Polymeric Compounds And Methods Of Making And Using The Same

FIELD

The present disclosure is directed, in part, to polycyclic compounds, or pharmaceutically acceptable salts thereof, for inhibiting the growth of a microbe; treating a mammal having a microbial infection, malaria, mucositis, an ophthalmic infection, an otic infection, a cancer, or a Mycobacterium infection; killing or inhibiting the growth of a Plasmodium species; inhibiting the growth of a Mycobacterium species; modulating an immune response in a mammal; or antagonizing unfractionated heparin, low molecular weight heparin, or a heparin/low molecular weight heparin derivative.

BACKGROUND

Antimicrobial peptides (AMPs) represent a first line of defense against microbes for many species. AMPs are typically small (12-80 amino acids) cationic amphiphiles. There are two types of AMPs comprising ribosomally and nonribosomally synthesized peptides. Over 700 AMPs have been identified and are generally α-helical (magainin and cecropin) or disulfide-rich β-sheets (bactenecin and defensin). Although the peptides are composed of many different sequences, their physiochemical properties are remarkably similar. They adopt an amphiphilic architecture with positively charged groups segregated to one side of the secondary structure and hydrophobic groups on the opposite surface. In mammals, the peptides are produced and secreted in skin, mucosal surfaces and neutrophils, and act locally in response to infection. It is the overall physiochemical properties that are largely responsible for biological activity of these peptides. Some AMPs display very broad spectrum action against bacteria, yeast, fungus, protozoa, and even viruses. Anti-parasitic activities have also been reported for a number of host defense peptides. AMPs have remained an effective weapon against bacterial infection over evolutionary time indicating that their mechanism of action thwarts bacterial responses which lead to resistance against toxic substances. This premise is supported by direct experimental data showing that no appreciable resistance to the action of the AMPs occurs after multiple serial passages of bacteria in the presence of sub-lethal concentrations of the peptides.

Several synthetic peptides and peptoids have been synthesized to mimic the activity of the natural host defense proteins (DeGrado, Adv. Protein Chem., 1988, 51-124; Hamuro et al., J. Am. Chem. Soc., 1999, 121, 12200-12201; Porter et al., Nature (London), 2000, 404, 565; Porter et al., J. Am. Chem. Soc., 2002, 124, 7324-7330; Liu et al., J. Am. Chem. Soc., 2001, 123, 7553-7559; Patch et al., J. Am. Chem. Soc., 2003, 125, 12092-12093; and Seurynck et al., Biophysical Journal, 2003, 84, 298A-298A) and several of these have been shown to selectively kill tumorigenic cells (Papo et al., Biochemistry, 2003, 42, 9346-9354; Papo et al., Cancer Res., 2004, 64, 5779-5786; and Shin et al., Biochim. Biophys. Acta, 2000, 1463, 209-218).

World-wide, 41% of the population live in areas where malaria is transmitted, such as parts of Africa, Asia, Middle East, Central and South America, Hispaniola, and Oceania. Each year between 350 and 500 million cases of malaria occur worldwide, and over one million people die, most of them young children in sub-Saharan Africa. In 2002, malaria was the fourth cause of death in children in developing countries. In addition, malaria caused 10.7% of all children's deaths in developing countries. AMPs appear to kill protozoa by interacting with the cytoplasmic membrane causing excessive permeability, lysis and death. Because the site of action is at the membrane and not to any specific receptor or intracellular target, the development of resistance to the cytotoxic properties of the AMPs is highly unlikely. With regard to anti-malarial activities, natural host defense proteins and their analogs have been shown to inhibit oocyst development of several Plasmodium species in various mosquito hosts (Gwadz et al., Infect. Immun., 1989, 57, 2628-2633; and Possani et al., Toxicon, 1998, 36, 1683-1692) and are directly cytotoxic against early sporogonic stages of Plasmodium in cell culture (Arrighi et al., Antimicrob. Agents Chemother., 2002, 46, 2104-2110). Furthermore, several AMPs have been identified which selectively kill intraerthrocytic parasites (plasmodia life forms growing in red blood cells) by either attacking the infected erythrocyte while sparring normal erthrocytes (Feder et al., J. Biol. Chem., 2000, 275, 4230-4238; and Krugliak et al., Antimicrob. Agents Chemother., 2000, 44, 2442-2451) or interacting with and killing the intracellular parasite without harming the infected red blood cell (Dagan et al., Antimicrob. Agents Chemother., 2002, 46, 1059-1066; and Efron et al., J. Biol. Chem., 2002, 277, 24067-24072).

Tuberculosis (TB) is a highly contagious disease that affects one-third of the world's population today. There are 8 million newly reported cases each year and 3.1 million people die from the disease annually. TB is the leading cause of death of women, AIDS patients, and the young in the world. There are more deaths from TB than any other single infectious disease. Worldwide, 30 to 50% of AIDS deaths are caused by TB. Globally, the population weighted mean of multi-drug resistant (MDR) TB among all TB cases is estimated at about 5%. Extensively-drug resistant (XDR) TB is more expensive and difficult to treat than MDR-TB and outcomes for XDR-TB patients are much worse. Mycobacterium tuberculosis (M. tuberculosis) is the primary infectious agent for TB, and drug resistance has become a paramount issue, accounting for over 50 million infections world wide. Although several anti-infective agents have been identified that combat M. tuberculosis and other tuberculosis-causing organisms, the emergence of MDR and XDR organisms has severely limited their effectiveness. A current therapeutic strategy for active disease is to treat with multiple drugs for 6 to 9 months; a course of therapy that is difficult to manage for compliance, thereby exacerbating the development of resistance. Furthermore, many of the anti-TB agents interfere with HIV therapy creating a dangerous upward spiral in disease progression and severity in co-infected individuals.

Oral ulcerative mucositis is a common, painful, dose-limiting toxicity of chemotherapy and radiation therapy for cancer (Sonis, Nat. Rev. Cancer, 2004, 4, 277-284; Keefe et al., Cancer, 2007, 109, 820-831; Belim et al., Support Care Cancer, 2000, 8, 33-39; and Parulekar et al., Oral Oncol., 1998, 34, 63-71). The disorder is characterized by breakdown of the oral mucosa and results in the formation of ulcerative lesions. It can significantly affect nutritional intake, mouth care, and quality of life (Lalla et al., Dent. Clin. North Am., 2005, 49, 167-184; and Duncan et al., Head Neck, 2005, 27, 421-428). The ulcerations that accompany mucositis are frequent portals of entry for oral bacteria often leading to sepsis or bacteremia. For patients receiving high-dose chemotherapy prior to hematopoietic cell transplantation, oral mucositis has been reported to be the single most debilitating complication of transplantation (Belim et al., Support Care Cancer, 2000, 8, 33-39). Infections associated with the oral mucositis lesions can cause life-threatening systemic sepsis during periods of immunosuppression (Rapoport et al., J. Clin. Oncol., 1999, 17, 2446-2453). Mucositis results in increased hospital stays and re-admission rates, and can result in interruptions or early cessation of treatment regimens (Pico et al., The Oncologist, 1998, 3, 446-451; and Elting et al., Cancer, 2003, 98, 1531-1539). Moderate to severe mucositis occurs in virtually all patients who receive radiation therapy for tumors of the head and neck. Among patients who are treated with induction therapy for leukemia or with many of the conditioning regimens for bone marrow transplant, is not unusual for more than three-quarters of patients to develop moderate to severe mucositis (Belim et al., Support Care Cancer, 2000, 8, 33-39). Annually, nearly 60,000 patients receive a diagnosis of head and neck cancer (Jemal et al., CA Cancer J. Clin., 2002, 52, 23-47) and severe mucositis occurs in up to 92% of these treated patients (Parulekar et al., Oral Oncol., 1998, 34, 63-71; Sonis et al., Cancer, 85, 2103-2113). In addition to quality of life issues, there is a substantial impact of oral mucositis on medical care resources and costs, estimated to be $17,000 per patient, which are related to increased hospitalization stays, medical treatments and medications (Nonzee et al., Cancer, 2008, 113, 1446-1452). Despite its frequency, severity and impact on patients' ability to tolerate cancer treatment, there is currently only one approved pharmaceutical for the prevention or treatment for oral mucositis. Palifermin (Kepivance®, recombinant human keratinocyte growth factor-1) was approved for a mucositis indication in patients with hematologic malignancies receiving stem cell transplants. Its efficacy may be related to mitogenic effects on mucosal epithelium and/or alteration of cytokine profiles, including down-regulation of TNF (Logan et al., Cancer Treatment Rev., 2007, 33, 448-460). Palifermin is not widely used due in part to concerns on the potential impact of a growth factor on antineoplastic treatment. Available agents include topical analgesics (lidocaine), barrier devices (GelClair), or rinses (Caphosol). Another agent proposed to be used for treatment of mucositis is NX002, which is a peptide derived from AMP-18 (see, U.S. Pat. Nos. 7,910,543 and 7,629,317).

Periodontitis is the most common cause of tooth loss in adults in the United States (Borrell et al., J. Dent. Res., 2005, 84, 924-930), occurring in 15-25% of the US population. Its etiology can be considered due to bacterial colonization by a variety of pathogenic microorganisms, including Porphyromonas gingivalis, which is associated with chronic periodontitis, and Aggregatibacter actinomycetemcomitans, which is associated with aggressive periodontitis. This colonization and subsequent invasion into the gingival epithelium leads to an innate immune response, including the production of such mediators as IL-1 and tumor necrosis factor (TNF)-α (Graves et al., J. Periodontol., 2003, 74, 391-401). This leads to inflammation, which ultimately results in the bone loss seen in this disease (reviewed in Cochran, J. Periodontol., 2008, 79, 1569-1576). While standard treatment involves mechanical removal of the biofilm, the use of systemic antibiotics has also been examined (reviewed in Herrera et al., J. Clin. Periodontol., 2008, 35, 45-66), as has the identification of therapeutic targets in the inflammatory response (reviewed in Kirkwood et al., Periodontol. 2000, 2007, 43, 294-315). While periodontal disease is ultimately of bacterial etiology, from multispecies biofilms of Gram-negative anaerobic microorganisms, much of the deleterious effects are due to the resultant epithelial inflammatory response. Thus, development of a treatment that combines both anti-biofilm antibiotic activity with anti-inflammatory activity would be of great utility. Metabolic assays as well as culture and biomass measurement assays have demonstrated that mPE exhibits potent activity against biofilm cultures of both species. Furthermore, as little as 2 μg/mL mPE was sufficient to inhibit IL-1β-induced secretion of IL-8 in both gingival epithelial cells and THP-1 cells. This anti-inflammatory activity is associated with a reduction in activation of NF-κB, suggesting that mPE can act both as an anti-biofilm agent in an anaerobic environment as well as an anti-inflammatory agent in infected tissues.

Treatment and prevention of thrombosis are major clinical issues for medical and surgical patients. Heparin, a highly sulfated polysaccharide, is commonly used as prophylaxis against venous thromboembolism and to treat venous thrombosis, pulmonary embolism, unstable angina and myocardial infarction (see, for example, Walenga et al., “Factor Xa inhibition in mediating antithrombotic actions: application of a synthetic heparin pentasaccharide” In. Paris: Universite Pierre et Marie Curie, Paris VI; 1987; and Hirsh et. al., Chest, 2001, 119, 64-94). Heparin is also used as an anticoagulant during the extracorporeal blood circulation for kidney dialysis and coronary bypass surgery. Although heparin is an efficacious anticoagulant, there are many limitations associated with its clinical use. For example, heparin's heterogeneity and polydispersity lead to nonspecific protein binding and poorly predictive pharmacokinetic properties upon subcutaneous (s.c.), and even intravenous, injection (see, for example, Bendetowicz et. al., Thromb. Hemostasis., 1994, 71, 305-313). As a result, infusions of unfractionated heparin (UFH) are performed in the hospital where its anticoagulant effect can be measured to minimize the risk of bleeding. In addition to hemorrhage, administration of UFH is associated with 1-2% incidence of heparin-induced thrombocytopenia (HIT) (see, for example, Morabia, Lancet, 1986, 1, 1278-1279; Mureebe et. al., Vase. Endovasc. Surg., 2002, 36, 163-170; and Lubenow et. al., Chest, 2002, 122, 37-42).

To address some of the shortcomings of UFH, low molecular weight heparins (LMWHs) have been developed. LMWHs are fragments of UFH produced by chemical or enzymatic depolymerization (see, for example, Hirsh et. al., Blood, 1992, 79, 1-17). Due to their smaller size and lower polydispersity, LMWHs are more reproducibly bioavailable after s.c. administration and have more predictable pharmacokinetics leading to greater safety (see, for example, Ofosu et. al., “Mechanisms of action of low molecular weight heparins and heparinoids.” In: Hirsh J (ed). Antithrombotic Therapy, Bailliere's Clinical Haematology (Volume 3). London, UK: Bailliere Tindall, 1990, pp. 505-529). The smaller size of LMWHs is also associated with a lower ratio of anti-thrombin to anti-FXa activity (see, for example, Hirsh et. al., Chest, 2001, 119, 64-94). LMWHs are being used with greater frequency owing to their ease of administration, longer duration or action and reduced incidence of heparin-induced thrombocytopenia (see, for example, Hirsh et. al., Chest, 2004, 126 (Suppl 3), 188S-203S). LMWHs are commonly used to treat deep vein thrombosis, unstable angina, and acute pulmonary embolism, as well as thromboprophylactic agents in a wide range of clinical situations including orthopedic surgery, high risk pregnancy, and cancer therapy (see, for example, Hirsh et. al., Chest, 2004, 126 (Suppl 3), 188S-203S; Becker, J. Thrombosis and Thrombolysis, 1999, 7, 195; Antman et. al., Circulation, 1999, 100, 1593-601; Cohen et. al., New England J. Med., 1997, 337, 447; and Lee et. al., J. Clin. Oncol., 2005, 23, 2123-9). Fondaparinux is a heparin-derived pentasaccharide that represents the smallest fragment of heparin that is capable of accelerating antithrombin-mediated factor Xa inhibition (see, for example, Walenga et. al., Exp. Opin. Invest. Drugs, 2005, 14, 847-58). Fondaparinux is currently approved for the prophylaxis of deep vein thrombosis following hip repair and/or replacement, knee replacement and abdominal surgery and the treatment of DVT/PE when used in conjunction with warfarin. The most common complication of anticoagulation with LMWHs is hemorrhage. Many published clinical studies report 1% to 4% major (life-threatening) bleeding associated with LMWH therapy and there is a 5-fold increase in the overall death rate for acute coronary syndrome patients receiving anti-coagulant therapy that experience major bleeding (see, for example, Hirsh et. al., Chest, 2001, 119, 64-94; and Mehta et. al., J. Am. Coll. Cardiol., 2007, 50, 1742-1751).

Protamine, an arginine-rich heterogeneous peptide mixture isolated from fish sperm, is used routinely to neutralize the effects of heparin in patients who bleed while under treatment (see, for example, Ando et. al., in Kleinzeller, A. (ed): “Protamine: Molecular biology, biochemistry and biophysics” Vol 12. 1973. New York, Springer-Verlag, 1-109). Polycationic protamine binds to anionic heparin through electrostatic interactions, thereby neutralizing the anticoagulant effects of heparin. Although protamine is commonly used to neutralize UFH following coronary bypass surgery, it is unable to completely reverse the anticoagulant effects of LMWHs (see, for example, Hubbard et. al., Thromb. Haemost., 1985, 53, 86-89; Poon et. al., Thromb. Haemost., 1982, 47, 162-165; Massonnet-Castel et. al., Haemostasis, 1986, 16, 139-146; and Doutremepuich et. al., Semin. Thromb. Hemost., 1985, 11, 318-322) or fondaparinux (see, for example, Walenga, “Factor Xa inhibition in mediating antithrombotic actions: application of a synthetic heparin pentasaccharide” In. Paris: Universite Pierre et Marie Curie, Paris VI; 1987).

In addition, use of protamine for heparin reversal is associated with adverse reactions including systemic vasodilation and hypotension, bradycardia, pulmonary artery hypertension, pulmonary vasoconstriction, thrombocytopenia, and neutropenia (see, for example, Metz et. al., “Protamine and newer heparin antagonists” in Stoetling, R. K. (ed): Pharmacology and Physiology in Anesthetic Practice. Vol. 1. Philadelphia, Pa., J B Lippincott, 1-15, 1994; Weiler et. al., J. Allergy Clin. Immunol., 1985, 75, 297-303; Horrow, Anest. Analg., 1985, 64, 348-361; and Porsche et. al., Heart Lung J. Acute Crit. Care, 1999, 28, 418-428).

Therefore, there is a strong medical need for the development of a safe and effective antagonist for UFH and/or LMWH. The lack of an effective antagonist has limited the clinical use of the LMWHs and fondaparinux, especially in bypass procedures and instances where near term surgical procedures may be needed. There is also a strong medical need for an efficacious, nontoxic substitute for protamine. Further, efficacy against the anticoagulation properties of the LMWHs would substantially address an important and expanding medical market for which no effective antidote is available.

SUMMARY OF THE DISCLOSURE

The present disclosure provides compounds of Formula I

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wherein: X is S, O, or N; R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nN(CH₃)₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂—NC(═N)NH₂, —C(═O)(CH₂)_nNH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂NC(═N)NH₂, where n is 2, 3, or 4; R²is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; and R³is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; or a pharmaceutically acceptable salt thereof; provided that: when X is S, and R²and R³are H, then R¹is not —C(═O)(CH₂)₂NH₂; and when X is S, R³is H, and R²is Cl or —CF₃, then R¹is not —(CH₂)₃N(CH₃)₂.

The present disclosure also provides compounds of Formula II

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wherein: X is N, O, or S; R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R²is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; and R³is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula III

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The present disclosure also provides compounds of Formula IV

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wherein: each of R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, and R⁹is, independently, H, halo, haloC_1-8alkyl, —NH₂, C_1-8alkyl, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or substituted or unsubstituted piperazine, substituted or unsubstituted piperidine, substituted or unsubstituted pyrrolidine, substituted or unsubstituted aromatic, or substituted or unsubstituted heteroaromatic; or —X—Y wherein X is —(CH₂)_rwhere r is 1 to 8, O, S, —CH═CH, —CH≡CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkyl, haloC_1-8alkyl, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, substituted or unsubstituted C_1-8alkyl aromatic, substituted or unsubstituted C_1-8alkyl heteroaromatic, or any one of

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or

—X(Z¹)(Z²), where X is —CH or —N, and Z¹and Z²are, independently, —NH₂, C_1-8alkyl, haloC_1-8alkyl, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, substituted or unsubstituted C_1-8alkyl aromatic, substituted or unsubstituted C_1-8alkyl heteroaromatic; wherein each substituent is, independently, C₁-C₆alkyl, C₁-C₆alkenyl, C₁-C₆alkynyl, C₅-C₆aryl, C₁-C₆alkoxy, C₃-C₅heteroaryl, C₃-C₆cycloalkyl, C₅-C₆aryloxy, —CN, —OH, oxo, halo, haloalkyl, —NO₂, —CO₂H, —NH₂, —NH(C₁-C₈alkyl), —N(C₁-C₈alkyl)₂, —NH(C₆aryl), —N(C₅-C₆aryl)₂, —CHO, —CO(C₁-C₆alkyl), —CO((C₅-C₆)aryl), —CO₂((C₁-C₆)alkyl), or —CO₂((C₅-C₆)aryl); or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula V

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wherein: X is O, N, or S; R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or —NC(═N)NH₂, where n is 2, 3, or 4; and R²is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —C═C—(CH₂)₂—NC(═N)NH₂, or —NC(═N)NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula VI

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wherein: X is N, O, S, or C; Y is N, O, S, or C; Z is N, O, S, or C; R¹is H or

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R²is

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each R³is, independently, H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; each R⁴is, independently, H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C═C—CH₂NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and each R⁵is, independently, H, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C═C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula VII

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wherein: X is C, O, S, or N; Y is C, O, S, or N; Z is O or S; R¹is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; R²is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; R³is H, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or

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where n is 2, 3, or 4; R⁴is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —C≡C—CH₂NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or

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where n is 2, 3, or 4; R⁵is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or

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where n is 2, 3, or 4; and R⁶is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or

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where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula VIII

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wherein: X is C, O, S, or N; Y is C, O, S, or N; Z is O or S; R¹is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; R²is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; R³is —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and R⁴is —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula IX

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The present disclosure also provides compounds of Formula X

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wherein: X is O or S; R¹is H or

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R²is H or

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R³is H or

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each R⁴is, independently, H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; each R⁵is, independently, H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and each R⁶is, independently, H, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XI

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wherein: X is N, C, O, or S; Y is N, C, O, or S; Z is N, C, O, or S; and R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —C≡C—CH₂NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XII

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wherein: X is N, O, C, or S; R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R²is —NH₂, —N((CH₂)_nNH₂)₂, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and R³is —NH₂, —N((CH₂)_nNH₂)₂, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, —N(CH₂CH₂NH₂)₂, or NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof; provided that: when X is N, then R¹, R², and R³are not all —(CH₂)₃NH₂; and when X is N, and R¹is —(CH₂)₃NH₂, then R²and R³are not both —(CH₂)₂NH₂, —O—(CH₂)₃NH₂, or —O—(CH₂)₂NH₂.

The present disclosure also provides compounds of Formula XIII

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wherein: X is N, C, O, or S; R¹is H, halo, haloalkyl, —NH₂, C_1-3alkyl, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —C≡C—CH₂NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R²is H, halo, haloalkyl, —NH₂, C_1-6alkyl, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —C≡C—CH₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R³is —NH(CH₂)_nNH₂, —C(═O)N(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —C═C—CH₂NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and R⁴is —C(═O)N(CH₂)_nNH₂, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XIV

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The present disclosure also provides compounds of Formula XV

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wherein: X is C(═O), O, S, or —C(halo)₂; R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R²is —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R³is —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and R⁴is —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XVI

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wherein: X is C, S, O, or N; R¹is H, —NH(CH₂)NH₂, —NH(CH₂) NC(═N)NH₂, —(CH₂) NH₂, —(CH₂)NC(═N)NH₂, —O—(CH₂)NH₂, —O—(CH₂)NC(═N)NH₂, —C(═O)N(CH₂)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —C═C—(CH₂)₂NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or

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where n is 2, 3, or 4; R²is H, —(CH₂)NH₂, —NH(CH₂)NH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)NH₂, —CH═CH—CH₂NH₂, —O—(CH₂)NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —C═C—CH₂NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C(═O)N(CH₂)NH₂, —C═C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —C═C—(CH₂)₂—NC(═N)NH₂, —N((CH₂)_nNH₂)₂,

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where n is 2, 3, or 4; R³is H, —NH(CH₂) NH₂, —NH(CH₂)NC(═N)NH₂, —(CH₂)NH₂, —(CH₂)NC(═N)NH₂, —O—(CH₂) NH₂, —O—(CH₂) NC(═N)NH₂, —C(═O)N(CH₂)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C═C—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —C═C—(CH₂)₂NH₂, —C═C—(CH₂)₂—NC(═N)NH₂, or

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where n is 2, 3, or 4; R⁴is H, —NH(CH₂)NH₂, —NH(CH₂)NC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —C═C—(CH₂)₂—NC(═N)NH₂, —C(═O)N(CH₂)_nNH₂, —(CH₂)_nN((CH₂)_nNH₂)₂, —N((CH₂)_nNH₂)₂,

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where n is 2, 3, or 4; R⁵is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C_1-3alkyl, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁶is H, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁷is H, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁸is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; and R⁹is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; or a pharmaceutically acceptable salt thereof; provided that: when R¹, R³, R⁵, R⁶, R⁷, R⁸, and R⁹are H, and X is S, then R²and R⁴are not both —(CH₂)₂NH₂, —(CH₂)₃NC(═N)NH₂, —(CH₂)₃NH₂, or —CH₂NH₂; when R¹, R², R³, R⁴, R⁵, R⁸, and R⁹are H, and X is S, then R⁶and R⁷are not both —(CH₂)₃NH₂; when R¹, R³, R⁵, R⁶, R⁷, R⁸, and R⁹are H, and X is N, then R²and R⁴are not both —CH₂NH₂or —(CH₂)₃NH₂; when R¹, R³, R⁵, R⁶, R⁷, R⁸, and R⁹are H, and X is O, then R²and R⁴are not both —(CH₂)₃NH₂; when R¹, R³, R⁶, R⁷, R⁸, and R⁹are H, X is N, and R⁵is —CH₂CH₃, then R²and R⁴are not both —(CH₂)₃NH₂; when R⁵, R⁶, R⁷, R⁸, are R⁹, are H, and X is O, then R¹, R², R³, and R⁴are not all —O—(CH₂)₃NH₂; when R⁶, R⁷, R⁸, are R⁹, are H, X is N, and R⁵is —CH₂CH₃, then R¹, R², R³, and R⁴are not all —O—(CH₂)₃NH₂; and when R⁵, R⁶, R⁷, R⁸, are R⁹, are H, and X is S, then R¹, R², R³, and R⁴are not all —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂.

The present disclosure also provides compounds of Formula XVII

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wherein: R¹is H, halo, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R²is H, halo, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R³is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, —CH((CH₂)_nNH₂)₂, or —CH((CH₂)_nNC(═N)NH₂)₂, where n is 2, 3, or 4; R⁴is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —C≡C—CH₂NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH((CH₂)_nNH₂)₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —C═C—(CH₂)₂—NC(═N)NH₂, or —CH((CH₂)_nNC(═N)NH₂)₂, where n is 2, 3, or 4; R⁵is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; and R⁶is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; and R⁷is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁸is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and R⁹is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; or a pharmaceutically acceptable salt thereof; provided that: when R⁵, R⁶, R⁷, R⁸, and R⁹are H, and R¹and R²are Br, then R³and R⁴are not both —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂.

The present disclosure also provides compounds of Formula XVIII

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wherein: X is N, C, O, or S; Y is N, C, O, or S; R¹is —NH(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R²is —NH(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R³is —NH(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁴is —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—CH₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XIX

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The present disclosure also provides compounds of Formula XX

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The present disclosure also provides compounds of Formula XXI

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The present disclosure also provides compounds of Formula XXII

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The present disclosure also provides compounds of Formula XXIII

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wherein: R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R²is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R³is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁴is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁵is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁶is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁷is H, halo, C_1-6alkyl, or haloalkyl; R⁸is H, halo, C_1-6alkyl, or haloalkyl; and R⁹is H, halo, C_1-6alkyl, or haloalkyl; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XXIV

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wherein: R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R²is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C═C—CH₂NH₂, —C═C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R³is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁴is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁵is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and R⁶is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XXV

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wherein: R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R²is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R³is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁴is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁵is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁶is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and R⁷is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XXVI

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wherein: R¹is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R²is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R³is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁴is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁵is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and R⁶is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C═C—CH₂NH₂, —C═C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XXVII

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wherein: R¹is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R²is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R³is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁴is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁵is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and R⁶is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C═C—CH₂NH₂, —C═C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XXVIII

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wherein: R¹is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R²is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R³is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁴is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; R⁵is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and R⁶is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or a pharmaceutically acceptable salt thereof.

The present disclosure also provides pharmaceutical compositions comprising any one or more of the foregoing compounds, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.

The present disclosure also provides methods of inhibiting the growth of a microbe comprising contacting the microbe with any one or more of the foregoing compounds, or pharmaceutically acceptable salt thereof.

The present disclosure also provides methods of treating malaria in a mammal comprising administering to the mammal in need thereof a therapeutically effective amount of any one or more of the foregoing compounds, or a pharmaceutically acceptable salt thereof.

The present disclosure also provides methods of killing or inhibiting the growth of a Plasmodium species comprising contacting the species with an effective amount of any one or more of the foregoing compounds, or a pharmaceutically acceptable salt thereof.

The present disclosure also provides methods of inhibiting the growth of a Mycobacterium species comprising contacting the Mycobacterium species with an effective amount of any one or more of the foregoing compounds, or a pharmaceutically acceptable salt thereof.

The present disclosure also provides methods of treating a mammal having a Mycobacterium infection comprising administering to the mammal in need thereof a therapeutically effective amount of any one or more of the foregoing compounds, or a pharmaceutically acceptable salt thereof.

The present disclosure also provides methods of treating oral mucositis in a mammal comprising administering to the mammal in need thereof a therapeutically effective amount of any one or more of the foregoing compounds, or a pharmaceutically acceptable salt thereof.

The present disclosure also provides methods for antagonizing unfractionated heparin, low molecular weight heparin, or a heparin/low molecular weight heparin derivative comprising administering to a mammal in need thereof any one or more of the foregoing compounds, or a pharmaceutically acceptable salt thereof.

The present disclosure also provides methods of inhibiting anti-Factor Xa in a mammal comprising administering to the mammal in need thereof a therapeutically effective amount of any one or more of the foregoing compounds, or a pharmaceutically acceptable salt thereof.

The present disclosure also provides methods of treating a microbial infection in an eye of a mammal comprising administering to one or more tissues of the eye of the mammal in need thereof an effective amount of any one or more of the foregoing compounds, or a pharmaceutically acceptable salt thereof.

The present disclosure also provides methods of treating a microbial infection in an ear of a mammal comprising administering to one or more tissues of the ear of the mammal in need thereof an effective amount of any one or more of the foregoing compounds, or a pharmaceutically acceptable salt thereof.

The present disclosure also provides methods for treating or reducing cancer, or inhibiting growth of a cancer cell, or inhibiting tumor growth, or reducing spread or metastasis of cancer in a mammal comprising administering to the mammal in need thereof an effective amount of any one or more of the foregoing compounds, or a pharmaceutically acceptable salt thereof.

The present disclosure also provides methods of modulating an immune response in a mammal comprising administering to the mammal in need thereof a therapeutically effective amount of any one or more of the foregoing compounds, or a pharmaceutically acceptable salt thereof.

The present disclosure also provides any one or more of the foregoing compounds for inhibiting anti-Factor Xa in a mammal; inhibiting the growth of a microbe; treating a mammal having a microbial infection; treating malaria in a mammal; killing or inhibiting the growth of a Plasmodium species; inhibiting the growth of a Mycobacterium species; treating a mammal having a Mycobacterium infection; treating oral mucositis in a mammal; treating a microbial infection in an ear of a mammal; treating a microbial infection in an eye of a mammal; treating or reducing cancer, or inhibiting growth of a cancer cell, or inhibiting tumor growth, or reducing spread or metastasis of cancer in a mammal; modulating an immune response in a mammal; or antagonizing unfractionated heparin, low molecular weight heparin, or a heparin/low molecular weight heparin derivative.

The present disclosure also provides any one or more of the foregoing compounds for use in the manufacture of a medicament for inhibiting anti-Factor Xa in a mammal; inhibiting the growth of a microbe; treating a mammal having a microbial infection; treating malaria in a mammal; killing or inhibiting the growth of a Plasmodium species; inhibiting the growth of a Mycobacterium species; treating a mammal having a Mycobacterium infection; treating oral mucositis in a mammal; treating a microbial infection in an ear of a mammal; treating a microbial infection in an eye of a mammal; treating or reducing cancer, or inhibiting growth of a cancer cell, or inhibiting tumor growth, or reducing spread or metastasis of cancer in a mammal; modulating an immune response in a mammal; or antagonizing unfractionated heparin, low molecular weight heparin, or a heparin/low molecular weight heparin derivative.

The present disclosure also provides uses of any one or more of the foregoing compounds for inhibiting anti-Factor Xa in a mammal; inhibiting the growth of a microbe; treating a mammal having a microbial infection; treating malaria in a mammal; killing or inhibiting the growth of a Plasmodium species; inhibiting the growth of a Mycobacterium species; treating a mammal having a Mycobacterium infection; treating oral mucositis in a mammal; treating a microbial infection in an ear of a mammal; treating a microbial infection in an eye of a mammal; treating or reducing cancer, or inhibiting growth of a cancer cell, or inhibiting tumor growth, or reducing spread or metastasis of cancer in a mammal; modulating an immune response in a mammal; or antagonizing unfractionated heparin, low molecular weight heparin, or a heparin/low molecular weight heparin derivative.

The present disclosure also provides uses of any one or more of the foregoing compounds in the manufacture of a medicament for inhibiting anti-Factor Xa in a mammal; inhibiting the growth of a microbe; treating a mammal having a microbial infection; treating malaria in a mammal; killing or inhibiting the growth of a Plasmodium species; inhibiting the growth of a Mycobacterium species; treating a mammal having a Mycobacterium infection; treating oral mucositis in a mammal; treating a microbial infection in an ear of a mammal; treating a microbial infection in an eye of a mammal; treating or reducing cancer, or inhibiting growth of a cancer cell, or inhibiting tumor growth, or reducing spread or metastasis of cancer in a mammal; modulating an immune response in a mammal; or antagonizing unfractionated heparin, low molecular weight heparin, or a heparin/low molecular weight heparin derivative.

DESCRIPTION OF EMBODIMENTS

Unless defined otherwise, all technical and scientific terms have the same meaning as is commonly understood by one of ordinary skill in the art to which the embodiments disclosed belongs.

As used herein, the terms “a” or “an” means that “at least one” or “one or more” unless the context clearly indicates otherwise.

As used herein, the term “about” means that the numerical value is approximate and small variations would not significantly affect the practice of the disclosed embodiments. Where a numerical limitation is used, unless indicated otherwise by the context, “about” means the numerical value can vary by ±10% and remain within the scope of the disclosed embodiments.

As used herein, the term “acylamino” means an amino group substituted by an acyl group (e.g., —O—C(═O)—H or —O—C(═O)-alkyl). An example of an acylamino is —NHC(═O)H or —NHC(═O)CH₃. The term “lower acylamino” refers to an amino group substituted by a loweracyl group (e.g., —O—C(═O)—H or —O—C(═O)—C_1-6alkyl). An example of a lower acylamino is —NHC(═O)H or —NHC(═O)CH₃.

As used herein, the term “alkenyl” means a straight or branched alkyl group having one or more double carbon-carbon bonds and 2-20 carbon atoms, including, but not limited to, ethenyl, 1-propenyl, 2-propenyl, 2-methyl-1-propenyl, 1-butenyl, 2-butenyl, and the like. In some embodiments, the alkenyl chain is from 2 to 10 carbon atoms in length, from 2 to 8 carbon atoms in length, from 2 to 6 carbon atoms in length, or from 2 to 4 carbon atoms in length.

As used herein, the term “alkoxy” means a straight or branched —O-alkyl group of 1 to 20 carbon atoms, including, but not limited to, methoxy, ethoxy, n-propoxy, isopropoxy, t-butoxy, and the like. In some embodiments, the alkoxy chain is from 1 to 10 carbon atoms in length, from 1 to 8 carbon atoms in length, from 1 to 6 carbon atoms in length, from 1 to 4 carbon atoms in length, from 2 to 10 carbon atoms in length, from 2 to 8 carbon atoms in length, from 2 to 6 carbon atoms in length, or from 2 to 4 carbon atoms in length.

As used herein, the term “alkyl” means a saturated hydrocarbon group which is straight-chained or branched. An alkyl group can contain from 1 to 20, from 2 to 20, from 1 to 10, from 2 to 10, from 1 to 8, from 2 to 8, from 1 to 6, from 2 to 6, from 1 to 4, from 2 to 4, from 1 to 3, or 2 or 3 carbon atoms. Examples of alkyl groups include, but are not limited to, methyl (Me), ethyl (Et), propyl (e.g., n-propyl and isopropyl), butyl (e.g., n-butyl, t-butyl, isobutyl), pentyl (e.g., n-pentyl, isopentyl, neopentyl), hexyl, isohexyl, heptyl, 4,4-dimethylpentyl, octyl, 2,2,4-trimethylpentyl, nonyl, decyl, undecyl, dodecyl, 2-methyl-1-propyl, 2-methyl-2-propyl, 2-methyl-1-butyl, 3-methyl-1-butyl, 2-methyl-3-butyl, 2-methyl-1-pentyl, 2,2-dimethyl-1-propyl, 3-methyl-1-pentyl, 4-methyl-1-pentyl, 2-methyl-2-pentyl, 3-methyl-2-pentyl, 4-methyl-2-pentyl, 2,2-dimethyl-1-butyl, 3,3-dimethyl-1-butyl, 2-ethyl-1-butyl, and the like.

As used herein, the term “alkylamino” means an amino group substituted by an alkyl group having from 1 to 6 carbon atoms. An example of an alkylamino is —NHCH₂CH₃.

As used herein, the term “alkylene” or “alkylenyl” means a divalent alkyl linking group. An example of an alkylene (or alkylenyl) is methylene or methylenyl (—CH₂—).

As used herein, the term “alkylthio” means an —S-alkyl group having from 1 to 6 carbon atoms. An example of an alkylthio group is —SCH₂CH₃.

As used herein, the term “alkynyl” means a straight or branched alkyl group having one or more triple carbon-carbon bonds and 2-20 carbon atoms, including, but not limited to, acetylene, 1-propylene, 2-propylene, and the like. In some embodiments, the alkynyl chain is 2 to 10 carbon atoms in length, from 2 to 8 carbon atoms in length, from 2 to 6 carbon atoms in length, or from 2 to 4 carbon atoms in length.

As used herein, the term “amidino” means —C(═NH)NH₂.

As used herein, the term “amino” means —NH₂.

As used herein, the term “aminoalkoxy” means an alkoxy group substituted by an amino group. An example of an aminoalkoxy is —OCH₂CH₂NH₂.

As used herein, the term “aminoalkyl” means an alkyl group substituted by an amino group. An example of an aminoalkyl is —CH₂CH₂NH₂.

As used herein, the term “aminosulfonyl” means —S(═O)₂NH₂.

As used herein, the term “aminoalkylthio” means an alkylthio group substituted by an amino group. An example of an aminoalkylthio is —SCH₂CH₂NH₂.

As used herein, the term “amphiphilic” means a three-dimensional structure having discrete hydrophobic and hydrophilic regions. An amphiphilic compound suitably has the presence of both hydrophobic and hydrophilic elements.

As used herein, the term “animal” includes, but is not limited to, humans and non-human vertebrates such as wild, domestic, and farm animals.

As used herein, the term “antagonize” or “antagonizing” means reducing or completely eliminating an effect, such as the anticoagulant effect of heparin.

As used herein, the phrase “anti-microbial effective amount” of a compound can be measured by the anti-microbial effectiveness of the compound. In some embodiments, an anti-microbial effective amount inhibits growth of a particular microbe by at least 10%, by at least 20%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 80%, by at least 90%, or by at least 95%. In some embodiments, an “anti-microbial effective amount” is also a “therapeutically effective amount” whereby the compound reduces or eliminates at least one harmful effect of a microbe on a mammal.

As used herein, the term “anti-TB” means that the compound inhibits, prevents, or destroys the growth or proliferation of a tuberculosis-causing organism, such as a Mycobacterium species.

As used herein, the term “aryl” means a monocyclic, bicyclic, or polycyclic (e.g., having 2, 3 or 4 fused rings) aromatic hydrocarbons. In some embodiments, aryl groups have from 6 to 20 carbon atoms or from 6 to 10 carbon atoms. Examples of aryl groups include, but are not limited to, phenyl, naphthyl, anthracenyl, phenanthrenyl, indanyl, indenyl, tetrahydronaphthyl, and the like.

As used herein, the term “arylalkyl” means a C_1-6alkyl substituted by aryl.

As used herein, the term “arylamino” means an amino group substituted by an aryl group. An example of an arylamino is —NH(phenyl).

As used herein, the term “arylene” means an aryl linking group, i.e., an aryl group that links one group to another group in a molecule.

As used herein, the term “cancer” means a spectrum of pathological symptoms associated with the initiation or progression, as well as metastasis, of malignant tumors.

As used herein, the term “carbamoyl” means —C(═O)—NH₂.

As used herein, the term “carbocycle” means a 5- or 6-membered, saturated or unsaturated cyclic ring, optionally containing O, S, or N atoms as part of the ring. Examples of carbocycles include, but are not limited to, cyclopentyl, cyclohexyl, cyclopenta-1,3-diene, phenyl, and any of the heterocycles recited above.

As used herein, the term “carrier” means a diluent, adjuvant, or excipient with which a compound is administered. Pharmaceutical carriers can be liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. The pharmaceutical carriers can also be saline, gum acacia, gelatin, starch paste, talc, keratin, colloidal silica, urea, and the like. In addition, auxiliary, stabilizing, thickening, lubricating and coloring agents can be used.

As used herein, the term “chemically nonequivalent termini” means a functional group such as an ester, amide, sulfonamide, or N-hydroxyoxime that, when reversing the orientation of the functional group (e.g., —(C═O)O—) produces different chemical entities (e.g., —R¹C(═O)OR²— vs. —R¹OC(═O)R²—).

As used herein, the term, “compound” means all stereoisomers, tautomers, and isotopes of the compounds described herein.

As used herein, the terms “comprising” (and any form of comprising, such as “comprise”, “comprises”, and “comprised”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”), or “containing” (and any form of containing, such as “contains” and “contain”), are inclusive or open-ended and do not exclude additional, unrecited elements or method steps.

As used herein, the term “contacting” means bringing together of two elements in an in vitro system or an in vivo system. For example, “contacting” a heparin or LMWH with a compound includes the administration of a compound to an individual or patient, such as a human, having been administered a heparin, as well as, for example, introducing a compound into a sample containing a cellular or purified preparation containing the heparin, or before an individual has been administered a heparin.

As used herein, the term “cyano” means —CN.

As used herein, the term “cycloalkyl” means non-aromatic cyclic hydrocarbons including cyclized alkyl, alkenyl, and alkynyl groups that contain up to 20 ring-forming carbon atoms. Cycloalkyl groups can include mono- or polycyclic ring systems such as fused ring systems, bridged ring systems, and spiro ring systems. In some embodiments, polycyclic ring systems include 2, 3, or 4 fused rings. A cycloalkyl group can contain from 3 to 15, from 3 to 10, from 3 to 8, from 3 to 6, from 4 to 6, from 3 to 5, or 5 or 6 ring-forming carbon atoms. Ring-forming carbon atoms of a cycloalkyl group can be optionally substituted by oxo or sulfido. Examples of cycloalkyl groups include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl, cyclononyl, cyclopentenyl, cyclohexenyl, cyclohexadienyl, cycloheptatrienyl, norbornyl, norpinyl, norcarnyl, adamantyl, and the like. Also included in the definition of cycloalkyl are moieties that have one or more aromatic rings fused (having a bond in common with) to the cycloalkyl ring, for example, benzo or thienyl derivatives of pentane, pentene, hexane, and the like (e.g., 2,3-dihydro-1H-indene-1-yl, or 1H-inden-2(3H)-one-1-yl).

As used herein, the term “cycloalkylalkyl” means a C_1-6alkyl substituted by cycloalkyl.

As used herein, the term “dialkylamino” means an amino group substituted by two alkyl groups, each having from 1 to 6 carbon atoms.

As used herein, the term “diazamino” means —N(NH₂)₂.

As used herein, the term “facially amphiphilic” or “facial amphiphilicity” means compounds with polar (hydrophilic) and nonpolar (hydrophobic) side chains that adopt conformation(s) leading to segregation of polar and nonpolar side chains to opposite faces or separate regions of the structure or molecule.

As used herein, the phrase “groups with chemically nonequivalent termini” means functional groups such as esters amides, sulfonamides and N-hydroxyoximes where reversing the orientation of the substituents, e.g. R¹C(═O)OR²vs. R¹O(O═)CR², produces unique chemical entities.

As used herein, the term “guanidino” means —NH(═NH)NH₂.

As used herein, the term “halo” means halogen groups including, but not limited to fluoro, chloro, bromo, and iodo.

As used herein, the term “haloalkoxy” means an —O-haloalkyl group. An example of an haloalkoxy group is OCF₃.

As used herein, the term “haloalkyl” means a C_1-6alkyl group having one or more halogen substituents. Examples of haloalkyl groups include, but are not limited to, CF₃, C₂F₅, CHF₂, CCl₃, CHCl₂, C₂Cl₅, CH₂CF₃, and the like.

As used herein, the term “heparin” means naturally occurring unfractionated heparin and low molecular weight heparin, which can be used as an anticoagulant in diseases that feature thrombosis, as well as for prophylaxis in situations that lead to a high risk of thrombosis. The term “heparin” further includes anticoagulant agents that are derivatives of unfractionated heparin and/or LMWH, for example, by chemical modification or through enzymatic process. Examples of such heparin derivatives (for example, chemically modified unfractionated heparin and/or LMWH; or pentasaccharide) include fondaparinux. Examples of LMWH include, but are limited to, enoxaparin, reviparin, and tinzaparin.

As used herein, the term “heteroaryl” means an aromatic heterocycle having up to 20 ring-forming atoms (e.g., C) and having at least one heteroatom ring member (ring-forming atom) such as sulfur, oxygen, or nitrogen. In some embodiments, the heteroaryl group has at least one or more heteroatom ring-forming atoms, each of which are, independently, sulfur, oxygen, or nitrogen. In some embodiments, the heteroaryl group has from 3 to 20 ring-forming atoms, from 3 to 10 ring-forming atoms, from 3 to 6 ring-forming atoms, or from 3 to 5 ring-forming atoms. In some embodiments, the heteroaryl group contains 2 to 14 carbon atoms, from 2 to 7 carbon atoms, or 5 or 6 carbon atoms. In some embodiments, the heteroaryl group has 1 to 4 heteroatoms, 1 to 3 heteroatoms, or 1 or 2 heteroatoms. Heteroaryl groups include monocyclic and polycyclic (e.g., having 2, 3 or 4 fused rings) systems. Examples of heteroaryl groups include, but are not limited to, pyridyl, pyrimidinyl, pyrazinyl, pyridazinyl, triazinyl, furyl, quinolyl, isoquinolyl, thienyl, imidazolyl, thiazolyl, indolyl (such as indol-3-yl), pyrryl, oxazolyl, benzofuryl, benzothienyl, benzthiazolyl, isoxazolyl, pyrazolyl, triazolyl, tetrazolyl, indazolyl, 1,2,4-thiadiazolyl, isothiazolyl, benzothienyl, purinyl, carbazolyl, benzimidazolyl, indolinyl, pyranyl, oxadiazolyl, isoxazolyl, triazolyl, thianthrenyl, pyrazolyl, indolizinyl, isoindolyl, isobenzofuranyl, benzoxazolyl, xanthenyl, 2H-pyrrolyl, pyrrolyl, 3H-indolyl, 4H-quinolizinyl, phthalazinyl, naphthyridinyl, quinazolinyl, phenanthridinyl, acridinyl, perimidinyl, phenanthrolinyl, phenazinyl, isothiazolyl, phenothiazinyl, isoxazolyl, furazanyl, phenoxazinyl groups, and the like. Suitable heteroaryl groups include 1,2,3-triazole, 1,2,4-triazole, 5-amino-1,2,4-triazole, imidazole, oxazole, isoxazole, 1,2,3-oxadiazole, 1,2,4-oxadiazole, 3-amino-1,2,4-oxadiazole, 1,2,5-oxadiazole, 1,3,4-oxadiazole, pyridine, and 2-aminopyridine.

As used herein, the term “heteroarylalkyl” means a C_1-6alkyl group substituted by a heteroaryl group.

As used herein, the term “heteroarylamino” means an amino group substituted by a heteroaryl group. An example of a heteroarylamino is —NH-(2-pyridyl).

As used herein, the term “heteroarylene” means a heteroaryl linking group, i.e., a heteroaryl group that links one group to another group in a molecule.

As used herein, the term “heterocycle” or “heterocyclic ring” means a 5- to 7-membered mono- or bicyclic or 7- to 10-membered bicyclic heterocyclic ring system any ring of which may be saturated or unsaturated, and which consists of carbon atoms and from one to three heteroatoms chosen from N, O and S, and wherein the N and S heteroatoms may optionally be oxidized, and the N heteroatom may optionally be quaternized, and including any bicyclic group in which any of the above-defined heterocyclic rings is fused to a benzene ring. Particularly useful are rings containing one oxygen or sulfur, one to three nitrogen atoms, or one oxygen or sulfur combined with one or two nitrogen atoms. The heterocyclic ring may be attached at any heteroatom or carbon atom which results in the creation of a stable structure. Examples of heterocyclic groups include, but are not limited to, piperidinyl, piperazinyl, 2-oxopiperazinyl, 2-oxopiperidinyl, 2-oxopyrrolodinyl, 2-oxoazepinyl, azepinyl, pyrrolyl, 4-piperidonyl, pyrrolidinyl, pyrazolyl, pyrazolidinyl, imidazolyl, imidazolinyl, imidazolidinyl, pyridyl, pyrazinyl, pyrimidinyl, pyridazinyl, oxazolyl, oxazolidinyl, isoxazolyl, isoxazolidinyl, morpholinyl, thiazolyl, thiazolidinyl, isothiazolyl, quinuclidinyl, isothiazolidinyl, indolyl, quinolinyl, isoquinolinyl, benzimidazolyl, thiadiazoyl,benzopyranyl, benzothiazolyl, benzoxazolyl, furyl, tetrahydrofuryl, tetrahydropyranyl, thienyl,benzothienyl, thiamorpholinyl, thiamorpholinyl sulfoxide, thiamorpholinyl sulfone, and oxadiazolyl. Morpholino is the same as morpholinyl.

As used herein, the term “heterocycloalkyl” means non-aromatic heterocycles having up to 20 ring-forming atoms including cyclized alkyl, alkenyl, and alkynyl groups, where one or more of the ring-forming carbon atoms is replaced by a heteroatom such as an O, N, or S atom. Heterocycloalkyl groups can be mono or polycyclic (e.g., fused, bridged, or spiro systems). In some embodiments, the heterocycloalkyl group has from 1 to 20 carbon atoms, or from 3 to 20 carbon atoms. In some embodiments, the heterocycloalkyl group contains 3 to 14 ring-forming atoms, 3 to 7 ring-forming atoms, or 5 or 6 ring-forming atoms. In some embodiments, the heterocycloalkyl group has 1 to 4 heteroatoms, 1 to 3 heteroatoms, or 1 or 2 heteroatoms. In some embodiments, the heterocycloalkyl group contains 0 to 3 double bonds. In some embodiments, the heterocycloalkyl group contains 0 to 2 triple bonds. Examples of heterocycloalkyl groups include, but are not limited to, morpholino, thiomorpholino, piperazinyl, tetrahydrofuranyl, tetrahydrothienyl, 2,3-dihydrobenzofuryl, 1,3-benzodioxole, benzo-1,4-dioxane, piperidinyl, pyrrolidinyl, isoxazolidinyl, oxazolidinyl, isothiazolidinyl, pyrazolidinyl, thiazolidinyl, imidazolidinyl, pyrrolidin-2-one-3-yl, and the like. In addition, ring-forming carbon atoms and heteroatoms of a heterocycloalkyl group can be optionally substituted by oxo or sulfido. For example, a ring-forming S atom can be substituted by 1 or 2 oxo (form a S(O) or S(O)₂). For another example, a ring-forming C atom can be substituted by oxo (form carbonyl). Also included in the definition of heterocycloalkyl are moieties that have one or more aromatic rings fused (having a bond in common with) to the nonaromatic heterocyclic ring including, but not limited to, pyridinyl, thiophenyl, phthalimidyl, naphthalimidyl, and benzo derivatives of heterocycles such as indolene, isoindolene, 4,5,6,7-tetrahydrothieno[2,3-c]pyridine-5-yl, 5,6-dihydrothieno[2,3-c]pyridin-7(4H)-one-5-yl, isoindolin-1-one-3-yl, and 3,4-dihydroisoquinolin-1(2H)-one-3-yl groups. Ring-forming carbon atoms and heteroatoms of the heterocycloalkyl group can be optionally substituted by oxo or sulfido.

As used herein, the term “heterocycloalkylalkyl” refers to a C_1-6alkyl substituted by heterocycloalkyl.

As used herein, the term “hydroxy” or “hydroxyl” means an —OH group.

As used herein, the term “hydroxyalkyl” or “hydroxylalkyl” means an alkyl group substituted by a hydroxyl group. Examples of a hydroxylalkyl include, but are not limited to, —CH₂OH and —CH₂CH₂OH.

As used herein, the term “individual” or “patient,” used interchangeably, means any animal, including mammals, such as mice, rats, other rodents, rabbits, dogs, cats, swine, cattle, sheep, horses, or primates, such as humans.

As used herein, the phrase “inhibiting the growth” means reducing by any measurable amount the growth of one or more microbes, such as bacteria. In some embodiments, the inhibition of growth may result in cell death of the microbe.

As used herein, the phrase “in need thereof” means that the animal or mammal has been identified as having a need for the particular method or treatment. In some embodiments, the identification can be by any means of diagnosis. In any of the methods and treatments described herein, the animal or mammal can be in need thereof. In some embodiments, the animal or mammal is in an environment or will be traveling to an environment in which a particular disease, disorder, or condition is prevelant.

As used herein, the phrase “in situ gellable” means embracing not only liquids of low viscosity that form gels upon contact with the eye or with lacrimal fluid in the exterior of the eye, but also more viscous liquids such as semi-fluid and thixotropic gels that exhibit substantially increased viscosity or gel stiffness upon administration to the eye.

As used herein, the phrase “integer from 1 to 5” means 1, 2, 3, 4, or 5.

As used herein, the term “isolated” means that the compounds described herein are separated from other components of either (a) a natural source, such as a plant or cell, such as a bacterial culture, or (b) a synthetic organic chemical reaction mixture, such as by conventional techniques.

As used herein, the term “malarialcidal” means that the compound inhibits, prevents, or destroys the growth or proliferation of a Plasmodium species.

As used herein, the term “mammal” means a rodent (i.e., a mouse, a rat, or a guinea pig), a monkey, a cat, a dog, a cow, a horse, a pig, or a human. In some embodiments, the mammal is a human.

As used herein, the phrases “MDR-TB”, “multi-drug resistant TB”, and “multi-drug resistant Tuberculosis” mean TB with resistance to isoniazid and rifampicin, the two most powerful first line drugs.

As used herein, the term “microbe” means a bacteria, fungi, protozoa, or virus.

As used herein, the term “nitro” means —NO₂.

As used herein, the term “n-membered”, where n is an integer, typically describes the number of ring-forming atoms in a moiety, where the number of ring-forming atoms is n. For example, pyridine is an example of a 6-membered heteroaryl ring and thiophene is an example of a 5-membered heteroaryl ring.

As used herein, the phrase “ophthalmically acceptable” means having no persistent detrimental effect on the treated eye or the functioning thereof, or on the general health of the subject being treated. However, it will be recognized that transient effects such as minor irritation or a “stinging” sensation are common with topical ophthalmic administration of drugs and the existence of such transient effects is not inconsistent with the composition, formulation, or ingredient (e.g., excipient) in question being “ophthalmically acceptable” as herein defined.

As used herein, the phrase “optionally substituted” means that substitution is optional and therefore includes both unsubstituted and substituted atoms and moieties. A “substituted” atom or moiety indicates that any hydrogen on the designated atom or moiety can be replaced with a selection from the indicated substituent groups, provided that the normal valency of the designated atom or moiety is not exceeded, and that the substitution results in a stable compound. For example, if a methyl group is optionally substituted, then 3 hydrogen atoms on the carbon atom can be replaced with substituent groups.

As used herein, the phrase “otically acceptable” means having no persistent detrimental effect on the treated ear or the functioning thereof, or on the general health of the subject being treated.

As used herein, the phrase “pharmaceutically acceptable” means those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with tissues of humans and animals. In some embodiments, “pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans.

As used herein, the phrase “pharmaceutically acceptable salt(s),” includes, but is not limited to, salts of acidic or basic groups. Compounds that are basic in nature are capable of forming a wide variety of salts with various inorganic and organic acids. Acids that may be used to prepare pharmaceutically acceptable acid addition salts of such basic compounds are those that form non-toxic acid addition salts, i.e., salts containing pharmacologically acceptable anions including, but not limited to, sulfuric, thiosulfuric, citric, maleic, acetic, oxalic, hydrochloride, hydrobromide, hydroiodide, nitrate, sulfate, bisulfate, bisulfite, phosphate, acid phosphate, isonicotinate, borate, acetate, lactate, salicylate, citrate, acid citrate, tartrate, oleate, tannate, pantothenate, bitartrate, ascorbate, succinate, maleate, gentisinate, fumarate, gluconate, glucaronate, saccharate, formate, benzoate, glutamate, methanesulfonate, ethanesulfonate, benzenesulfonate, p-toluenesulfonate, bicarbonate, malonate, mesylate, esylate, napsydisylate, tosylate, besylate, orthophoshate, trifluoroacetate, and pamoate (i.e., 1,1′-methylene-bis-(2-hydroxy-3-naphthoate)) salts. Compounds that include an amino moiety may form pharmaceutically acceptable salts with various amino acids, in addition to the acids mentioned above. Compounds that are acidic in nature are capable of forming base salts with various pharmacologically acceptable cations. Examples of such salts include, but are not limited to, alkali metal or alkaline earth metal salts and, particularly, calcium, magnesium, ammonium, sodium, lithium, zinc, potassium, and iron salts. The present disclosure also includes quaternary ammonium salts of the compounds described herein, where the compounds have one or more tertiary amine moiety.

As used herein, the term “phenyl” means —C₆H₅. A phenyl group can be unsubstituted or substituted with one, two, or three suitable substituents.

As used herein, the terms “prevention” or “preventing” mean a reduction of the risk of acquiring a particular disease, condition, or disorder.

As used herein, the term “prodrug” means a derivative of a known direct acting drug, which derivative has enhanced delivery characteristics and therapeutic value as compared to the drug, and is transformed into the active drug by an enzymatic or chemical process.

As used herein, the term “purified” means that when isolated, the isolate contains at least 90%, at least 95%, at least 98%, or at least 99% of a compound described herein by weight of the isolate.

As used herein, the phrase “quaternary ammonium salts” means derivatives of the disclosed compounds with one or more tertiary amine moieties wherein at least one of the tertiary amine moieties in the parent compound is modified by converting the tertiary amine moiety to a quaternary ammonium cation via alkylation (and the cations are balanced by anions such as Cl⁻, CH₃COO⁻, and CF₃COO⁻), for example methylation or ethylation.

As used herein, the term “semicarbazone” means ═NNHC(═O)NH₂.

As used herein, the phrase “solubilizing agent” means agents that result in formation of a micellar solution or a true solution of the drug.

As used herein, the term “solution/suspension” means a liquid composition wherein a first portion of the active agent is present in solution and a second portion of the active agent is present in particulate form, in suspension in a liquid matrix.

As used herein, the phrase “substantially isolated” means a compound that is at least partially or substantially separated from the environment in which it is formed or detected.

As used herein, the phrase “suitable substituent” or “substituent” means a group that does not nullify the synthetic or pharmaceutical utility of the compounds described herein or the intermediates useful for preparing them. Examples of suitable substituents include, but are not limited to: C₁-C₆alkyl, C₁-C₆alkenyl, C₁-C₆alkynyl, C₅-C₆aryl, C₁-C₆alkoxy, C₃-C₅heteroaryl, C₃-C₆cycloalkyl, C₅-C₆aryloxy, —CN, —OH, oxo, halo, haloalkyl, —NO₂, —CO₂H, —NH₂, —NH(C₁-C₈alkyl), —N(C₁-C₈alkyl)₂, —NH(C₆aryl), —N(C₅-C₆aryl)₂, —CHO, —CO(C₁-C₆alkyl), —CO((C₅-C₆)aryl), —CO₂((C₁-C₆)alkyl), and —CO₂((C₅-C₆)aryl). One of skill in art can readily choose a suitable substituent based on the stability and pharmacological and synthetic activity of the compounds described herein.

As used herein, the phrase “therapeutically effective amount” means the amount of active compound or pharmaceutical agent that elicits the biological or medicinal response that is being sought in a tissue, system, animal, individual or human by a researcher, veterinarian, medical doctor or other clinician. The therapeutic effect is dependent upon the disorder being treated or the biological effect desired. As such, the therapeutic effect can be a decrease in the severity of symptoms associated with the disorder and/or inhibition (partial or complete) of progression of the disorder, or improved treatment, healing, prevention or elimination of a disorder, or side-effects. The amount needed to elicit the therapeutic response can be determined based on the age, health, size and sex of the subject. Optimal amounts can also be determined based on monitoring of the subject's response to treatment.

As used herein, the terms “treat,” “treated,” or “treating” mean both therapeutic treatment and prophylactic or preventative measures wherein the object is to prevent or slow down (lessen) an undesired physiological condition, disorder or disease, or obtain beneficial or desired clinical results. For purposes of this disclosure, beneficial or desired clinical results include, but are not limited to, alleviation of symptoms; diminishment of extent of condition, disorder or disease; stabilized (i.e., not worsening) state of condition, disorder or disease; delay in onset or slowing of condition, disorder or disease progression; amelioration of the condition, disorder or disease state or remission (whether partial or total), whether detectable or undetectable; an amelioration of at least one measurable physical parameter, not necessarily discernible by the patient; or enhancement or improvement of condition, disorder or disease. Treatment includes eliciting a clinically significant response without excessive levels of side effects. Treatment also includes prolonging survival as compared to expected survival if not receiving treatment. Thus, “treatment of cancer” or “treating cancer” means an activity that prevents, alleviates or ameliorates any of the primary phenomena (initiation, progression, metastasis) or secondary symptoms associated with the disease.

As used herein, the term “tumor” means a new growth of tissue in which the multiplication of cells is uncontrolled and progressive. The tumor that is particularly relevant to the disclosure is the malignant tumor, one in which the primary tumor has the properties of invasion or metastasis or which shows a greater degree of anaplasia than do benign tumors.

As used herein, the term “ureido” means —NHC(═O)—NH₂.

As used herein, the phrases “XDR-TB”, “extensively drug resistant TB”, and “extensively drug resistant Tuberculosis” mean MDR-TB with resistance to any one of the fluoroquinolone drugs and to at least one of the following three injectable second-line drugs: amikacin, capreomycin, or kanamycin.

At various places in the present specification, substituents of compounds may be disclosed in groups or in ranges. It is specifically intended that the disclosure include each and every individual subcombination of the members of such groups and ranges. For example, the term “C_1-6alkyl” is specifically intended to individually disclose methyl, ethyl, propyl, C₄alkyl, C₅alkyl, and C₆alkyl.

For compounds in which a variable appears more than once, each variable can be a different moiety selected from the Markush group defining the variable. For example, where a structure is described having two R groups that are simultaneously present on the same compound, the two R groups can represent different moieties selected from the Markush groups defined for R. In another example, when an optionally multiple substituent is designated in the form, for example,

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then it is understood that substituent R can occur s number of times on the ring, and R can be a different moiety at each occurrence. Further, in the above example, where the variable T¹is defined to include hydrogens, such as when T¹is CH₂, NH, etc., any H can be replaced with a substituent.

It is further appreciated that certain features of the disclosure, which are, for clarity, described in the context of separate embodiments, can also be provided in combination in a single embodiment. Conversely, various features of the disclosure which are, for brevity, described in the context of a single embodiment, can also be provided separately or in any suitable subcombination.

It is understood that the present disclosure encompasses the use, where applicable, of stereoisomers, diastereomers and optical stereoisomers of the compounds of the disclosure, as well as mixtures thereof. Additionally, it is understood that stereoisomers, diastereomers, and optical stereoisomers of the compounds of the disclosure, and mixtures thereof, are within the scope of the disclosure. By way of non-limiting example, the mixture may be a racemate or the mixture may comprise unequal proportions of one particular stereoisomer over the other. Additionally, the compounds can be provided as a substantially pure stereoisomers, diastereomers and optical stereoisomers (such as epimers).

The compounds described herein can be asymmetric (e.g., having one or more stereocenters). All stereoisomers, such as enantiomers and diastereomers, are intended to be included within the scope of the disclosure unless otherwise indicated. Compounds that contain asymmetrically substituted carbon atoms can be isolated in optically active or racemic forms. Methods of preparation of optically active forms from optically active starting materials are known in the art, such as by resolution of racemic mixtures or by stereoselective synthesis. Many geometric isomers of olefins, C═N double bonds, and the like can also be present in the compounds described herein, and all such stable isomers are contemplated in the present disclosure. Cis and trans geometric isomers of the compounds are also included within the scope of the disclosure and can be isolated as a mixture of isomers or as separated isomeric forms. Where a compound capable of stereoisomerism or geometric isomerism is designated in its structure or name without reference to specific R/S or cis/trans configurations, it is intended that all such isomers are contemplated.

Resolution of racemic mixtures of compounds can be carried out by any of numerous methods known in the art, including, for example, fractional recrystallizaion using a chiral resolving acid which is an optically active, salt-forming organic acid. Suitable resolving agents for fractional recrystallization methods include, but are not limited to, optically active acids, such as the D and L forms of tartaric acid, diacetyltartaric acid, dibenzoyltartaric acid, mandelic acid, malic acid, lactic acid, and the various optically active camphorsulfonic acids such as β-camphorsulfonic acid. Other resolving agents suitable for fractional crystallization methods include, but are not limited to, stereoisomerically pure forms of α-methylbenzylamine (e.g., S and R forms, or diastereomerically pure forms), 2-phenylglycinol, norephedrine, ephedrine, N-methylephedrine, cyclohexylethylamine, 1,2-diaminocyclohexane, and the like. Resolution of racemic mixtures can also be carried out by elution on a column packed with an optically active resolving agent (e.g., dinitrobenzoylphenylglycine). Suitable elution solvent compositions can be determined by one skilled in the art.

Compounds may also include tautomeric forms. Tautomeric forms result from the swapping of a single bond with an adjacent double bond together with the concomitant migration of a proton. Tautomeric forms include prototropic tautomers which are isomeric protonation states having the same empirical formula and total charge. Examples of prototropic tautomers include, but are not limited to, ketone-enol pairs, amide-imidic acid pairs, lactam-lactim pairs, amide-imidic acid pairs, enamine-imine pairs, and annular forms where a proton can occupy two or more positions of a heterocyclic system including, but not limited to, 1H- and 3H-imidazole, 1H-, 2H- and 4H-1,2,4-triazole, 1H- and 2H-isoindole, and 1H- and 2H-pyrazole. Tautomeric forms can be in equilibrium or sterically locked into one form by appropriate substitution.

Compounds also include hydrates and solvates, as well as anhydrous and non-solvated forms.

Compounds can also include all isotopes of atoms occurring in the intermediates or final compounds. Isotopes include those atoms having the same atomic number but different mass numbers. For example, isotopes of hydrogen include tritium and deuterium.

Compounds can also include various charged states. For example, one or more moieties of any of the compounds described herein can be charged. In some instances, any moiety having an amino group can be —NH₃⁺. Thus, each amino group existing in any compound described herein can, independently, be either —NH₂or —NH₃⁺.

In some embodiments, the compounds, or salts thereof, are substantially isolated. Partial separation can include, for example, a composition enriched in the compound of the disclosure. Substantial separation can include compositions containing at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 97%, or at least about 99% by weight of the compound of the disclosure, or salt thereof. Methods for isolating compounds and their salts are routine in the art.

Although the disclosed compounds are suitable, other functional groups can be incorporated into the compound with an expectation of similar results. In particular, thioamides and thioesters are anticipated to have very similar properties. The distance between aromatic rings can impact the geometrical pattern of the compound and this distance can be altered by incorporating aliphatic chains of varying length, which can be optionally substituted or can comprise an amino acid, a dicarboxylic acid or a diamine. The distance between and the relative orientation of monomers within the compounds can also be altered by replacing the amide bond with a surrogate having additional atoms. Thus, replacing a carbonyl group with a dicarbonyl alters the distance between the monomers and the propensity of dicarbonyl unit to adopt an anti arrangement of the two carbonyl moiety and alter the periodicity of the compound. Pyromellitic anhydride represents still another alternative to simple amide linkages which can alter the conformation and physical properties of the compound. Modern methods of solid phase organic chemistry (E. Atherton and R. C. Sheppard, Solid Phase Peptide Synthesis A Practical Approach IRL Press Oxford 1989) now allow the synthesis of homodisperse compounds with molecular weights approaching 5,000 Daltons. Other substitution patterns are equally effective.

The compounds also include derivatives referred to as prodrugs.

Some of the compounds may be capable of adopting amphiphilic conformations that allow for the segregation of polar and nonpolar regions of the molecule into different spatial regions and provide the basis for a number of uses. For example, some compounds may adopt amphiphilic conformations that are capable of binding to heparin (including, for example, unfractionated heparin, low molecular weight heparin, and synthetically modified heparin or low molecular heparin derivatives). Although not wishing to be bound by any particular theory, it is believed that compounds can interact with heparin through electrostatic interactions.

Compounds containing an amine function can also form N-oxides. A reference herein to a compound that contains an amine function also includes the N-oxide. Where a compound contains several amine functions, one or more than one nitrogen atom can be oxidized to form an N-oxide. Examples of N-oxides include N-oxides of a tertiary amine or a nitrogen atom of a nitrogen-containing heterocycle. N-Oxides can be formed by treatment of the corresponding amine with an oxidizing agent such as hydrogen peroxide or a per-acid (e.g., a peroxycarboxylic acid) (see, Advanced Organic Chemistry, by Jerry March, 4th Edition, Wiley Interscience).

The present disclosure provides compounds of Formula I

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wherein:

X is S, O, or N;

R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nN(CH₃)₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂—NC(═N)NH₂, —C≡C—CH₂NH₂, —C(═O)(CH₂)_nNH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂NC(═N)NH₂, where n is 2, 3, or 4;

R²is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; and

R³is H, halo, haloalkyl, —NH₂, or C_1-3alkyl;

or a pharmaceutically acceptable salt thereof;

provided that:

when X is S, and R²and R³are H, then R¹is not —C(═O)(CH₂)₂NH₂; and

when X is S, R³is H, and R²is Cl or —CF₃, then R¹is not —(CH₂)₃N(CH₃)₂.

In some embodiments, R¹is —(CH₂)_nNH₂, —(CH₂)_nN(CH₃)₂, or —C(═O)(CH₂)_nNH₂, where n is 2, 3, or 4. In some embodiments, R¹is —(CH₂)₃NH₂, —(CH₂)₃N(CH₃)₂, or —C(═O)(CH₂)₂NH₂.

In some embodiments, R²is H, halo, or haloalkyl. In some embodiments, R²is H, —CF₃, F, Br, or Cl.

In some embodiments, R³is H or —NH₂.

In some embodiments, X is S or O.

In some embodiments, X is S or O; R¹is —(CH₂)₃NH₂, —(CH₂)₃N(CH₃)₂, or —C(═O)(CH₂)₂NH₂; R²is H, —CF₃, or Cl; and R³is H or —NH₂.

In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula II

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wherein:

X is N, O, or S;

R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

R²is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; and

R³is H, halo, haloalkyl, —NH₂, or C_1-3alkyl;

or a pharmaceutically acceptable salt thereof.

In some embodiments, X is N.

In some embodiments, R¹is —(CH₂)_nNH₂. In some embodiments, R¹is —(CH₂)₃NH₂.

In some embodiments, R²is H or halo. In some embodiments, R²is H or —Br.

In some embodiments, R³is H or halo. In some embodiments, R³is H or —Br.

In some embodiments, X is N; R¹is —(CH₂)₃NH₂; R²is H or —Br; and R³is H or —Br.

In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula III

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wherein:

R²is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

or a pharmaceutically acceptable salt thereof.

In some embodiments, R¹is —(CH₂)₄NH₂, —(CH₂)₃NH₂, or —(CH₂)₂NH₂.

In some embodiments, R²is —(CH₂)₄NH₂, —(CH₂)₃NH₂, or —(CH₂)₂NH₂.

In some embodiments, R¹is —(CH₂)₄NH₂, —(CH₂)₃NH₂, or —(CH₂)₂NH₂; and R²is —(CH₂)₄NH₂, —(CH₂)₃NH₂, or —(CH₂)₂NH₂.

In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula IV

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wherein:

R¹is H, halo, haloC_1-8alkyl, —NH₂, C_1-8alkyl, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or substituted or unsubstituted piperazine, substituted or unsubstituted piperidine, substituted or unsubstituted pyrrolidine, substituted or unsubstituted aromatic, or substituted or unsubstituted heteroaromatic; or —X—Y wherein X is —(CH₂)_rwhere r is 1 to 8, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkyl, haloC_1-8alkyl, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, substituted or unsubstituted C_1-8alkyl aromatic, substituted or unsubstituted C_1-8alkyl heteroaromatic, or any one of

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R²is H, halo, haloC_1-8alkyl, —NH₂, C_1-8alkyl, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or substituted or unsubstituted piperazine, substituted or unsubstituted piperidine, substituted or unsubstituted pyrrolidine, substituted or unsubstituted aromatic, or substituted or unsubstituted heteroaromatic; or —X—Y wherein X is —(CH₂)_rwhere r is 1 to 8, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkyl, haloC_1-8alkyl, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, substituted or unsubstituted C_1-8alkyl aromatic, substituted or unsubstituted C_1-8alkyl heteroaromatic, or any one of

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R³is H, halo, haloC_1-8alkyl, —NH₂, C_1-8alkyl, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or substituted or unsubstituted piperazine, substituted or unsubstituted piperidine, substituted or unsubstituted pyrrolidine, substituted or unsubstituted aromatic, or substituted or unsubstituted heteroaromatic; or —X—Y wherein X is —(CH₂)_rwhere r is 1 to 8, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkyl, haloC_1-8alkyl, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, substituted or unsubstituted C_1-8alkyl aromatic, substituted or unsubstituted C_1-8alkyl heteroaromatic, or any one of

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R⁴is H, halo, haloC_1-8alkyl, —NH₂, C_1-8alkyl, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or substituted or unsubstituted piperazine, substituted or unsubstituted piperidine, substituted or unsubstituted pyrrolidine, substituted or unsubstituted aromatic, or substituted or unsubstituted heteroaromatic; or —X—Y wherein X is —(CH₂)_rwhere r is 1 to 8, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkyl, haloC_1-8alkyl, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, substituted or unsubstituted C_1-8alkyl aromatic, substituted or unsubstituted C_1-8alkyl heteroaromatic, or any one of

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or

—X(Z)(Z²), where X is —CH or —N, and Z¹and Z²are, independently, —NH₂, C_1-8alkyl, haloC_1-8alkyl, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, substituted or unsubstituted C_1-8alkyl aromatic, substituted or unsubstituted C_1-8alkyl heteroaromatic; wherein each substituent is, independently, C₁-C₆alkyl, C₁-C₆alkenyl, C₁-C₆alkynyl, C₅-C₆aryl, C₁-C₆alkoxy, C₃-C₅heteroaryl, C₃-C₆cycloalkyl, C₅-C₆aryloxy, —CN, —OH, oxo, halo, haloalkyl, —NO₂, —CO₂H, —NH₂, —NH(C₁-C₈alkyl), —N(C₁-C₈alkyl)₂, —NH(C₆aryl), —N(C₅-C₆aryl)₂, —CHO, —CO(C₁-C₆alkyl), —CO((C₅-C₆)aryl), —CO₂((C₁-C₆)alkyl), or —CO₂((C₅-C₆)aryl);

R⁵is H, halo, haloC_1-8alkyl, —NH₂, C_1-8alkyl, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or substituted or unsubstituted piperazine, substituted or unsubstituted piperidine, substituted or unsubstituted pyrrolidine, substituted or unsubstituted aromatic, or substituted or unsubstituted heteroaromatic; or —X—Y wherein X is —(CH₂)_rwhere r is 1 to 8, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkyl, haloC_1-8alkyl, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, substituted or unsubstituted C_1-8alkyl aromatic, substituted or unsubstituted C_1-8alkyl heteroaromatic, or any one of

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R⁶is H, halo, haloC_1-8alkyl, —NH₂, C_1-8alkyl, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or substituted or unsubstituted piperazine, substituted or unsubstituted piperidine, substituted or unsubstituted pyrrolidine, substituted or unsubstituted aromatic, or substituted or unsubstituted heteroaromatic; or —X—Y wherein X is —(CH₂)_rwhere r is 1 to 8, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkyl, haloC_1-8alkyl, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, substituted or unsubstituted C_1-8alkyl aromatic, substituted or unsubstituted C_1-8alkyl heteroaromatic, or any one of

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R⁷is H, halo, haloC_1-8alkyl, —NH₂, C_1-8alkyl, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or substituted or unsubstituted piperazine, substituted or unsubstituted piperidine, substituted or unsubstituted pyrrolidine, substituted or unsubstituted aromatic, or substituted or unsubstituted heteroaromatic; or —X—Y wherein X is —(CH₂)_rwhere r is 1 to 8, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkyl, haloC_1-8alkyl, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, substituted or unsubstituted C_1-8alkyl aromatic, substituted or unsubstituted C_1-8alkyl heteroaromatic, or any one of

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R⁸is H, halo, haloC_1-8alkyl, —NH₂, C_1-8alkyl, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or substituted or unsubstituted piperazine, substituted or unsubstituted piperidine, substituted or unsubstituted pyrrolidine, substituted or unsubstituted aromatic, or substituted or unsubstituted heteroaromatic; or —X—Y wherein X is —(CH₂)_rwhere r is 1 to 8, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkyl, haloC_1-8alkyl, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, substituted or unsubstituted C_1-8alkyl aromatic, substituted or unsubstituted C_1-8alkyl heteroaromatic, or any one of

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R⁹is H, halo, haloC_1-8alkyl, —NH₂, C_1-8alkyl, —NH(CH₂)_nNH₂, —(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; or substituted or unsubstituted piperazine, substituted or unsubstituted piperidine, substituted or unsubstituted pyrrolidine, substituted or unsubstituted aromatic, or substituted or unsubstituted heteroaromatic; or —X—Y wherein X is —(CH₂)_rwhere r is 1 to 8, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkyl, haloC_1-8alkyl, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, substituted or unsubstituted C_1-8alkyl aromatic, substituted or unsubstituted C_1-8alkyl heteroaromatic, or any one of

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In some embodiments, R¹is H, halo, haloalkyl, —NH₂, C_1-3alkyl, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4. In some embodiments, R¹is halo, —CF₃, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(C—C)CH₂NH₂, —(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—CH₂NH₂, or —(C—C)CH₂NC(═N)NH₂. In some embodiments, R¹is halo, —CF₃, —(CH₂)₂NH₂, —(CH₂)₃NH₂, —O—(CH₂)₃NH₂, —(CH₂)₃NC(═N)NH₂, —(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—CH₂NH₂, —(C≡C)CH₂NH₂, or —(C≡C)CH₂NC(═N)NH₂. In some embodiments, R¹is —X—Y wherein X is CH₂, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, or any one of

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In some embodiments, R¹is —X(Z¹)(Z²), where X is —CH or —N, and Z¹and Z²are, independently, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, or C_1-6cyclioalkyl substituted C_1-3alkylamidine; wherein each substituent is, independently, C₁-C₆alkyl, C₁-C₆alkenyl, C₁-C₆alkynyl, C₅-C₆aryl, C₁-C₆alkoxy, C₃-C₅heteroaryl, C₃-C₆cycloalkyl, C₅-C₆aryloxy, —CN, —OH, oxo, halo, haloalkyl, —NO₂, —CO₂H, —NH₂, —NH(C₁-C₈alkyl), —N(C₁-C₈alkyl)₂, —NH(C₆aryl), —N(C₅-C₆aryl)₂, —CHO, —CO(C₁-C₆alkyl), —CO((C₅-C₆)aryl), —CO₂((C₁-C₆)alkyl), or —CO₂((C₅-C₆)aryl).

In some embodiments, R²is H, halo, haloalkyl, —NH₂, C_1-3alkyl, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4. In some embodiments, R²is halo, —CF₃, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—CH₂NH₂, —(C≡C)CH₂NH₂, or —(C≡C)CH₂NC(═N)NH₂. In some embodiments, R²is halo, —CF₃, —(CH₂)₂NH₂, —(CH₂)₃NH₂, —O—(CH₂)₃NH₂, —(CH₂)₃NC(═N)NH₂, —(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NH₂, —(C≡C)CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —(C≡C)CH₂NC(═N)NH₂. In some embodiments, R²is —X—Y wherein X is CH₂, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, or any one of

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In some embodiments, R²is —X(Z¹)(Z²), where X is —CH or —N, and Z¹and Z²are, independently, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, or C_1-6cyclioalkyl substituted C_1-3alkylamidine; wherein each substituent is, independently, C₁-C₆alkyl, C₁-C₆alkenyl, C₁-C₆alkynyl, C₅-C₆aryl, C₁-C₆alkoxy, C₃-C₅heteroaryl, C₃-C₆cycloalkyl, C₅-C₆aryloxy, —CN, —OH, oxo, halo, haloalkyl, —NO₂, —CO₂H, —NH₂, —NH(C₁-C₈alkyl), —N(C₁-C₈alkyl)₂, —NH(C₆aryl), —N(C₅-C₆aryl)₂, —CHO, —CO(C₁-C₆alkyl), —CO((C₅-C₆)aryl), —CO₂((C₁-C₆)alkyl), or —CO₂((C₅-C₆)aryl).

In some embodiments, R³is H, halo, haloalkyl, —NH₂, C_1-3alkyl, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4. In some embodiments, R³is H, —CF₃, —O—(CH₂)_nNH₂, or —O—(CH₂)_nNC(═N)NH₂. In some embodiments, R³is H, —CF₃, —O—(CH₂)₃NH₂, or —O—(CH₂)₃NC(═N)NH₂. In some embodiments, R³is —X—Y wherein X is CH₂, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, or any one of

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In some embodiments, R³is —X(Z¹)(Z²), where X is —CH or —N, and Z¹and Z²are, independently, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, or C_1-6cyclioalkyl substituted C_1-3alkylamidine; wherein each substituent is, independently, C₁-C₆alkyl, C₁-C₆alkenyl, C₁-C₆alkynyl, C₅-C₆aryl, C₁-C₆alkoxy, C₃-C₅heteroaryl, C₃-C₆cycloalkyl, C₅-C₆aryloxy, —CN, —OH, oxo, halo, haloalkyl, —NO₂, —CO₂H, —NH₂, —NH(C₁-C₈alkyl), —N(C₁-C₈alkyl)₂, —NH(C₆aryl), —N(C₅-C₆aryl)₂, —CHO, —CO(C₁-C₆alkyl), —CO((C₅-C₆)aryl), —CO₂((C₁-C₆)alkyl), or —CO₂((C₅-C₆)aryl). In some embodiments, R³is —X—Y wherein X is —NH—C(═O) and Y is any one of

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In some embodiments, R⁴is H, halo, haloalkyl, —NH₂, C_1-3alkyl, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C═C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4. In some embodiments, R⁴is H, halo, —O—(CH₂)_nNH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —(C≡C)CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—CH₂NH₂, —(C≡C)(CH₂)_nNH₂, or —(C≡C)(CH₂)_nNC(═N)NH₂. In some embodiments, R⁴is H, halo, —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, —(CH₂)₂NC(═N)NH₂, —(C≡C)CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —(C≡C)(CH₂)₂NH₂, —(C≡C)CH₂NC(═N)NH₂, or —(C≡C)(CH₂)₂NC(═N)NH₂. In some embodiments, R⁴is —X—Y wherein X is CH₂, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, or any one of

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In some embodiments, R⁴is —X(Z¹)(Z²), where X is —CH or —N, and Z¹and Z²are, independently, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, or C_1-6cyclioalkyl substituted C_1-3alkylamidine; wherein each substituent is, independently, C₁-C₆alkyl, C₁-C₆alkenyl, C₁-C₆alkynyl, C₅-C₆aryl, C₁-C₆alkoxy, C₃-C₅heteroaryl, C₃-C₆cycloalkyl, C₅-C₆aryloxy, —CN, —OH, oxo, halo, haloalkyl, —NO₂, —CO₂H, —NH₂, —NH(C₁-C₈alkyl), —N(C₁-C₈alkyl)₂, —NH(C₆aryl), —N(C₅-C₆aryl)₂, —CHO, —CO(C₁-C₆alkyl), —CO((C₅-C₆)aryl), —CO₂((C₁-C₆)alkyl), or —CO₂((C₅-C₆)aryl).

In some embodiments, R⁵is H, halo, haloalkyl, —NH₂, C_1-3alkyl, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4. In some embodiments, R⁵is H, halo, —O—(CH₂)_nNH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—CH₂NH₂, —(C≡C)(CH₂)_nNH₂, or —(C≡C)(CH₂)_nNC(═N)NH₂. In some embodiments, R⁵is H, halo, —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, —(CH₂)₂NC(═N)NH₂, —(C≡C)CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—CH₂NH₂, —(C≡C)(CH₂)₂NH₂, —(C≡C)CH₂NC(═N)NH₂, or —(C≡C)(CH₂)₂NC(═N)NH₂. In some embodiments, R⁵is —X—Y wherein X is CH₂, O, S, —CH═CH, —CH≡CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, or any one of

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In some embodiments, R⁵is —X(Z¹)(Z²), where X is —CH or —N, and Z¹and Z²are, independently, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, or C_1-6cyclioalkyl substituted C_1-3alkylamidine; wherein each substituent is, independently, C₁-C₆alkyl, C₁-C₆alkenyl, C₁-C₆alkynyl, C₅-C₆aryl, C₁-C₆alkoxy, C₃-C₅heteroaryl, C₃-C₆cycloalkyl, C₅-C₆aryloxy, —CN, —OH, oxo, halo, haloalkyl, —NO₂, —CO₂H, —NH₂, —NH(C₁-C₈alkyl), —N(C₁-C₈alkyl)₂, —NH(C₆aryl), —N(C₅-C₆aryl)₂, —CHO, —CO(C₁-C₆alkyl), —CO((C₅-C₆)aryl), —CO₂((C₁-C₆)alkyl), or —CO₂((C₅-C₆)aryl).

In some embodiments, R⁶is H, halo, haloalkyl, —NH₂, C_1-3alkyl, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C═C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4. In some embodiments, R⁶is H, —(CH₂)_nNH₂, or —O—(CH₂)_nNC(═N)NH₂. In some embodiments, R⁶is H, —(CH₂)₃NH₂, or —O—(CH₂)₃NC(═N)NH₂. In some embodiments, R⁶is —X—Y wherein X is CH₂, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, or any one of

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In some embodiments, R⁶is —X(Z¹)(Z²), where X is —CH or —N, and Z and Z are, independently, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, or C_1-6cyclioalkyl substituted C_1-3alkylamidine; wherein each substituent is, independently, C₁-C₆alkyl, C₁-C₆alkenyl, C₁-C₆alkynyl, C₅-C₆aryl, C₁-C₆alkoxy, C₃-C₅heteroaryl, C₃-C₆cycloalkyl, C₅-C₆aryloxy, —CN, —OH, oxo, halo, haloalkyl, —NO₂, —CO₂H, —NH₂, —NH(C₁-C₈alkyl), —N(C₁-C₈alkyl)₂, —NH(C₆aryl), —N(C₅-C₆aryl)₂, —CHO, —CO(C₁-C₆alkyl), —CO((C₅-C₆)aryl), —CO₂((C₁-C₆)alkyl), or —CO₂((C₅-C₆)aryl).

In some embodiments, R⁷is H, halo, haloalkyl, —NH₂, C_1-3alkyl, —NH(CH₂)NH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)NH₂, —O—(CH₂)NC(═N)NH₂, —C═C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C═C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4. In some embodiments, R⁷is H, —(CH₂)_nNH₂, or —O—(CH₂)_nNC(═N)NH₂. In some embodiments, R⁷is H, —(CH₂)₃NH₂, or —O—(CH₂)₃NC(═N)NH₂. In some embodiments, R⁷is —X—Y wherein X is CH₂, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, or any one of

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In some embodiments, R⁷is —X(Z¹)(Z²), where X is —CH or —N, and Z¹and Z²are, independently, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, or C_1-6cyclioalkyl substituted C_1-3alkylamidine; wherein each substituent is, independently, C₁-C₆alkyl, C₁-C₆alkenyl, C₁-C₆alkynyl, C₅-C₆aryl, C₁-C₆alkoxy, C₃-C₅heteroaryl, C₃-C₆cycloalkyl, C₅-C₆aryloxy, —CN, —OH, oxo, halo, haloalkyl, —NO₂, —CO₂H, —NH₂, —NH(C₁-C₈alkyl), —N(C₁-C₈alkyl)₂, —NH(C₆aryl), —N(C₅-C₆aryl)₂, —CHO, —CO(C₁-C₆alkyl), —CO((C₅-C₆)aryl), —CO₂((C₁-C₆)alkyl), or —CO₂((C₅-C₆)aryl).

In some embodiments, R⁸is H, halo, haloalkyl, —NH₂, C_1-3alkyl, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4. In some embodiments, R⁸is H or halo. In some embodiments, R⁸is —X—Y wherein X is CH₂, O, S, —CH═CH, —CH—CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, or any one of

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In some embodiments, R⁸is —X(Z¹)(Z²), where X is —CH or —N, and Z¹and Z²are, independently, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, or C_1-6cyclioalkyl substituted C_1-3alkylamidine; wherein each substituent is, independently, C₁-C₆alkyl, C₁-C₆alkenyl, C₁-C₆alkynyl, C₅-C₆aryl, C₁-C₆alkoxy, C₃-C₅heteroaryl, C₃-C₆cycloalkyl, C₅-C₆aryloxy, —CN, —OH, oxo, halo, haloalkyl, —NO₂, —CO₂H, —NH₂, —NH(C₁-C₈alkyl), —N(C₁-C₈alkyl)₂, —NH(C₆aryl), —N(C₅-C₆aryl)₂, —CHO, —CO(C₁-C₆alkyl), —CO((C₅-C₆)aryl), —CO₂((C₁-C₆)alkyl), or —CO₂((C₅-C₆)aryl).

In some embodiments, R⁹is H, halo, haloalkyl, —NH₂, C_1-3alkyl, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4. In some embodiments, R⁹is H or halo. In some embodiments, R⁹is —X—Y wherein X is CH₂, O, S, —CH═CH, —CH≡CH, —C(═O)O, —C(═O)NH, —NH, —NH—C(═O), —NH—C(═O)NH, —NH—C(═S)NH, —S(═O), —S(═O)₂, or —S(═O)₂NH, and Y is H, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, C_1-6cyclioalkyl substituted C_1-3alkylamidine, or any one of

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In some embodiments, R⁹is —X(Z¹)(Z²), where X is —CH or —N, and Z¹and Z²are, independently, —NH₂, C_1-8alkylamine, C_0-8alkyl-substituted C_1-3alkylamine, C_1-6cycloalkylamine, C_1-6cycloalkyl substituted C_1-3alkylamine amine, C_0-8alkylguanidine, C_0-8alkyl substituted C_1-3alkylguanidine, C_1-6cycloalkylguanidine, C_1-6cyclioalkyl substituted C_1-3alkylguanidine, C_0-8alkylamidine, C_0-8alkyl substituted C_1-3alkylamidine, C_1-6cycloalkylamidine, or C_1-6cyclioalkyl substituted C_1-3alkylamidine; wherein each substituent is, independently, C₁-C₆alkyl, C₁-C₆alkenyl, C₁-C₆alkynyl, C₅-C₆aryl, C₁-C₆alkoxy, C₃-C₅heteroaryl, C₃-C₆cycloalkyl, C₅-C₆aryloxy, —CN, —OH, oxo, halo, haloalkyl, —NO₂, —CO₂H, —NH₂, —NH(C₁-C₈alkyl), —N(C₁-C₈alkyl)₂, —NH(C₆aryl), —N(C₅-C₆aryl)₂, —CHO, —CO(C₁-C₆alkyl), —CO((C₅-C₆)aryl), —CO₂((C₁-C₆)alkyl), or —CO₂((C₅-C₆)aryl).

In some embodiments, R¹is halo, —CF₃, —(CH₂)₂NH₂, —(CH₂)₃NH₂, —O—(CH₂)₃NH₂, —(CH₂)₃NC(═N)NH₂, —(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—CH₂NH₂, —(C≡C)CH₂NH₂, or —(C≡C)CH₂NC(═N)NH₂; R²is halo, —CF₃, —(CH₂)₂NH₂, —(CH₂)₃NH₂, —O—(CH₂)₃NH₂, —(CH₂)₃NC(═N)NH₂, —(CH₂)₂NC(═N)NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—CH₂NH₂, (C≡C)CH₂NH₂, or —(C≡C)CH₂NC(═N)NH₂; R³is H, —CF₃, —O—(CH₂)₃NH₂, or —O—(CH₂)₃NC(═N)NH₂; R⁴is H, halo, —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, —(CH₂)₂NC(═N)NH₂, —(C≡C)CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—CH₂NH₂, —(C≡C)(CH₂)₂NH₂, —(C≡C)CH₂NC(═N)NH₂, or —(C≡C)(CH₂)₂NC(═N)NH₂; R⁵is H, halo, —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, —(CH₂)₂NC(═N)NH₂, —(C≡C)CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —(C≡C)(CH₂)₂NH₂, —(C≡C)CH₂NC(═N)NH₂, or —(C≡C)(CH₂)₂NC(═N)NH₂; R⁶is H, —(CH₂)₃NH₂or —O—(CH₂)₃NC(═N)NH₂; R⁷is H, —(CH₂)₃NH₂or —O—(CH₂)₃NC(═N)NH₂; R⁸is H or halo; and R⁹is H or halo.

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R⁴is H, halo, —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, —(CH₂)₂NC(═N)NH₂, —(C≡C)CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—CH₂NH₂, —(C≡C)(CH₂)₂NH₂, —(C≡C)CH₂NC(═N)NH₂, or —(C≡C)(CH₂)₂NC(═N)NH₂; R⁵is H, halo, —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, —(CH₂)₂NC(═N)NH₂, —(C≡C)CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —(C≡C)(CH₂)₂NH₂, —(C≡C)CH₂NC(═N)NH₂, or —(C≡C)(CH₂)₂NC(═N)NH₂; R⁶is H, —(CH₂)₃NH₂or —O—(CH₂)₃NC(═N)NH₂; R⁷is H, —(CH₂)₃NH₂or —O—(CH₂)₃NC(═N)NH₂; R⁸is H or halo; and R⁹is H or halo.

In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula V

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wherein:

X is O, N, or S;

R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or —NC(═N)NH₂, where n is 2, 3, or 4; and

R²is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or —NC(═N)NH₂, where n is 2, 3, or 4;

or a pharmaceutically acceptable salt thereof.

In some embodiments, X is O.

In some embodiments, R¹is —NC(═N)NH₂.

In some embodiments, R²is —NC(═N)NH₂.

In some embodiments, X is O; R¹is —NC(═N)NH₂; and R²is —NC(═N)NH₂.

In some embodiments, the compound is

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The present disclosure also provides compounds of Formula VI

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wherein:

X is N, O, S, or C;

Y is N, O, S, or C;

Z is N, O, S, or C;

R¹is H or

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R²is

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each R³is, independently, H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

each R⁴is, independently, H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and

each R⁵is, independently, H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

or a pharmaceutically acceptable salt thereof.

In some embodiments, X is N or C.

In some embodiments, Y is O or C.

In some embodiments, Z is O, S, or C.

In some embodiments, R¹is H or

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wherein: R³is —(CH₂)₂NC(═N)NH₂, R⁴is H, and R⁵is H; or R³is —CH₂NH₂, R⁴is H, and R⁵is H; or R³is —CH₂NH₂, R⁴is H, and R⁵is —CH₂NH₂; or R³is —(CH₂)₂NC(═N)NH₂, R⁴is H, and R⁵is —(CH₂)₂NC(═N)NH₂.

In some embodiments, R²is

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In some embodiments, X is N or C; Y is O or C; Z is O, S, or C; R¹is H; R²is

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and R³is —(CH₂)₂NH₂, R⁴is H, and R⁵is H; or R³is —CH₂NH₂, R⁴is H, and R⁵is —CH₂NH₂.

In some embodiments, X is N or C; Y is O or C; Z is O, S, or C; R¹and R²are

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and R³is —(CH)₂NH₂; R⁴is H, and R⁵is H; or R³is —(CH₂)₂NC(═N)NH₂, R⁴is H, and R⁵is H; or R³is —CH₂NH₂, R⁴is H, and R⁵is H; or R³is —(CH)₂NH₂, R⁴is H, and R⁵is —(CH)₂NH₂; or R³is —(CH₂)₂NC(═N)NH₂, R⁴is H, and R⁵is —(CH₂)₂NC(═N)NH₂. In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula VII

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wherein:

X is C, O, S, or N;

Y is C, O, S, or N;

Z is O or S;

R¹is H, halo, haloalkyl, —NH₂, or C_1-3alkyl;

R²is H, halo, haloalkyl, —NH₂, or C_1-3alkyl;

R³is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or

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where n is 2, 3, or 4;

R⁴is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or

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where n is 2, 3, or 4;

R⁵is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or

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where n is 2, 3, or 4; and

R⁶is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or

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where n is 2, 3, or 4;

or a pharmaceutically acceptable salt thereof.

In some embodiments, X is C or N.

In some embodiments, Y is C or N.

In some embodiments, Z is O.

In some embodiments, R¹is H, halo, or haloalkyl. In some embodiments, R¹is H, F, Cl, Br, or CF₃.

In some embodiments, R²is H, halo, or haloalkyl. In some embodiments, R²is H, F, Cl, Br, or CF₃.

In some embodiments, R³is H, —(CH₂)₃NH₂, or

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In some embodiments, R⁴is H, —(CH₂)₃NH₂, or

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In some embodiments, R⁵is H or

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In some embodiments, R⁶is H or

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In some embodiments, X is C or N; Y is C or N; Z is O; R¹is H, F, Cl, Br, or CF₃; R²is H, F, Cl, Br, or CF₃; R³is H, —(CH₂)₃NH₂, or

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R⁴is H, —(CH₂)₃NH₂, or,

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R⁵is H or

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and R⁶is H or

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In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula VIII

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wherein:

X is C, O, S, or N;

Y is C, O, S, or N;

Z is O or S;

R¹is H, halo, haloalkyl, —NH₂, or C_1-3alkyl;

R²is H, halo, haloalkyl, —NH₂, or C_1-3alkyl;

R³is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and

R⁴is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

or a pharmaceutically acceptable salt thereof.

In some embodiments, X is S.

In some embodiments, Y is N.

In some embodiments, Z is O.

In some embodiments, R¹is H, halo, or haloalkyl. In some embodiments, R¹is H, F, Cl, Br, or CF₃.

In some embodiments, R²is H, halo, or haloalkyl. In some embodiments, R²is H, F, Cl, Br, or CF₃.

In some embodiments, R³is —(CH₂)_nNH₂. In some embodiments, R³is —(CH₂)₃NH₂.

In some embodiments, R⁴is —(CH₂)_nNH₂. In some embodiments, R⁴is —(CH₂)₃NH₂.

In some embodiments, X is S; Y is N; Z is O; R¹is H, F, Cl, Br, or CF₃; R²is H, F, Cl, Br, or CF₃; R³is —(CH₂)₃NH₂; and R⁴is —(CH₂)₃NH₂.

In some embodiments, the compound is

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The present disclosure also provides compounds of Formula IX

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wherein:

R⁵is H, halo, haloalkyl, —NH₂, or C_1-3alkyl;

R⁶is H, halo, haloalkyl, —NH₂, or C_1-3alkyl;

R⁷is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; and

R⁸is H, halo, haloalkyl, —NH₂, or C_1-3alkyl;

or a pharmaceutically acceptable salt thereof.

In some embodiments, R¹is —O—(CH₂)_nNH₂, —(CH₂)_nNH₂, or —(CH₂)_nNC(═N)NH₂. In some embodiments, R¹is —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, or —(CH₂)₂NC(═N)NH₂.

In some embodiments, R²is —O—(CH₂)_nNH₂, —(CH₂)_nNH₂, or —(CH₂)_nNC(═N)NH₂. In some embodiments, R²is —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, or —(CH₂)₂NC(═N)NH₂.

In some embodiments, R³is —O—(CH₂)_nNH₂, —(CH₂)_nNH₂, or —(CH₂)_nNC(═N)NH₂. In some embodiments, R³is —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, or —(CH₂)₂NC(═N)NH₂.

In some embodiments, R⁴is —O—(CH₂)_nNH₂, —(CH₂)_nNH₂, or —(CH₂)_nNC(═N)NH₂. In some embodiments, R⁴is —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, or —(CH₂)₂NC(═N)NH₂.

In some embodiments, R⁵is H, halo, or haloalkyl. In some embodiments, R⁵is H or F, Cl, Br or —CF₃.

In some embodiments, R⁶is H, halo, or haloalkyl. In some embodiments, R⁶is H or F, Cl, Br or —CF₃.

In some embodiments, R⁷is H, halo, haloalkyl, or C_1-3alkyl. In some embodiments, R⁷is H or F, Cl, Br, —CF₃, or —CH₃.

In some embodiments, R is H, halo, haloalkyl, or C_1-3alkyl. In some embodiments, R⁸is H or F, Cl, Br, —CF₃, or —CH₃.

In some embodiments, R¹is —O—(CH₂)_nNH₂, —(CH₂)_nNH₂, or —(CH₂)_nNC(═N)NH₂; R²is —O—(CH₂)_nNH₂, —(CH₂)_nNH₂, or —(CH₂)_nNC(═N)NH₂; R³is —O—(CH₂)_nNH₂, —(CH₂)_nNH₂, or —(CH₂)_nNC(═N)NH₂; R⁴is —O—(CH₂)_nNH₂, —(CH₂)_nNH₂, or —(CH₂)_nNC(═N)NH₂; R⁵is H, halo, or —CF₃; R⁶is H, halo, or —CF₃; R⁷is H, halo, —CF₃, or —CH₃; and R⁸is H, halo, —CF₃, or —CH₃;

In some embodiments, R¹is —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, or —(CH₂)₂NC(═N)NH₂; R²is —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, or —(CH₂)₂NC(═N)NH₂; R³is —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, or —(CH₂)₂NC(═N)NH₂; R⁴is —O—(CH₂)₃NH₂, —(CH₂)₂NH₂, or —(CH₂)₂NC(═N)NH₂; R⁵is H, F, Cl, Br, or —CF₃; R⁶is H, F, Cl, Br, or —CF₃; R⁷is H, F, Cl, Br, —CF₃, or —CH₃; and R⁸is H, F, Cl, Br, —CF₃, or —CH₃.

In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula X

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wherein:

X is O or S;

R¹is H or

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R²is H or

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R³is H or

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each R⁴is, independently, H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —C═C—(CH₂)₂NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

each R⁵is, independently, H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and

each R⁶is, independently, H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

or a pharmaceutically acceptable salt thereof.

In some embodiments, X is O.

In some embodiments, each R⁴is, independently, —(CH₂)_nNH₂or —O—(CH₂)_nNH₂. In some embodiments, each R⁴is, independently, —(CH₂)₂NH₂or —O—(CH₂)₃NH₂.

In some embodiments, each R⁶is, independently, H or —O—(CH₂)_nNH₂. In some embodiments, each R⁶is, independently, H or —O—(CH₂)₃NH₂.

In some embodiments, X is O; R¹is

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R²is

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and R³is H; and each R⁴is, independently, —(CH₂)_nNH₂, where n is 2, 3, or 4; each R⁵is H; and each R⁶is H. In some embodiments, X is O; R¹is H; R²is

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and R³is

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and each R⁴is, independently, —(CH₂)_nNH₂, where n is 2, 3, or 4; each R⁵is H; and each R⁶is H.

In some embodiments, X is O; R¹is

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R²is

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and R³is

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and each R⁴is, independently, —(CH₂)_nNH₂, where n is 2, 3, or 4; each R⁵is H; and each R⁶is H.

In some embodiments, X is O; R¹is

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R²is

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and R³is H; and each R⁴is, independently, —O—(CH₂)_nNH₂, where n is 2, 3, or 4; each R⁵is H; and each R⁶is, independently, —O—(CH₂)_nNH₂, where n is 2, 3, or 4.

In some embodiments, X is O; R¹is H; R²is

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and R³is

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and each R⁴is, independently, —O—(CH₂)_nNH₂, where n is 2, 3, or 4; each R⁵is H; and each R⁶is, independently, —O—(CH₂)_nNH₂, where n is 2, 3, or 4.

In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula XI

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wherein:

X is N, C, O, or S;

Y is N, C, O, or S;

Z is N, C, O, or S; and

or a pharmaceutically acceptable salt thereof.

In some embodiments, X is O.

In some embodiments, Y is N.

In some embodiments, Z is N.

In some embodiments, R¹is —(CH₂)_nNH₂. In some embodiments, R¹is —(CH₂)₃NH₂.

In some embodiments, X is O; Y is N; Z is N; and R¹is —(CH₂)_nNH₂.

In some embodiments, the compound is

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The present disclosure also provides compounds of Formula XII

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wherein:

X is N, O, C, or S;

R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

R²is —NH₂, —N((CH₂)_nNH₂)₂, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and

R³is —NH₂, —N((CH₂)_nNH₂)₂, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; —N(CH₂CH₂NH₂)₂, or NH₂;

or a pharmaceutically acceptable salt thereof;

provided that:

when X is N, then R¹, R², and R³are not all —(CH₂)₃NH₂; and

when X is N, and R¹is —(CH₂)₃NH₂, then R²and R³are not both —(CH₂)₂NH₂, —O—(CH₂)₃NH₂, or —O—(CH₂)₂NH₂.

In some embodiments, X is N.

In some embodiments, R¹is —(CH₂)_nNC(═N)NH₂or —(CH₂)_nNH₂. In some embodiments, R¹is —(CH₂)₃NC(═N)NH₂or —(CH₂)₃NH₂.

In some embodiments, R²is —NH₂, —(CH₂)NC(═N)NH₂, or —N((CH₂)_nNH₂)₂. In some embodiments, R²is —NH₂, —(CH₂)₃NC(═N)NH₂, or —N(CH₂CH₂NH₂)₂.

In some embodiments, R³is —NH₂, —(CH₂)NC(═N)NH₂, or —N((CH₂)_nNH₂)₂. In some embodiments, R³is —NH₂, —(CH₂)₃NC(═N)NH₂, or —N(CH₂CH₂NH₂)₂.

In some embodiments, X is N; R¹is —(CH₂)_nNC(═N)NH₂or —(CH₂)_nNH₂; R²is —NH₂, —(CH₂)_nNC(═N)NH₂, or —N((CH₂)_nNH₂)₂; and R³is —NH₂, —(CH₂)_nNC(═N)NH₂, or —N((CH₂)_nNH₂)₂.

In some embodiments, X is N; R¹is —(CH₂)₃NC(═N)NH₂or —(CH₂)₃NH₂; R²is —NH₂, —(CH₂)₃NC(═N)NH₂, or —N(CH₂CH₂NH₂)₂; and R³is —NH₂, —(CH₂)₃NC(═N)NH₂, or —N(CH₂CH₂NH₂)₂.

In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula XIII

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wherein:

X is N, C, O, or S;

R¹is H, halo, haloalkyl, —NH₂, C_1-3alkyl, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

R²is H, halo, haloalkyl, —NH₂, C_1-6alkyl, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —C≡C—CH₂NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

R³is —C(═O)N(CH₂)_nNH₂, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and

R⁴is —C(═O)N(CH₂)_nNH₂, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

or a pharmaceutically acceptable salt thereof.

In some embodiments, X is N or C.

In some embodiments, R¹is H or —(CH₂)_nNH₂. In some embodiments, R¹is H or —(CH₂)₃NH₂.

In some embodiments, R²is H, halo, or —C_1-6alkyl. In some embodiments, R²is H, Br, or —(CH₂)₅CH₃.

In some embodiments, R³is —O—(CH₂)_nNH₂or —C(═O)N(CH₂)_nNH₂. In some embodiments, R³is —O—(CH₂)₃NH₂or —C(═O)N(CH₂)₂NH₂.

In some embodiments, R⁴is —O—(CH₂)_nNH₂or —C(═O)N(CH₂)_nNH₂. In some embodiments, R⁴is —O—(CH₂)₃NH₂or —C(═O)N(CH₂)₂NH₂.

In some embodiments, X is N or C; R¹is H or —(CH₂)_nNH₂; R²is H, halo, or C_1-6alkyl; R³is —C(═O)N(CH₂)_nNH₂or —O—(CH₂)_nNH₂; and R⁴is —C(═O)N(CH₂)_nNH₂or —O—(CH₂)_nNH₂.

In some embodiments, X is N or C; R¹is H or —(CH₂)₃NH₂; R²is H, Br, or —(CH₂)₅CH₃; R³is —O—(CH₂)₃NH₂or —C(═O)N(CH₂)₂NH₂; and R⁴is —O—(CH₂)₃NH₂or —C(═O)N(CH₂)₂NH₂.

In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula XIV

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wherein:

R⁴is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C═C—CH₂NH₂, —C═C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

or a pharmaceutically acceptable salt thereof.

In some embodiments, R¹is —O—(CH₂)_nNH₂. In some embodiments, R¹is —O—(CH₂)₃NH₂.

In some embodiments, R²is —O—(CH₂)_nNH₂. In some embodiments, R²is —O—(CH₂)₃NH₂.

In some embodiments, R³is —O—(CH₂)_nNH₂. In some embodiments, R³is —O—(CH₂)₃NH₂.

In some embodiments, R⁴is —O—(CH₂)_nNH₂. In some embodiments, R⁴is —O—(CH₂)₃NH₂.

In some embodiments, R¹is —O—(CH₂)_nNH₂; R²is —O—(CH₂)_nNH₂; R³is —O—(CH₂)_nNH₂; and R⁴is —O—(CH₂)_nNH₂.

In some embodiments, the compound is

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The present disclosure also provides compounds of Formula XV

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wherein:

X is C(═O), O, S, or —C(halo)₂;

or a pharmaceutically acceptable salt thereof.

In some embodiments, X is C(═O) or —C(halo)₂. In some embodiments, X is C(═O) or —CF₂.

In some embodiments, R¹is —O—(CH₂)_nNH₂. In some embodiments, R¹is —O—(CH₂)₃NH₂.

In some embodiments, R²is —O—(CH₂)_nNH₂. In some embodiments, R²is —O—(CH₂)₃NH₂.

In some embodiments, R³is —O—(CH₂)_nNH₂. In some embodiments, R³is —O—(CH₂)₃NH₂.

In some embodiments, R⁴is —O—(CH₂)_nNH₂. In some embodiments, R⁴is —O—(CH₂)₃NH₂.

In some embodiments, X is C(═O) or —C(halo)₂; R¹is —O—(CH₂)_nNH₂; R²is —O—(CH₂)_nNH₂; R³is —O—(CH₂)_nNH₂; and R⁴is —O—(CH₂)_nNH₂.

In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula XVI

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wherein:

X is C, S, O, or N;

R¹is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —C(═O)N(CH₂)_nNH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or

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where n is 2, 3, or 4;

R²is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C(═O)N(CH₂)_nNH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, —N((CH₂)_nNH₂)₂, —(CH₂)_nN((CH₂)_nNH₂)₂,

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where n is 2, 3, or 4;

R³is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —C(═O)N(CH₂)_nNH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, or

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where n is 2, 3, or 4;

R⁴is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C═C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, —C(═O)N(CH₂)_nNH₂, —N((CH₂)_nNH₂)₂, —(CH₂)_nN((CH₂)_nNH₂)₂,

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where n is 2, 3, or 4;

R⁵is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —C_1-3alkyl, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C═C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH═CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

R⁷is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

R⁸is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; and

R⁹is H, halo, haloalkyl, —NH₂, or C_1-3alkyl;

or a pharmaceutically acceptable salt thereof;

provided that:

when R¹, R³, R⁵, R⁶, R⁷, R⁸, and R⁹are H, and X is S, then R²and R⁴are not both —(CH₂)₂NH₂, —(CH₂)₃NC(═N)NH₂, —(CH₂)₃NH₂, or —CH₂NH₂;

when R¹, R², R³, R⁴, R⁵, R⁸, and R⁹are H, and X is S, then R⁶and R⁷are not both —(CH₂)₃NH₂;

when R¹, R³, R⁵, R⁶, R⁷, R⁸, and R⁹are H, and X is N, then R²and R⁴are not both —CH₂NH₂or —(CH₂)₃NH₂;

when R¹, R³, R⁵, R⁶, R⁷, R⁸, and R⁹are H, and X is O, then R²and R⁴are not both —(CH₂)₃NH₂;

when R¹, R³, R⁶, R⁷, R⁸, and R⁹are H, X is N, and R⁵is —CH₂CH₃, then R²and R⁴are not both —(CH₂)₃NH₂;

when R⁵, R⁶, R⁷, R⁸, are R⁹, are H, and X is O, then R¹, R², R³, and R⁴are not all —O—(CH₂)₃NH₂;

when R⁶, R⁷, R⁸, are R⁹, are H, X is N, and R⁵is —CH₂CH₃, then R¹, R², R³, and R⁴are not all —O—(CH₂)₃NH₂; and

when R⁵, R⁶, R⁷, R⁸, are R⁹, are H, and X is S, then R¹, R², R³, and R⁴are not all —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂.

In some embodiments, X is S, O, or N.

In some embodiments, R¹is H, —C(═O)N(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, or

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In some embodiments, R¹is H, —C(═O)N(CH₂)₂NH₂, —C(═O)N(CH₂)₃NH₂, —O—(CH₂)₃NC(═N)NH₂, —O—(CH₂)₃NH₂, or

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In some embodiments, R²is H, —C(═O)N(CH₂)_nNH₂, —(CH₂)_nN((CH₂)_nNH₂)₂, —N(CH₂)_nNH₂)₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂,

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In some embodiments, R²is H, —C(═O)N(CH₂)₂NH₂, —N(CH₂CH₂NH₂)₂, —C(═O)N(CH₂)₃NH₂, —CH₂N(CH₂CH₂NH₂)₂, —CH₂N(CH₂CH₂CH₂NH₂)₂, —O—(CH₂)₃NH₂, —O—(CH₂)₃NC(═N)NH₂,

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In some embodiments, R³is H, —C(═O)N(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, or

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In some embodiments, R³is H, —C(═O)N(CH₂)₂NH₂, —C(═O)N(CH₂)₃NH₂, —O—(CH₂)₃NC(═N)NH₂, —O—(CH₂)₃NH₂, or

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In some embodiments, R⁴is H, —C(═O)N(CH₂)_nNH₂, —(CH₂)_nN((CH₂)_nNH₂)₂, —N((CH₂)_nNH₂)₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂,

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In some embodiments, R⁴is H, —C(═O)N(CH₂)₂NH₂, —N(CH₂CH₂NH₂)₂, —C(═O)N(CH₂)₃NH₂, —CH₂N(CH₂CH₂NH₂)₂, —CH₂N(CH₂CH₂CH₂NH₂)₂, —O—(CH₂)₃NH₂, —O—(CH₂)₃NC(═N)NH₂,

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In some embodiments, R⁵is H, —C_1-6alkyl, or —(CH₂)_nNH₂. In some embodiments, R⁵is H, —CH₂CH₃, or —(CH₂)₃NH₂.

In some embodiments, R⁶is H, —N(CH₂)_nNH₂, —O—(CH₂)_nNH₂, or —O—(CH₂)_nNC(═N)NH₂. In some embodiments, R⁶is H, —N(CH₂)₂NH₂, —O—(CH₂)₃NH₂, or —O—(CH₂)₃NC(═N)NH₂.

In some embodiments, R⁷is H, —N(CH₂)_nNH₂, —O—(CH₂)_nNH₂, or —O—(CH₂)_nNC(═N)NH₂. In some embodiments, R⁷is H, —N(CH₂)₂NH₂, —O—(CH₂)₃NH₂, or —O—(CH₂)₃NC(═N)NH₂.

In some embodiments, R⁸is H, halo, or haloalkyl. In some embodiments, R⁸is H, F, Cl, Br, or CF₃.

In some embodiments, R⁹is H, halo, or haloalkyl. In some embodiments, R⁹is H, F, Cl, Br, or CF₃.

In some embodiments, X is S, O, or N; R¹is H, —C(═O)N(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, or

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R²is H, —C(═O)N(CH₂)_nNH₂, —(CH₂)_nN((CH₂)_nNH₂)₂, —N((CH₂)_nNH₂)₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂,

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R³is H, —C(═O)N(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, or

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R⁴is H, —C(═O)N(CH₂)_nNH₂, —(CH₂)_nN((CH₂)_nNH₂)₂, —N((CH₂)_nNH₂)₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂,

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R⁵is H, —C_1-6alkyl, or —(CH₂)_nNH₂; R⁶is H, —N(CH₂)_nNH₂, —O—(CH₂)_nNH₂, or —O—(CH₂)_nNC(═N)NH₂; R⁷is H, —N(CH₂)_nNH₂, —O—(CH₂)_nNH₂, or —O—(CH₂)_nNC(═N)NH₂; R⁹is H, halo, or haloalkyl; and R⁹is H, halo, or haloalkyl.

In some embodiments, X is S, O, or N; R¹is H, —C(═O)N(CH₂)₂NH₂, —C(═O)N(CH₂)₃NH₂, —O—(CH₂)₃NC(═N)NH₂, —O—(CH₂)₃NH₂, or

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R²is H, —C(═O)N(CH₂)₂NH₂, —C(═O)N(CH₂)₃NH₂, —CH₂N(CH₂CH₂NH₂)₂, —N(CH₂CH₂NH₂)₂, —CH₂N(CH₂CH₂CH₂NH₂)₂, —O—(CH₂)₃NH₂, —O—(CH₂)₃NC(═N)NH₂,

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R³is H, —C(═O)N(CH₂)₂NH₂, —C(═O)N(CH₂)₃NH₂, —O—(CH₂)₃NH₂, —O—(CH₂)₃NC(═N)NH₂, or

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R⁴is H, —C(═O)N(CH₂)₂NH₂, —O—(CH₂)₃NH₂, —C(═O)N(CH₂)₃NH₂, —CH₂N(CH₂CH₂NH₂)₂, —N(CH₂CH₂NH₂)₂, —CH₂N(CH₂CH₂CH₂NH₂)₂, —O—(CH₂)₃NC(═N)NH₂,

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R⁵is H, —CH₂CH₃, or —(CH₂)₃NH₂; R⁶is H, —N(CH₂)₂NH₂, —O—(CH₂)₃NH₂, or —O—(CH₂)₃NC(═N)NH₂; R⁷is H, —N(CH₂)₂NH₂, —O—(CH₂)₃NH₂, or —O—(CH₂)₃NC(═N)NH₂; R⁸is H, F, Cl, Br, or —CF₃; and R⁹is H, F, Cl, Br, or —CF₃.

In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula XVII

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wherein:

R¹is H, halo, —NH(CH₂)NH₂, —NH(CH₂)NC(═N)NH₂, —(CH₂)NH₂, —O—(CH₂)NH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)NC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C═C—CH₂NH₂, —C═C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

R²is H, halo —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

R³is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)_nNH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, —CH((CH₂)_nNH₂)₂, or —CH((CH₂)_nNC(═N)NH₂)₂, where n is 2, 3, or 4;

R⁴is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)_nNH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, —C≡C—(CH₂)₂—NC(═N)NH₂, —CH((CH₂)_nNH₂)₂, or —CH((CH₂)_nNC(═N)NH₂)₂, where n is 2, 3, or 4;

R⁵is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; and

R⁶is H, halo, haloalkyl, —NH₂, or C_1-3alkyl; and

R⁸is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4; and

R⁹is H, halo, haloalkyl, —NH₂, or C_1-3alkyl;

or a pharmaceutically acceptable salt thereof;

provided that:

when R⁵, R⁶, R⁷, R⁸, and R⁹are H, and R¹and R²are Br, then R³and R⁴are not both —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂.

In some embodiments, R¹is H, halo, —(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, or —O—(CH₂)_nNH₂. In some embodiments, R¹is H, Br, —(CH₂)₂NC(═N)NH₂, —(CH₂)₂NH₂, or —O—(CH₂)₃NH₂.

In some embodiments, R²is H, halo, —(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, or —O—(CH₂)_nNH₂. In some embodiments, R²is H, Br, —(CH₂)₂NC(═N)NH₂, —(CH₂)₂NH₂, or —O—(CH₂)₃NH₂.

In some embodiments, R³is —(CH₂)_nNC(═N)NH₂, —CH((CH₂)_nNH₂)₂, —(CH₂)_nNH₂, —CH((CH₂)_nNC(═N)NH₂)₂, or —O—(CH₂)_nNH₂. In some embodiments, R³is —CH(CH₂NH₂)₂, —(CH₂)₂NC(═N)NH₂, —CH(CH₂NC(═N)NH₂)₂, —(CH₂)₂NH₂, or —O—(CH₂)₃NH₂.

In some embodiments, R⁴is —(CH₂)_nNC(═N)NH₂, —CH((CH₂)_nNH₂)₂, —CH((CH₂)_nNC(═N)NH₂)₂, —(CH₂)_nNH₂, or —O—(CH₂)_nNH₂. In some embodiments, R⁴is —(CH₂)₂NC(═N)NH₂, —CH(CH₂NH₂)₂, —CH(CH₂NC(═N)NH₂)₂, —(CH₂)₂NH₂, or —O—(CH₂)₃NH₂.

In some embodiments, ⁵is H, halo, or haloalkyl. In some embodiments, R⁵is H, F, Cl, Br, or —CF₃.

In some embodiments, R⁶is H, halo, or haloalkyl. In some embodiments, R⁶is H, F, Cl, Br, or —CF₃.

In some embodiments, R⁷is H, —(CH₂)_nNH₂, or —(CH₂)_nNC(═N)NH₂. In some embodiments, R⁷is H, —(CH₂)₂NH₂, or —(CH₂)₂NC(═N)NH₂.

In some embodiments, R⁸is H, —(CH₂)_nNH₂, or —(CH₂)_nNC(═N)NH₂. In some embodiments, R⁸is H, —(CH₂)₂NH₂, or —(CH₂)₂NC(═N)NH₂.

In some embodiments, R⁹is H or halo, or haloalkyl. In some embodiments, R⁹is H, F, Cl, Br, or —CF₃.

In some embodiments, R¹is H, halo, —(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, or —O—(CH₂)_nNH₂; R²is H, halo, —(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, or —O—(CH₂)_nNH₂; R³is —(CH₂)_nNC(═N)NH₂, —CH((CH₂)_nNH₂)₂, —CH((CH₂)_nNC(═N)NH₂)₂, —(CH₂)_nNH₂, or —O—(CH₂)_nNH₂; R⁴is —(CH₂)_nNC(═N)NH₂, —CH((CH₂)_nNH₂)₂, —CH((CH₂)_nNC(═N)NH₂)₂, —(CH₂)_nNH₂, or —O—(CH₂)_nNH₂; R⁵is H, halo, or haloalkyl; R⁶is H, halo, or haloalkyl; R⁷is H, —(CH₂)_nNH₂, or —(CH₂)_nNC(═N)NH₂; R⁸is H, —(CH₂)_nNH₂, or —(CH₂)_nNC(═N)NH₂; and R⁹is H, halo, or haloalkyl.

In some embodiments, R¹is H, Br, —(CH₂)₂NC(═N)NH₂, —(CH₂)₂NH₂, or —O—(CH₂)₃NH₂; R²is H, Br, —(CH₂)₂NC(═N)NH₂, —(CH₂)₂NH₂, or —O—(CH₂)₃NH₂; R³is —(CH₂)₂NC(═N)NH₂, —CH(CH₂NH₂)₂, —CH(CH₂NC(═N)NH₂)₂, —(CH₂)₂NH₂, or —O—(CH₂)₃NH₂; R⁴is —(CH₂)₂NC(═N)NH₂, —CH(CH₂NH₂)₂, —CH(CH₂NC(═N)NH₂)₂, —(CH₂)₂NH₂, or —O—(CH₂)₃NH₂; R⁵is H, F, Cl, Br, or —CF₃; R⁶is H, F, Cl, Br, or —CF₃; R⁷is H, —(CH₂)₂NH₂, or —(CH₂)₂NC(═N)NH₂; R⁸is H, —(CH₂)₂NH₂, or —(CH₂)₂NC(═N)NH₂; and R⁹is H, F, Cl, Br, or —CF₃.

In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula XVIII

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wherein:

X is N, C, O, or S;

Y is N, C, O, or S;

or a pharmaceutically acceptable salt thereof.

In some embodiments, X is N.

In some embodiments, Y is S.

In some embodiments, R¹is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂. In some embodiments, R¹is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂.

In some embodiments, R²is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂. In some embodiments, R²is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂.

In some embodiments, R³is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂. In some embodiments, R³is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂.

In some embodiments, R⁴is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂. In some embodiments, R⁴is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂.

In some embodiments, X is N; Y is S; R¹is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂; R²is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂; R³is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂; and R⁴is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂.

In some embodiments, X is N; Y is S; R¹is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂; R²is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂; R³is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂; and R⁴is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂.

In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula XIX

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wherein:

or a pharmaceutically acceptable salt thereof.

In some embodiments, R¹is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂. In some embodiments, R¹is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂.

In some embodiments, R²is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂. In some embodiments, R²is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂.

In some embodiments, R³is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂. In some embodiments, R³is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂. In some embodiments, R⁴is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂. In some embodiments, R⁴is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂.

In some embodiments, R¹is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂; R²is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂; R³is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂; and R⁴is —(CH₂)_nNH₂or —(CH₂)_nNC(═N)NH₂.

In some embodiments, R¹is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂; R²is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂; R³is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂; and R⁴is —(CH₂)₂NH₂or —(CH₂)₂NC(═N)NH₂.

In some embodiments, the compound is chosen from

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The present disclosure also provides compounds of Formula XX

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wherein:

or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XXI

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wherein:

or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XXII

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wherein:

R¹is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C═C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XXIII

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wherein:

R⁵is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

R⁶is —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

R⁷is H, halo, C_1-6alkyl, or haloalkyl;

R⁸is H, halo, C_1-6alkyl, or haloalkyl; and

R⁹is H, halo, C_1-6alkyl, or haloalkyl;

or a pharmaceutically acceptable salt thereof.

In some embodiments, R⁷is H, F, Cl, Br, —CH₃, or —CF₃.

In some embodiments, R⁸is H, F, Cl, Br, —CH₃, or —CF₃.

In some embodiments, R⁹is H, F, Cl, Br, —CH₃, or —CF₃.

The present disclosure also provides compounds of Formula XXIV

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wherein:

or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XXV

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wherein:

or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XXVI

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wherein:

R¹is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

R²is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XXVII

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wherein:

R²is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

or a pharmaceutically acceptable salt thereof.

The present disclosure also provides compounds of Formula XXVIII

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wherein:

R²is H, —NH(CH₂)_nNH₂, —NH(CH₂)_nNC(═N)NH₂, —(CH₂)_nNH₂, —O—(CH₂)_nNH₂, —(CH₂)_nNC(═N)NH₂, —O—(CH₂)_nNC(═N)NH₂, —CH═CH—CH₂NH₂, —CH═CH—CH₂NC(═N)NH₂, —CH═CH—(CH₂)₂NH₂, —CH═CH—(CH₂)₂NC(═N)NH₂, —C≡C—CH₂NH₂, —C≡C—(CH₂)₂NH₂, —CH≡CH—CH₂NC(═N)NH₂, or —C≡C—(CH₂)₂—NC(═N)NH₂, where n is 2, 3, or 4;

or a pharmaceutically acceptable salt thereof.

Polyamides and polyesters that are useful for the present disclosure can be prepared by typical condensation polymerization and addition polymerization processes (see, for example, G. Odian, Principles of Polymerization, John Wiley & Sons, Third Edition (1991), and M. Steven, Polymer Chemistry, Oxford University Press (1999)). Most commonly, the polyamides are prepared by a) thermal dehydration of amine salts of carboxylic acids, b) reaction of acid chlorides with amines, and c) aminolysis of esters. Methods a) and c) are of limited use in polymerizations of aniline derivatives which are generally prepared utilizing acid chlorides. The skilled chemist, however, will recognize that there are many alternative active acylating agents, for example phosphoryl anhydrides, active esters or azides, which may replace an acid chloride and which, depending of the particular polymer being prepared, may be superior to an acid chloride. The acid chloride route is probably the most versatile and has been used extensively for the synthesis of aromatic polyamides.

Homopolymers derived from substituted aminobenzoic acid derivatives can also prepared in a stepwise fashion. A stepwise process comprises coupling an N-protected amino acid to an amine (or hydroxy group) and subsequently removing the amine-protecting group and repeating the process. These techniques have been highly refined for synthesis of specific peptides, allow for the synthesis of specific sequences, and both solid-phase and solution techniques for peptide synthesis are directly applicable to the present disclosure. An alternative embodiment of the present disclosure is the corresponding polysulfonamides that can be prepared in analogous fashion by substituting sulfonyl chlorides for carboxylic acid chlorides.

The most common method for the preparation of polyureas is the reaction of diamines with diisocyanates (see, Yamaguchi et al., Polym. Bull., 2000, 44, 247). This exothermic reaction can be carried out by solution techniques or by interfacial techniques. One skilled in organic and polymer chemistry will appreciate that the diisocyanate can be replaced with a variety of other bis-acylating agents, such as phosgene or N,N′-(diimidazolyl)carbonyl, with similar results. Polyurethanes are prepared by comparable techniques using a diisocyanate and a dialcohol or by reaction of a diamine with a bis-chloroformate.

The syntheses of compounds described herein can be carried out by routine and/or known methods such as those disclosed in, for example, U.S. Patent Application Publication Nos. 2005-0287108, 2006-0041023, U.S. Pat. No. 7,173,102, International Publication Nos. WO 2005/123660, WO 2004/082643, and WO 2006/093813, and U.S. Application Publication No. 2010-0081665, each of which is incorporated herein by reference in its entirety. Numerous pathways are available to incorporate polar and nonpolar side chains. Phenolic groups on the monomer can be alkylated. Alkylation of the commercially available phenol will be accomplished with standard Williamson ether synthesis for the non-polar side chain with ethyl bromide as the alkylating agent. Polar sidechains can be introduced with bifunctional alkylating agents such as BOC—NH(CH₂)₂Br. Alternately, the phenol group can be alkylated to install the desired polar side chain function by employing the Mitsonobu reaction with BOC—NH(CH₂)₂—OH, triphenyl phosphine, and diethyl acetylenedicarboxylate. Standard conditions for reduction of the nitro groups and hydrolysis of the ester afford the amino acid. With the aniline and benzoic acid in hand, coupling can be effected under a variety of conditions. Alternatively, the hydroxy group of the (di)nitrophenol can be converted to a leaving group and a functionality introduced under nucleophilic aromatic substitution conditions. Other potential scaffolds that can be prepared with similar sequences are methyl 2-nitro-4-hydroxybenzoate and methyl 2-hydroxy-4-nitrobenzoate.

Compounds described herein can also be synthesized by solid-phase synthetic procedures well know to those of skill in the art (see, Tew et al., Proc. Natl. Acad. Sci. USA, 2002, 99, 5110-5114; Barany et al., Int. J. Pept. Prot. Res., 1987, 30, 705-739; Solid-phase Synthesis: A Practical Guide, Kates, S. A., and Albericio, F., eds., Marcel Dekker, New York (2000); and Dörwald, F. Z., Organic Synthesis on Solid Phase: Supports, Linkers, Reactions, 2nd Ed., Wiley-VCH, Weinheim (2002)).

The compounds described herein can also be designed using computer-aided computational techniques, such as de novo design techniques, to embody the amphiphilic properties. In general, de novo design of compounds is performed by defining a three-dimensional framework of the backbone assembled from a repeating sequence of monomers using molecular dynamics and quantum force field calculations. Next, side groups are computationally grafted onto the backbone to maximize diversity and maintain drug-like properties. The best combinations of functional groups are then computationally selected to produce a cationic, amphiphilic structures. Representative compounds can be synthesized from this selected library to verify structures and test their biological activity. Novel molecular dynamic and coarse grain modeling programs have also been developed for this approach because existing force fields developed for biological molecules, such as peptides, were unreliable in these oligomer applications (see, Car et al., Phys. Rev. Lett., 1985, 55, 2471-2474; Siepmann et al., Mol. Phys., 1992, 75, 59-70; Martin et al., J. Phys. Chem., 1999, 103, 4508-4517; and Brooks et al., J. Comp. Chem., 1983, 4, 187-217). Several chemical structural series of compounds have been prepared. See, for example, International Publication No. WO 2002/100295, which is incorporated herein by reference in its entirety. The compounds described herein can be prepared in a similar manner. Molecular dynamic and coarse grain modeling programs can be used for a design approach. See, for example, U.S. Application Publication No. 2004-0107056, and U.S. Application Publication No. 2004-0102941, each of which is incorporated herein by reference in its entirety.

After verifying the suitability of the force field by comparing computed predictions of the structure and thermodynamic properties to molecules that have similar torsional patterns and for which experimental data are available, the fitted torsions can then be combined with bond stretching, bending, one-four, van der Waals, and electrostatic potentials borrowed from the CHARMM (see, Brooks et al., J. Comp. Chem., 1983, 4, 187-217) and TraPPE (Martin et al., J. Phys. Chem., 1999, 103, 4508-4517; and Wick et al., J. Phys. Chem., 2000, 104, 3093-3104) molecular dynamics force fields. To identify conformations that can adopt periodic folding patterns with polar groups and apolar groups lined up on the opposite sides, initial structures can be obtained with the Gaussian package (see, Frisch et al., Gaussian 98 (revision A.7) Gaussian Inc., Pittsburgh, Pa. 1998). Then, the parallelized plane-wave Car-Parrinello CP-MD (see, Car et al., Phys. Rev. Lett., 1985, 55, 2471-2474) program, (see, Röthlisberger et al., J. Chem. Phys., 1996, 3692-3700) can be used to obtain energies at the minimum and constrained geometries. The conformations of the compounds without side-chains can be investigated in the gas phase. Both MD and MC methods can be used to sample the conformations. The former is useful for global motions of the compound. With biasing techniques (see, Siepmann et al., Mol. Phys., 1992, 75, 59-70; Martin et al., J. Phys. Chem., 1999, 103, 4508-4517; and Vlugt et al., Mol. Phys., 1998, 94, 727-733), the latter allows efficient sampling for compounds with multiple local minimum configurations that are separated by relatively large barriers.

The potential conformations are examined for positions to attach pendant groups that will impart amphiphilic character to the secondary structure. Compounds selected from the gas phase studies with suitable backbone conformations and with side-chains at the optimal positions to introduce amphiphilicity can be further evaluated in a model interfacial system. n-hexane/water can be chosen because it is simple and cheap for calculations while it mimics well the lipid/water bilayer environment. Compound secondary structures that require inter-compound interactions can be identified by repeating the above-mentioned calculations using a periodically repeated series of unit cells of various symmetries (so called variable cell molecular dynamics or Monte Carlo technique) with or without solvent. The results of these calculations can guide the selection of candidates for synthesis.

The compounds described herein can be administered in any conventional manner by any route where they are active. Administration can be systemic, topical, or oral. For example, administration can be, but is not limited to, parenteral, subcutaneous, intravenous, intramuscular, intraperitoneal, transdermal, oral, buccal, sublingual, or ocular routes, or intravaginally, by inhalation, by depot injections, or by implants. The mode of administration can depend on the pathogen or microbe to be targeted. The selection of the specific route of administration can be selected or adjusted by the clinician according to methods known to the clinician to obtain the desired clinical response.

In some embodiments, it may be desirable to administer one or more compounds, or a pharmaceutically acceptable salt thereof, locally to an area in need of treatment. This may be achieved, for example, and not by way of limitation, by local infusion during surgery, topical application, e.g., in conjunction with a wound dressing after surgery, by injection, by means of a catheter, by means of a suppository, or by means of an implant, wherein the implant is of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers.

The compounds described herein can be administered either alone or in combination (concurrently or serially) with other pharmaceuticals. For example, the compounds can be administered in combination with another anti-heparin agent, including, but not limited to, protamine molecules. The compounds can also be administered in combination with other anti-cancer or anti-neoplastic agents, or in combination with other cancer therapies other than chemotherapy, such as, for example, surgery or radiotherapy. In some embodiments, the compounds described herein can also be administered in combination with (i.e., as a combined formulation or as separate formulations) with antibiotics, such as, for example: 1) protein synthesis inhibitors including, but not limited to, amikacin, anisomycin, apramycin, azithromycin, blasticidine S, brefeldin A, butirosin, chloramphenicol, chlortetracycline, clindamycin, clotrimazole, cycloheximide, demeclocycline, dibekacin, dihydrostreptomycin, doxycycline, duramycin, emetine, erythromycin, fusidic acid, G 418, gentamicin, helvolic acid, hygromycin B, josamycin, kanamycin, kirromycin, lincomycin, meclocycline, mepartricin, midecamycin, minocycline, neomycin, netilmicin, nitrofurantoin, nourseothricin, oleandomycin, oxytetracycline, paromomycin, puromycin, rapamycin, ribostamycin, rifampicin, rifamycin, rosamicin, sisomicin, spectinomycin, spiramycin, streptomycin, tetracycline, thiamphenicol, thiostrepton, tobramycin, tunicamycin, tylosin, viomycin, and virginiamycin; 2) DNA synthesis interfering agents including, but not limited to, camptothecin, 10-deacetylbaccatin III, azacytidine, 7-aminoactinomycin D, 8-quinolinol, 9-dihydro-13-acetylbaccatin III, aclarubicin, actinomycin D, actinomycin I, actinomycin V, bafilomycin A1, bleomycin, capreomycin, chromomycin, cinoxacin, ciprofloxacin, cis-diammineplatinum(II) dichloride, coumermycin A1, L(+)-lactic acid, cytochalasin B, cytochalasin D, dacarbazine, daunorubicin, distamycin A, doxorubicin, echinomycin, enrofloxacin, etoposide, flumequine, formycin, fumagillin, ganciclovir, gliotoxin, lomefloxacin, metronidazole, mithramycin A, mitomycin C, nalidixic acid, netropsin, nitrofurantoin, nogalamycin, nonactin, novobiocin, ofloxacin, oxolinic acid, paclitaxel, phenazine, phleomycin, pipemidic acid, rebeccamycin, sinefungin, streptonigrin, streptozocin, succinylsulfathiazole, sulfadiazine, sulfadimethoxine, sulfaguanidine purum, sulfamethazine, sulfamonomethoxine, sulfanilamide, sulfaquinoxaline, sulfasalazine, sulfathiazole, trimethoprim, tubercidin, 5-azacytidine, cordycepin, and formycin A; 3) cell wall synthesis interfering agents including, but not limited to, (+)-6-aminopenicillanic acid, 7-Aminodesacetoxycephalosporanic acid, amoxicillin, ampicillin, azlocillin, bacitracin, carbenicillin, cefaclor, cefamandole, cefazolin, cefinetazole, cefoperazone, cefotaxime, cefsulodin, ceftriaxone, cephalexin, cephalosporin C, cephalothin, cephradine, cloxacillin, D-cycloserine, dicloxacillin, D-penicillamine, econazole, ethambutol, lysostaphin, moxalactam, nafcillin, nikkomycin Z, nitrofurantoin, oxacillin, penicillic, penicillin G, phenethicillin, phenoxymethylpenicillinic acid, phosphomycin, pipemidic acid, piperacillin, ristomycin, and vancomycin; 4) cell membrane permeability interfering agents (ionophores) including, but not limited to, 2-mercaptopyridine, 4-bromocalcimycin A23187, alamethicin, amphotericin B, calcimycin A23187, chlorhexidine, clotrimazole, colistin, econazole, hydrocortisone, filipin, gliotoxin, gramicidin A, gramicidin C, ionomycin, lasalocid A, lonomycin A, monensin, N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide, narasin, nigericin, nisin, nonactin, nystatin, phenazine, pimaricin, polymyxin B, DL-penicillamine, polymyxin B, praziquantel, salinomycin, surfactin, and valinomycin; 5) enzyme inhibitors including, but not limited to, (+)-usnic acid, (±)-miconazole, (S)-(+)-camptothecin, 1-deoxymannojirimycin, 2-heptyl-4-hydroxyquinoline N-oxide, cordycepin, 1,10-phenanthroline, 6-diazo-5-oxo-L-norleucine, 8-quinolinol, antimycin, antipain, ascomycin, azaserine, bafilomycin, cerulenin, chloroquine, cinoxacin, ciprofloxacin, mevastatin, concanamycin A, concanamycin C, coumermycin A1, L(+)-lactic acid, cyclosporin A, econazole, enrofloxacin, etoposide, flumequine, formycin A, furazolidone, fusaric acid, geldanamycin, gliotoxin, gramicidin A, gramicidin C, herbimycin A, indomethacin, irgasan, lomefloxacin, mycophenolic acid, myxothiazol, N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide, nalidixic acid, netropsin, niclosamide, nikkomycin, N-methyl-1-deoxynojirimycin, nogalamycin, nonactin, novobiocin, ofloxacin, oleandomycin, oligomycin, oxolinic acid, piericidin A, pipemidic acid, radicicol, rapamycin, rebeccamycin, sinefungin, staurosporine, stigmatellin, succinylsulfathiazole, succinylsulfathiazole, sulfadiazine, sulfadimethoxine, sulfaguanidine, sulfamethazine, sulfamonomethoxine, sulfanilamide, sulfaquinoxaline, sulfasalazine, sulfathiazole, triacsin C, trimethoprim, and vineomycin A1; and 6) membrane modifiers including, but not limited to, paracelsin.

The means and methods for administration are known in the art and an artisan can refer to various pharmacologic references for guidance (see, for example, Modem Pharmaceutics, Banker & Rhodes, Marcel Dekker, Inc. (1979); and Goodman & Gilman's The Pharmaceutical Basis of Therapeutics, 6th Edition, MacMillan Publishing Co., New York (1980)).

The amount of compound to be administered is that amount which is therapeutically effective. The dosage to be administered will depend on the characteristics of the subject being treated, e.g., the particular animal treated, age, weight, health, types of concurrent treatment, if any, and frequency of treatments, and can be easily determined by one of skill in the art (e.g., by the clinician). The standard dosing for protamine can be used and adjusted (i.e., increased or decreased) depending upon the factors described above. The selection of the specific dose regimen can be selected or adjusted or titrated by the clinician according to methods known to the clinician to obtain the desired clinical response.

The amount of a compound described herein that will be effective in the treatment and/or prevention of a particular disease, condition, or disorder will depend on the nature and extent of the disease, condition, or disorder, and can be determined by standard clinical techniques. In addition, in vitro or in vivo assays may optionally be employed to help identify optimal dosage ranges. The precise dose to be employed in the compositions will also depend on the route of administration, and the seriousness of the disorder, and should be decided according to the judgment of the practitioner and each patient's circumstances. However, a suitable dosage range for oral administration is, generally, from about 0.001 milligram to about 200 milligrams per kilogram body weight, from about 0.01 milligram to about 100 milligrams per kilogram body weight, from about 0.01 milligram to about 70 milligrams per kilogram body weight, from about 0.1 milligram to about 50 milligrams per kilogram body weight, from 0.5 milligram to about 20 milligrams per kilogram body weight, or from about 1 milligram to about 10 milligrams per kilogram body weight. In some embodiments, the oral dose is about 5 milligrams per kilogram body weight.

In some embodiments, suitable dosage ranges for intravenous (i.v.) administration are from about 0.01 mg to about 500 mg per kg body weight, from about 0.1 mg to about 100 mg per kg body weight, from about 1 mg to about 50 mg per kg body weight, or from about 10 mg to about 35 mg per kg body weight. Suitable dosage ranges for other modes of administration can be calculated based on the forgoing dosages as known by those skilled in the art. For example, recommended dosages for intradermal, intramuscular, intraperitoneal, subcutaneous, epidural, sublingual, intracerebral, intravaginal, transdermal administration or administration by inhalation are in the range of from about 0.001 mg to about 200 mg per kg of body weight, from about 0.01 mg to about 100 mg per kg of body weight, from about 0.1 mg to about 50 mg per kg of body weight, or from about 1 mg to about 20 mg per kg of body weight. Effective doses may be extrapolated from dose-response curves derived from in vitro or animal model test systems. Such animal models and systems are well known in the art.

The compounds described herein can be formulated for parenteral administration by injection, such as by bolus injection or continuous infusion. The compounds can be administered by continuous infusion subcutaneously over a period of about 15 minutes to about 24 hours. Formulations for injection can be presented in unit dosage form, such as in ampoules or in multi-dose containers, with an added preservative. The compositions can take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and can contain formulatory agents such as suspending, stabilizing and/or dispersing agents. In some embodiments, the injectable is in the form of short-acting, depot, or implant and pellet forms injected subcutaneously or intramuscularly. In some embodiments, the parenteral dosage form is the form of a solution, suspension, emulsion, or dry powder.

For oral administration, the compounds described herein can be formulated by combining the compounds with pharmaceutically acceptable carriers well known in the art. Such carriers enable the compounds to be formulated as tablets, pills, dragees, capsules, emulsions, liquids, gels, syrups, caches, pellets, powders, granules, slurries, lozenges, aqueous or oily suspensions, and the like, for oral ingestion by a patient to be treated. Pharmaceutical preparations for oral use can be obtained by, for example, adding a solid excipient, optionally grinding the resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients include, but are not limited to, fillers such as sugars, including, but not limited to, lactose, sucrose, mannitol, and sorbitol; cellulose preparations such as, but not limited to, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and polyvinylpyrrolidone (PVP). If desired, disintegrating agents can be added, such as, but not limited to, the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.

Orally administered compositions can contain one or more optional agents, for example, sweetening agents such as fructose, aspartame or saccharin; flavoring agents such as peppermint, oil of wintergreen, or cherry; coloring agents; and preserving agents, to provide a pharmaceutically palatable preparation. Moreover, where in tablet or pill form, the compositions may be coated to delay disintegration and absorption in the gastrointestinal tract thereby providing a sustained action over an extended period of time. Selectively permeable membranes surrounding an osmotically active driving compound are also suitable for orally administered compounds. Oral compositions can include standard vehicles such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, etc. Such vehicles are suitably of pharmaceutical grade.

Dragee cores can be provided with suitable coatings. For this purpose, concentrated sugar solutions can be used, which can optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments can be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.

Pharmaceutical preparations which can be used orally include, but are not limited to, push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active compounds can be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers can be added.

For buccal administration, the compositions can take the form of, such as, tablets or lozenges formulated in a conventional manner.

For administration by inhalation, the compounds described herein can be delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, such as dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit can be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, such as gelatin for use in an inhaler or insufflator can be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

The compounds described herein can also be formulated in rectal compositions such as suppositories or retention enemas, such as containing conventional suppository bases such as cocoa butter or other glycerides. The compounds described herein can also be formulated in vaginal compositions such as vaginal creams, suppositories, pessaries, vaginal rings, and intrauterine devices.

In transdermal administration, the compounds can be applied to a plaster, or can be applied by transdermal, therapeutic systems that are consequently supplied to the organism. In some embodiments, the compounds are present in creams, solutions, powders, fluid emulsions, fluid suspensions, semi-solids, ointments, pastes, gels, jellies, and foams, or in patches containing any of the same.

The compounds described herein can also be formulated as a depot preparation. Such long acting formulations can be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection. Depot injections can be administered at about 1 to about 6 months or longer intervals. Thus, for example, the compounds can be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.

In yet another embodiment, the compounds can be delivered in a controlled release system. In one embodiment, a pump may be used (see Langer, supra; Sefton, CRC Crit. Ref. Biomed. Eng., 1987, 14, 201; Buchwald et al., Surgery, 1980, 88, 507 Saudek et al., N. Engl. J. Med., 1989, 321, 574). In another embodiment, polymeric materials can be used (see Medical Applications of Controlled Release, Langer and Wise (eds.), CRC Pres., Boca Raton, Fla. (1974); Controlled Drug Bioavailability, Drug Product Design and Performance, Smolen and Ball (eds.), Wiley, New York (1984); Ranger et al., J. Macromol. Sci. Rev. Macromol. Chem., 1983, 23, 61; see, also Levy et al., Science, 1985, 228, 190; During et al., Ann. Neurol., 1989, 25, 351; Howard et al., J. Neurosurg., 1989, 71, 105). In yet another embodiment, a controlled-release system can be placed in proximity of the target of the compounds described herein, such as the liver, thus requiring only a fraction of the systemic dose (see, e.g., Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115-138 (1984)). Other controlled-release systems discussed in the review by Langer, Science, 1990, 249, 1527-1533) may be used.

It is also known in the art that the compounds can be contained in such formulations with pharmaceutically acceptable diluents, fillers, disintegrants, binders, lubricants, surfactants, hydrophobic vehicles, water soluble vehicles, emulsifiers, buffers, humectants, moisturizers, solubilizers, preservatives and the like. The pharmaceutical compositions can also comprise suitable solid or gel phase carriers or excipients. Examples of such carriers or excipients include, but are not limited to, calcium carbonate, calcium phosphate, various sugars, starches, cellulose derivatives, gelatin, and polymers such as polyethylene glycols. In some embodiments, the compounds described herein can be used with agents including, but not limited to, topical analgesics (e.g., lidocaine), barrier devices (e.g., GelClair), or rinses (e.g., Caphosol).

In some embodiments, the compounds described herein can be delivered in a vesicle, in particular a liposome (see, Langer, Science, 1990, 249, 1527-1533; Treat et al., in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and Fidler (eds.), Liss, New York, pp. 353-365 (1989); Lopez-Berestein, ibid., pp. 317-327; see generally ibid.).

Suitable compositions include, but are not limited to, oral non-absorbed compositions. Suitable compositions also include, but are not limited to saline, water, cyclodextrin solutions, and buffered solutions of pH 3-9.

The compounds described herein, or pharmaceutically acceptable salts thereof, can be formulated with numerous excipients including, but not limited to, purified water, propylene glycol, PEG 400, glycerin, DMA, ethanol, benzyl alcohol, citric acid/sodium citrate (pH3), citric acid/sodium citrate (pH5), tris(hydroxymethyl)amino methane HCl (pH7.0), 0.9% saline, and 1.2% saline, and any combination thereof. In some embodiments, excipient is chosen from propylene glycol, purified water, and glycerin.

In some embodiments, the excipient is a multi-component system chosen from 20% w/v propylene glycol in saline, 30% w/v propylene glycol in saline, 40% w/v propylene glycol in saline, 50% w/v propylene glycol in saline, 15% w/v propylene glycol in purified water, 30% w/v propylene glycol in purified water, 50% w/v propylene glycol in purified water, 30% w/v propylene glycol and 5 w/v ethanol in purified water, 15% w/v glycerin in purified water, 30% w/v glycerin in purified water, 50% w/v glycerin in purified water, 20% w/v Kleptose in purified water, 40% w/v Kleptose in purified water, and 25% w/v Captisol in purified water. In some embodiments, the excipient is chosen from 50% w/v propylene glycol in purified water, 15% w/v glycerin in purified water, 20% w/v Kleptose in purified water, 40% w/v Kleptose in purified water, and 25% w/v Captisol in purified water. In some embodiments, the excipient is chosen from 20% w/v Kleptose in purified water, 20% w/v propylene glycol in purified water, and 15% w/v glycerin in purified water.

In some embodiments, the composition comprises 50 mg/mL of compound in 20% w/v Kleptose in purified water.

In some embodiments, the formulation can be lyophilized to a solid and reconstituted with, for example, water prior to use.

When administered to a mammal (e.g., to an animal for veterinary use or to a human for clinical use) the compounds can be administered in isolated form.

When administered to a human, the compounds can be sterile. Water is a suitable carrier when a compound is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid carriers, particularly for injectable solutions. Suitable pharmaceutical carriers also include excipients such as starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. The present compositions, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents.

The compositions described herein can take the form of a solution, suspension, emulsion, tablet, pill, pellet, capsule, capsule containing a liquid, powder, sustained-release formulation, suppository, aerosol, spray, or any other form suitable for use. Examples of suitable pharmaceutical carriers are described in Remington's Pharmaceutical Sciences, A.R. Gennaro (Editor) Mack Publishing Co.

In one embodiment, the compounds are formulated in accordance with routine procedures as a pharmaceutical composition adapted for administration to humans. Typically, compounds are solutions in sterile isotonic aqueous buffer. Where necessary, the compositions can also include a solubilizing agent. Compositions for intravenous administration may optionally include a local anesthetic such as lidocaine to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent. Where the compound is to be administered by infusion, it can be dispensed, for example, with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the compound is administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients may be mixed prior to administration.

The pharmaceutical compositions can be in unit dosage form. In such form, the composition can be divided into unit doses containing appropriate quantities of the active component. The unit dosage form can be a packaged preparation, the package containing discrete quantities of the preparations, for example, packeted tablets, capsules, and powders in vials or ampules. The unit dosage form can also be a capsule, cachet, or tablet itself, or it can be the appropriate number of any of these packaged forms.

The ophthalmic and otic compositions of the present disclosure can take the form of a liquid or solid, including, e.g., but not limited to, a solution, a suspension, an emulsion, a gel, an ointment, or a solid article that can be inserted in a suitable location in the eye or ear.

In some embodiments, a composition of the present disclosure is in the form of a liquid wherein the active agent (i.e., one of the compounds disclosed herein) is present in solution, in suspension, as an emulsion, or as a solution/suspension. In some embodiments, the liquid composition is in the form of a gel. In other embodiments, the liquid composition is aqueous. In other embodiments, the composition is in the form of an ointment.

In yet other embodiments, the composition is in the form of a solid article. For example, in some embodiments, the ophthalmic composition is a solid article that can be inserted in a suitable location in the eye, such as between the eye and eyelid or in the conjunctival sac, where it releases the active agent as described, for example, U.S. Pat. No. 3,863,633; U.S. Pat. No. 3,867,519; U.S. Pat. No. 3,868,445; U.S. Pat. No. 3,960,150; U.S. Pat. No. 3,963,025; U.S. Pat. No. 4,186,184; U.S. Pat. No. 4,303,637; U.S. Pat. No. 5,443,505; and U.S. Pat. No. 5,869,079. Release from such an article is usually to the cornea, either via the lacrimal fluid that bathes the surface of the cornea, or directly to the cornea itself, with which the solid article is generally in intimate contact. Solid articles suitable for implantation in the eye in such fashion are generally composed primarily of polymers and can be bioerodible or non-bioerodible. Bioerodible polymers that can be used in the preparation of ocular implants carrying one or more of the anti-microbial compounds in accordance with the present disclosure include, but are not limited to, aliphatic polyesters such as polymers and copolymers of poly(glycolide), poly(lactide), poly(epsilon-caprolactone), poly-(hydroxybutyrate) and poly(hydroxyvalerate), polyamino acids, polyorthoesters, polyanhydrides, aliphatic polycarbonates and polyether lactones. Suitable non-bioerodible polymers include silicone elastomers.

The ophthalmic and otic compositions are preferably sterile and have physical properties (e.g., osmolality and pH) that are specially suited for application to ophthalmic or otic tissues, including tissues that have been compromised as the result of preexisting disease, trauma, surgery or other physical conditions. For example, aqueous compositions of the disclosure typically have a pH in the range of from 4.5 to 8.0, from 6.0 to 8.0, from 6.5 to 8.0, or from 7.0 to 8.0.

Suitable ophthalmically acceptable compositions, formulations, and excipients are those that cause no substantial detrimental effect, even of a transient nature.

Suitable otically acceptable compositions, formulations, and excipients are those that cause no substantial detrimental effect, even of a transient nature.

Ophthalmically and otically acceptable excipients include, but are not limited to, viscosity-enhancing agents, preservatives, stabilizers, antioxidants, suspending agents, solubilizing agents, buffering agents, lubricating agents, ophthalmically or otically acceptable salts, and combinations thereof.

For example, aqueous ophthalmic compositions of the present disclosure, when in suspension or solution form, are suitably viscous or mucoadhesive, or both viscous or mucoadhesive, and thus comprise a viscosity-enhancing agent. Examples of suitable viscosity-enhancing agents include, but are not limited to, glycerin, polyvinyl alcohol, polyvinyl pyrrolidone, methylcellulose, hydroxypropylmethylcellulose, hydroxyethyl-cellulose, carboxymethylcellulose, hydroxypropylcellulose, and/or various gelling agents. For example, in some embodiments, the viscosity-enhancing agent is chosen from methylcellulose, hydroxypropyl-methylcellulose, polyvinyl alcohol, and glycerol. Such agents are generally employed in the compositions of the disclosure at a concentration of about 0.01% to about 3% by weight.

Thus, for ophthalmic compositions, in some embodiments, the ophthalmically acceptable excipient is a viscosity-enhancing agent or a promoter of mucoadhesion, such as carboxymethylcellulose. In such embodiments, the concentration of carboxymethylcellulose in the aqueous suspension or solution is 0.1% to 5% by weight or about 0.1% to about 2.5% by weight. The carboxymethylcellulose is preferably in the form of sodium carboxymethylcellulose substituted to a degree that the sodium content of the sodium carboxymethylcellulose is about 1% to about 20%.

In other embodiments, the ophthalmic composition is an in situ gellable aqueous composition such as an in situ gellable aqueous solution. Such a composition comprises a gelling agent in a concentration effective to promote gelling upon contact with the eye or with lacrimal fluid in the exterior of the eye, enabling the composition to remain in the eye for a prolonged period without loss by lacrimal drainage. Suitable gelling agents non-restrictively include thermosetting polymers such as tetra-substituted ethylene diamine block copolymers of ethylene oxide and propylene oxide (e.g., poloxamine 1307); polycarbophil; and polysaccharides such as gellan, carrageenan (e.g., kappa-carrageenan and iota-carrageenan), chitosan and alginate gums.

For example, in some embodiments of the present disclosure, the ophthalmic composition is an in situ gellable aqueous solution, suspension or solution/suspension, comprising from about 0.1% to about 6.5% or from about 0.5% to about 4.5% by weight, based on the total weight of the composition, of one or more compounds. A suitable gelling agent in this embodiment is polycarbophil. In other embodiments, the composition is an in situ gellable aqueous solution, suspension or solution/suspension, such as a solution, comprising about 0.1% to about 2% by weight of a polysaccharide that gels when it contacts an aqueous medium having the ionic strength of lacrimal fluid. A suitable polysaccharide is gellan gum, or a low acetyl clarified grade of gellan gum such as that sold under the trademark Gelrite®. Suitable partially deacylated gellan gums are disclosed in U.S. Pat. No. 5,190,927.

In yet other embodiments, the composition is an in situ gellable aqueous solution, suspension or solution/suspension, comprising about from 0.2% to about 3% or from about 0.5% to about 1% by weight of a gelling polysaccharide, chosen from gellan gum, alginate gum and chitosan, and about 1% to about 50% of a water-soluble film-forming polymer, preferably selected from alkylcelluloses (e.g., methylcellulose, ethylcellulose), hydroxyalkylcelluloses (e.g., hydroxyethylcellulose, hydroxypropyl methylcellulose), hyaluronic acid and salts thereof, chondroitin sulfate and salts thereof, polymers of acrylamide, acrylic acid and polycyanoacrylates, polymers of methyl methacrylate and 2-hydroxyethyl methacrylate, polydextrose, cyclodextrins, polydextrin, maltodextrin, dextran, polydextrose, gelatin, collagen, natural gums (e.g., xanthan, locust bean, acacia, tragacanth and carrageenan gums and agar), polygalacturonic acid derivatives (e.g., pectin), polyvinyl alcohol, polyvinylpyrrolidone and polyethylene glycol. The composition can optionally contain a gel-promoting counterion such as calcium in latent form, for example encapsulated in gelatin.

In yet other embodiments, the composition is an in situ gellable aqueous solution, suspension or solution/suspension comprising about 0.1% to about 5% of a carrageenan gum, e.g., a carrageenan gum having no more than 2 sulfate groups per repeating disaccharide unit, such as e.g., kappa-carrageenan, having 18-25% ester sulfate by weight, iota-carrageenan, having 25-34% ester sulfate by weight, and mixtures thereof.

In still other embodiments, the composition comprises a bioerodible polymer substantially as disclosed in U.S. Pat. No. 3,914,402.

In some embodiments, the composition comprises an ophthalmically acceptable mucoadhesive polymer, chosen from, for example, hydroxypropylmethylcellulose, carboxymethylcellulose, carbomer (acrylic acid polymer), poly(methylmethacrylate), polyacrylamide, polycarbophil, polyethylene oxide, acrylic acid/butyl acrylate copolymer, sodium alginate, and dextran.

Ophthalmic compositions of the disclosure can incorporate a means to inhibit microbial growth, for example through preparation and packaging under sterile conditions and/or through inclusion of an antimicrobially effective amount of an ophthalmically acceptable preservative.

Suitable preservatives include, but are not limited to, mercury-containing substances such as phenylmercuric salts (e.g., phenylmercuric acetate, borate and nitrate) and thimerosal; stabilized chlorine dioxide; quaternary ammonium compounds such as benzalkonium chloride, cetyltrimethylammonium bromide and cetylpyridinium chloride; imidazolidinyl urea; parabens such as methylparaben, ethylparaben, propylparaben and butylparaben, and salts thereof; phenoxyethanol; chlorophenoxyethanol; phenoxypropanol; chlorobutanol; chlorocresol; phenylethyl alcohol; disodium EDTA; and sorbic acid and salts thereof.

Several preservatives may precipitate in the presence of other excipients in the composition and/or in the presence of the compounds in the ophthalmic compositions. For example, benzalkonium chloride can precipitate in a composition using iota-carrageenan as a gelling agent. Thus, in those embodiments of the disclosure in which a preservative is present, the preservative is one that does not precipitate but remains in solution in the composition.

In some embodiments, the ophthalmic composition further comprises an additional ophthalmically acceptable excipient. The additional ophthalmically acceptable excipient is selected from a buffering agent, a solubilizing agent, a surfactant, a lubricating agent, and an ophthalmically acceptable salt, or any combination thereof.

Optionally one or more stabilizers can be included in the compositions to enhance chemical stability where required. Suitable stabilizers include, but are not limited to, chelating agents or complexing agents, such as, for example, the calcium complexing agent ethylene diamine tetraacetic acid (EDTA). For example, an appropriate amount of EDTA or a salt thereof, e.g., the disodium salt, can be included in the composition to complex excess calcium ions and prevent gel formation during storage. EDTA or a salt thereof can suitably be included in an amount of about 0.01% to about 0.5%. In those embodiments containing a preservative other than EDTA, the EDTA or a salt thereof, more particularly disodium EDTA, can be present in an amount of about 0.025% to about 0.1% by weight.

One or more antioxidants can also be included in the ophthalmic compositions. Suitable antioxidants include, but are not limited to, ascorbic acid, sodium metabisulfite, sodium bisulfite, acetylcysteine, polyquaternium-1, benzalkonium chloride, thimerosal, chlorobutanol, methyl paraben, propyl paraben, phenylethyl alcohol, edetate disodium, sorbic acid, or other agents know to those of skill in the art. Such preservatives are typically employed at a level of from about 0.001% to about 1.0% by weight.

In some embodiments, the compounds are solubilized at least in part by an ophthalmically acceptable solubilizing agent. Certain ophthalmically acceptable nonionic surfactants, for example polysorbate 80, can be useful as solubilizing agents, as can ophthalmically acceptable glycols, polyglycols, e.g., polyethylene glycol 400 (PEG-400), and glycol ethers.

Suitable solubilizing agents for solution and solution/suspension compositions are cyclodextrins. Suitable cyclodextrins can be chosen from α-cyclodextrin, β-cyclodextrin, γ-cyclodextrin, alkylcyclodextrins (e.g., methyl-β-cyclodextrin, dimethyl-β-cyclodextrin, diethyl-β-cyclodextrin), hydroxyalkylcyclodextrins (e.g., hydroxyethyl-β-cyclodextrin, hydroxypropyl-β-cyclodextrin), carboxy-alkylcyclodextrins (e.g., carboxymethyl-β-cyclodextrin), sulfoalkylether cyclodextrins (e.g., sulfobutylether-β-cyclodextrin), and the like. Ophthalmic applications of cyclodextrins have been reviewed in Rajewski et al., Journal of Pharmaceutical Sciences, 1996, 85, 1155-1159.

An ophthalmically acceptable cyclodextrin can optionally be present in an ophthalmic composition at a concentration from about 1 to about 200 mg/mL, from about 5 to about 100 mg/mL, or from about 10 to about 50 mg/mL.

In some embodiments, the ophthalmic composition optionally contains a suspending agent. For example, in those embodiments in which the ophthalmic composition is an aqueous suspension or solution/suspension, the composition can contain one or more polymers as suspending agents. Useful polymers include, but are not limited to, water-soluble polymers such as cellulosic polymers, for example, hydroxypropyl methylcellulose, and water-insoluble polymers such as cross-linked carboxyl-containing polymers. However, in some embodiments, ophthalmic compositions do not contain substantial amounts of solid particulate matter, whether of the anti-microbial compound, an excipient, or both, as solid particulate matter, if present, can cause discomfort and/or irritation of a treated eye.

One or more ophthalmically acceptable pH adjusting agents and/or buffering agents can be included in the ophthalmic compositions, including acids such as acetic, boric, citric, lactic, phosphoric and hydrochloric acids; bases such as sodium hydroxide, sodium phosphate, sodium borate, sodium citrate, sodium acetate, sodium lactate and tris-hydroxymethylaminomethane; and buffers such as citrate/dextrose, sodium bicarbonate and ammonium chloride. Such acids, bases and buffers are included in an amount required to maintain pH of the composition in an ophthalmically acceptable range.

One or more ophthalmically acceptable salts can be included in the compositions of the disclosure in an amount required to bring osmolality of the composition into an ophthalmically acceptable range. Such salts include, but are not limited to, those having sodium, potassium or ammonium cations and chloride, citrate, ascorbate, borate, phosphate, bicarbonate, sulfate, thiosulfate or bisulfite anions. In some embodiments, salts include sodium chloride, potassium chloride, sodium thiosulfate, sodium bisulfite and ammonium sulfate. In some embodiments, the salt is sodium chloride.

Optionally an ophthalmically acceptable xanthine derivative such as caffeine, theobromine or theophylline can be included in the compositions, e.g., as disclosed in U.S. Pat. No. 4,559,343. Inclusion of the xanthine derivative can reduce ocular discomfort associated with administration of the composition.

Optionally one or more ophthalmically acceptable surfactants, preferably nonionic surfactants, or co-solvents can be included in the compositions to enhance solubility of the components of the compositions or to impart physical stability, or for other purposes. Suitable nonionic surfactants include, but are not limited to, polyoxyethylene fatty acid glycerides and vegetable oils, e.g., polyoxyethylene (60) hydrogenated castor oil; and polyoxyethylene alkylethers and alkylphenyl ethers, e.g., octoxynol 10, octoxynol 40; polysorbate 20, 60 and 80; polyoxyethylene/polyoxypropylene surfactants (e.g., Pluronic® F-68, F84 and P-103); cyclodextrin; or other agents known to those of skill in the art. Typically, such co-solvents or surfactants are employed in the compositions at a level of from about 0.01% to about 2% by weight.

One or more ophthalmic lubricating agents can also be included optionally in the compositions to promote lacrimation or as a “dry eye” medication. Such agents include, but are not limited to, polyvinyl alcohol, methylcellulose, hydroxypropyl methylcellulose, polyvinylpyrrolidone, and the like. It will be understood that promotion of lacrimation is beneficial in the present disclosure only where lacrimation is naturally deficient, to restore a normal degree of secretion of lacrimal fluid. Where excessive lacrimation occurs, residence time of the composition in the eye can be reduced.

Ophthalmic compositions of the present disclosure typically include a combination of one or more of the optional excipients listed above. For example, in some embodiments, the ophthalmic composition can optionally further comprise glycerin in an amount from about 0.5% to about 5%, from about 1% to about 2.5%, or from about 1.5% to about 2% by weight. Glycerin can be useful to increase viscosity of the composition and for adjustment of osmolality. Independently of the presence of glycerin, the composition can also further comprise a cyclodextrin, such as hydroxypropyl-β-cyclodextrin, in an amount from about 0.5% to about 25% by weight, as a solubilizing agent, and an antimicrobially effective amount of a preservative, e.g., imidazolidinyl urea in an amount from about 0.03% to about 0.5%; methylparaben in an amount from about 0.015% to about 0.25%; propylparaben in an amount from about 0.005% to about 0.01%; phenoxyethanol in an amount from about 0.25% to about 1%; disodium EDTA in an amount from about 0.05% to about 0.2%; thimerosal in an amount from 0.001% to about 0.15%; chlorobutanol in an amount from about 0.1% to about 0.5%; and/or sorbic acid in an amount from about 0.05% to about 0.2%; all by weight.

The otic compositions also optionally comprise one or more otically acceptable excipients. Otically acceptable excipients include, but are not limited to, one or more of the preservatives, stabilizers, antioxidants, viscosity-enhancing agents, buffering agents, solubilizing agents, surfactants, lubricating agents, or acceptable salts described above, or combinations thereof, as described above for the ophthalmic compositions.

Thus, for example, in some embodiments, an otic composition optionally comprises one or more buffering agents, solubilizing agents, and antioxidants, typically in an aqueous solution. In some embodiments, the otic composition further comprises glycerin (e.g., anhydrous glycerin) or propylene glycol as a viscosity-enhancing agent. The otic composition may also comprise a surfactant in combination with the glycerin or propylene glycol to aid in the removal of cerum (ear wax). Sodium bicarbonate may also be used if wax is to be removed from the ear.

Thus, e.g., in some embodiments, the otic composition is a sterile aqueous solution comprising one or more of the disclosed compounds, glycerin, sodium bicarbonate, and, optionally, a preservative, in purified water.

The ophthalmic and otic compositions can be prepared by methods known in the art and described in patents and publications cited herein and incorporated herein by reference.

The compounds described herein can also be incorporated into compositions such as, for example, polishes, paints, sprays, or detergents formulated for application to a surface to inhibit the growth of a Mycobacterium species thereon. These surfaces include, but are not limited to, countertops, desks, chairs, laboratory benches, tables, floors, bed stands, tools, equipment, doorknobs, windows, and the like. The compounds described herein can also be incorporated into soaps and hand lotions. The present compositions, including the cleansers, polishes, paints, sprays, soaps, and detergents, can contain one or more of the compounds described herein. In addition, the compositions can optionally contain one or more of each of the following: solvents, carriers, thickeners, pigments, fragrances, deodorizers, emulsifiers, surfactants, wetting agents, waxes, and/or oils. For example, in some embodiments, the compounds can be incorporated into a formulation for external use as a pharmaceutically acceptable skin cleanser, particularly for the surfaces of human hands. Cleansers, polishes, paints, sprays, soaps, hand lotions, and detergents and the like containing the compounds described herein can be useful in homes and institutions, particularly but not exclusively, in hospital settings for the prevention of nosocomial infections.

The present disclosure also provides pharmaceutical packs or kits comprising one or more containers filled with one or more compounds described herein. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration for treating a condition, disease, or disorder described herein. In some embodiments, the kit contains more than one compound described herein. In some embodiments, the kit comprises a compound described herein in a single injectable dosage form, such as a single dose within an injectable device such as a syringe with a needle.

The present disclosure also provides methods of inhibiting the growth of a microbe comprising contacting the microbe with one or more compounds described above, or a pharmaceutically acceptable salt thereof. In some embodiments, the compound can act as an antiseptic agent for cleansing surfaces, such as in, for example, kitchens and bathrooms. In these embodiments, the compound can be formulated for such uses by procedures well known to the skilled artisan.

The present disclosure also provides methods of treating a mammal having a microbial infection comprising administering to the mammal in need thereof an anti-microbial effective amount of one or more compounds described above, or a pharmaceutically acceptable salt thereof. In some embodiments, the mammal can be pre-diagnosed with a microbial infection prior to treatment. In some embodiments, no formal diagnosis may have been made; in such embodiments, the mammal may be suspected of having a microbial infection for which treatment is recognized as being desirable.

In some embodiments, the microbe is, or the microbial infection is due to, a gram-negative aerobe, a gram-positive aerobe, a gram-negative anaerobe, a gram-positive anaerobe, or a yeast. In some embodiments, the gram-negative aerobe is selected from, but not limited to, Escherichia coli, Citrobacter freundii, Citrobacter diverus, Citrobacter koseri, Enterobacter cloacae, Enterobacter faecalis, Klebsiella pneumonia, Klebsiella oxytoca, Morganella morganii, Providencia stuartii, Proteus vulgaris, Proteus mirabilis, Serratia marcescens, Acinetobacter haemolyticus, Acinetobacter junii, Acinetobacter lwoffii, Haemophilus influenzae, Stenotrophomonas maltophilia, and Pseudomonas aeruginosa. In some embodiments, the gram-positive aerobe is selected from, but not limited to, Enterococcus faecalis, Enterococcus faecium, Mycobacterium tuberculosis, Staphylococcus aureus, Staphylococcus pneumoniae, Staphylococcus epidermidis, Staphylococcus saprophyticus, Staphylococcus colmii, Staphylococcus sciuri, Staphylococcus warneri, Streptococcus agalactiae, Streptococcus pyogenes, Streptococcus anginosus, Streptococcus mitis, and Streptococcus oralis. In some embodiments, the gram-negative anaerobe is Bacteroides fragilis. In some embodiments, the gram-positive anaerobe is Clostridium difficile or Clostridium perfringens. In some embodiments, the mycobacterium is Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium canetti, or Mycobacterium microti. In some embodiments, the yeast is selected from, but not limited to, Candida albicans and Candida krusei. In some embodiments, the microbe is an antibiotic-resistant strain of bacteria, such as those recited in the Examples below.

The present disclosure also provides one or more compounds described above, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising one or more compounds described above, for treating a microbial infection.

The present disclosure also provides the use of one or more compounds described above, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising one or more compounds described above, in the inhibition of growth of a microbe.

The ophthalmic or otic compositions possess anti-microbial activity and can be used in methods of treating or preventing ophthalmic infections in an eye of an animal, or otic infections in the ear of an animal.

Ophthalmic infections for which the compositions and methods are useful include, but are not limited to, infections of one or more tissues of the eye, including, for example, conjunctivitis, keratitis (including ulcerative keratitis with bacterial infection), keratoconjunctivitis (including, e.g., keratoconjunctivitis sicca (KCS) commonly found in dogs), blepharitis, blepharoconjunctivitis, dacyrocystitis, hordeolum, corneal ulcers, orbital and preseptal cellulitis, and endophthalmitis. In some embodiments, the infected tissue is one that is directly bathed by the lacrimal fluid, as in conjunctivitis, keratitis, keratoconjunctivitis, blepharitis, and blepharoconjunctivitis. The ophthalmic compositions may also be used prophylactically in connection with various ophthalmic surgical procedures that create a risk of infection.

Otic infections for which the compositions and methods are useful include, but are not limited to, otitis externa and otitis media. With respect to the treatment of otitis media, the compositions are primarily useful in cases where the tympanic membrane has ruptured or tympanostomy tubes have been implanted. The otic compositions may also be used to treat infections associated with otic surgical procedures, such as tympanostomy, or to prevent such infections.

The ophthalmic and otic compositions are effective in killing or inhibiting the growth of a broad spectrum of pathogens or microbes often associated with ophthalmic and/or otic infections, including a range of bacteria (both gram-postive and gram-negative), fungi and viruses. For example, the ophthalmic and otic compositions are useful in killing or inhibiting the growth of any of the following clinically relevant ocular or otic pathogens, and can be administered topically to treat and/or prevent ophthalmic or otic infections caused by the following pathogens or mixtures of the following pathogens: Staphylococcus spp. (e.g., Staphylococcus aureus, Staphylococcus epidermidis), Streptococcus spp. (e.g., Streptococcus viridans, Streptococcus pneumoniae), Enterococcus spp., Bacillus spp., Corynebacterium spp., Propionibacterium spp., Chlamydia spp., Moraxella spp. (e.g., Moraxella lacunata and Moraxella catarrhalis), Haemophilus spp. (e.g., Haemophilus influenza and Haemophilus aegyptius), Pseudomonas spp. (e.g., Pseudomonas aeruginosa, and, for otic infections, Pseudomonas otitidis), Serratia spp. (e.g., Serratia marcescens), Neisseria spp., and Mycoplasma spp., as well as Enterobacter spp. (e.g., Enterobacter aerogenes), Eschericia spp. (e.g., Eschericia coli), Klebsiella spp. (e.g., Klebsiella pneumoniae), Proteus spp. (e.g., Proteus mirabillis and Proteus vulgaris), Acinetobacter spp. (e.g., Acinetobacter calcoaceticus), Prevotella spp., Fusobacterium spp., Porphyromonas spp., and Bacteroides spp. (e.g., Bacteroides fragilis). This list of microbes is purely illustrative and is in no way to be interpreted as restrictive.

Thus, for example, the ophthalmic compositions can be administered to treat or prevent a bacterial infection of the eye caused by one or more of the following species: Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus viridans, Enterococcus faecalis, Corynebacterium spp., Propionibacterium spp., Moraxella catarrhalis and Haemophilus influenzae.

Treatment of bacterial conjunctivitis by administering an ophthalmic composition of the present disclosure is appropriate where infection with one or more of the following species is present: Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus viridans, Enterococcus faecalis, Corynebacterium spp., Propionibacterium spp., Moraxella catarrhalis and Haemophilus influenzae.

Treatment of bacterial blepharitis by administering an ophthalmic composition of is appropriate where infection with one or more of the following species is present: Staphylococcus aureus, Staphylococcus epidermidis and Streptococcus pneumoniae.

Treatment of bacterial keratitis by administering an ophthalmic composition is also appropriate where infection with one or more of the following species is present: Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae and Streptococcus viridans.

The otic compositions can also be administered to treat or prevent a bacterial infection of the ear caused by one or more of the following species: Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, Moraxella catarrhalis, Pseudomonas otitidis, and Proteus spp. (e.g., Proteus mirabillis and Proteus vulgaris), as well as one or more of the following anaerobes: Prevotella spp., Fusobacterium spp., Porphyromonas spp., and Bacteroides spp. (e.g., Bacteroides fragilis). Thus, for example, treatment of chronic suppurative otitis media by administering an otic composition is appropriate where infection with one or more of the following species is present: Staphylococcus aureus, Pseudomonas aeruginosa, Eschericia coli, Klebsiella spp. (e.g., Klebsiella pneumoniae), Proteus spp. (e.g., Proteus mirabillis and Proteus vulgaris), Prevotella spp., Fusobacterium spp., Porphyromonas spp., and Bacteroides spp. (e.g., Bacteroides fragilis).

The ophthalmic or otic compositions are also useful in killing or inhibiting the growth of clinically relevant ocular or otic fungi, and can be administered topically to treat and/or prevent ophthalmic or otic infections caused by one or more species of fungi, or a mixture of species of fungi, including, but not limited to, Aspergillus spp. (e.g., Aspergillus fumigatus, Aspergillus favus, Aspergillus niger and Aspergillus terreus), Fusarium spp. (e.g., Fusarium solani, Fusarium moniliforme and Fusarium proliferartum), Malessezia spp. (e.g., Malessezia pachydermatis), and/or Candida spp. (e.g., Candida albicans), as well as Chrysosporium parvum, Metarhizium anisopliae, Phaeoisaria clematidis, and Sarcopodium oculorum. This list of microbes is purely illustrative and is in no way to be interpreted as restrictive.

The ophthalmic compositions can be administered to treat or prevent a fungal infection of the eye caused by one or more of the following species: Aspergillus spp., Fusarium spp., Chrysosporium parvum, Metarhizium anisopliae, Phaeoisaria clematidis, and Sarcopodium oculorum. For example, the ophthalmic composition can be administered to treat fungal keratitis caused by one or more Aspergillus spp. and/or Fusarium spp.

The otic compositions can also be administered to treat or prevent a fungal infection of the ear caused by one or more of the following species: Candida spp., Aspergillus spp., and/or Malessezia spp. (e.g., Malessezia pachydermatis).

The ophthalmic or otic compositions are also useful in killing or inhibiting the growth of clinically relevant ocular or otic viruses and can be administered topically to treat and/or prevent ophthalmic or otic infections caused by one or more viruses, including, but not limited to, adenoviruses and herpes viruses (including, e.g., Herpes simplex 1 virus and/or varicella-zoster virus), Eneroviruses and Cytomegaloviruses. Thus, for example, the ophthalmic compositions can be administered to treat or prevent a viral infection of the eye, e.g., Herpes keratitis, caused by Herpes simplex 1 virus.

In some embodiments, the ophthalmic or otic compositions are useful and effective in killing and/or preventing the growth of microbes that have developed significant levels of resistance to anti-microbial agents other than the disclosed compounds. For example, in some embodiments, the ophthalmic compositions and otic compositions are especially effective in methods of treating ophthalmic infections or otic infections cased by bacterial strains that have developed resistance to ciprofloxacin, e.g., Ciprofloxacin Resistant (CR) S. aureus and CR S. epidermidis, or to fluoroquinolone, or bacterial strains that have developed resistance to penicillin.

In some embodiments, the compositions are administered topically to one or more tissues of the eye or ear to treat an existing microbial infection, or as a prophylactic measure to prevent a microbial infection. Thus, for example, in some embodiments, an ophthalmic composition is administered topically to one or more tissues of the eye to treat an existing microbial infection, e.g., conjunctivitis, keratitis, blepharitis, or blepharoconjunctivitis.

In other embodiments, an ophthalmic composition is administered topically to one or more tissues of the eye as a prophylactic measure. That is, the compositions are administered for prophylactic uses, e.g., in connection with various ophthalmic surgical procedures that create a risk of infection. Thus, for example, a composition can be administered in a method of post-traumatic prophylaxis, especially post-surgical prophylaxis, to prevent infection after ocular surgery, or in a method of prophylaxis prior to ocular surgery, for example, administered prior to surgery to prevent infection as a consequence of surgery.

The ophthalmic and otic compositions possess broad-spectrum anti-microbial activity. As a consequence, an ophthalmic infection or an otic infection can be treated or prevented by administering only one of the compositions, rather than by administering two or more separate antimicrobial compositions or one antimicrobial composition containing a combination of antimicrobial agents.

For example, because the ophthalmic compositions can be used to treat or prevent both viral and bacterial ophthalmic infections in an eye, only one of the present compositions needs to be administered to the eye to treat a viral ophthalmic infection where there is a risk of a secondary bacterial infection. Similarly, for an eye infection caused by multiple strains of bacteria (e.g., by both gram-positive bacteria and gram-negative bacteria), only one composition containing one of the disclosed compounds needs to be administered, rather than a composition containing multiple anti-microbial agents, or a combination of separate treatments administered concurrently.

In some embodiments, the ophthalmic or otic compositions are administered with an additional anti-microbial agent, such as, e.g., an anti-bacterial, anti-fungal, or anti-viral agent. For example, the additional anti-microbial agent can be a second compound disclosed herein, or the additional anti-microbial agent can be another anti-microbial agent such as, for example, an antibiotic selected from the group consisting of aminoglycosides, cephalosporins, diaminopyridines, fluoroquinolones, sulfonamides and tetracyclines. Examples of useful antibiotics which can serve as additional anti-microbials include, but are not limited to, amikacin, azithromycin, cefixime, cefoperazone, cefotaxime, ceftazidime, ceftizoxime, ceftriaxone, chloramphenicol, ciprofloxacin, clindamycin, colistin, domeclocycline, doxycycline, erythromycin, gentamicin, mafenide, methacycline, minocycline, neomycin, norfloxacin, ofloxacin, oxytetracycline, polymyxin B, pyrimethamine, silver sulfadiazine, sulfacetamide, sulfisoxazole, tetracycline, tobramycin, and trimethoprim.

In those embodiments in which the ophthalmic or otic composition is administered with another anti-microbial agent, the present disclosure provides methods of treating or preventing multiple bacterial infections in an eye or an ear, the method comprising application to the eye or ear in co-therapy (including co-formulation) one or more compounds disclosed herein and one or more additional anti-microbial agents. “Co-therapy” herein means administration to the eye or ear, at the same time or sequentially, of an ophthalmically or otically acceptable composition comprising one or more of the compounds disclosed herein and a separate ophthalmically or otically acceptable composition of the additional anti-microbial agent, in a treatment regimen intended to provide a beneficial effect from co-action of the two types of antimicrobial agents. “Co-formulation” herein means that the compound and the additional anti-microbial agent are administered to the eye or ear as components of a single ophthalmically or otically acceptable composition.

The ophthalmic or otic compositions can also be used in co-therapy with one or more drugs, or medicaments, other than anti-microbial agents. Such medicaments other than anti-microbial agents can be co-administered to the eye or ear together with a composition. Thus, e.g., an ophthalmic composition disclosure can further comprise, in co-formulation with the compounds described herein, a therapeutically and/or prophylactically effective amount of one or more medicaments that are other than anti-microbial agents.

These additional medicaments other than the compounds described herein can cooperate with the compounds described herein in treating and/or preventing an infective disease of the eye or ear, or can be used to treat a related or unrelated conditions simultaneously affecting the eye or ear.

Any medicament having utility in an ophthalmic or otic application can be used in co-therapy, co-administration or co-formulation with an ophthalmic or otic composition as described above. Such additional medicaments include, but are not limited to, anti-inflammatory agents (e.g., steroidal anti-inflammatory agents, non-steroidal anti-inflammatory agents (NSAIDs), and selective cyclooxygenase-2 inhibitors); topical and/or regional anesthetic agents; anti-allergic agents (e.g., anti-histamines); demulcents; acetylcholine blocking agents; adrenergic agonists, beta-adrenergic blocking agents and other anti-glaucoma agents; anti-hypertensives; anti-cataract agents; anti-microbial agents, and anti-allergic agents.

For example, ophthalmic and otic infections are frequently accompanied by inflammation of the infected ophthalmic and/or otic tissues and surrounding tissues. In addition, ophthalmic and otic surgical procedures that create a risk of microbial infections frequently also causes inflammation of the affected tissues. Thus, the ophthalmic and otic compositions can be co-formulated with an anti-inflammatory agent to combine the anti-infective activity of one or more antibiotics with the anti-inflammatory activity of one or more steroid or non-steroid agents in a single composition.

The anti-inflammatory agents can be steroidal or non-steroidal. Examples of suitable steroidal anti-inflammatory agents include, but are not limited to, dexamethasone; dexamethasone derivatives such as those disclosed in U.S. Pat. No. 5,223,492; rimexolone; prednisolone; fluorometholone; and hydrocortisone.

Examples of suitable non-steroidal anti-inflammatory agents include, but are not limited to, prostaglandin H synthetase inhibitors (Cos I or Cox II), also referred to as cyclooxygenase type I and type II inhibitors, such as diclofenac, flurbiprofen, ketorolac, suprofen, nepafenac, amfenac, indomethacin, naproxen, ibuprofen, bromfenac, ketoprofen, meclofenamate, piroxicam, sulindac, mefanamic acid, diflusinal, oxaprozin, tolmetin, fenoprofen, benoxaprofen, nabumetome, etodolac, phenylbutazone, aspirin, oxyphenbutazone, tenoxicam and carprofen; cyclooxygenase type II selective inhibitors, such as vioxx, celecoxib, etodolac; PAF antagonists, such as apafant, bepafant, minopafant, nupafant and modipafant; PDE IV inhibitors, such as ariflo, torbafylline, rolipram, filaminast, piclamilast, cipamfylline, and roflumilast; inhibitors of cytokine production, such as inhibitors of the NFkB transcription factor; or other anti-inflammatory agents know to those skilled in the art.

Examples of suitable topical or regional anesthetic agents include, but are not limited to, benzocaine.

Examples of suitable anti-allergic agents include, but are not limited to, pemirolast, olopatadine, and the corticosteroids (prednisolone, fluorometholone, loteprenol and dexamthasone).

The additional medicament can be administered in co-therapy (including co-formulation) with the one or more facially amphiphilic polymers of the ophthalmic or otic composition. For example, in some embodiments, an ophthalmic composition of the present disclosure comprising one of the anti-microbial compounds disclosed herein is administered in co-therapy with an anti-inflammatory agent, e.g., a glucocorticoid. The glucocorticoid can be co-formulated with the compound in a single ophthalmically acceptable composition, which is administered to one or more tissues of an eye, to not only treat or prevent an ophthalmic infection but also to treat and/or prevent inflammation.

The ophthalmic or otic compositions can be administered by any appropriate route of administration. In some aspects of the disclosure, the ophthalmic and otic compositions are administered topically, for example, the composition is topically administered in an antimicrobially effective amount to one or more tissues of the eye of the animal, or to one or more tissues of the ear of an animal.

In some embodiments, the response of the ophthalmic or otic infection to treatment is monitored and the treatment regimen is adjusted if necessary in light of such monitoring.

Frequency of administration is typically such that the dosing interval, for example, the period of time between one dose and the next, during waking hours is from about 2 to about 12 hours, from about 3 to about 8 hours, or from about 4 to about 6 hours. It will be understood by those of skill in the art that an appropriate dosing interval is dependent to some degree on the length of time for which the selected composition is capable of maintaining a concentration of the compound(s) in the lacrimal fluid and/or in the target tissue (e.g., the conjunctiva) above the MIC₉₀(the minimum concentration of the compound which inhibits microbial growth by 90%). Ideally the concentration remains above the MIC₉₀for at least 100% of the dosing interval. Where this is not achievable it is desired that the concentration should remain above the MIC₉₀for at least about 60% of the dosing interval, or should remain above the MIC₉₀for at least about 40% of the dosing interval.

In some embodiments, the ophthalmic composition is formulated as an in situ gellable aqueous liquid and is administered as eye drops. Typically each drop, generated by a conventional dispensing means, has a volume from about 10 to about 40 μL. From 1 to about 6 such drops typically provides a suitable dose of the compound in from about 25 to about 150 μL of the composition. For example, no more than 3 drops, no more than 2 drops, or no more than 1 drop, should contain the desired dose of the compound for administration to an eye. Where the composition is administered in a form other than eye drops, for example, as an ophthalmic ointment or as a solid implant, an equivalent dose is provided. Such a dose can be administered as needed, but typically administration to the eye 1 to about 6 times per day, in most cases from 2 to 4 times a day, provides adequate continuing relief or prevention of the infective disease indicated.

The ophthalmic compositions, such as aqueous suspension compositions, can be packaged in single-dose non-reclosable containers. Such containers can maintain the composition in a sterile condition and thereby eliminate need for preservatives such as mercury-containing preservatives, which can sometimes cause irritation and sensitization of the eye. Alternatively, multiple-dose reclosable containers can be used, in which case it is preferred to include a preservative in the composition.

In some embodiments, the ophthalmic composition is an aqueous solution, suspension or solution/suspension which is administered in the form of eye drops. In these embodiments, a desired dosage of the active agent can be administered by means of a suitable dispenser as a known number of drops into the eye. Examples of suitable dispensers are disclosed in International Patent Publication No. WO 96/06581.

The ophthalmic or otic compositions can be tested for anti-microbial activity by methods known to those of skill in the art. For example, anti-microbial assays suitable for testing the antimicrobial activity of the ophthalmic or otic compositions of the disclosure are described, for example, US Pat. Appl. Publ. No. US 2006-0041023 A1; Tew et al., Proc. Natl. Acad. Sci. USA, 2002, 99, 5110-5114; and Liu et al., J. Amer. Chem. Soc., 2001, 123, 7553-7559.

The activity of antimicrobials is generally expressed as the minimum concentration of a compound (active agent) required to inhibit the growth of a specified pathogen. This concentration is also referred to as the “minimum inhibitory concentration” or “MIC.” The term “MIC₉₀” refers to the minimum concentration of an antimicrobial active agent required to inhibit the growth of ninety percent (90%) of the tested isolates for one particular organism. The concentration of a compound required to totally kill a specified bacterial species is referred to as the “minimum bactericidal concentration” or “MBC.”

In some embodiments, an effective concentration of the compound in the composition will generally be from about 0.01% to about 20% by weight (wt %) of the composition, from about 0.05% to about 10% by weight, from about 0.1% to about 8.0% by weight, from about 0.5% to about 5.0% by weight, from about 1.0% to about 5.0% by weight, or from about 2.0% to about 4.0% of the composition. For example, in ophthalmic compositions in the form of solid suspensions, such as ointments, an effective concentration of the antimicrobial compound will generally be from about 1% to about 5% by weight (wt %) of the composition.

The present disclosure is also directed to a method for treating or preventing a microbial infection in an eye of an animal by administering to one or more tissues of the eye an antimicrobial ophthalmic composition, wherein the composition comprises a compound described herein in an amount effective to treat or prevent the infection.

In some embodiments of the methods of the present disclosure, the antimicrobial ophthalmic composition is administered topically to one or more tissues of the eye of the animal.

In some embodiments of the methods present disclosure, the ophthalmic composition is in a form selected from a solution, a suspension, an emulsion, a gel, an ointment, and a solid article suitable for ocular implant. In other embodiments, the ophthalmic composition is administered 2 to 4 times daily. In yet other embodiments, the compound in the ophthalmic composition is present in the composition at a concentration of about 0.01% to about 20% by weight.

In some embodiments of the methods of the present disclosure, the microbial ophthalmic infection is a bacterial infection. For example, in some embodiments, the bacterial infection is caused by Staphylococcus, Streptococcus, Enterococcus, Bacillus, Corynebacterium, Moraxella, Haemophilus, Serratia, Pseudomonas, or Neisseria spp. In other embodiments, the microbial infection is a fungal infection. For example, in some embodiments, the fungal infection is caused by Aspergillus or Fusarium spp. In yet other embodiments, the microbial infection is a viral infection. For example, in some embodiments, the viral infection is caused by a herpes virus. In some embodiments of the methods of the present disclosure, the ophthalmic infection is selected from bacterial keratitis, bacterial conjunctivitis, and corneal ulcers.

The present disclosure is also directed to an otic composition, comprising an effective amount of a compound described herein and an otically acceptable excipient.

The present disclosure is also directed to an antimicrobial otic composition, the composition comprising a) a compound described herein, or a pharmaceutically acceptable salt or solvate thereof, in an amount effective for treatment and/or prophylaxis of a microbial infection of an ear of an animal; and b) an otically acceptable excipient, wherein the composition is suitable for administration to one or more tissues of the ear.

The present disclosure is also directed to an otic composition for use in treatment or prevention of a microbial infection in an ear of an animal, wherein the composition comprises a compound described herein, or an acceptable salt or solvate thereof, in an amount effective to treat or prevent the infection when the composition is administered to one or more tissues of the ear.

The present disclosure is also directed to any of the otic compositions disclosed herein, wherein the composition is suitable for topical administration to one or more tissues of an ear of an animal.

The present disclosure is also directed to any of the otic compositions disclosed herein, wherein the composition is in a form selected from a solution, a suspension, an emulsion, a gel, an ointment, and a solid article suitable for otic implant.

The present disclosure is also directed to any of the otic compositions disclosed herein, wherein the compound is present in the otic composition at a concentration of about 0.01% to about 20% by weight.

The present disclosure is also directed to any of the otic compositions disclosed herein, wherein the otically acceptable excipient is selected from a preservative, a stabilizer, an antioxidant, and a viscosity-enhancing agent, or any combination thereof, such as any of those discussed above.

In some embodiments, the otic composition further comprises an additional medicament. The additional medicament is selected from an anti-inflammatory agent, an antimicrobial agent, an anesthetic agent, and an anti-allergic agent.

The present disclosure is further directed to a method of treating or preventing a microbial infection in an ear of an animal, the method comprising administering to an ear of an animal in need of the treating or preventing an effective amount of an otic composition.

The present disclosure is also directed to a method for treating or preventing a microbial infection in an ear of an animal by administering to one or more tissues of the ear an antimicrobial otic composition, wherein the composition comprises a compound described herein, in an amount effective to treat or prevent the infection.

In some embodiments, the antimicrobial otic composition is administered topically to one or more tissues of the ear of the animal.

In some embodiments, the otic composition is in a form selected from a solution, a suspension, an emulsion, a gel, an ointment, and a solid article suitable for otic implant. In other embodiments, the otic composition is administered 2 to 4 times daily. In yet other embodiments, the compound is present in the otic composition at a concentration of about 0.01% to about 20% by weight.

In some embodiments, the microbial otic infection is a bacterial infection. In other embodiments, the infection is a fungal infection. In yet other embodiments, the infection is a viral infection.

In some embodiments, the otic infection is selected from otitis externa and otitis media.

The present disclosure also provides methods of treating malaria in an animal comprising administering to the animal a therapeutically effective amount of a compound, or a pharmaceutically acceptable salt thereof. In any of the above embodiments, the malaria can be chloroquine-sensitive or chloroquine-resistant.

The present disclosure also provides methods of killing or inhibiting the growth of a Plasmodium species comprising contacting the species with an effective amount of a compound, or a pharmaceutically acceptable salt thereof. In any of the above embodiments, the malaria can be chloroquine-sensitive or chloroquine-resistant.

The anti-malarial compounds can be useful as anti-malarial agents in a number of applications. For example, compounds can be used therapeutically to treat malaria in animals, including humans and non-human vertebrates such as wild, domestic and farm animals. The malarial infection in an animal can be treated by administering to the animal an effective amount of a compound, or a pharmaceutical composition comprising the same. The compound, or composition thereof, can be administered systemically or topically and can be administered to any body site or tissue.

The present disclosure also provides compounds, or a salt thereof, or compositions comprising the same, for use in treating a malarial infection in an animal. The present disclosure also provides compounds, or a salt thereof, or compositions comprising the same, for use in killing or inhibiting the growth of a Plasmodium species. The present disclosure also provides compounds, or a salt thereof, or compositions comprising the same, for use in preparation of a medicament for treating a malarial infection in an animal. The present disclosure also provides compounds, or a salt thereof, or compositions comprising the same, for use in preparation of a medicament for killing or inhibiting the growth of a Plasmodium species.

The compounds described herein can be combined with one, two, or three other anti-malarial compounds described herein to form a cocktail. This cocktail can also include other anti-malarial compounds. Other anti-malarial compounds include, but are not limited to, any one or more of artemisinin, quinine, artesunate, sulfadoxine-pyrimethamine, hydroxychloroquine, chloroquine, amodiaquine, pyrimethamine, sulphadoxine, proguanil, mefloquine, atovaquone, primaquine, halofantrine, doxycycline, and clindamycin.

One of skill in the art will recognize that the compounds can be tested for anti-malarial activity by methods well known to those of skill in the art. Any compound found to be active can be purified to homogeneity and re-tested to obtain an accurate IC₅₀.

Thus, the present disclosure provides methods of treating malaria in an animal comprising administering to the animal in need thereof an effective amount of a compound or a slat thereof. The present disclosure provides methods of treating malaria in an animal comprising administering to the animal in need thereof a composition comprising a compound, or a salt thereof. The present disclosure provides methods of killing or inhibiting the growth of a Plasmodium species comprising contacting the species with an effective amount of a compound, or salt thereof. The present disclosure provides methods of killing or inhibiting the growth of a Plasmodium species comprising contacting the species with a composition comprising a compound, or salt thereof. The present disclosure provides methods of killing or inhibiting the growth of a chloroquine-sensitive or chloroquine-resistant Plasmodium species comprising contacting the species with an effective amount of a compound, or salt thereof. The present disclosure provides methods of killing or inhibiting the growth of a chloroquine-sensitive or chloroquine-resistant Plasmodium species comprising contacting the species with a composition comprising a compound, or salt thereof. The present disclosure provides methods of disrupting a food vacuole of a Plasmodium species comprising contacting the species with an effective amount of a compound, or salt thereof. The present disclosure provides methods of disrupting a food vacuole of a Plasmodium species comprising contacting the species with a composition comprising a compound, or salt thereof.

The present disclosure also provides methods of inhibiting the growth of a Mycobacterium species comprising contacting the Mycobacterium species with an effective amount of a compound described herein, or salt or pharmaceutically acceptable salt thereof.

In some embodiments, some of the compounds described herein rapidly kill M. tuberculosis (for example in vitro). In some embodiments, some of the compounds described herein possess low cytotoxicity against mammalian cells. In some embodiments, the EC₅₀of the compounds used in the present disclosure (for mammalian cells) is greater than about 200 μM or greater than about 300 μM. In some embodiments, some of the compounds described herein have high selectivity against M. tuberculosis over mammalian cells. In some embodiments, the selective index (SI) values (the SI value is calculated by dividing the EC₅₀by the IC₉₀) of some of the compounds described herein is greater than about 10, greater than about 20, greater than about 30, greater than about 40, greater than about 50, greater than about 60, greater than about 70, greater than about 80, greater than about 90, greater than about 100, greater than about 120, greater than about 150, or greater than about 200.

The present disclosure also provides methods of treating an animal having a Mycobacterium infection comprising administering to the animal a therapeutically effective amount of a compound or a pharmaceutically acceptable salt thereof. In some embodiments, the Mycobacterium infection is caused by a Mycobacterium species, such as Mycobacterium tuberculosis. In some embodiments, the Mycobacterium species is active, dormant, or semi-dormant. In some embodiments, the active, dormant, or semi-dormant Mycobacterium species is not killed or inhibited by known TB drugs. In some embodiments, the Mycobacterium species is multi-drug resistant TB, with resistance to isoniazid and rifampicin. In some embodiments, the Mycobacterium species is extensively drug resistant TB, with resistance to any one of the fluoroquinolone drugs and to at least one of the following three injectable second-line drugs: amikacin, capreomycin, or kanamycin. In some embodiments, the Mycobacterium tuberculosis is multi-drug resistant TB, with resistance to isoniazid and rifampicin. In some embodiments, the Mycobacterium tuberculosis is extensively drug resistant TB, with resistance to any one of the fluoroquinolone drugs and to at least one of the following three injectable second-line drugs: amikacin, capreomycin, or kanamycin. In some embodiments, the methods described herein create or cause no new drug resistance. In some embodiments, the compound is present within a pharmaceutical composition.

In some embodiments, the animal being treated, such as a human, is “in need thereof.” That is, the animal is in need of treatment. Thus, in some embodiments, the animal is treated for the purpose of treating the Mycobacterium infection. In some embodiments, the animal has been diagnosed with a Mycobacterium infection or is suspected of having a Mycobacterium infection. In some embodiments, the animal, or human, is in a population at risk of having a Mycobacterium infection, such as in a prison or hospital.

Those skilled in the art will recognize that the compounds described herein can be tested for anti-TB activity by methods well known to those of skill in the art (see, e.g., Collins et al., Antimicrobial Agents and Chemotherapy, 1997, 41, 1004-1009). Any compound found to be active can be purified to homogeneity and re-tested to obtain an accurate IC₉₀or IC₅₀. Because these compounds can work by directly lysing bacterial cell membranes (rather than working on any specific receptor or intracellular target), the same mechanism utilized by the host defense proteins, drug resistance to these compounds is unlikely to develop. This premise is supported by experimental data showing that a negligible incidence of resistance development was observed in vitro in serial passage challenge assays using S. aureus. Thus, targeting bacterial cell membranes rather than any specific receptor or intracellular target represents a highly innovative and novel approach for treating TB (including MDR-TB and/or XRD-TB) and serves as one manner to distinguish the present disclosure from others in this field.

In any of the methods described above and herein, the Mycobacterium species can be Mycobacterium tuberculosis. In some embodiments, the Mycobacterium species is active, dormant, or semi-dormant. In some embodiments, the active, dormant, or semi-dormant Mycobacterium species is not killed or inhibited by known TB drugs. In some embodiments, the Mycobacterium species is multi-drug resistant TB, with resistance to isoniazid and rifampicin. In some embodiments, the Mycobacterium species is extensively drug resistant TB, with resistance to any one of the fluoroquinolone drugs and to at least one of the following three injectable second-line drugs: amikacin, capreomycin, or kanamycin.

The present disclosure also provides compounds described herein, or compositions or pharmaceutical compositions comprising the same, for use in preparation of a medicament for treating a Mycobacterium infection (including Mycobacterium tuberculosis, including MDR-TB and XDR-TB) in an animal and/or for inhibiting the growth of a Mycobacterium species. The present disclosure also provides compounds described herein, or compositions comprising the same, for treating a Mycobacterium infection (including Mycobacterium tuberculosis, including MDR-TB and XDR-TB) in an animal and/or for inhibiting the growth of a Mycobacterium species.

The present disclosure also provides methods of treating and/or preventing mucositis in a mammal comprising administering to the mammal in need thereof a therapeutically effective amount of a compound described herein.

The compounds described herein may be useful for treating and/or preventing mucositis by administering to the patient an effective amount of a compound or a salt thereof, or a pharmaceutical composition comprising a compound or a salt thereof. The compound or salt, or composition thereof, can be administered systemically or topically and can be administered to any body site or tissue.

In some embodiments, the present methods for treating and/or preventing mucositis can be used in a patient who receives chemotherapy and/or radiation therapy for cancer. In some embodiments, the patient is receiving or will be receiving high-dose chemotherapy prior to hematopoietic cell transplantation. In some embodiments, the patient is receiving or will be receiving radiation therapy for tumors of the head and neck. In some embodiments, the patient is receiving or will be receiving induction therapy for leukemia. In some embodiments, the patient is receiving or will be receiving conditioning regimens for bone marrow transplant. In some embodiments, the patient is experiencing or will be experiencing basal epithelial cell death.

The present disclosure also provides compounds, or compositions comprising the same, for use in treating and/or preventing mucositis in a patient. The present disclosure also provides compounds, or compositions comprising the same, for use in treating and/or preventing mucositis. The present disclosure also provides compounds, or compositions comprising the same, for use in preparation of a medicament for treating and/or preventing mucositis in a patient.

The compounds described herein can also be administered in combination with other active ingredients such as, for example, palifermin and/or NX002, or other known compounds useful for treating and/or preventing mucositis.

The present disclosure also provides methods for treating and/or preventing mucositis in an animal comprising administering to the animal in need thereof an effective amount of a compound described herein. The present disclosure also provides methods for treating and/or preventing mucositis in an animal comprising administering to the animal in need thereof a composition of the disclosure. The present disclosure also provides methods for treating and/or preventing mucositis comprising administering to the animal an effective amount of a compound.

The present disclosure also provides methods of treating or reducing a cancer, inhibiting tumor growth, or treating or preventing spread or metastasis of cancer in a mammal comprising administering to the mammal in need thereof a therapeutically effective amount of a compound described herein or pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising the compound described herein or pharmaceutically acceptable salt thereof. In some embodiments, one or more compounds may be combined in the same composition for any of the methods disclosed herein.

The present disclosure also provides methods for killing or inhibiting growth of a cancer cell comprising contacting the cancer cell with an effective amount of a compound or pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising the compound or salt.

Thus, the compounds can be used as anti-cancer and anti-tumor agents, e.g., the compounds can kill or inhibit the growth of cancer cells. The compounds can also be used in methods of reducing cancer in an animal, or in methods of treating or preventing the spread or metastasis of cancer in an animal, or in methods of treating an animal afflicted with cancer. The compounds can also be used in methods of killing or inhibiting the growth of a cancer cell, or in methods of inhibiting tumor growth. In some embodiments, the compounds of the disclosure can act directly on the cancer cell rather than by acting indirectly such as by inhibition of angiogenesis.

The compounds can be tested for anti-cancer activity by methods known to those of skill in the art. Examples of anti-cancer assays include, but are not limited to, standard cell viability assays, such as the XTT assay, or by metabolic activity assays.

Generally, cancer refers to any malignant growth or tumor caused by abnormal and uncontrolled cell division; it may spread to other parts of the body through the lymphatic system or the blood stream. Cancers include both solid tumors and blood-borne tumors. Cancers that are treatable are broadly divided into the categories of carcinoma, lymphoma and sarcoma. Examples of carcinomas include, but are not limited to: adenocarcinoma, acinic cell adenocarcinoma, adrenal cortical carcinomas, alveoli cell carcinoma, anaplastic carcinoma, basaloid carcinoma, basal cell carcinoma, bronchiolar carcinoma, bronchogenic carcinoma, renaladinol carcinoma, embryonal carcinoma, anometroid carcinoma, fibrolamolar liver cell carcinoma, follicular carcinomas, giant cell carcinomas, hepatocellular carcinoma, intraepidermal carcinoma, intraepithelial carcinoma, leptomanigio carcinoma, medullary carcinoma, melanotic carcinoma, menigual carcinoma, mesometonephric carcinoma, oat cell carcinoma, squamal cell carcinoma, sweat gland carcinoma, transitional cell carcinoma, and tubular cell carcinoma. Sarcomas include, but are not limited to: amelioblastic sarcoma, angiolithic sarcoma, botryoid sarcoma, endometrial stroma sarcoma, ewing sarcoma, fascicular sarcoma, giant cell sarcoma, granulositic sarcoma, immunoblastic sarcoma, juxaccordial osteogenic sarcoma, coppices sarcoma, leukocytic sarcoma (leukemia), lymphatic sarcoma (lympho sarcoma), medullary sarcoma, myeloid sarcoma (granulocitic sarcoma), austiogenci sarcoma, periosteal sarcoma, reticulum cell sarcoma (histiocytic lymphoma), round cell sarcoma, spindle cell sarcoma, synovial sarcoma, and telangiectatic audiogenic sarcoma. Lymphomas include, but are not limited to: Hodgkin's disease and lymphocytic lymphomas, such as Burkitt's lymphoma, NPDL, NML, NH and diffuse lymphomas.

Thus, examples of cancers that can be treated using the compounds described herein include, but are not limited to, Hodgkin's disease, non-Hodgkin's lymphomas, acute lymphocytic leukemia, multiple myeloma, breast carcinomas, ovarian carcinomas, lung carcinomas, Wilms' tumor, testicular carcinomas, soft-tissue sarcomas, chronic lymphocytic leukemia, primary macroglobulinemia, bladder carcinomas, chronic granulocytic leukemia, primary brain carcinomas, malignant melanoma, small-cell lung carcinomas, stomach carcinomas, colon carcinomas, malignant pancreatic insulinoma, malignant carcinoid carcinomas, malignant melanomas, choriocarcinomas, mycosis fungoides, head and neck carcinomas, osteogenic sarcoma, pancreatic carcinomas, acute granulocytic leukemia, hairy cell leukemia, rhabdomyosarcoma, Kaposi's sarcoma, genitourinary carcinomas, thyroid carcinomas, esophageal carcinomas, malignant hypercalcemia, renal cell carcinomas, endometrial carcinomas, polycythemia vera, essential thrombocytosis, adrenal cortex carcinomas, skin cancer, and prostatic carcinomas.

In some embodiments, the cancer is lung cancer (such as non-small cell lung cancer), breast cancer, prostate cancer, ovarian cancer, testicular cancer, colon cancer, renal cancer, bladder cancer, pancreatic cancer, glioblastoma, neuroblastoma, sarcomas such as Kaposi's sarcoma and Ewing's sarcoma, hemangiomas, solid tumors, blood-borne tumors, rhabdomyosarcoma, CNS cancer (such as brain cancer), retinoblastoma, neuroblastoma, leukemia, melanoma, kidney or renal cancer, and osteosarcoma.

The compounds can be used in methods of killing or inhibiting the growth of cancer cells, either in vivo or in vitro, or inhibiting the growth of a cancerous tumor.

Angiogenesis is also associated with blood-borne tumors, such as leukemias, any of various acute or chronic neoplastic diseases of the bone marrow in which unrestrained proliferation of white blood cells occurs, usually accompanied by anemia, impaired blood clotting, and enlargement of the lymph nodes, liver and spleen. It is believed to that angiogenesis plays a role in the abnormalities in the bone marrow that give rise to leukemia-like tumors.

Suitable angiogenesis-mediated disorders that may be treated or prevented with the compounds described herein include, but are not limited to, tumors and cancer associated disorders (e.g., retinal tumor growth), benign tumors (e.g., hemangiomas, acoustic neuromas, neurofibromas, trachomas, and pyogenic granulomas), solid tumors, blood borne tumors (e.g., leukemias, angiofibromas, and Kaposi sarcoma), tumor metastases, and other cancers which require neovascularization to support tumor growth, ocular neovascular-disorders (e.g., diabetic retinopathy, macular degeneration, retinopathy of prematurity, neovascular glaucoma, corneal graft rejection, and other ocular angiogenesis-mediated disorders), inflammatory disorders (e.g., immune and non-immune inflammation, rheumatoid arthritis, chronic articular rheumatism, inflammatory bowel diseases, psoriasis, and other chronic inflammatory disorders), endometriosis, other disorders associated with inappropriate or inopportune invasion of vessels (e.g., retrolental fibroplasia, rubeosis, and capillary proliferation in atherosclerotic plaques and osteoporosis), Osler-Webber Syndrome, myocardial angiogenesis, plaque neovascularization, telangiectasia, hemophiliac joints, and wound granulation. Other diseases in which angiogenesis plays a role in the maintenance or progression of the pathological state are known to those skilled in the art and are similarly intended to be included within the meaning of the term angiogenesis-mediated used herein.

Other diseases, conditions, or disorders include blindness, corneal transplant, myopic degeneration, complications related to AIDS, arthritis, scleroderma, stroke, heart disease, ulcers and infertility. For example, but not limited to, cancers, inflammatory arthritis (such as rheumatoid arthritis), diabetic retinopathy, as well as other neovascular diseases of the eye (or example, corneal neovascularization, neovascular glaucoma, retrolental fibroblasia and macular degeneration), arteriovenous malformations, conditions of excessive bleeding (menorrhagia), and angiofibroma.

The anti-angiogenic compositions provided herein are also useful in the treatment of diseases of excessive or abnormal stimulation of endothelial cells. These diseases include, but are not limited to, intestinal adhesions, Crohn's disease, atherosclerosis, scleroderma, and hypertrophic scars (i.e., keloids).

In some embodiments, the compounds are used in conjunction with other angiogenesis inhibitors. Angiogenic inhibitors are known in the art and can be prepared by known methods. For a description of angiogenic inhibitors and targets see, for example, Chen et al., Cancer Res. 55:4230-4233 (1995), Good et al., Proc. Natl. Acad. Sci. USA 87:6629-6628 (1990), O'Reilly et al., Cell 79:315-328 (1994), Parangi et al., Proc. Natl. Acad. Sci. USA 93:2002-2007 (1996), Rastinejad et al., Cell 56:345-355 (1989), Gupta et al., Proc. Natl. Acad. Sci. USA 92:7799-7803 (1995), Maione et al., Science 247:77-79 (1990), Angiolillo et al., J. Exp. Med. 182:155-162 (1995), Strieter et al., Biochem. Biophys. Res. Comm. 210:51-57 (1995); Voest et al., J. Natl. Cancer Inst. 87:581-586 (1995), Cao et al., J. Exp. Med. 182:2069-2077 (1995), and Clapp et al., Endocrinology 133:1292-1299 (1993), which are hereby incorporated by reference in their entirety. For a description of additional angiogenic inhibitors see, for example, Blood et al., Bioch. Biophys Acta., 1032:89-118 (1990), Moses et al., Science, 248:1408-1410 (1990), Ingber et al., Lat Invest., 59:44-51 (1988), and U.S. Pat. Nos. 5,092,885 and 5,112,946, which are hereby incorporated by reference in their entirety.

In another embodiment, the compounds are used in conjunction with other therapies, such as standard anti-inflammatory therapies, standard ocular therapies, standard dermal therapies, radiotherapy, tumor surgery, and conventional chemotherapy directed against solid tumors and for the control of establishment of metastases. The administration of the angiogenesis inhibitor is typically conducted during or after chemotherapy at time where the tumor tissue should respond to toxic assault by inducing angiogenesis to recover by the provision of a blood supply and nutrients to the tumor tissue. Additionally, the compounds are administered after surgery where solid tumors have been removed as a prophylaxis against metastasis. Cytotoxic or chemotherapeutic agents are those known in the art such as aziridine thiotepa, alkyl sulfonate, nitrosoureas, platinum complexes, NO classic alkylators, folate analogs, purine analogs, adenosine analogs, pyrimidine analogs, substituted urea, antitumor antibiotics, microtubulle agents, and asprignase.

The present disclosure also provides methods for inhibiting angiogenesis-mediated processes alone or in combination with other existing anti-inflammatory, anti-angiogenesis, anti-cancer, and ocular therapies.

The present disclosure also provides methods of modulating an immune response in a mammal comprising administering to the mammal in need thereof a therapeutically effective amount of a compound described herein or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising a compound described herein or a pharmaceutically acceptable salt thereof.

For the above-mentioned methods, the method of modulating an immune response comprises decreasing the production of a cytokine. In some embodiments, the cytokine is chosen from TNFalpha, IL-1Beta, IL-1alpha, IL-8, IL-6, IL-10, IL-11, IL-12, TGF-Beta, and IFNgamma. In some embodiments, more than one cytokine is decreased. A decrease in a cytokine can be either at the nucleic acid level, the protein level, or the activity of the protein.

In some embodiments, the immune response is against an oral pathogen. In some embodiments, the oral pathogen is chosen from: Aggregatibacter spp. such as, for example, Aggregatibacter actinomycetemcomitans; Porphyromonas spp. such as, for example, Porphyromonas gingivalis; Streptococcus spp. such as, for example, Streptococcus sanguis and Streptococcus mutans, Candida spp. such as, for example, Candida albicans, Candida glabrata, Candida krusei, Candida dubliniensis, Candida parapsilosis, and Candida tropicalis; Actinomyces spp. such as, for example, Actinomyces viscosus; and Lactobacillus spp. such as, for example, Lactobacillus casei.

In some embodiments, the immune response is against a bacterial pathogen. In some embodiments, the bacterial pathogen is chosen from: Staphylococcus spp., such as, for example, Staphylococcus aureus, methicillin-resistant Staphylococcus aureus, and Staphylococcus epidermidis; Streptococcus spp. such as, for example, Streptococcus pneumoniae, Streptococcus pyogenes, and Streptococcus viridans; Escherichia spp. such as, for example, E. coli; Enterococcus spp. such as, for example, Enterococcus faecalis and Enterococcus faecium; Psuedomonas spp. such as, for example, Pseudomonas aeruginosa; Acinetobacter spp. such as, for example, A. baumannii; Haemophilus spp. such as, for example, Haemophilus influenzae; Serratia spp. such as, for example, Serratia marcescens; Moraxella spp. such as, for example, Moraxella catarrhalis; Klebsiella spp. such as, for example, Klebsiella pneumoniae; Proteus spp. such as, for example, Proteus vulgaris and Proteus mirabilis; Bacteroides spp. such as, for example, Bacteroides fragalis; Clostridium spp. such as, for example, Clostridium difficile and Clostridium perfringens; and Propionibacterium spp. such as, for example, Propionibacterium acnes.

In some embodiments, the modulation of an immune response decreases or eliminates an immune response. In some embodiments, the methods of the present disclosure can decrease an immune response by greater than about 50%, greater than about 60%, greater than about 70%, greater than about 80%, greater than about 85%, greater than about 88%, greater than about 90%, greater than about 92%, greater than about 95%, greater than about 98%, greater than about 99%, greater than about 99.2%, greater than about 99.5%, greater than about 99.8%, or greater than about 99.9%. The % decrease in an immune response can be measured by routine immune assays such as, for example, measuring the amount of a particular cytokine produced (at the protein level, nucleic acid level, or protein activity level).

In some embodiments, the modulation or decrease of the immune response takes place in an epithelial cell and/or a myeloid-derived cell. In some embodiments, the cell is a T cell, B cell, or monocyte such as a macrophage. In some embodiments, the cell is a neutrophil.

The present disclosure also provides methods for antagonizing an anticoagulant agent (such as heparin including, for example, unfractionated heparin, low molecular weight heparin, synthetically modified heparin, and low molecular heparin derivatives) comprising administering to a mammal a compound described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising the same. The present disclosure provides methods for antagonizing an anticoagulant effect of heparin in an animal comprising administering to the animal in need thereof an effective amount of a compound, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising the same. The present disclosure also provides methods for antagonizing the anticoagulant effect of heparin comprising contacting the heparin with an effective amount of a compound, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising the same. The present disclosure also provides methods for inhibiting anti-Factor Xa comprising administering to a mammal a compound described herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising the same.

The compounds may be useful as anti-heparin agents (i.e., antagonizing the anticoagulant effect of an anticoagulant such as unfractionated heparin, low molecular heparin, and a derivative of heparin or low molecular heparin) in a number of applications. For example, compounds may be used therapeutically to antagonize the anticoagulant effect of an anticoagulant agent (for example unfractionated heparin, low molecular heparin, or a derivative of heparin or low molecular heparin), present in a mammal. The anticoagulant effect of the anticoagulant agent (for example unfractionated heparin, low molecular heparin, or a derivative of heparin or low molecular heparin) present in a mammal may be antagonized by administering to the mammal an effective amount of a compound or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition comprising the same.

Natural heparins have polysaccharide chains of varying lengths, or molecular weights (including salts). Natural heparin has polysaccharide chains of molecular weight from about 5000 to over 40,000 Daltons. Low-molecular-weight heparins (LMWHs), in contrast, are fragments of unfractionated heparins, and have short chains of polysaccharide (including salts). LMWHs have an average molecular weight of less than 8000 Da and at least 60% of all chains have a molecular weight less than 8000 Da.

In some embodiments, the methods of the present disclosure can effectively antagonize the anticoagulant effect of unfractionated heparin. In some embodiments, the methods of the present disclosure can effectively antagonize the anticoagulant effect of a low molecular weight heparin such as enoxaparin. In some embodiments, the methods of the present disclosure can effectively antagonize the anticoagulant effect of a synthetically modified heparin derivative such as fondaparinux.

In some embodiments, the method of the present disclosure can antagonize greater than about 50%, greater than about 60%, greater than about 70%, greater than about 80%, greater than about 85%, greater than about 88%, greater than about 90%, greater than about 92%, greater than about 95%, greater than about 98%, greater than about 99%, greater than about 99.2%, greater than about 99.5%, greater than about 99.8%, or greater than about 99.9% of the anticoagulant effect of heparin (including, for example, unfractionated heparin, low molecular weight heparin, and synthetically modified heparin or low molecular heparin derivatives). In some embodiments, the compound or salt thereof used in the present disclosure antagonizes the anticoagulant effect of an anticoagulant agent (including, for example, unfractionated heparin, low molecular weight heparin, and synthetically modified heparin or low molecular heparin derivatives) more effectively than protamine.

In some embodiments, the compound or salt thereof used in the present disclosure binds to heparin (including, for example, unfractionated heparin, low molecular weight heparin, and synthetically modified heparin or low molecular heparin derivatives) with an EC₅₀of less than about 100, less than about 90, less than about 80, less than about 70, less than about 60, less than about 50, less than about 40, less than about 30, less than about 20, less than about 15, less than about 10, less than about 5, less than about 2, less than about 1, less than about 0.9, less than about 0.8, less than about 0.7, less than about 0.6, less than about 0.5, less than about 0.4, less than about 0.3, less than about 0.2, less than about 0.1, less than about 0.09, less than about 0.08, less than about 0.07, less than about 0.06, less than about 0.05, less than about 0.02, less than about 0.01, less than about 0.001, less than about 0.0001, or less than about 0.00001 μg/mL.

In some embodiments, the compound or salt thereof used in the present disclosure binds to heparin (including, for example, unfractionated heparin, low molecular weight heparin, and synthetically modified heparin or low molecular heparin derivatives) with an EC₅₀less than about 100, less than about 90, less than about 80, less than about 70, less than about 60, less than about 50, less than about 40, less than about 30, less than about 20, less than about 15, less than about 10, less than about 5, less than about 2, less than about 1, less than about 0.9, less than about 0.8, less than about 0.7, less than about 0.6, less than about 0.5, less than about 0.4, less than about 0.3, less than about 0.2, less than about 0.1, less than about 0.09, less than about 0.08, less than about 0.07, less than about 0.06, less than about 0.05, less than about 0.02, less than about 0.01, less than about 0.001, less than about 0.0001, or less than about 0.00001 μM.

In some embodiments, the compound or salt thereof used in the present disclosure can effectively antagonize the anticoagulant effect of an anticoagulant agent (including, for example, unfractionated heparin, low molecular weight heparin, and synthetically modified heparin or low molecular heparin derivatives) with a dosage of less than about 10, less than about 9, less than about 8, less than about 7, less than about 6, less than about 5, less than about 4, less than about 3, less than about 2, or 1 equivalent (by weight) to the heparin.

In some embodiments, the compound or salt thereof used in the present disclosure can effectively antagonize the anticoagulant effect of an anticoagulant agent (including, for example, unfractionated heparin, low molecular weight heparin, and synthetically modified heparin or low molecular heparin derivatives) through antagonizing the AT activity of the heparin, the anti-factor Xa activity of the heparin, the anti-factor IIa activity of the heparin, or any combination thereof.

In some embodiments, the method of the present disclosure can rapidly antagonize the anticoagulant effect of an anticoagulant agent (including, for example, unfractionated heparin, low molecular weight heparin, and synthetically modified heparin or low molecular heparin derivatives), for example, antagonize (or neutralize) greater than about 40%, greater than about 50%, greater than about 60%, greater than about 70%, greater than about 80, greater than about 90%, greater than about 95%, greater than about 98%, greater than about 99%, or greater than about 99.5% of the anticoagulant effect of the heparin in less than about 30, less than about 20, less than about 15, less than about 10, less than about 8, less than about 5, less than about 2, less than about 1, less than about 0.9, less than about 0.8, less than about 0.7, less than about 0.6, less than about 0.5, less than about 0.4, less than about 0.3, less than about 0.2, or less than about 0.1 minute.

In some embodiments, after the anticoagulant effect of heparin in a mammal during anticoagulant therapy is antagonized (for example, by 80% or more) by methods of the present disclosure, a new dose of heparin can effectively restore the anticoagulant therapy, for example, greater than about 80% or 90% of the anticoagulant effect of heparin of the new dose can be achieved in less than about 20, less than about 15, less than about 10, less than about 8, less than about 5, less than about 2, or less than about 1 minute.

In some embodiments, the present disclosure provides methods for antagonizing the anticoagulant effect of heparin with low or no toxicity, hemodynamic and/or hematological adverse side effects. In some embodiments, the methods have low or no side effects associated with use of protamine such as one or more selected from systemic vasodilation and hypotension, bradycardia, pulmonary artery hypertension, pulmonary vasoconstriction, thrombocytopenia, and neutropenia. In some embodiments, the methods have low or no side effects associated with use of protamine such as anaphylactic-type reactions involving both nonimmunogenic and immunogenic-mediated pathways. In some embodiments, the compounds and/or the salts have low or no antigenicity and/or immunogenicity comparing to those of protamine molecules. In some embodiments, the present methods for antagonizing the anticoagulant effect of heparin can preserve hemodynamic stability, such as during and/or following infusion.

In some embodiments, the present methods for antagonizing the anticoagulant effect of heparin can be used in a patient who receives anticoagulant therapy, for example, who uses fondaparinux for the prophylaxis of deep vein thrombosis following hip repair/replacement, knee replacement and abdominal surgery; uses UFH or LMWH for coronary bypass surgery; or uses UFH or LMWH during and/or following blood infusion.

In some embodiments, the unfractionated heparin is antagonized. In some embodiments, the low molecular weight heparin is antagonized. In some embodiments, the low molecular weight heparin is enoxaparin, reviparin, or tinzaparin. In some embodiments, the heparin/low molecular weight heparin derivative is antagonized. In some embodiments, the heparin/low molecular weight heparin derivative is fondaparinux. In some embodiments, the mammal is a human.

In some embodiments, the weight ratio of the compound, or pharmaceutically acceptable salt thereof, to be administered, to the unfractionated heparin, low molecular weight heparin, or heparin/low molecular weight heparin derivative is less than about 10:1. In some embodiments, the weight ratio of the compound, or pharmaceutically acceptable salt thereof, to be administered, to the unfractionated heparin, low molecular weight heparin, or heparin/low molecular weight heparin derivative is less than about 5:1, less than about 10:1, less than about 25:1, or less than about 30:1. In some embodiments, the weight ratio of the compound, or pharmaceutically acceptable salt thereof, to be administered, to the unfractionated heparin, low molecular weight heparin, or heparin/low molecular weight heparin derivative is from about 1:1 to about 5:1, from about 1:1 to about 10:1, or from about 1:1 to about 25:1.

The present disclosure also provides compounds of any of the preceding embodiments, or a pharmaceutical composition comprising said compound, for antagonizing unfractionated heparin, low molecular weight heparin, or a heparin/low molecular weight heparin derivative in a mammal.

The present disclosure also provides for use of compounds of any of the preceding embodiments, or a pharmaceutical composition comprising said compound, for antagonizing unfractionated heparin, low molecular weight heparin, or a heparin/low molecular weight heparin derivative in a mammal.

The present disclosure also provides for use of compounds of any of the preceding embodiments, or a pharmaceutical composition comprising said compound, in the manufacture of a medicament for antagonizing unfractionated heparin, low molecular weight heparin, or a heparin/low molecular weight heparin derivative in a mammal.

In order that the disclosure disclosed herein may be more efficiently understood, examples are provided below. It should be understood that these examples are for illustrative purposes only and are not to be construed as limiting the disclosure in any manner.

Throughout these examples, molecular cloning reactions, and other standard recombinant DNA techniques, were carried out according to methods described in Maniatis et al., Molecular Cloning—A Laboratory Manual, 2nd ed., Cold Spring Harbor Press (1989), using commercially available reagents, except where otherwise noted.

EXAMPLES
Example 1
Synthesis of Compounds
General Procedure for Sonogashira Coupling Reaction

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The iodobenzene (1 mmol), Pd(PPh₃)₂Cl₂(0.36 mmol), CuI (0.369 mmol) and DIEA (4.5 mL) were added in 6 mL toluene. The mixture was flushed with argon for 5 minutes and then heated to 70° C. The ethynylbenzene (1 mmol) in 2 mL of toluene was added over ten minutes. The mixture was stirred at 70° C. for another 3 hours. The mixture was filtered and evaporated. The product was purified by flash column.

General Procedure for Guanylation

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The amine (0.04 mmol) was dissolved in 6 mL acetonitrile and was added TEA (2 equiv) and pyrazole reagent (1.2 equiv). The reaction mixture was stirred overnight. The solvent was evaporated and the product was purified by flash column.

General Procedure for Bromination of Methyl Benzene

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The methylbenzene (23.6 mmol), NBS (1.1 equiv) and AIBN (0.11 equiv) were mixed in 100 mL of benzene. The mixture was heated to reflux for eight hours. After benzene was removed, the solid was dissolved in DCM and filtered, and purified on flash column.

General Procedure to Synthesize Nitrile

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The bromide (13.4 mmol) was dissolved in EtOH/water (40 mL/12 mL), and was added NaCN (1.6 equiv). The reaction mixture was heated to reflux for 4 hours before the solvent was removed on a rotovap. The residue was redissolved in EtOAc, washed with water. The organic layer was concentrated and purified on a flash column.

General Procedure to Synthesize Amine from Nitrile

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The nitrile (11.8 mmol) was dissolved in 22 mL of THF and cooled to 0° C. To the solution 46.3 mL of BF3.THF (1.0 M solution) was added dropwise over 10 minutes. The mixture was heated to reflux overnight. The reaction mixture was concentrated and redissolved in 5 mL of MeOH. The solution was cooled to 0° C. and was added 10 mL of concentrated HCl. After stirred at 0° C. for 1 hour, MeOH was removed on a rotovap. To the residue was added 10 mL of water. The mixture was cooled to 0° C. and its pH was adjusted to 12 with solid KOH. EtOAc was added to the mixture. The organic layer was concentrated to dryness and redissolved in 15 mL of THF. To the solution (Boc)₂O (1.03 equiv) and TEA (3 mL) were added. The resulting mixture was stirred at room temperature for 4 hours. The mixture was diluted with EtOAc and washed with NaHCO₃. The organic layer was dried, concentrated and purified on a flash column.

General Procedure to Remove Boc Protecting Group by TFA

The Boc protected compound (100 mg) was dissolved in 1.5 mL of DCM and was added 1.5 mL of TFA. The reaction mixture was stirred at room temperature for 4 hours. The mixture was concentrated and trituated with ether. The solid was washed with ether for 3 times and dried under vacuum overnight.

General Method of Direct Arylation

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The heterocycle (0.32 mmol), iodobenzene (1 equiv), Ag₂CO₃(28 equiv), Pd(dppf)Cl₂(0.16 equiv) and PPh₃(1 equiv) were mixed in 2 mL of water and stirred at 60° C. overnight. The mixture was filtered through celite and added water and EtOAc. The organic layer was died and concentrated. The product was purified on a flash column.

the Synthesis of General Intermediate A:

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Intermediate A was synthesized from (3-iodophenyl)acetonitrile using the general method for the synthesis of amine from nitrile.

The synthesis of general intermediate B

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Intermediate B was synthesized from 1-iodo-3,5-dimethylbenzene using the general method for the bromination of methyl benzene, the general method for the synthesis of nitrile and the general method for the synthesis of amine from nitrile.

The Synthesis of General Intermediate C

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Intermediate C was prepared from 1-bromo-3,5-diiodobenzene and Boc amino propyne using the general procedure for Sonogashira coupling.

The Synthesis of Intermediate D

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Intermediate C (0.242 mmol) and 1,3-phenyl-boronic ester (0.107 mmol) were mixed and were added K₂CO₃(1.1 mmol) in water (0.75 mL) and dioxane (1.5 mL), followed by the addition of Pd(PPh₃)₄(0.039 mmol). The mixture was flashed with argon and then sealed and irradiated in a microwave reactor at 95° C. for 1.5 hours. The mixture was filtered through celite and diluted with EtOAc. The organic layer was concentrated and purified on a flash column to produce intermediate D.

Example 1A
Synthesis of Compound 128

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Benzaldehyde (36 mmol) and hydroxylamine (49 mmol) were mixed in pyridine (14 mL) and heated to 85-90° C. for 15 minutes. The reaction mixture was diluted with EtOAc and water, and washed with 20% AcOH (25 mL) to remove pyridine. The organic layer was then neutralized with NaHCO₃, washed with brine and dried, concentrated. No purification was performed. Yield=4.65 g.

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The oxime (27 mmol) was dissolved in DMF and treated with N-chlorosuccinimide (31.2 mmol). The mixture was stirred at room temperature overnight. The mixture was added water and filtered. The collected solid was mixed with 1,3-diethynylbenzene (1.7 mL) in 56 mL of toluene and then was added 8.09 g of K₂CO₃. The mixture was heated at reflux overnight. After the solvent was removed, the product was isolated on a flash column using EtOAc in Hexanes. Yield=3.57 g.

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The compound was made using the general method for bromination of methyl benzene, and the general method for the synthesis of nitrile.

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Compound 128 was made using the general method for the synthesis of amine from nitrile, and the general method for Boc deprotection.

Example 1B
Synthesis of Compound 129

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Compound 129 was made from Compound 128 by the general method of guanylation, followed by the general method of Boc deprotection.

Example 1C
Synthesis of Compound 130

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The thioamide (10 mmol) and chlorodiol (6.5 equiv) were mixed in 12 mL of EtOH. The mixture was heated to reflux overnight. After the solvent was removed, the product was purified on a flash column.

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Compound 130 was made from the phenyl thiazole using 1) the general method of direct arylation with intermediate A, 2) the general method of Boc deprotection.

Example 1D
Synthesis of Compound 131

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Compound 131 was made from Compound 132 by using the general method of guanylation and the general method of Boc deprotection.

Example 1E
Synthesis of Compound 132 and Compound 133

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Diiodobenzene (3 mmol), oxazole (2.3 equiv), Pd(PPh₃)₄(0.11 equiv) and tBuLi (4.1 equiv) were mixed with 10 mL of dioxane in a sealed tube. The mixture was stirred at 120-125° C. overnight. The mixture was filtered and was added EtOAc and water. The organic layer was concentrated and purified on a flash column.

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Compound 132 and Compound 133 were made from the phenyl oxazole and intermediate A by using 1) general method of direct arylation with A, 2) general method of Boc deprotection.

Example 1F
Synthesis of Compound 134

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Compound 134 was made from Compound 132 using the general method of guanylation and the general method of Boc deprotection.

Example 1G
Synthesis of Compound 189

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The amine was made from intermediate B and 1,3-diethynylbenzene using the general procedure of Sonogashira coupling reaction, followed by the general method of Boc deprotection.

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Compound 189 was made from the amine using the general method of guanlyation followed by the general method of Boc deprotection.

Example 1H
Synthesis of Compound 190

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The benzaldehyde (1.05 mmol), nitromethane (2.5 mL) and Al₂O₃(1.8 equiv) were mixed in a sealed tube. The mixture was irradiated in a microwave reactor at 150° C. for 30 minutes. The benzaldehyde (1.05 mmol), nitromethane (2.5 mL) and Al₂O₃(1.8 equiv) were mixed in a sealed tube. The mixture was irradiated in a microwave reactor at 150° C. for 30 minutes, and then at 175° C. for 30 minutes. The mixture was filtered and evaporated to dryness. The product was purified on a flash column.

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The nitro compound (0.69 mmol) was dissolved in THF/water (3 mL/0.9 mL). To the solution was added 0.75 mL of concentrated HCl and In metal (1.18 g). The mixture was stirred overnight. The mixture was filtered and was neutralized with KOH. EtOAc and water was added to extract the amine. After the solvent was removed, the residue was redissolved in THF. To the solution (Boc)₂O (2 equiv) and TEA (4 equiv) were added. The resulting mixture was stirred at room temperature for 4 hours. The mixture was diluted with EtOAc and washed with NaHCO₃. The organic layer was dried, concentrated and purified on a flash column.

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Compound 190 was made from the dibromide and 1,3-diethynylbenzene using the general procedure of Sonogashira coupling reaction, followed by the general method of Boc deprotection.

Example 11
Synthesis of Compound 196

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The thioamide (15 mmol) and chlorodiol (4 mL) were mixed in 18 mL of EtOH. The mixture was heated to reflux overnight. After the solvent was removed, the product was purified on a flash column.

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The thiazole (3.25 mmol) was dissolved in ACN (4 mL), and was added TEA (4 mL), TMS-acetylene (1.6 equiv), CuI (0.16 equiv), and Pd(PPh₃)₂Cp₂(0.1 equiv) sequentially. The mixture was stirred at 65° C. for 6 hours. The mixture was filtered, evaporated and purified on a flash column. The collected fractions were dried and treated with 1 M TBAF in THF for two hours. The solvent was removed on a rotovap. The residue was added EtOAc and water. The organic layer was dried, evaporated and purified on a column.

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The thiazole was prepared following the general procedure for Sonogashira coupling.

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Compound 196 was prepared from the thiazole and intermediate B using the general procedure for direct arylation, followed by the general method for Boc deprotection.

Example 1J
Synthesis of Compound 135 and Compound 136

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Compound 135 and Compound 136 were prepared from the symmetric phenyl thiazole and intermediate B following the general procedure for direct arylation and the general method for Boc deprotection.

Example 1K
Synthesis of Compound 197

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Compound 197 was prepared from Compound 196 using the general method for guanylation, followed by the general method for Boc deprotection.

Example 1L
Synthesis of Compound 137

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Compound 137 was prepared from Compound 135 using the general method for guanylation, followed by the general method for Boc deprotection.

Example 1M
Synthesis of Compound 191

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Compound 191 was prepared from Compound 190 using the general method for guanylation, followed by the general method for Boc deprotection.

Example 1N
Synthesis of Compound 192

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1,5-dibromo-2,4-difluorobenzene (6.4 mmol) was dissolved in ACN (12 mL), and was added TEA (2.6 mL), TMS-acetylene (1.6 equiv), CuI (0.16 equiv), and Pd(PPh₃)₂Cp₂(0.1 equiv) sequentially. The mixture was stirred at 65° C. for 6 hours. The mixture was filtered, evaporated and purified on a flash column. The collected fractions were dried and treated with 1 M TBAF in THF for two hours. The solvent was removed on a rotovap. The residue was added EtOAc and water. The organic layer was dried, evaporated and purified on a column.

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Compound 192 was made from intermediate B and 1,5-diethynyl-2,4-difluorobenzene using the general procedure of Sonogashira coupling reaction, followed by the general method of Boc deprotection.

Example 1O
Synthesis of Compound 193

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Compound 193 was prepared from Compound 192 using the general method for guanylation, followed by the general method for Boc deprotection.

Example 1P
Synthesis of Compound 198

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Compound 198 was made from 1,4-diethynylbenzene and intermediate B using the general procedure for Sonogashira coupling followed by the general method of Boc deprotection.

Example 1Q
Synthesis of Compound 199

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Compound 199 was made from Compound 198 using the general method for guanylation followed by the general method of Boc deprotection.

Example 1R
Synthesis of Compound 194

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The bromide was made using the general method for bromination of methyl benzene.

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The nitrile was made using the general method for preparation of nitrile from bormide.

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The amine was prepared follow the general procedure of the synthesis of amine form nitrile.

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Compound 194 was prepared using the general procedure for Sonogashira coupling, followed by the general method of Boc deprotection.

Example 1S
Synthesis of Compound 195

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Compound 195 was made from Compound 194 using the general method for guanylation, followed by the general method for Boc deprotection.

Example 1T
Synthesis of Compound 115

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Intermediate B (0.4 mmol) and 1,3-phenylenediboronic acid (0.17 mmol) were added 0.4 mL 0.4M K₂CO₃in water and Pd(PPh₃)₄(0.07 mmol) sequentially. The mixture was heated to 95° C. for 3 hours and let stand over the weekend at room temperature. The mixture was filtered through celite and diluted with EtOAc and brine. The organic layer was evaporated and purified on a flash column. The combined fraction was concentrated and treated by TFA in DCM to produce Compound 115.

Example 1U
Synthesis of Compound 116

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Compound 116 was prepared from Compound 115 using the general procedure for guanylation, followed by the general procedure for Boc deprotection.

Example 1V
Synthesis of Compound 138

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In a argon flushed vial were sequentially added 1,3diiodobenzene (12.4 mmol), thiophene-2-boronic acid (2 equiv), Pd(PPh₃)₄(0.087 equiv) and K₂CO₃(5.8 equiv) in water and dioxane. The mixture was heated at 100° C. overnight. The mixture was filtered through celite, diluted with EtOAc. The organic layer was concentrated and purified on a flash column.

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Compound 138 was prepared from the phenylthiophene and intermediate B using the general procedure for direct arylation, followed by the general procedure for Boc deprotection.

Example 1W
Synthesis of Compound 117

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Intermediate D (0.11 mmol) were dissolved in 40 mL of MeOH and was added 49 mg Pd/C (49 mg). The mixture was put on a Parr shaker and shaked under 52 Psi hydrogen over night. The mixture was filtered. The filtrated was purified on a flash column. The combined fractions were concentrated and treated with TFA/DCM to yield Compound 117.

Example 1X
Synthesis of Compound 118

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Compound 118 was prepared from Compound 117 using the general procedure for guanylation, followed by the general procedure for Boc deprotection.

Example 1Y
Synthesis of Compound 139

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Compound 139 was prepared from Compound 138 using the general procedure for guanylation followed by the general procedure for Boc deprotection.

Example 1Z
Synthesis of Compound 124

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Compound 124 was prepared from intermediate D using the general procedure for Boc deprotection.

Example 1AB
Synthesis of Compound 123

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Compound 123 was prepared from Compound 124 using the general procedure for guanylation followed by the general procedure for boc deprotection.

Example 1AC
Synthesis of Compound 125 and Compound 126

Compound 125 and Compound 126 were prepared following similar procedures for the synthesis of Compound 124 and Compound 123. Trifluoromethylbenzene boronic acid was used in the Suzuki coupling step.

Example 1AD
Synthesis of Compound 100

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Synthesis of Intermediate 1

To an ice-cold solution of phenothiazine (0.4 g, 2 mmol) in DMF (2 mL) was added NaH (0.24 g, 60% in mineral oil) in three portions. Then N-3-(bromopropyl)phthalimide (1.07 g, 4 mmol) was added. The resulting mixture was stirred at room temperature for 4 hours. Water was added to quench the reaction. EtOAc was used to do extraction. The organic layer was washed with brine, dried over Na₂SO₄and evaporated under vacuum. The residue was purified using silica gel column (eluent; EtOAc/hexanes=0/100 to 20/100). A white solid (0.30 g, 40%) was obtained as compound 1. LC-MS agreed.

The solid (0.18 g, 0.47 mmol) from the above reaction and hydrazine (0.24 g, 0.75 mmol) were stirred in 1 mL n-butanol at 80° C. over night. EtOAc (10 mL) was added and the mixture was stirred for additional 30 minutes. Then the mixture was filtrated. The organic solution was washed with brine, dried over Na₂SO₄, and evaporated under vacuum. HCl in dioxane (1 mL, 4 M) was added into the residue. The mixture was stirred for 40 minutes at room temperature. Then the mixture was evaporated and the residue was washed with ether. A white solid (0.10 g) was obtained as the product after freeze-dry. LC-MS and ¹HNMR agreed.

Example 1AE
Synthesis of Compound 101

Following similar synthetic procedure of Compound 100, Compound 101 was obtained starting from 2-(trifluoromethyl)phenothiazine instead.

Example 1AF
Synthesis of Compound 102

Following similar synthetic procedure of Compound 100, Compound 102 was obtained starting from carbazole instead.

Example 1AG
Synthesis of Compound 105

Following similar synthetic procedure of Compound 100, Compound 105 was obtained starting from phenoxazine instead.

Example 1AH
Synthesis of Compound 103

Following similar synthetic procedure of Compound 100, Compound 103 was obtained starting from 2-chlorophenothiazine instead.

Example 1AI
Synthesis of Compound 110

1,3-Benzenediboronic acid (0.34 g, 2 mmol) and 3-(3-bromophenyl)propanenitrile (4.8 mmol, 1.0 g) were added into a microwave tube under Argon. Dioxane (10 mL), Pd(PPh₃)₄(0.4 mmol, 0.46 g) and K₂CO₃(16 mmol, 4 mL, 4 M) were added. The mixture was under microwave irradiation (120° C., 15 minutes) with stirring. Then the reaction was cooled down to room temperature and extracted with EtOAc and brine. The organic layer was dried over Na₂SO₄and evaporated under vacuum. The residue was purified with silica column (eluent: EtOAc/hexanes=1/2, v/v). A yellow oil (0.64 g, 95%) was obtained. This oil was stirred in 40 mL BH₃-THF (1 M in THF) at room temperature over night. Then methanol was added dropwise till no bubble appeared. The mixture was evaporated under vacuum to dry. The residue was dispersed between EtOAc and sat. NaHCO₃. The organic layer was dried and evaporated in vacuum. The residue was stirred in HCl in dioxane (10 mL, 4 M). The mixture was stirred for 40 minutes at room temperature. Then the mixture was evaporated and the residue was washed with ether and purified using HPLC. A white solid (0.04 g) was obtained as the product after freeze-dry. LC-MS and ¹HNMR agreed.

Example 1AJ
Synthesis of Compound 104

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Synthesis of Intermediate 1

To an ice-cold solution of 7-nitro-2-(trifluoromethyl)phenothiazine (1.0 g, 3.2 mmol) in DMF (3 mL) was added NaH (0.4 g, 60% in mineral oil) in three portions. Then N-3-(bromopropyl)phthalimide (1.7 g, 6.4 mmol) was added. The resulting mixture was stirred at room temperature for 4 hours. Water was added to quench the reaction. EtOAc was used to do extraction. The organic layer was washed with brine, dried over Na₂SO₄and evaporated under vacuum. The residue was purified using silica gel column (eluent; EtOAc/hexanes=0/100 to 20/100). A red solid (0.38 g, 24%) was obtained as compound 1. LC-MS OK.

Synthesis of Intermediate 2

The red solid was dissolved in EtOH (20 mL) and CH₂Cl₂(4 mL). Pd/C (10%, 0.038 g) was added. Hydrogen was supplied to the mixture after flushing the flask. The reaction was stirred at room temperature over night. Then the mixture was filtered through celite. After evaporation under vacuum, the residue was used as such in the subsequent reactions.

Synthesis of Compound 104

The residue (0.1 g) from above reaction and hydrazine (0.24 g, 0.75 mmol) were stirred in 1 mL n-butanol at 80° C. over night. EtOAc (10 mL) was added and the mixture was stirred for additional 30 minutes. Then the mixture was filtrated. The organic solution was washed with brine, dried over Na₂SO₄, and evaporated. HCl in dioxane (4 mL, 4 M) was added into the residue. The mixture was stirred for 40 minutes at room temperature. Then the mixture was evaporated and the residue was washed with ether. A white solid (0.04 g) was obtained as the product after freeze-dry. LC-MS and ¹HNMR agreed.

Example 1AK
Synthesis of Compound 143

The intermediate 2 (0.2 g) from synthesis of Compound 104 and TEA (0.056 mL) were stirred in dioxane in ice-water bath. Phosgene solution (0.106 mL, 20% in toluene) was added dropwise. The resulting mixture was stirred at room temperature over night. Water and EtOAc were used to work up the reaction. The organic layer was dried, and evaporated under vacuum. The residue was purified with silica gel column (eluent: EtOAC/Hexanes=0/100-34/100). A solid (40 mg) was obtained. This solid and hydrazine (0.24 g, 0.75 mmol) were stirred in 1 mL n-butanol at 80° C. over night. EtOAc (10 mL) was added and the mixture was stirred for additional 30 minutes. Then the mixture was filtrated. The organic solution was washed with brine, dried over Na₂SO₄, and evaporated. HCl in dioxane (2 mL, 4 M) was added into the residue. The mixture was stirred for 40 minutes at room temperature. Then the mixture was evaporated and the residue was washed with ether and purified using reverse phase HPLC. A white solid (0.005 g) was obtained as the product after freeze-dry. LC-MS and ¹HNMR agreed.

Example 1AL
Synthesis of Compound 107

1,3-Sithynylbenzene (0.126 g, 1 mmol) was added into a THF/H₂O (5 mL/5 mL) solution of tert-butyl 4-azidobutylcarbamate (0.42 g, 2.1 mmol), which was prepared according to literature, CuSO₄.5H₂O (0.053 g, 0.21 mmol) and sodium ascorbate (0.083 g, 0.42 mmol). The resulting mixture was stirred at room temperature over night. Then the mixture was poured into ice-water, extracted with EtOAc. The organic layer was dried over Na₂SO₄and evaporated under vacuum. The residue was purified using silica gel column (Eluent: MeOH/DCM: 1% to 5%). A white solid (0.1 g, 19%) was obtained. This solid was stirred in TFA/DCM (0.5 mL/1 mL) at room temperature for 4 hours. Then the mixture was evaporated under vacuum. Ether was added. The white solid (0.1 g) was obtained as Compound 107. LC-MS and ¹HNMR agreed.

Example 1AM
Synthesis of Compound 108

Following the same synthetic procedure as Compound 107, Compound 108 was obtained using tert-butyl 3-azidopropylcarbamate as starting material.

Example 1AN
Synthesis of Compound 109

Following the same synthetic procedure as Compound 107, Compound 109 was obtained using tert-butyl 2-azidoethylcarbamate as starting material.

Example 1AO
Synthesis of Compound 127

Mercury (II) chloride (0.65 g, 2.4 mmol) was added to a solution of 2,5-bis(4-aminophenyl)-1,3-oxadiazole (0.25 g, 1 mmol), 1,3-bis(t-butoxycarbonyl)-2-methyl-2-thiopseudourea (0.64 g, 2.2 mmol) and TEA (1 mL, 7.2 mmol) in DMF (8 mL). The resulting mixture was stirred at room temperature over night. Then the mixture was poured into ice-water, extracted with EtOAc. The organic layer was washed with saturated NaHCO₃, dried over Na₂SO₄and evaporated under vacuum. The residue was purified using silica gel column (Eluent: EtOAc/hexanes: 1% to 30%). A white solid (0.08 g, 11%) was obtained. This solid was stirred in TFA/DCM (0.5 mL/1 mL) at room temperature for 4 hours. Then the mixture was evaporated under vacuum. Ether was added. The white solid (0.056 g) was obtained as Compound 127. LC-MS and ¹HNMR agreed.

Example 1AP
Synthesis of Compound 157

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Synthesis of Intermediate 1

Pyrazole-4-boronic acid pinacol ester (0.78 g, 4.0 mmol) was stirred in anhydrous DMF (10 mL) at room temperature under Ar. NaH (0.16 g, 4.2 mmol, dispersed in mineral oil at 60% in weight) was added in three portions. The mixture was stirred at 64° C. for 30 minutes. Then tert-butyl (3-bromopropyl)carbamate (1.0 g, 4.2 mmol) was added. The resulting mixture was stirred at 64° C. for 5 hours. The reaction was quenched with ice water. EtOAc was added to extract the mixture. The organic layer was washed with brine, dried over Na₂SO₄, and evaporated under vacuum. The residue was purified with silica gel column (eluent: EtOAc/hexanes=0/100-50/100). The yellow oil (0.62 g, 43%) was obtained as compound 1.

Synthesis of Compound 157

Intermediate 1 (0.7 mmol, 0.246 g) and 2,8-dibromodibenzo[b,d]furan (0.3 mmol, 0.10 g) were added into a microwave tube under Argon. Dioxane (2 mL) and aqueous K₂CO₃(2 mmol, 1 mL, 2 M) were added. Then Pd(PPh₃)₄(0.07 mmol, 0.082 g) was added. The mixture was under microwave irradiation (95° C., 1 hour then 104° C. 24 minutes) with stirring. The reaction was cooled down to room temperature and extracted with EtOAc and brine. The organic layer was dried over NaSO₄and evaporated under vacuum. The residue was purified with silica column (eluent: EtOAc/hexanes=0/100 to 50/100, v/v). The obtained white solid was stirred in 1 mL dichloromethane and 0.5 mL at room temperature for 4 hours. Then the mixture was evaporated and the residue was washed with ether. A white solid (0.022 g) was obtained as the product after freeze-dry. LC-MS and ¹HNMR agreed.

Example 1AQ
Synthesis of Compound 141

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Synthesis of compound 1

2-(4-Boc-piperazine)pyridine-5-boronic acid pinacol ester (0.42 g, 1.07 mmol) and 2-Fluoro-4-bromoaniline (1 mmol, 0.19 g) were added into a microwave tube under Argon. Dioxane (4 mL) and aqueous K₂CO₃(4 mmol, 4 mL, 2 M) were added. Then Pd(PPh₃)₄(0.1 mmol, 0.1 g) was added. The mixture was under microwave irradiation (95° C., 1 hour then 104° C. 24 minutes) with stirring. The reaction was cooled down to room temperature and extracted with EtOAc and brine. The organic layer was dried over Na₂SO₄and evaporated under vacuum. The residue was purified with silica gel column (eluent: EtOAc/hexanes=0/100 to 40/100, v/v). A yellow solid (0.24 g) was obtained as product. LC-MS OK.

Synthesis of Compound 141

To a solution of compound 1 (0.12 g, 0.3 mmol) in 5 mL anhydrous THF was added TEA (0.11 mL, 0.8 mmol) and triphosgene (0.032 g, 0.108 mmol) at room temperature. The resulting mixture was stirred for 1 hour. Then saturated NaHCO₃was added to quench the reaction. The mixture was dispersed in EtOAc and brine. A yellow sold appeared between organic and aqueous layers. The yellow solid (0.06 g, 48%) was collected and was stirred in 1 mL dichloromethane and 0.5 mL at room temperature for 4 hours. Then the mixture was evaporated and the residue was washed with ether. A white solid (0.02 g) was obtained as the product after freeze-dry. LC-MS and ¹HNMR agreed.

Example 1AR
Synthesis of Compound 140

Following similar synthetic method used in Compound 141, Compound 140 was obtained as white solid using tert-butyl 3-(3-bromophenyl)propylcarbamate, which was synthesized from 3-(3-bromophenyl)propanenitrile by BH₃reduction and Boc protection, as starting material.

Example 1AS
Synthesis of Compound 142

Following similar synthetic method use in Compound 141, Compound 142 is obtained as white solid using 2-(4-tert-Butoxycarbonylpiperazin-1-yl)pyridine-4-boronic acid, pinacol ester as starting material.

Example 1AT
Synthesis of Compound 106

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Synthesis of intermediate 1

4,4′-Dibromo-2-nitro-biphenyl (2.04 g, 5.42 mmol) and PPh₃(3.80 g, 14.3 mmol) were refluxing in 1,2-dichlorobenzen (14 mL) under Ar over night. Then the solvent is removed by evaporation under vacuum. The residue was purified with silica chromatography (eluent: dichloromethane/hexanes=0% to 44%). A brown solid (1.29 g, 70%) was obtained as intermediate 1.

Synthesis of intermediate 2

Intermediate 1 (0.65 g) was stirred in DMF (7 mL) at room temperature. NaH (0.17 g, 60% in mineral oil) was added in three portions. Then t-butyl-(3-bromopropeyl)carbonate (1.0 g) was added. The resulting mixture was stirred at room temperature over night. The mixture was extracted with dichloromethane and washed with brine. The organic layer was dried over Na₂SO₄and evaporated. The residue was washed with dichloromethane (5 mL) and hexanes (10 mL) to give a white solid (0.59 g) as desire product.

Synthesis of Compound 106

The solid (0.09 g) from above reaction was stirred in 4 mL dichloromethane and 2 mL TFA at room temperature for 4 hours. Then the mixture was evaporated and the residue was washed with ether. The solid was purified by reverse phase column. A white solid (0.058 g) was obtained. LC-MS and ¹HNMR agreed.

Example 1AU
Synthesis of Compound 158

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Synthesis of Compound 2

tert-Butyl 3-(2,7-dibromo-9H-carbazol-9-yl)propylcarbamate (1 mmol, 0.48 g) and tert-butyl 3-(3-bromophenyl)propylcarbamate (3 mmol, 1.08 g) were added into a microwave tube under Argon. Dioxane (8 mL) and aqueous K₂CO₃(8 mmol, 4 mL, 2 M) were added. Then Pd(PPh₃)₄(0.2 mmol, 0.2 g) was added. The mixture was under microwave irradiation (95° C., 1 hour then 104° C. 24 minutes) with stirring. The reaction was cooled down to room temperature and extracted with EtOAc and brine. The organic layer was dried over Na₂SO₄and evaporated under vacuum. The residue was purified with silica column (eluent: EtOAc/hexanes=0/100 to 50/100, v/v). A white solid (0.23 g) was obtained as product 2. LC-MS OK.

Synthesis of Compound 158

The solid from above reaction was stirred in 4 mL dichloromethane and 2 mL TFA at room temperature for 4 hours. Then the mixture was evaporated and the residue was washed with ether. Half of the residue (0.1 g) was stirred in 1.5 mL CH₃CN and 1 mL of water. DIPEA (0.14 mL) was added and followed by N,N′-bis(t-butoxycarbonyl)-1H-pyrazole-1-carboxamidine (0.124 g). The resulting mixture was stirred at room temperature over night. The mixture was evaporated under vacuum to dry. The residue was purified using silica gel column (eluent: hexanes/DCM/EtOAc=100/1/1-72/14/14, v/v/v). A white solid (100 mg) was obtained. This solid was stirred in 1.5 mL dichloromethane and 0.5 mL TFA at room temperature for 4 hours. Then the mixture was evaporated and the residue was washed with ether. The solid was purified by reverse phase column. A white solid (0.040 g) was obtained. LC-MS and ¹HNMR agreed.

Example 1AV
Synthesis of Compound 161

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Synthesis of compound 1

To a dichloromethane solution (300 mL) of 1-bromo-3,5-dimethoxaybenzene (8.00 g, 36.9 mmol) in ice bath was added BBr₃(25.00 g, 100 mmol) dropwise. After 2 hours, the mixture was allowed to warm to room temperature and stirred over night. Methanol (10 mL) was added dropwise to terminate the reaction. The mixture was poured into water and stirred for 2 hours, then saturated sodium bicarbonate (100 mL) was added and extracted with dichloromethane. The organic layer was washed with saturated sodium bicarbonate, brine, and then dried over Na₂SO₄. The residue, after concentration, was purified using chromatography (eluent: methoh/DCM: 2/98, v/v). A white solid (1.0 g) was obtained as product. LC-MS and HNMR are nice.

Synthesis of Compound 2

Compound 1 (0.76 g, 4 mmol) and potassium carbonate (2.8 g, 20 mmol) were stirred in DMF (5 mL) and water (0.5 mL) at room temperature for 10 minutes, then heated to 44° C. 3-(Boc-amino)propyl bromide (3.0 g, 12.6 mmol) was added. The resulting mixture was stirred at 44° C. over night. The mixture was cooled down to room temperature and poured into a mixture of ethyl acetate and water. The organic layer was washed with brine and dried over Na₂SO₄. The residue after concentration was purified with chromatography. A white solid (1.7 g, 84%) was obtained. LC-MS and HNMR are great.

Synthesis of Compound 3

Compound 2 (1.01 g, 2 mmol) and 4,4,5,5-tetramethyl-2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3,2-dioxaborolane (0.61 g, 2.4 mmol) and potassium acetate (0.98 g, 10 mmol) were stirred in DMSO (10 mL) at room temperature under Ar protection. Then PdCl₂(pddf) (0.082 g, 0.1 mmol) was added. The resulting mixture was stirred at 80° C. over night. Then the reaction was cooled to room temperature. The mixture was filtered through celite and washed with ethyl acetate. The organic layer was washed with water, brine then dried over Na₂SO₄. Then residue after concentration is purified by chromatography (eluent: ethyl acetate/hexanes=1/4). A white solid (2.6 g, 75%) was obtained as the product.

Synthesis of Compound 161

Compound 3 (0.11 g, 0.2 mmol) and tert-butyl 3-(3-bromo-9H-carbazol-9-yl)propylcarbamate (0.080 g, 0.2 mmol), which was synthesized from 3-bromo-9H-carbazole using method of Compound 106, and potassium carbonate solution (1 mL, 2 mmol, 2 M) were stirred in dioxane (2 mL) at room temperature under Ar protection. Then Pd(PPh₃)₄(0.02 g, 0.02 mmol) was added. The mixture was irradiated under microwave at two stages: stage 1, 94° C., 3 hours; stage 2, 104° C., 1.5 hours. The reaction mixture was cooled down to room temperature then poured into a mixture of ethyl acetate and water. The organic layer was washed with brine and dried over Na₂SO₄. The residue after concentration was purified with chromatography (eluent: ethyl acetate/DCM/hexanes=10/10/80 to 33/33/34, v/v/v). A white solid (0.07 g) was obtained as compound 4. LC-MS is fine.

The solid from above was stirred in a mixture of TFA and DCM (3 mL, 1/2, v/v) at room temperature for 4 hours. Then the mixture was concentrated. Ether was added to triturate the residue. The solid obtained was purified with prep-HPLC. A white solid (54 mg) was obtained after freeze-dry. LC-MS and ¹HNMR agreed.

Example 1AW
Synthesis of Compound 162

Following the same procedure of Compound 161, Compound 162 was obtained using 7-Dibromo-9H-carbazole instead of 3-bromo-9H-carbazole as starting material.

Example 1AX
Synthesis of Compound 167

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Synthesis of Intermediate 1

2-Chloro-4,6-dimethoxy-1,3,5-triazole (0.88 g, 5 mmol) and N-methyl morpholine (1.1 mL, 10 mmol) were stirred in anhydrous THF (20 mL) for 20 minutes. 5-Bromoisophthalic acid (0.5 g, 2 mmol) and tert-butyl-N-(2-aminoethyl)carbamate (0.8 g, 5 mmol) were added. The resulting mixture was stirred at room temperature over night. The reaction mixture was poured into a mixture of ethyl acetate and water. The organic layer was washed with brine and dried over Na₂SO₄. A white solid (0.8 g, 76%) was obtained as product. LC-MS and HNMR agreed.

Synthesis of Compound 167

Following similar procedure of synthesis of Compound 161, Compound 167 was obtained as a white solid using 8-(dihydroxyboryl)dibenzo[b,d]thiophen-2-ylboronic acid and compound 1 above as starting materials.

Example 1AY
Synthesis of Compound 163

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Synthesis of Intermediate 2

Following the similar procedure as the synthesis of intermediate 3, compound 2 was obtained as off-white solid.

Synthesis of Compound 163

Following similar procedure as the synthesis of Compound 161, Compound 163 was obtained as white solid using compound 2 and 2-bromo-7-hexyl-9H-fluorene as starting materials.

Example 1AZ
Synthesis of Compound 168

Following similar procedure as the synthesis of Compound 163, Compound 168 was obtained as white solid using 2,8-dibromodibenzofuran to replace 2-bromo-7-hexyl-9H-fluorene as starting material.

Example 1BA
Synthesis of Compound 169

Following similar procedure as the synthesis of Compound 163, Compound 169 was obtained as white solid using 3,6-Dibromo-9-ethylcarbazole to replace 2-bromo-7-hexyl-9H-fluorene as starting material.

Example 1BB
Synthesis of Compound 170

Following similar procedure as the synthesis of Compound 167, Compound 170 was obtained using piperazine-1-carboxylic acid tert-butyl ester, instead of tert-butyl-N-(2-aminoethyl)carbamate, as starting material.

Example 1BC
Synthesis of Compound 171

Following similar procedure as the synthesis of Compound 167, Compound 171 was obtained using tert-butyl-N-(3-aminopropyl)carbamate, instead of tert-butyl-N-(2-aminoethyl)carbamate, as starting material.

Example 1BD
Synthesis of Compound 172

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Synthesis of compound 3

Following similar procedure of 19.2.4 synthesis of Compound 161, compound 3 was obtained as white solid using compound 1 and 2 as starting materials.

Synthesis of Compound 172

Following similar procedure of synthesis of compound 633, Compound 172 was obtained as white solid using compound 3 as starting materials.

Example 1BE
Synthesis of Compound 159

3-Aminophenylboronic acid (0.07 g, 0.48 mmol) and tert-butyl 3-(2,7-dibromo-9H-carbazol-9-yl)propylcarbamate (0.1 g, 0.2 mmol) were added into a microwave tube under Argon. Dioxane (2 mL) and aqueous K₂CO₃(1 mL, 2 M) were added. Then Pd(PPh₃)₄(0.02 mmol, 0.02 g) was added. The mixture was under microwave irradiation (95° C., 1 hour then 104° C., 24 minutes) with stirring. The reaction was cooled down to room temperature and extracted with EtOAc and brine. The organic layer was dried over Na₂SO₄and evaporated under vacuum. The residue was purified with silica column (eluent: MeOH/DCM=0/100 to 5/100, v/v). The obtained white solid (0.51 g) was stirred in 2 mL dichloromethane and 1 mL TFA at room temperature for 4 hours. Then the mixture was evaporated and the residue was washed with ether. A brown solid (0.5 g) was obtained as Compound 159, LC-MS and HNMR agreed.

Example 1BF
Synthesis of Compound 173
Synthesis of tert-butyl 2-(4-bromophenylamino)ethylcarbamate

4-Bromoaniline (0.13 g, 0.75 mmol), tert-butyl formylmethylcarbamate (0.12 g, 0.75 mmol) and NaBH(OAc)₃(0.84 g, 4 mmol) were stirred in DCE (4 mL) at room temperature over night. Then the reaction mixture was poured into EtOAc. The organic layer was washed with bring and water, then dried over Na₂SO₄and evaporated under vacuum. The residue was purified using silica gel column (Eluent: EtOAc/hexanes=0/100 to 25/100). The portion with desired MS was collected as the product.

Synthesis of the Compound 173

Following similar procedure of synthesis of Compound 161, Compound 173 was obtained as a white solid using 8-(dihydroxyboryl)dibenzo[b,d]thiophen-2-ylboronic acid and tert-butyl 2-(4-bromophenylamino)ethylcarbamate obtained above as starting materials.

Example 1BG
Synthesis of Compound 174
Synthesis of N1-(3-bromobenzyl)-N2-Boc-N-(2-(methylamino)ethyl)ethane-1,2-diamine

N,N-Di-BOC-diethylenetriamine (0.61 g, 2 mmol), 1-bromo-3-(bromomethyl)benzene (0.5 g, 2 mmol) and potassium carbonate (0.138 g, 10 mmol) were stirred in MeCN at room temperature for 30 minutes then 60° C. over night. The mixture was poured into water and extracted with EtOAc. The organic layer was washed with brine and water, dried over Na₂SO₄and evaporated under vacuum. The residue was purified with silica gel column (eluent: MeOH/DCM=0/100 to 4/100) to give a white solid as product.

Synthesis of Compound 174

Following similar procedure of the synthesis of Compound 161, Compound 174 was obtained as a white solid using 8-(dihydroxyboryl)dibenzo[b,d]thiophen-2-ylboronic acid and of N1-(3-bromobenzyl)-N2-Boc-N1-(2-(methylamino)ethyl)ethane-1,2-diamine obtained above as starting materials.

Example 1BH
Synthesis of Compound 180

Following similar procedure as synthesis of Compound 174, Compound 180 was obtained using 2-bromo-4-(bromomethyl)-1-fluorobenzene to replace 1-bromo-3-(bromomethyl)benzene as starting material.

Example 1BI
Synthesis of Compound 160

3-Aminophenylboronic acid (0.07 g, 0.48 mmol) and tert-butyl 3-(2,7-dibromo-9H-carbazol-9-yl)propylcarbamate (0.1 g, 0.2 mmol) were added into a microwave tube under Argon. Dioxane (2 mL) and aqueous K₂CO₃(1 mL, 2 M) were added. Then Pd(PPh₃)₄(0.02 mmol, 0.02 g) was added. The mixture was under microwave irradiation (95° C., 1 hour then 104° C., 24 minutes) with stirring. The reaction was cooled down to room temperature and extracted with EtOAc and brine. The organic layer was dried over Na₂SO₄and evaporated under vacuum. The residue was purified with silica column (eluent: MeOH/DCM=0/100 to 5/100, v/v). The obtained white solid (15 mg), tert-butyl formylmethylcarbamate (25 mg) and NaBH(OAc)₃(40 mg) were stirred in DCE (2 mL) at room temperature for 3 days. The mixture was poured into water and extracted with EtOAc. The organic layer was washed with brine and water, dried over Na₂SO₄and evaporated under vacuum. The residue was purified with silica gel column (eluent: MeOH/DCM=0/100 to 4/100) to give a white solid, which was stirred in TFA/DCM (0.5 mL/1 mL) are room temperature for 4 hours. A white solid (12 mg) was obtained after evaporation under vacuum and ether washing. LC-MS and HNMR agreed.

Example 1BJ
Synthesis of Compound 175

Following similar procedure as synthesis of Compound 174, Compound 175 was obtained as a white solid using 1-Boc piperazine to replace N,N-Di-BOC-diethylenetriamine as starting material.

Example 1BK
Synthesis of Compound 176

Following similar procedure as synthesis of Compound 160, Compound 176 was obtained as a white solid using 3,6-dibromo-9-ethyl-9H-carbazole to replace tert-butyl 3-(2,7-dibromo-9H-carbazol-9-yl)propylcarbamate as starting material.

Example 1BL
Synthesis of Compound 177

Following similar procedure as synthesis of Compound 160, Compound 177 was obtained as a white solid using 3,6-dibromo-9H-carbazole to replace tert-butyl 3-(2,7-dibromo-9H-carbazol-9-yl)propylcarbamate as starting material.

Example 1BM
Synthesis of Compound 178

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Synthesis of Compound 1

N1-(3-bromobenzyl)-N2-Boc-N1-(2-(methylamino)ethyl)ethane-1,2-diamine (0.47 g, 1 mmol) and 4,4,5,5-tetramethyl-2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3,2-dioxaborolane (0.31 g, 2.4 mmol) and potassium acetate (0.98 g, 10 mmol) were stirred in DMSO (5 mL) at room temperature under Ar protection. Then PdCl₂(pddf) (0.042 g, 0.05 mmol) was added. The resulting mixture was stirred at 80° C. over night. Then the reaction was cooled to room temperature. The mixture was filtered through celite and washed with ethyl acetate. The organic layer was washed with water, brine then dried over Na₂SO₄. Then residue after concentration is purified by chromatography (eluent: ethyl acetate/hexanes=1/2). A white solid was obtained as compound 1.

Synthesis of Compound 178

Following similar procedure as synthesis of Compound 159, Compound 178 was obtained as white solid using compound 1 from above to replace 3-aminophenylboronic acid as starting material.

Example 1BN
Synthesis of Compound 144

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Synthesis of Compound 1

To a dichloromethane solution (300 mL) of 1-bromo-3.5-dimethoxaybenzene (8.00 g, 36.9 mmol) in ice bath was added BBr₃(25.00 g, 100 mmol) dropwise. After 2 hours the mixture was allowed to warm to room temperature and stirred over night. Methanol (10 mL) was added dropwise to terminate the reaction. The mixture was poured into water and stirred for 2 hours. Then saturated sodium bicarbonate (100 mL) was added and extracted with dichloromethane. The organic layer was washed with saturated sodium bicarbonate, brine, and then dried over Na₂SO₄. The residue, after concentration, was purified using chromatography (eluent: methoh/DCM: 2/98, v/v). A white solid (1.0 g) was obtained as product. LC-MS and HNMR are nice.

Synthesis of Compound 2

Compound 1 (0.76 g, 4 mmol) and potassium carbonate (2.8 g, 20 mmol) were stirred in DMF (5 mL) and water (0.5 mL) at room temperature for 10 minutes, then heated to 44° C. 3-(Boc-amino) propyl bromide (3.0 g, 12.6 mmol) was added. The resulting mixture was stirred at 44° C. over night. The mixture was cooled down to room temperature and poured into a mixture of ethyl acetate and water. The organic layer was washed with brine and dried over Na₂SO₄. The residue after concentration was purified with chromatography. A white solid (1.7 g, 84%) was obtained. LC-MS and HNMR are great.

Synthesis of Compound 3

Synthesis of Compound 4

Cu(OAc)₂(0.73 g) and 3-bromophenylboranic acid (1.6 g) were stirred at 100° C. in DMF (16 mL) in open flask for 1 hour. Then the mixture was filtered through celite and washed with EtOAc. The organic layer was washed with water and dried over Na₂SO₄and evaporated under vacuum. The oil reside was purified using hexane as eluent. Yellow oil (1.0 g) was obtained as product.

Synthesis of Compound 5

Compound 4 (0.025 g, 0.08 mmol) and compound 3 (0.090 g, 0.16 mmol) and potassium carbonate solution (0.4 mL, 2 M) were stirred in dioxane (0.8 mL) at room temperature under Ar protection. Then Pd(PPh₃)₄(0.015 g, 0.016 mmol) was added. The mixture was irradiated under microwave at two stages: stage 1, 94° C., 3 hours; stage 2, 104° C., 1.5 hours. The reaction mixture was cooled down to room temperature then poured into a mixture of ethyl acetate and water. The organic layer was washed with brine and dried over Na₂SO₄. The residue after concentration was purified with chromatography TLC (eluent: ethyl acetate/DCM/hexanes=1/1/1, v/v/v). A yellowish solid was obtained as product. LC-MS is fine.

Synthesis of Compound 144

The solid from the previous step was stirred in a mixture of TFA and DCM (2 mL, 1/1, v/v) at room temperature for 4 hours. Then the mixture was concentrated. Ether was added. The solid obtained was purified with prep-HPLC. A white solid (36 mg) was obtained after freeze-dry.

Example 1BO
Synthesis of Compound 149, Compound 147, Compound 148, Compound 146, and Compound 145

Compounds 149, 147, 148, 146, and 145 were made following same procedure as that of Compound 144.

Example 1BP
Synthesis of Compound 179

Following similar procedure as synthesis of Compound 178, Compound 179 was obtained as white solid using 3,6-dibromo-9H-carbazole to replace tert-butyl 3-(2,7-dibromo-9H-carbazol-9-yl)propylcarbamate as starting material.

Example 1BQ
Synthesis of Compound 181

Following similar procedure as synthesis of Compound 174, Compound 181 was obtained using N,N-di-Boc-dipropylenetriamine to replace N,N-Di-BOC-diethylenetriamine as starting material.

Example 1BR
Synthesis of Compound 152

1,3-Dibromo-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-one (0.037 g, 0.1 mmol) and tert-butyl 3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenethylcarbamate (0.077 g, 0.22 mmol) and potassium carbonate solution (0.4 mL, 2 M) were stirred in dioxane (0.8 mL) at room temperature under Ar protection. Then Pd(PPh₃)₄(0.01 g, 0.01 mmol) was added. The mixture was irradiated under microwave at two stages: stage 1, 94° C., 3 hours; stage 2, 104° C., 1.5 hours. The reaction mixture was cooled down to room temperature then poured into a mixture of ethyl acetate and water. The organic layer was washed with brine and dried over Na₂SO₄. The residue after concentration was purified with chromatography TLC (eluent: ethyl acetate/DCM/hexanes=1/1/1, v/v/v). A white solid was obtained as product. LC-MS is fine. The white solid was stirred in a mixture of TFA and DCM (2 mL, 1/1, v/v) at room temperature for 4 hours. Then the mixture was concentrated. Ether was added to the residue. The solid obtained was purified with prep-HPLC. A white solid (26 mg) was obtained after freeze-dry. LC-MS and HNMR agreed.

Example 1BS
Synthesis of Compound 153

Following similar procedure as the synthesis of Compound 152, Compound 153 was obtained using 3,7-Dibromo-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-one to replace 1,3-Dibromo-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-one as starting material

Example 1BT
Synthesis of Compound 154

Following similar procedure as the synthesis of Compound 152, Compound 154 was obtained using 1,3,7-tribromo-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-one to replace 1,3-Dibromo-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-one as starting material

Example 1BU
Synthesis of Compound 155

Following similar procedure as the synthesis of Compound 152, Compound 155 was obtained using compound 4 in the syntheses procedure of compound 3 of Compound 144 to replace tert-butyl 3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenethylcarbamate as starting material

Example 1BV
Synthesis of Compound 156

Following similar procedure as synthesis of Compound 152, Compound 156 was obtained using compound 4 in the syntheses procedure of compound 3 of Compound 144 to replace tert-butyl 3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenethylcarbamate and 3,7-Dibromo-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-one to replace 1,3-Dibromo-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-one as starting materials.

Example 1BW
Synthesis of Compound 187

1,3-Diethynylbenzene (0.025 g, 0.2 mmol), compound 2 from the synthesis of compound 2 of Compound 144 (0.20 g, 0.4 mmol), CuI (0.007 g, 0.04 mmol) and TEA (0.1 g, 1 mmol) were stirred in acetonitrile (4 mL) at room temperature. Then Pd(PPh₃)₄(0.04 g, 0.04 mmol) was added. The mixture was irradiated under microwave at two stages: stage 1, 54° C., 4 hours 45 minutes; stage 2, 64° C., 4 hours 45 minutes. The reaction mixture was cooled down to room temperature then poured into a mixture of ethyl acetate and water. The organic layer was washed with brine and dried over Na₂SO₄. The residue after concentration was purified with silica gel chromatography (eluent: ethyl acetate/DCM/hexanes=1/1/1, v/v/v). Yellow oil was obtained. LC-MS is fine. The oil was stirred in a mixture of TFA and DCM (2 mL, 1/1, v/v) at room temperature for 4 hours. Then the mixture was concentrated. Ether was added to the residue. The white solid (0.035 g) obtained after freeze-dry. LC-MS and HNMR agreed.

Example 1BX
Synthesis of Compound 188

Following similar procedure as the synthesis of Compound 187, Compound 188 was obtained using 1,3-diethynyl-5-fluorobenzene to replace 1,3-diethynylbenzene as starting material.

Example 1BY
Synthesis of Compound 166

Following similar procedure as the synthesis of Compound 152, Compound 166 was obtained using bis(p-bromophenyl)difluoromethane to replace 1,3-Dibromo-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-one as starting material.

Example 1BZ
Synthesis of Compound 164

Following similar procedure as the synthesis of Compound 152, Compound 164 was obtained using compound 2 from the synthesis of compound 2 of Compound 144 to replace 1,3-Dibromo-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-one as starting material.

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Example 1CA
Synthesis of Compound 150
Synthesis of Compound 1

1-Bromo-3,5-bis(bromomethyl)benzene (0.39 g, 1 mmol) and sodium cyanide (0.49 g, 10 mmol) was stirred in acetonitrile (20 mL) and water (2 mL) at room temperature for 15 minutes, then heated to 64° C. for 30 minutes. The mixture was cooled to room temperature and evaporated under vacuum. The left-over was poured into a mixture of dichloromethane and water. The organic layer was washed with water and dried over Na₂SO₄. The residue after concentration was purified with silica gel chromatography (eluent: ethyl acetate/DCM/hexanes=1/1/1, v/v/v). A white solid (0.25 g, 89%) was obtained as compound 1. LC-MS is fine.

Synthesis of Compound 2

Compound 1 (0.25 g, 0.9 mmol) was stirred in anhydrous THF (2 mL) at 0° C. Borane-THF (14 mL, 1 M) was added dropwise. The resulting mixture was stirred at 0° C. for 30 minutes and then refluxing over night. The reaction was quenched using methanol (dropwise). Then the mixture was evaporated under vacuum. The residue was stirred in HCl in methanol (10 mL, 4 M) at room temperature for 4 hours and then was evaporated again. The oily residue was dissolved in EtOAc (20 mL) and KOH solution (100 mL, 1 M). The aqueous layer was extracted with EtOAc again. The organic layer was combined and evaporated under vacuum. The residue (compound 2) was used in subsequent reaction without purification.

Synthesis of Compound 3

Compound 2 and (Boc)₂O (0.52 g, 2.4 mmol) were stirred in THF (5 mL) with TEA (0.22 g, 2.2 mol) at room temperature over night. The mixture was poured into a mixture of ethyl acetate and water. The organic layer was washed with brine and dried over Na₂SO₄. The residue after concentration was purified with chromatography (EtOAc/DCM/hexanes=0/50/50-20/40/40, v/v/v). A white solid (0.17 g, 84%) was obtained. LC-MS and HNMR are agreed.

Synthesis of Compound 4

Compound 3 (0.2 g, 0.4 ol) and 4,4,5,5-tetramethyl-2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1,3,2-dioxaborolane (0.112 g, 0.44 mmol) and potassium acetate (0.2 g, 2 mmol) were stirred in DMSO (2 mL) at room temperature under Ar protection. Then PdCl₂(pddf) (0.02 g, 0.01 mmol) was added. The resulting mixture was stirred at 80° C. over night. Then the reaction was cooled to room temperature. The mixture was filtered through celite and washed with ethyl acetate. The organic layer was washed with water, brine then dried over Na₂SO₄. Then residue after concentration is purified by chromatography (eluent: ethyl acetate/hexanes=1/4). A white solid (0.14 g, 70%) was obtained as the product.

Synthesis of Compound 5

Cu(OAc)₂(0.182 g, 1 mmol) and 3-bromo-5-fluorobenzeneboronic acid (0.44 g, 2 mmol) were stirred at 100° C. in DMF (4 mL) in open flask for 1 hour. Then the mixture was filtered through celite and washed with EtOAc. The organic layer was washed with water and dried over Na₂SO₄and evaporated under vacuum. The residue was uses as such without further purification.

Synthesis of Compound 150

Compound 4 (0.059 g, 0.128 mmol) and compound 5 (0.02 g, 0.06 mmol) and potassium carbonate solution (0.4 mL, 2 M) were stirred in dioxane (0.8 mL) at room temperature under Ar protection. Then Pd(PPh₃)₄(0.012 g, 0.012 mmol) was added. The mixture was irradiated under microwave: 100° C., 1 hour. The reaction mixture was cooled down to room temperature then poured into a mixture of ethyl acetate and water. The organic layer was washed with brine and dried over Na₂SO₄. The residue after concentration was purified with chromatography TLC (eluent: ethyl acetate/DCM/hexanes=1/1/1, v/v/v). A yellowish solid was obtained as product. LC-MS is fine.

The solid was stirred in a mixture of TFA and DCM (2 mL, 1/1, v/v) at room temperature for 4 hours. Then the mixture was concentrated. Ether was added. The solid obtained was purified with prep-HPLC. A white solid (10 mg) was obtained after freeze-dry. LC-MS and HNMR agreed.

Example 1CB
Synthesis of Compound 151

Compound 150 (0.01 g) and TEA (0.01 g) were stirred in 1 mL MeOH and followed by N,N′-bis(t-butoxycarbonyl)-1H-pyrazole-1-carboxamidine (0.124 g). The resulting mixture was stirred at room temperature over night. The mixture was evaporated under vacuum to dry. The residue was purified using silica gel column (eluent: hexanes/EtOAc=100/1-70/30, v/v). A white solid (10 mg) was obtained. This solid was stirred in 1.5 mL dichloromethane and 0.5 mL TFA at room temperature for 4 hours. Then the mixture was evaporated and the residue was washed with ether. The solid was purified by reverse phase column. A white solid (0.007 g) was obtained. LC-MS and ¹HNMR agreed.

Example 1CC
Synthesis of Compound 184

Following similar procedure as the synthesis of compound 3 of the synthesis of Compound 172, Compound 184 was obtained using 3-(2,3-bis(3-(Boc-amino)propoxy)-5-bromophenoxy)-N-Boc-propan-1-amine, which was made from 5-bromo-1,2,3-trimethoxybenzene, to replace compound 1 as starting material.

Example 1CD
Synthesis of Compound 111

Following similar procedure as the synthesis of Compound 156, Compound III was obtained using 3,5-dibromobenzotrifluoride to replace 1,3-Dibromo-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5-one as starting material.

Example 1CE
Synthesis of Compound 186

Following similar procedure as the synthesis of Compound 151, Compound 186 was obtained using Compound 184 to replace Compound 150 as starting material.

Example 1CF
Synthesis of Compound 112

Following similar procedure as the synthesis of Compound 110, Compound 112 was obtained using 5-trifluoromethyl-1,3-phenylenediboronic acid to replace 1,3-benzenediboronic acid as starting material.

Example 1CG
Synthesis of Compound 114

Following similar procedure as the synthesis of Compound 151, Compound 114 was obtained using Compound 112 to replace Compound 150 as starting material.

Example 1CH
Synthesis of Compound 182

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Compound 1 (0.068 g, 0.1 mmol), compound 2 (0.051 g, 0.1 mmol) and compound 3 (0.027 g, 0.1 mmol) and potassium carbonate solution (0.4 mL, 2 M) were stirred in dioxane (0.8 mL) at room temperature under Ar protection. Then Pd(PPh₃)₄(0.012 g, 0.012 mmol) was added. The mixture was irradiated under microwave: 100° C., 1 hour. The reaction mixture was cooled down to room temperature then poured into a mixture of ethyl acetate and water. The organic layer was washed with brine and dried over Na₂SO₄. The residue after concentration was purified with chromatography TLC (eluent: ethyl acetate/DCM/hexanes=1/1/1, v/v/v). A white solid obtained was stirred in a mixture of TFA and DCM (2 mL, 1/1, v/v) at room temperature for 4 hours. Then the mixture was concentrated. Ether was added. The solid obtained was purified with prep-HPLC. A white solid (24 mg) was obtained after freeze-dry. LC-MS and HNMR agreed.

Example 1CI
Synthesis of Compound 183

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Synthesis of Compound 4

Following similar procedure as the synthesis of Compound 182 but before de-protection step, compound 4 was obtained using compound 1, which was obtained by converting Boc to Fmoc protection, as starting material.

Synthesis of compound 5 and Compound 183

Compound 4 (0.1 mmol) was stirred in THF (1 mL) with diethylamine (0.2 mL) at room temperature for 4 hours. Then the mixture was evaporated under vacuum to dry. The residue and was dissolved in methanol (1 mL) and DIPEA (0.1 mL), N,N′-bis(t-butoxycarbonyl)-1H-pyrazole-1-carboxamidine (0.1 g) was added. The resulting mixture was stirred at room temperature over night. The mixture was evaporated under vacuum to dry. The residue was purified using silica gel column (eluent: hexanes/DCM/EtOAc=100/1/1-72/14/14, v/v/v). A white solid (10 mg) was obtained as compound 5. This solid was stirred in 1.5 mL dichloromethane and 0.5 mL TFA at room temperature for 4 hours. Then the mixture was evaporated and the residue was washed with ether. The solid was purified by reverse phase column. A white solid (0.009 g) was obtained. LC-MS and ¹HNMR agreed.

Example 1CJ
Synthesis of Compound 185

Following similar procedure as the synthesis of Compound 183, Compound 185 was obtained using compound 1 in the synthesis of Compound 182 to replace compound 2 in the synthesis of Compound 183 as starting material.

Example 1CK
Synthesis of Compound 113

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Following similar procedure in the syntheses procedure of Compound 144, Compound 113 was obtained using compound 2, which was synthesized from 4,6-dibromobenzene-1,3-diol (1), and 3-(trifluoromethyl)phenylboronic acid as starting materials.

Example 2
Antimicrobial Activity—Minimum Inhibitory Concentrations (MIC)

The compounds were screened for antimicrobial activity against a number of ATCC bacterial strains. Minimum Inhibitory Concentrations (MIC) of each of the compounds were determined using standard CLSI procedures modified by the Hancock protocol against E. Coli ATCC 25922, Staphylococcus aureus ATCC 27660, Enterococcus faecalis ATCC 29212, Pseudomonas aeruginosa ATCC 10145, and Klebsiella pneumoniae ATCC 13883.

General Procedures:

This procedure is a modification of the standard microbroth dilution assay recommended by the National Committee for Clinical Laboratory Standards (NCCLS) which has been developed for determining in vitro antimicrobial activities of cationic agents (Steinberg et al., Antimicrob. Agents Chemother., 1997, 41, 1738; and Yan et al., Antimicrob. Agents Chemother., 2001, 45, 1558). The modifications were made to minimize loss of the antimicrobial agent due to adsorption onto glass or plastic surfaces and by precipitation at high concentrations.

Three mL of Mueller-Hinton II Broth (cation-adjusted) was inoculated with 5 μL of frozen bacterial stock and incubated at 37° C. on a shaker platform (at 250 rpm) overnight. Compound stock solutions were prepared in DMSO and serial two-fold dilutions of compound were made in 0.01% acetic acid, 0.2% bovine serum albumin directly in the wells of the polypropylene plate at 10 μL/well. DMSO concentrations did not exceed 1% in the assay. All samples were performed in duplicate. The overnight bacteria suspension was diluted to approximately 10⁶cfu/mL and inoculated into a polypropylene (Costar) 96-well round bottom plate (90 μL volumes). One set of control wells included broth-only samples with dilution buffer for testing sterility and providing blank values for the assay readings. Vehicle-control wells containing the bacterial suspension with DMSO (no compound) were also included. Following the overnight incubation (18 hours), the cell growth was assessed by observing the presence of “acceptable growth”, defined by NCCLS as a ≧2 mm button or definite turbidity.

Actual results from a representative MIC assay are shown below in Table 1. Data is expressed as MIC₅₀in μg/mL. The bacterial isolates were as follows: E. coli (25922); S. aureus (27660); E. faecalis (29212); P. aeruginosa (10145); and K. pneumoniae (13883).

TABLE 1

Compound

E. coli

S. aureus

E. faecalis

P. Aeruginosa

K. Pnuemnoiae

100
100
100
100
100
100

101
25
25
12.5
>100
50

102
50
25
3.13
>100
>100

103
>100
25
>100
>100
>100

104
100
100
>100
>100
>100

105
>100
>100
>100
>100
>100

106
12.5
12.5

100
25

107
>100
>100
>100
>100
>100

108
>100
>100
>100
>100
>100

109
>100
>100
>100
>100
>100

110
25
25
100
100
100

111
12.5
3.13
6.25
50
50

112
12.5
6.25
3.13
50
12.5

113
3.13
3.13
3.13
12.5
6.25

114
3.13
0.78
1.56
12.5
3.13

115
25
25
>50
>50
50

116
6.25
6.25
25
25
25

117
25
12.5
50
50
>50

118
0.78
0.78
12.5
12.5
12.5

119
1.56
0.78
0.78
12.5
3.13

120
1.56
1.56
1.56
6.25
1.56

121
6.25
1.56
3.13
25
3.13

122
3.13
1.56
1.56
12.5
3.13

123
3.13
0.78
0.78
6.25
12.5

124
50
50
25
50
>50

125
12.5
12.5
12.5
12.5
25

126
6.25
1.56
1.56
6.25
6.25

127
>100
50
>100
>100
>100

128
12.5
1.56
1.56
25
25

129
25
0.78
3.13
25
12.5-25

131
12.5
0.78
6.25
50
12.5

132
12.5
12.5
12.5
25
25

133
>50
50
25
>50
>50

134
12.5
0.78
12.5
25
50

135
50
6.25
>50
25
>50

136
>50
25
50
50
50

137
12.5
3.13
12.5
12.5
>50

138
12.5
0.39
1.56
12.5
25

139
6.25
0.39
0.78
12.5
3.13

140
>100
1.56

>100
>100

141
6.25
25

12.5
25

142
12.5
100

25
25

143
0.78
0.78
1.56
12.5
3.13

144
3.13
0.195
6.25
6.25
6.25

145
1.56-3.13
1.56
0.78-1.56
12.5
1.56-3.13

146
1.56-3.13
1.56
0.78-1.56
6.25
1.56-3.13

147
1.56
0.39
0.78
6.25
1.56

148
1.56
0.39
0.78
3.13
1.56

149
3.13
0.78
1.56
6.25
3.13

150
6.26
1.56
25
50
25

151
1.56
0.78
1.56
12.5
3.13

152
3.13
1.56
3.13
25
6.25

153
6.25
1.56
3.13
25
6.25

154
1.56
0.78
6.25
6.25
6.25

155
>50
1.56
>50
25
>50

156
3.13
0.098
12.5
6.25
12.5

157
50
6.25
25
25

158
3.13
1.56
6.25
25
3.13

159
12.5
1.56
12.5
100
12.5

160
1.56
0.39
6.25
12.5
6.25

161
>50
25
3.13
50
>50

162
50
0.39
0.39
12.5
>50

163
>50
0.39
12.5
>50
>50

164
>50
>50
>50
>50
>50

165
50
6.25
25
25
>50

166
3.13
0.39
1.56
6.25
6.25

167
>50
6.25
12.5
3.13
>50

168
>50
3.13
>50
>50
>50

169
25
3.13
>50
>50
>50

170
>100
>100
>100
>100
>100

171
>100
6.25
>100
>100
>100

172
0.78
0.049
0.78
6.25
0.78

173
6.25
0.195
1.56
>50
3.13

174
3.13
0.195
3.13
3.13
3.13

175
6.25
0.39
12.5
25
12.5

176
12.5
0.39
>50
12.5
>50

177
1.56
1.56
>50
12.5
>50

178
3.13
0.39
12.5
12.5
12.5

179
1.56
1.56
>50
25
>50

180
1.56
0.098
3.13
3.13
1.56

181
3.13
0.195
6.25
6.25
6.25

182
6.25
1.56
6.25
12.5
25

183
1.56
0.78
0.39
12.5
3.13

184
6.25
1.56
6.25
6.25
12.5

185
6.25
0.78
1.56
25
12.5

186
12.5
0.78
3.13
12.5
6.25

187
12.5
1.56
25
12.5
>50

188
3.13
0.195
0.78
6.25
12.5

189
1.56
3.9-7.8
6.25
6.25
1.56

190
1.56
0.78
0.39
12.5
3.13

191
3.13
1.56
3.13
6.25
6.25

192
12.5
3.13
12.5
50
>50

193
1.56
0.39
1.56
6.25
1.56

194
12.5
1.56
6.25
12.5
>50

195
3.13
0.78
1.56
12.5
6.25

196
25
3.13
25
25
>50

197
1.56
0.78
12.5
25
12.5

198
50
25
50
50
50

199
1.56
0.78
12.5
12.5
1.56

200
0.78
0.049
0.39
3.13
1.56

Example 3
Antimicrobial Activity Vs. Gram-Positive Clinical Isolates and Gram-Negative Clinical Isolates

The compounds can be evaluated in vitro in accordance with defined CLSI documents specific to the organisms (aerobic, anaerobic or yeast) tested in this study. Ampicillin, ceftazidime, cefuroxime, ciprofloxacin, linezolid, and vancomycin are tested alongside as comparator agents for aerobic bacteria; clindamycin and metronidazole are tested as comparators for anaerobes; fluconazole is tested as a comparator for yeast isolates. Stock solutions of compounds are prepared in dimethyl sulfoxide (DMSO). Ampicillin, ceftazidime, cefuroxime, ciprofloxacin, linezolid, vancomycin, metronidazole, clindamycin, and fluconazole are prepared each according to its manufacturer's guideline.

Aerobes (M7-A7)1

Minimum inhibitory concentrations (MICs) in g/mL are determined according to CLSI guideline M7-A7 by broth microdilution. All aerobes are tested using Mueller-Hinton broth medium with the exception of Streptococcus spp., which is tested using cation-adjusted Mueller-Hinton broth supplemented with 2-5% lysed horse blood.

Example 4
MICs with Staphylococcus Species with Defined Resistance Phenotypes

Evaluation of the susceptibility profiles of compounds against selected isolates can be carried out in vitro by broth microdilution methodology using Mueller-Hinton broth medium according to CLSI document M7-A7. CLSI interpretive breakpoints are applied where applicable as directed by CLSI document M100-S17.

Example 5
Cytotoxicity and Selectivity

Cytotoxicity of the compounds was evaluated in a colorimetric assay using a transformed human liver cell line (HepG2, HB-8065) and an embryonic mouse cell line (NIH/3T3 cells, CRL-1658). This assay measures the bioreduction of a novel tetrazolium compound to a soluble formazan product by viable cells. HepG2 cells were seeded in 96 well plates at 2×10⁴cells/well in MEM medium with 10% fetal bovine serum (FBS) 24 hours prior to use. NIH/3T3 cells were seeded in 96 well plates at 2×10⁴cells/well in DMEM medium with 10% bovine calf serum (BCS) 24 hours prior to use. Cell monolayers were rinsed in serum-free media and incubated for one hour with compounds in serum-free media. After incubation, the media is replaced with serum supplemented media and live cells were measured using the Cell Titer 96 Aqueous Non-Proliferation Assay kit (Promega, Madison, Wis.). EC₅₀values were determined using a four parameter logistic equation: Y=Bottom+(Top-Bottom)/(1+10̂((LogEC₅₀−X)*HillSlope)).

Actual results from a representative cytotoxicity assay are shown below in Table 2. Data is expressed as EC₅₀in μg/mL.

TABLE 2

Compound
NIH 3T3
HepG2

100
13
18

101
9

102
12
38

106
107
61.9

111
408.5
575

112
24.42
35.2

114
83.5
60.6

115
1130.7
>1164.6

116
675.5
973.9

119
113.3

120
99.0

121
37.0

122
14.5

123
114.7

124
192.4

125
26.1

126
59.7

128
22.3
46.95

129
35.77
57

131
41.66
31.65

132
23.48
50.13

133
70.15
130

134
33.44
70.88

135
34.49
134.5

136
250.2
4.12

137
26.64
55.6

140
>1000
>1000

141
404
24.4

142

105

144
320
448

145
146.3
302

146
35.82
58.6

147
50.94
164

148
53.77
244

149
59.19
98.5

150
427
486

151
72.14
254

152
20.9
27.5

153
53.3
80.6

154
53.4
85.4

155
177
330

156
49.4/88.1
74.2/143.7

157
713
461

158
131
100

159
45.7
64.7

160
451
853

161
>1000
790

162
307
341

163
84.4
102

164
>1000
>1000

165
357.3
355

166
83.99
137

167
56.3
71.8

168
32.4
72.6

169
450
312

170
436
>1000

171
46.5
236

172
41.4
35.7

173
trace

174
149
171

175
19.9
19.4

176
trace

177
487
>1000

178
trace
228

179
179
615

180
43.1
104

181
83.1
212

182
78.21
173

184
57
100

187
212.6
224.3

188
82.77
151

189
131.2
255.5

191
17.42
70.27

192
542
554

193
62.4
178

194
154.2
192.1

195
95.83
162.7

196
264.6
343.9

197
27.51
99.85

198
282.3
185.1

199
116.4
134.9

200
155
126

Cytotoxicity of the compounds is also evaluated in a hemolysis assay using human erythrocytes. Pooled whole human blood is centrifuged to separate the red blood cells (RBC). The isolated RBCs are rinsed and diluted in Tris-buffered saline (TBS buffer, pH 7.4) to obtain a 0.22% RBC stock suspension. 5 μL of compound stock solution is added to 45 μL of RBC suspension and incubated with shaking for 1 hour at 37° C. At the conclusion of the incubation time, samples are centrifuged and 30 μL of the supernatant is added to 100 μL of water. OD₄₁₄measurements are read for hemoglobin concentration. The bee venom peptide melittin is used as a positive control. EC₅₀values are determined as described above.

Example 6
Time-Kill

Time-kill studies of the compounds versus S. enteritidis ATCC 13076, E. coli ATCC25922, E. coli (lab strain) D31, and S. aureus ATCC27660 were determined in a standard protocol by measuring the time it takes to reduce the initial inoculums 3 log units. Three mL of cation-adjusted Mueller-Hinton medium was inoculated with 20 μL of frozen bacterial stock and incubated at 37° C. on a shaker platform (at 250 rpm) overnight. The suspension was diluted to approximately 5×10⁵cfu/mL and treated with 2×, 5×, 10×, and 20×MIC (MIC=1 μg/mL). The compound stock solutions were prepared at 10 mg/mL in DMSO. Time points were collected and viable bacteria were counted on MH Agar plates after an 18 hour incubation.

The time kill study was carried on Compound 200 against S. enteritidis ATCC 13076. The compound reduced more than 3 long bacterial growth at 3.75 hour with 2×MIC, at 1.55 hour with 5×MIC and at 1.35 hour with 10×MIC.

Example 7
Serial Passage Resistance in MSSA (ATCC 29213) and MRSA (ATCC 33591)

Frozen bacterial stocks (20 μL) of S. aureus ATCC29213 or methicillin-resistant S. aureus (MRSA ATCC 33591) are inoculated into 3 mL cation-adjusted Mueller-Hinton medium and incubated at 37° C. on a shaker platform (250 rpm) overnight. The suspension is diluted to approximately 5×10⁵cfu/mL and inoculated into a polypropylene (Costar) 96-well round bottom plate (90 μL volumes). Stock solutions of the compounds and norfloxacin (Sigma Aldrich, St. Louis, Mo.; Catalogue# N9890) are prepared in DMSO and serial two-fold dilutions of compound are made in 0.01% acetic acid, 0.2% bovine serum albumin directly in the wells of the polypropylene plate at 10 μL/well. Final concentrations of the compounds are 50, 25, 12.5, 6.25, 3.13, 1.56, 0.78, 0.39, 0.19, 0.098, 0.049, and 0.024 μg/mL. Final concentration ranges of norfloxacin are 100, 50, 25, 12.5, 6.25, 3.13, 1.56, 0.78, 0.39, 0.19, 0.098, and 0.049 μg/mL. DMSO concentrations do not exceed 1% in the assay. All samples are performed in triplicate. Following a 24 hour incubation at 37° C., cell growth is assessed by observing the presence of “acceptable growth”, defined by CLSI as a ≧2 mm button or definite turbidity. The MIC wells are defined as the lowest concentration where acceptable growth is not observed. For serial passage, 50 μL aliquots are taken from 2 of 3 replicate wells at 0.5×MIC and combined into 900 μL of fresh cation-adjusted Mueller-Hinton medium. The OD₆₀₀is measured and the cell suspensions are inoculated into polypropylene 96-well round bottom plates (90 μL volumes) at approximately 5×10⁵cfu/mL. Ten μL of compound stock solutions are added previously to the wells to achieve the concentration ranges for each compound described above. All samples are performed in triplicate. The plates are incubated for 24 hours at 37° C. This process is repeated for a total of 17 passages and MIC values are recorded at each passage.

Example 8
Anti-Biofilm Activity Against Methicillin-Resistant Staphylococcus aureus (MRSA)

The in vitro activity against biofilm was carried out by following the protocol for biofilm development and challenge using filter paper disks and 24-well plates. On day one, streak out MRSA for isolation on tryptic soy agar plate (TSA). On day two, grow up single colony of MRSA in about 5 mL tryptic soy broth (TSB). Filter papers were punched and autoclaved in 96-well plate. On the third day, a single filter paper disk was placed in each well of 24-well plate. The plate was inoculated with 300 μL/well of 0.01 adjusted OD₆₀₀bacteria inoculum in TSB supplemented with 1% glucose and 1.6% NaCl. The cells were allowed to grow for 48 hours on a shaker at 37° C. On day five, the challenge plate(s) were made in a 24-well plate(s), using eppendorf tubes to make dilutions and aliquoted into designated wells. The wash plates were filled in each well of a 24-well plate with 500 μL 0.9% saline. The disks were removed with forceps from the growth plate to the wash plate to challenge plate, flaming in between or where needed. Once disks are in challenge plate, incubated for 24 hours on shaker at 37° C. On day six, dilution plates were prepared with 180 μL/well deionized water for every compound tested (for 1:10 dilution, 20 μL of sonicate was added and 20 μL was carried down the plate). A 96-well sonication plate was prepared with 200 μL/well of recovery media. 24-well wash plates were prepared with 500 μL/well of 0.9% saline. The disks were moved from the challenge plate to the wash plate(s) to the sonication plate with forceps, with flaming in between or where needed. The, the plate was sonicated for 30 minutes at a temperature no higher than 40° C. 20 μL was transferred from each dilution series to the dilution plate and diluted down 1:10. Plate two of 5 μL sample to TSA and incubated overnight. On day seven, the colonies were counted.

Example 9
In Vitro Metabolic Stability of Compounds—Blood Plasma

Pooled plasma samples from human (mixed gender), rat (mixed breed and gender) and dog (mixed breed and gender) are incubated with the compounds (5 μM) at 37° C. for 0 and 60 minutes (duplicate samples). Incubations are terminated by addition of ice-cold precipitation solvent (acetonitrile: glacial acetic acid, 9:1 v/v). Supernatants are diluted with equal volume of 0.1% formic acid and analyzed by HPLC-MS/MS. Plasma stability is reported as % parent compound at 60 minutes relative to amount of parent at 0 minutes.

Example 10
Efficacy of Compounds in the Mouse Thigh Burden Model

Female 6-7-week old CD-1 mice are made neutropenic with cyclophosphamide (150 mg/kg, i.p.) on days 4 and 1 before i.m. inoculation with S. aureus (ATCC 13709). S. aureus inoculum is prepared by transferring colonies from 18-20-hour tryptic soy agar (TSA) cultures to sterile PBS. The density is adjusted to approximately 10⁶cfu/mL with the aid of a spectrophotometer, and the inoculum concentration is determined by the dilution plate count method. Mice are inoculated by injecting each posterior thigh with 0.1 mL of inoculum. The compounds are given to separate groups of mice (4 females/group) by i.v. bolus doses of 1 or 2 mg/kg/dose at 1 and 5, 1 and 9, or 1 and 13 hours post inoculation. A separate control group of mice receive the inoculum without antibiotic treatment. The compounds are dissolved 50%/50% v/v sterile USP purified water/PBS. Thighs are harvested at 25 hours after inoculation. Thigh muscle and bone tissue are homogenized, aliquots of serial dilutions are plated on TSA and incubated at 37° C. for 20 hours, and colony counts are obtained to calculate cfu/thigh.

Example 11
Efficacy vs. Vancomycin in The Rat Thigh Burden Model

For each experiment, female 8-9-week old femoral vein cannulated Crl:CD(SD) rats are made neutropenic with cyclophosphamide (150 mg/kg, i.p.) on days 4 and 1 before i.m. inoculation with S. aureus (ATCC 13507). A suspension of S. aureus is prepared from colonies obtained from an overnight culture, placed in PBS, and adjusted to approximately 10⁷cfu/mL with the aid of a spectrophotometer. Each rat is injected with 0.2 mL of inoculum into the thigh muscle of the right hind leg. Thighs are harvested at 25 hours after inoculation and processed to determine cfu/thigh. The compounds are given by i.v. bolus injection into a tail vein or 1-hour i.v. infusion, or 4-hour i.v. infusion via the femoral vein cannulae at different time intervals following inoculation. Separate inoculation control groups are included in each experiment, and vancomycin groups are included as comparative agents in the first and second experiments. Each group, including the controls and comparative agent, consists of 4 or more rats.

Example 12
Efficacy of Compounds in Mouse Sepsis Model: S. aureus Infection

Sterile saline, vancomycin, or the compounds are administered to separate groups of 8-week old female CD-1 mice (8 mice/group) 1 and 7 hours after i.p. injections of S. aureus (ATCC 13709, 5×10⁷cfu/mL in 5% mucin, 0.5 mL/mouse). The compounds were dissolved in 50%/50% v/v sterile USP purified water/TBS. A suspension of S. aureus is prepared from colonies transferred from the TSA plate to sterile PBS. An aliquot of the stock suspension is added to 5% mucin for a final concentration of about 5×10⁷cfu/mL. The mice are observed for 6 days following inoculation for mortality.

Example 13
Acute Toxicity Studies—Maximum Tolerated Doses

Maximum tolerated dose (MTD) determinations are made in ascending/descending dose studies in mice and rats. The compounds are administered by either i.v. bolus injection in the tail vein of mice and rats or by i.v. infusion via catheter in the femoral vein of rats. At each dose, two to three animals are administered compound and clinical signs are recorded over a 4 to 7 day period. Gross necropsy is performed at the conclusion of the study.

Example 14
Pharmacokinetics of Compounds in Rats

Crl:CD (SD) rats are administered compounds by i.v. bolus injection at the indicated dosages. Plasma is prepared from blood samples taken at 9 time points (n=3) over 28 hours. Compound levels are determined by HPLC-MS/MS. All animals are fitted with two jugular vein cannula (JVC), one each for dose administration and blood collection. Each route of administration is dosed as N=3. Animals are supplied with a commercial rodent diet and water ad libitum. Each rat receives a bolus dosed via the appropriate route of administration at time zero on the day of dosing.

Each blood sample is collected from the rats via a JVC and placed into chilled polypropylene tubes containing sodium EDTA as an anticoagulant. Samples are centrifuged at a temperature of 4° C. and at a speed of 13,000 rpm for 5 minutes. Samples are maintained chilled throughout processing. Each plasma sample is then transferred into labeled polypropylene tubes, placed on dry ice, and stored in a freezer set to maintain −60° C. to −80° C.

Plasma study samples are extracted and analyzed using a previously developed method. A single standard curve and six replicates of quality control samples at three concentrations are extracted using DMSO containing 0.1% formic acid. Plasma samples (50 μL) are added to 150 μL solvent and centrifuged. Supernatants are analyzed by LC/MSMS using a Perkin Elmer series 200 micropump and PE Sciex API4000 Electrospray mass spectrometer. Standard curves are prepared at concentrations of 10000, 5000, 1000, 500, 250, 100, 50 and 25 ng/mL. Quality control samples are prepared at concentrations of 5000, 500, and 50 ng/mL. The standard curve and quality control samples are prepared from independently prepared stock solutions. At least 5/8 of standards must have accuracy within ±15%, except at the LLOQ where ±20% is acceptable. Two thirds of the batch QCs must have accuracy within ±15% of nominal, and at least one QC must pass at each level in order for the run to be accepted.

Individual plasma concentration versus time data for the compounds is subjected to non-compartmental analysis using the pharmacokinetic program WinNonlin v4.1. Plasma concentrations below the limit of quantitation (25 ng/mL) are assigned a value of zero for pharmacokinetic analysis. Nominal dosing concentrations are used in all calculations.

Example 15
Ker-1

One purpose of the following experiments is to compare the efficacy of one or more compounds and vancomycin in the treatment of a fluoroquinolone-resistant, methicillin-resistant Staphylococcus aureus infection in the NZW rabbit keratitis model with or without intact corneal epithelia.

The next morning, the MRSA strain is suspended in sterile trypticase soy broth to a 0.5 McFarland Standard, containing approximately 5×10⁸cfu/mL of bacteria. The absorbance of the suspension is measured at 650 nm using a Beckman DU-70 spectrophotometer. OD readings of 0.07 corresponded to 5×10⁸cfu/mL of bacteria. This concentration is appropriately diluted in sterile trypticase soy broth to provide the inoculum of approximately 1,000 (1.0×10³) cfu/eye in 25 μl. Colony counts are performed on the inoculum to determine the actual cfu inoculated. Following general anesthesia with ketamine and xylazine and topical anesthesia with proparacaine and prior to bacterial inoculation in the left eyes, 6 mm areas of the corneal epithelia is removed centrally with an Amoils epithelial scrubber. Nothing is done to the right eyes. The 15 rabbits are then inoculated intrastromally in both eyes with 25 μl of the bacterial dilution of approximately 10³cfu/eye of the bacteria. The bacterial inoculation of the left eyes is directly under the epithelial defect created by the Amoils epithelial scrubber. The epithelia are removed in the left corneas in order to determine whether this layer of the cornea is a barrier for compound penetration when compared to the right cornea with an intact epithelium. A colony count is performed on the inoculum to determine the actual cfu inoculated. The rabbits are immediately treated with analgesia in the form of and intramuscular injection of ketoprofen, 1.5 mg/kg. After 4 hours, the 15 rabbits are divided into 4 treatment groups and one untreated control group sacrificed at the onset of therapy. Both eyes of each rabbit of the treatment groups are treated with one 37 μl drop of the coded solutions or control Saline or 1 drop of vancomycin from its dropper bottle. The compound concentrations are masked and labeled appropriately. The masked concentrations are appropriately labeled but the specific concentrations of solutions are not known to the lab workers who carried out the experiment. The vancomycin and control (Tris-Buffered Saline) are not masked.

Groups:

Rx -

Rabbit

Group
Left Eye
Right Eye
Both Eyes
Treatment Regimen
#

I
Abraded
Intact
Compound
Every 15 minutes for 5
1-3

Epithelium
Epithelium

hours (21 total doses)

II
Abraded
Intact
Compound
Every 15 minutes for 5
4-6

Epithelium
Epithelium

hours (21 total doses)

III
Abraded
Intact
Vancomycin
Every 15 minutes for 5
7-9

Epithelium
Epithelium
(50 mg/mL)
hours (21 total doses)

(Van)

IV
Abraded
Intact
Tris-Buffered
Every 15 minutes for 5
10-12

Epithelium
Epithelium
Saline (Con)
hours (21 total doses)

V
Abraded
Intact
Sacrifice at
None
13-15

Epithelium
Epithelium
Onset of

Therapy

(4 hours PI)

(ONSET)

Treatment is scheduled for every 15 minutes for 5 hours (21 total doses). The 3 rabbits in group V are sacrificed 4 hours PI and large 9.5 mm buttons are removed from the corneas. These are placed in 1 mL of PBS and kept on ice. The corneal buttons are homogenized for 25 seconds on ice using the motorized homogenizer. After homogenization, colony counts are done on the homogenates using 5% sheep blood agar plates to determine the amount of bacteria contained in the corneas at the onset of therapy. Following the completion of therapy, the eyes are examined for clinical signs of infection. One hour after the final treatment, the treated rabbits (Groups I-IV) are sacrificed and large 9.5 mm buttons are removed from the corneas. These are placed in 1 mL of PBS and kept on ice. The corneal buttons are homogenized for 25 seconds on ice using the motorized homogenizer. After homogenization, colony counts are performed on the homogenates using 5% sheep blood agar plates to determine the amount of bacteria contained in the corneas after treatment. The next morning, the plates are counted and the number of cfu/eye of Staphylococcus aureus was determined for each cornea.

Formulations: 1) the compounds, on the day of treatment, are dissolved in 5 mL of Tris-Buffered Saline (TBS) before use. The solution is stored at room temperature during the 5 hours of use. 37 μl drops are instilled using a Rainin EDP electronic pipet set in the multi-dispense mode. 2) 5% Vancomycin (50 mg/mL): Vancomycin (50 mg/mL) eye drops is purchased from the UPMC pharmacy as the fortified preparation used in patients. Vancomycin is administered using is supplied dropper bottle. 3) Control (Tris-Buffered Saline): 37 μl drops are instilled using a Rainin EDP electronic pipet set in the multi-dispense mode.

Example 16
Ker-2

One purpose of the following experiments is to compare the efficacy of 0.25% Compound, with and without 0.005% benzalkonium chloride, and 5% vancomycin in the treatment of a fluoroquinolone-resistant, methicillin-resistant Staphylococcus aureus infection in the NZW rabbit keratitis model with or without intact corneal epithelia. The 0.005% benzalkonium chloride is added to try to increase the penetration of 0.25% Compound through the corneal epithelium.

Fifteen rabbits are used from Myrtles' Rabbitry, Thompson Station, Tenn. The clinical isolate of fluoroquinolone-resistant, methicillin-resistant (MRSA) Staphylococcus aureus (K950) is subcultured on 5% sheep blood agar and incubated at 37° C. in 6% CO₂overnight. The next morning, the MRSA strain is suspended in sterile trypticase soy broth to a 0.5 McFarland Standard, containing approximately 5×10⁸cfu/mL of bacteria. The absorbance of the suspension is measured at 650 nm using a Beckman DU-70 spectrophotometer. OD readings of 0.07 corresponded to 5×10⁸cfu/mL of bacteria. This concentration is appropriately diluted in sterile trypticase soy broth to provide the inoculum of approximately 1,000 (1.0×10³) cfu/eye in 25 μl. Colony counts are performed on the inoculum to determine the actual cfu inoculated. Following general anesthesia with ketamine and xylazine and topical anesthesia with proparacaine and prior to bacterial inoculation in the left eyes, 6 mm areas of the corneal epithelia is removed centrally with an Amoils epithelial scrubber. Nothing is done to the right eyes. The 15 rabbits are then inoculated intrastromally in both eyes with 25 μl of the bacterial dilution of approximately 10³cfu/eye of the bacteria. The bacterial inoculation of the left eyes is directly under the epithelial defect created by the Amoils epithelial scrubber. The epithelia are removed in the left corneas in order to determine whether this layer of the cornea is a barrier for the Compound penetration when compared to the right cornea with an intact epithelium. A colony count is performed on the inoculum to determine the actual cfu inoculated. The rabbits are immediately treated with analgesia in the form of and intramuscular injection of ketoprofen, 1.5 mg/kg. After 4 hours, the 15 rabbits are divided into 4 treatment groups and one untreated control group sacrificed at the onset of therapy. Both eyes of each rabbit of the treatment groups are treated with one 37 μl drop of the solutions or control Saline or 1 drop of vancomycin from its dropper bottle.

Groups:

Rx -

Rabbit

Group
Left Eye
Right Eye
Both Eyes
Treatment Regimen
#

I
Abraded
Intact
0.25% Compound
Every 15 minutes for 5
1-3

Epithelium
Epithelium

hours (21 total doses)

II
Abraded
Intact
0.25% Compound
Every 15 minutes for 5
4-6

Epithelium
Epithelium
with 0.005% BAK
hours (21 total doses)

III
Abraded
Intact
Vancomycin
Every 15 minutes for 5
7-9

Epithelium
Epithelium
(50 mg/mL)
hours (21 total doses)

(Van)

IV
Abraded
Intact
Tris-Buffered
Every 15 minutes for 5
10-12

Epithelium
Epithelium
Saline (Con)
hours (21 total doses)

V
Abraded
Intact
Sacrifice at
None
13-15

Epithelium
Epithelium
Onset of

Therapy

(4 hours PI)

(ONSET)

Formulations: 1) 0.25% Compound, on the day of treatment, is dissolved in 6.04 mL of Tris-Buffered Saline (TBS) to yield 0.25% Compound. The solution is stored at room temperature during the 5 hours of use. 37 μl drops are instilled using a Rainin EDP electronic pipet set in the multi-dispense mode. 2) 0.25% Compound with 0.005% Benzalkonium Chloride (BAK), on the day of treatment, is dissolved in 6.288 mL of Tris-Buffered Saline (TBS) before use. Then, 0.032 mL (32 μL) of 1% Benzalkonium Chloride is added to the solution to yield a total volume of 6.32 mL of 0.25% Compound. The solution is stored at room temperature during the 5 hours of use. 37 μl drops are instilled using a Rainin EDP electronic pipet set in the multi-dispense mode. This solution is designated PMX-B. 3) 5% Vancomycin (50 mg/mL): Vancomycin (50 mg/mL) eye drops are purchased from the UPMC pharmacy as the fortified preparation used in patients. Vancomycin is administered using a supplied dropper bottle. 4) Control (Tris-Buffered Saline): 37 μl drops of Tris-Buffered Saline are instilled using a Rainin EDP electronic pipet set in the multi-dispense mode.

Example 17
Ker-3

One purpose of the following experiments is to determine the efficacy of 0.25% Compound, with and without 200 μM Farnesol, and 200 μM Farnesol in the treatment of a fluoroquinolone-resistant and methicillin-resistant Staphylococcus aureus infection in the NZW rabbit keratitis model with or without intact corneal epithelia. The 200 μM Farnesol is added to try to increase the efficacy and penetration of 0.25% compound through the corneal epithelium.

Fifteen rabbits are used from Myrtles' Rabbitry, Thompson Station, Tenn. The clinical isolate of fluoroquinolone-resistant and methicillin-resistant (MRSA) Staphylococcus aureus (K950) is subcultured on 5% sheep blood agar and incubated at 37° C. in 6% CO₂overnight. The next morning, the MRSA strain is suspended in sterile trypticase soy broth to a 0.5 McFarland Standard, containing approximately 5×10⁸CFU/mL of bacteria. The absorbance of the suspension is measured at 650 nm using a Beckman DU-70 spectrophotometer. OD readings of 0.07 corresponded to 5×10^sCFU/mL of bacteria. This concentration is appropriately diluted in sterile trypticase soy broth to provide the inoculum of approximately 1,000 (1.0×10³) CFU/eye in 25 μl. Colony counts are performed on the inoculum to determine the actual CFU inoculated. Following general anesthesia with ketamine and xylazine and topical anesthesia with proparacaine and prior to bacterial inoculation in the left eyes, 6 mm areas of the corneal epithelia are removed centrally from the left eyes with an Amoils epithelial scrubber. Nothing is done to the right eyes. The 15 rabbits are then inoculated intrastromally in both eyes with 25 μl of the bacterial dilution of approximately 10³cfu/eye of the bacteria. The bacterial inoculation of the left eyes is directly under the epithelial defect created by the Amoils epithelial scrubber. The epithelia are removed in the left corneas in order to determine whether this layer of the cornea is a barrier for drug penetration when compared to the right cornea with an intact epithelium. A colony count is performed on the inoculum to determine the actual CFU inoculated. The rabbits are immediately treated with analgesia in the form of an intramuscular injection of ketoprofen, 1.5 mg/kg. After 4 hours, the 15 rabbits are divided into 4 treatment groups and one untreated control group sacrificed at the onset of therapy. Both eyes of each rabbit of the treatment groups are treated with one 37 μl drop of the solutions or control Saline.

Groups:

Rx -

Rabbit

Group
Left Eye
Right Eye
Both Eyes
Treatment Regimen
#

I
Abraded
Intact
0.25% Compound
Every 15 minutes for 5
1-3

Epithelium
Epithelium

hours (21 total doses)

II
Abraded
Intact
0.25% Compound +
Every 15 minutes for 5
4-6

Epithelium
Epithelium
200 μM Farnesol
hours (21 total doses)

(P + F)

III
Abraded
Intact
200 nM Farnesol
Every 15 minutes for 5
7-9

Epithelium
Epithelium
(FARN)
hours (21 total doses)

IV
Abraded
Intact
Tris-Buffered
Every 15 minutes for 5
10-12

Epithelium
Epithelium
Saline (CON)
hours (21 total doses)

V
Abraded
Intact
Sacrifice at
None
13-15

Epithelium
Epithelium
Onset of

Therapy

(4 hours PI)

(ONSET)

Treatment is scheduled for every 15 minutes for 5 hours (21 total doses). The 3 rabbits in group V are sacrificed 4 hours PI and large 9.5 mm buttons are removed from the corneas. These are placed in 1 mL of PBS and kept on ice. The corneal buttons are homogenized for 25 seconds on ice using the motorized homogenizer. After homogenization, colony counts are done on the homogenates using 5% sheep blood agar plates to determine the amount of bacteria contained in the corneas at the onset of therapy. Following the completion of therapy, the eyes are examined for clinical signs of infection. One hour after the final treatment, the treated rabbits (Groups I-IV) are sacrificed and large 9.5 mm buttons are removed from the corneas. These are placed in 1 mL of PBS and kept on ice. The corneal buttons are homogenized for 25 seconds on ice using the motorized homogenizer. After homogenization, colony counts are done on the homogenates using 5% sheep blood agar plates to determine the amount of bacteria contained in the corneas after treatment. The next morning, the plates are counted and the number of CFU/eye of Staphylococcus aureus is determined for each cornea.

Formulations: 1) 0.25% Compound powder is stored at 4° C. until use. Upon use, the tube is removed from the refrigerator and 3.28 mL of S1 (sterile water for injection) is added and vortexed until the solid is completely dissolved. Then 3.28 mL of S2 (2×TBS) is added and vortexed for 10 seconds. 37 μl drops are instilled using a Rainin EDP electronic pipet set in the multi-dispense mode; 2) 0.25% Compound with 200 μM Farnesol (P+F): Tube G2 of Compound powder is stored at 4° C. until use. Upon use, the tube is removed from the refrigerator and 3.33 mL of S1 (sterile water for injection) is added and vortexed until the solid is completely dissolved. Then 3.33 mL of S3 (400 μM Framesol+2% Propylene Glycol in 2×TBS) is added and vortexed for 10 seconds. 37 μl drops are instilled using a Rainin EDP electronic pipet set in the multi-dispense mode; 3) 200 μM Framesol (FARN): Tube G3 containing about 8 mL of 200 μM Framesol in 1% Propylene Glycol (PG) and TBS is stored at 4° C. until use. 37 μl drops are instilled using a Rainin EDP electronic pipet set in the multi-dispense mode; 4) Control (Tris-Buffered Saline, CON): Tube G4 containing about 8 mL of Tris-Buffered Saline (10 mM TRIS, 150 mM NaCl, pH=7.4) is stored at 4° C. until use. 37 μl drops are instilled using a Rainin EDP electronic pipet set in the multi-dispense mode.

Example 18
Bacterial Strains and Culture

Aggregatibacter actinomycetemcomitans 1005 (Aa) (obtained from Dr. Helen Schreiner, New Jersey Dental School) are cultured on TSB agar (4% trypticase soy broth, 0.6% yeast extract, 0.8% dextrose, 0.4% NaHCO₃, 75 μg/mL bactracin, 5 μg/mL vancomycin) at 37° C., 10% CO₂. Single colonies are inoculated to TSB broth in 75-cm²tissue culture flasks. Biofilm is harvest upon the 90% confluence and resuspended into 1 mL PBS. Resuspension is vortexed vigorously for 1 minute and allowed to settle for 10 minutes. The supernatant is then diluted to 2.5×10⁷before seeded to 96-well plates to obtain even biofilms. Porphyromonas gingivalis W381 (obtained from Dr. Christopher Cutler, Stony Brook University Dental School) are cultured on TSB-blood agar (3% trypticase soy broth, 5% defibrinated sheep blood, 5 μg/mL hemin, 0.5 μg/mL menadione, and 0.2 mg/mL KNO₃) in an anaerobic chamber (80% N₂, 10% H₂, and 10% CO₂) at 37° C. For biofilm formation, the same protocol as Aa under anaerobic condition was used.

Example 19
Antimicrobial Assays

Aa biofilms are cultured into 96-well plates (tissue culture treated, Falcon) for 18 hours. Serial dilutions of the mimetic compounds are made in 100 μL RPMI-1640 without Phenol red and added directly to the wells. Plates are cultured at 37° C., 10% CO₂for 24 hours. Medium is removed, and cell viability is evaluated by XTT assay using the In Vitro Toxicology Assay Kit (Sigma) according to the manufacturer's protocol. Metabolic activity is measured by reading in a plate-reader at 450 nm. To determine cell viability by plating, the wells are scraped and resuspended in growth medium, and plated onto TSB agar. Colonies are counted after 72 hours. All assays are performed in duplicate.

Example 20
Cell Culture and Stimulation

The oral keratinocyte cell line OKF6/TERT (obtained from Dr. James Rhinewald, Harvard University) is cultured in Keratinocyte growth medium (Lonza) with hEGF, BPE (Bovine Pituitary Extract). Cells are subcultured in 6-well dishes 18 hours before stimulation. Cells are treated with 2 μg/mL, 5 μg/mL mPE with and without IL-1β stimulation (100 ng/mL, 24 hours) for 2 hours, 4 hours and 18 hours. THP-1 cells are grown in suspension at RPMI 1640 with 10% FBS, and stimulated similarly.

Example 21
Ophthalmic Ointment Formulation

The following represents an example of a typical ophthalmic ointment formulation comprising an antimicrobial compound.

Ophthalmic Ointment

Ingredient
Amount (weight %)

Compound
0.35

Mineral Oil, USP
2.0

White petrolatum, USP
q.s. 100

Example 22
Ophthalmic Ointment Formulation

The following represents an example of a typical ophthalmic ointment formulation comprising an antimicrobial compound and an anti-inflammatory agent.

Ophthalmic Ointment

Ingredient
Amount (weight %)

Compound
0.3

Dexamethasone
0.1

Chlorobutanol, Anhydrous, NF
0.5

Mineral Oil, USP
5.0

White petrolatum, USP
q.s. 100

Example 23
Ophthalmic/Otic Solution Formulation

The following represents an example of a typical ophthalmic/otic solution formulation comprising an antimicrobial compound.

Ophthalmic/Otic Solution

Ingredient
Amount (weight %)

Compound
0.35

Sodium Acetate
0.3

Acetic Acid
0.04

Mannitol
4.60

EDTA
0.05

Benzalkonium chloride
0.006

Water
q.s. 100

Example 24
Ophthalmic/Otic Suspension Formulation

The following represents an example of a typical ophthalmic/otic suspension formulation comprising an antimicrobial compound and an anti-inflammatory agent (dexamethasone).

Ophthalmic/Otic Suspension

Ingredient
Amount (weight %)

Compound
0.3

Dexamethasone, micronized USP
0.10

Benzalkonium chloride
0.01

Edetate Disodium USP
0.01

Sodium chloride USP
0.3

Sodium sulfate USP
1.2

Tyloxapol USP
0.05

Hydroxyethylcellulose
0.25

Sulfuric Acid and/or
q.s. for pH adjustment to 7.0-8.0

Sodium hydroxide, NF

Purified sterilized water
q.s. to 100

Example 25
Toxicity

The ocular toxicity of several concentrations of Compound, using the Draize ocular toxicity scoring system, in the NZW rabbit ocular toxicity model is carried out.

Nine rabbits are used from Myrtles' Rabbitry, Thompson Station, Tenn. and are subsequently divided into 5 groups:

Compound
N
N
Rabbit

Group
Concentration
Rabbits
Eyes
Numbers

I
1% Compound
2
4
1-2

II
0.25% Compound
2
4
3-4

III
0.1% Compound
2
4
5-6

IV
0.01% Compound
2
4
7-8

V
Tris-Buffered Saline
1
2
9

Rabbits are treated in both eyes with (37 μl) topical drops every 30 minutes for 3 hours (7 total doses). One rabbit is treated with Tris-Buffered Saline and serves as a negative control. Rabbits are evaluated in a masked fashion for ocular toxicity by an ophthalmologist with specialty training in corneal and external disease. Ocular toxicity is evaluated using the Draize scoring system after treatment on Day 0 and on Day 3 post treatment for any delayed toxicity (Draize et al., J. Pharmacol. Exp. Ther., 1944, 82, 377-390).

Formulations: 1) 1% Compound: 31.36 mg of Compound in powder form is stored at −20° C. until use. The vial containing Compound is removed from the freezer and 3.126 mL of Tris-Buffered Saline (TBS) is added to the vial to yield 3.126 mL of 1% (10 mg/mL) Compound; 2) 0.25% Compound: 0.5 mL of 1% Compound is added to 1.5 mL of TBS to yield 2 mL of 0.25% Compound; 3) 0.1% Compound: 0.2 mL of 1% Compound is added to 1.8 mL of TBS to yield 2 mL of 0.1% Compound; 4) 0.01% Compound: 0.2 mL of 0.1% Compound is added to 1.8 mL of TBS to yield 2 mL of 0.01% Compound; and 5) Tris-Buffered Saline: 25 mL of Tris-Buffered Saline (10 mM TRIS, 150 mM NaCl, pH=7.4) is filter sterilized prior to use in preparation of the above samples and use in rabbits.

A brief summary of the Draize scoring system for ocular lesions is provided below

1. Cornea

A. Opacity-degree of density (area most dense taken for reading)

No Opacity
0

Scattered or diffuse area, details of iris clearly visible
1

Easily discernible translucent areas, details of iris slightly obscured
2

Opalescent areas, no details of iris visible, size of pupil barely discernible
3

Opaque, iris invisible
4

B. Area of cornea involved

One quarter (or less) but not zero
1

Greater than one quarter, but less than half
2

Greater than half. but less than three quarters
3

Greater than three quarters, up to whole area
4

A × B × 5
Total Maximum = 80

2. Iris

A Values

Normal
0

Folds above normal, congestion, swelling, circumcorneal injection (any or all of

these or combination of any thereof) iris still reacting to light (sluggish reaction is

positive)
1

No reaction to light, hemorrhage, gross destruction (any or all of these)
2

A × 5
Total Maximum = 10

3. Conjunctivae

A. Redness (refers to palpebral and bulbar conjunctivas excluding cornea and iris)

Vessels normal
0

Vessels definitely injected above normal
1

More diffuse, deeper crimson red, individual vessels not easily discernible
2

Diffuse beefy red
3

B. Chemosis

No swelling
0

Any swelling above normal (includes nictitating membrane)
1

Obvious swelling with partial eversion of lids
2

Swelling with lids about half-closed
3

Swelling with lids about half-closed to completely closed
4

C. Discharge

No discharge
0

Any amount different from normal (does not include small amounts observed in

inner canthus of normal animals)
1

Discharge with moistening of the lids and hairs just adjacent to lids
2

Discharge with moistening of the lids and hairs, and considerable area around

the eye
3

Score (A + B + C) × 2
Total Maximum = 20

Total Maximum Score: 110 represents the sum of all scores obtained for the cornea, iris and

conjunctivae.

Classification of Eye Irritation Scores:

MMTS
Classification
Symbol

0.0-0.5
Non-Irritating
N

0.6-2.5
Practically Non-Irritating
PN

2.6-15.0
Minimally Irritating
M1

15.1-25.0
Mildly Irritating
M2

25.1-50.0
Moderately Irritating
M3

50.1-80.0
Severely Irritating
S

80.1-100.0
Extremely Irritating
E

100.1-110.0
Maximally Irritating
mx

MMTS = Maximum Mean Total Score (The mean total score per group)

Kay et al, J. Soc. Cos. Chem., 1962, 13, 281-289.

Example 26
Anti-Protozoan Activity Vs a Malarial Parasite

Compounds are screened in vitro against the malarial agent Plasmodium falciparum. P. falciparum is a protozoan parasite and is the infectious agent for the most prevalent and deadly forms of malaria. Anti-parasitic activities are measured in vitro using a human red blood cell assay. Active compounds are tested further to determine IC₅₀and IC₁₀₀values, or minimum concentrations resulting in 50% and 100% killing, respectively. Observations are also made during the 48 hour incubation period to assess the susceptibility of the parasite during lifecycle stages inside and outside the host erythrocyte. One goal of targeting parasite membranes, rather than proteins or metabolic pathways, represents a highly innovative and novel strategy for treating parasitic diseases and distinguishes this approach from most others in this field. Compounds are examined for disruption of food vacuoles as assayed by parasites expressing a marker for the food vacuole (plasmepsin II-YFP), with food vacuole integrity measured by standard fluorescence microscopy. In some embodiments, compounds 106 and 107 are screened in cultures of P. falciparum 3D7 and DD2 and compared to chloroquine. Flow cytometry is used for quantitation of parasitemia using SYOX Green on an LSRII.

Example 27
Anti-Malarial Activity

Numerous compounds are initially screened using a high throughput quantitative parasite growth assay that makes use of a strain of parasites expressing a cytoplasmic firefly luciferase (obtained from Dr. Kirk Deitsch, Cornell Medical College). These parasites are transfected with a vector containing the firefly luciferase gene using the malarial HRPII promoter. To grow parasites, culture dishes ranging from 96 well plates to 30 mL dishes are used. The 3D7 strain of P. falciparum for assays and transfections is primarily used because it has become the standard chloroquine sensitive reference strain and is used for the genome sequencing project. Parasites are cultured in human RBCs under an atmosphere of 5% O₂/7% CO₂/88% N₂in RPMI 1640 medium supplemented with 25 mM Hepes, 30 mg/L hypoxanthine, 0.225% (w/v) NaHCO₃and 0.5% (w/v) Albumax II (Life Technologies, Grand Island, N.Y.). Parasite growth is normally synchronized by a combination of serial D-sorbitol treatment for selection of ring stage parasites followed by selective purification of mature schizonts using a Super Macs II magnetic separator (Miltenyi Biotec).

A standard luminescent readout is used to measure the growth of parasites. Parasites are grown under normal conditions, lysed in the presence of the luminescence reagents (Bright Glo, Promega) and then measured. To initially test for growth, luciferase expressing parasites are synchronized using serial sorbitol treatments and then parasitemia, the percentage of RBCS infected with parasites, is adjusted using uninfected RBCs. 100 μl of total media is used in a 96 well format. Parasitized RBCs are incubated in 96 well plates at 37° C. and gassed with 5% CO₂, 5% O₂, 90% N₂. Parasites are allowed to grow for approximately 60 hours, until they successfully divide, rupture and reinvade new RBCs. At 10-15 hours post invasion, the cells are lysed, and luciferase levels are measured using an Analyst HT luminometer (Molecular Devices).

Example 28
Anti-Candida Activity

Anti-Candida activity is measured using the following protocol: To prepare RPMI/MOPS media, 8.4 g RPMI 1640, 34.52 g MOPS buffer and 2 g glucose are mixed and/or dissolved in 900 mL water, adjusted to pH 6.3 (using about 4 pellets of NaOH). The mixture is brought to 1 L and filter sterilized. FDGlu is suspended in 380 μL DMSO to make a 20 mM stock. A fresh plate of yeast is streaked onto a YPD plate and grown at 37° C. (35° C. would be optimal). Test compound(s) are diluted to 200 μg/mL in RPMI/MOPS (1:50, 4.8 μL of 10 mg/mL in 240 μL media). Ten 1:2 serial dilutions are prepared with RPMI/MOPS in a 96-well round bottom plate (120 μL/120 μL 2× dilutions). Column 12 has no compound. Fifty μL of compound dilutions is pipetted into a sterile TC-treated 96-well flat-bottom, black-sided polypropylene plate (in duplicate). One colony of yeast is resuspended in 5 mL PBS. OD₆₀₀is measured. Yeast (1 OD) is diluted 1:1000 in RPMI/MOPS supplemented with 20 μM FDGlu (for 1 plate 5 mL RPMI/MOPS, 5 μL FDGLu, 5 μL OD=1 yeast (i.e if OD=0.5 add 10 μL). Fifty L of diluted yeast is aliquoted to plates containing 50 μL of compound to all wells except 12E-H. Controls: 12 A-D cells, no compound. 12 E-H no cells, no compound; add 50 μL of RPMI/MOPS+20 μM FDGlu. The plate is mixed gently by hand and placed in ziplok bag in 37° C. incubator. The OD₆₀₀is read and fluorescence (485/530) at 24 and 48 hours.

Example 29
Susceptibility Assays versus M. tuberculosis (H37Rv Strain) and Cytotoxicity Assays versus Monkey VERO Cells

To evaluate the effects of compounds on inhibiting the growth of a M. tuberculosis species, susceptibility assays of some compounds on M. tuberculosis (H37Rv strain) and cytotoxicity assays of some compounds on monkey VERO cells are performed.

The antimicrobial screen is conducted against the H37Rv strain of M. tuberculosis in BACTEC 12B medium using the Microplate Alamar Blue Assay (MABA) (see, e.g., Collins et al., Antimicrobial Agents and Chemotherapy, 1997, 41 (5), 1004-1009). Compounds are tested in ten 2-fold dilutions to determine IC₉₀values (an IC₉₀value is defined as the concentration effecting a reduction in fluorescence of 90% relative to controls). Viability in the VERO cell cytotoxicity assay is measured after a 72 hour exposure using a luminescent cell viability assay that determines the number of viable cells based on quantitation of ATP. Cytotoxicity is determined using a curve fitting program to calculate EC₅₀values. An SI (Selectivity Index) value is calculated by dividing the EC₅₀by the IC₉₀.

Example 30
Clotting and Amidolytic Assays

aPTT Clotting Assay:

Unfractionated heparin is mixed with plasma at a final concentration of 0.4 U/mL (or concentration which increases aPTT time to between 120 and 300 seconds). Different concentrations of test compound are added (typically 0.15 to 20 μg/mL range). The ACL Elite Hemostasis analyzer (Beckman Coulter™) is used to add aPTT reagent (HemosIL SynthASil) to supplemented plasma. Clotting is initiated by addition of CaCl₂and time to clot is recorded. EC₅₀values are determined using a curve fit program (GraphPad Prism 5).

FXa Amidolytic Assay:

LMWH (enoxaparin or tinzaparin) at final concentrations of 0.1 μg/mL, UFH at final concentrations of 0.03 units/mL, or fondaparinux at a final concentration of 0.02 μg/mL (or concentration which fully inhibits factor Xa) is combined with human antithrombin at a final concentration of 0.036 units/mL. Two μL of test agent are added (range between 0.01 and 23 μg/mL) and incubated for 5 minutes at 23° C. Bovine Factor Xa was added to a final concentration of 0.636 nkat/mL and incubated for a further 10 minutes at 23° C. Using a SpectraMax 250 (Molecular Devices, Inc.) and SoftMax Pro V.5 software, the plate is read every 30 seconds for 4 minutes, with a 10 second shaking before first read and maximum interval shaking. Fit curve to report an EC₅₀(50% reversal of anticoagulant effects) value for each compound: P(C_p)=1/[1+(K/C_p)ⁿ].

Example 31
In Vivo Neutralization of Unfractionated Heparain in the Rat

The male Sprague-Dawley are obtained from Charles River Laboratories, Raleigh. They are nine-weeks-old at the start of the study and their weights range from 279-334 g. Rats are pre-treated with UFH administered by IV injection in a tail vein at 100 U/kg in a dose volume of 1 mL/kg. The rats are then treated with a single IV injection of saline, protamine or the appropriate test compound at doses of 0.25, 0.5 and 1.0 mg/kg. All treatments are dosed in a volume of 1 mL/kg. Blood is collected via the orbital sinus from three rats per group at the following time points after treatment: predose, 1, 3, 10, 30 and 60. At each time point, 1 mL of blood is collected from each animal into a single tube. The blood is analyzed using an AMEX Destiny Plus Coagulation Analyzer for activated partial thromboplastintime (APTT) and anti-Factor Xa.

Example 32
In Vivo Neutralization of Enoxaparin in the Rat

Compounds are tested for their ability to neutralize enoxaparin coagulation inhibition in rats. Male Sprague-Dawley rats are used in this study (Charles River Laboratories). They are ten-weeks-old at the start of the study and their weights range from 319-362 g. Enoxaparin (2 mg/kg) is administered by IV injection to groups of six rats. After 3 min, saline, protamine or a test compound is administered by IV injection. Blood is collected before dosing with enoxaparin, and at 1, 3, 10, 30 and 60 min after dosing with the standard and test compounds. All treatments are dosed in a volume of 1 mL/kg. Blood is collected via the orbital sinus from three rats per group. At each time point, 1 mL of blood is collected from each animal into a single tube. The blood is analyzed using an AMEX Destiny Plus Coagulation Analyzer for activated partial thromboplastin time (APTT) and anti-Factor Xa (low-molecular weight).

Example 33
Normalization of Enoxaparin-Extended Bleeding Times in a Rat Tail Transection Model

Studies are performed to examine effects on extended bleeding times caused by enoxaparin treatment. Male Sprague Dawley rats (Charles River) are administered 2 mg/kg enoxaparin by IV injection in the tail vein, followed 3 minutes later by test agent (IV, tail vein) at 2 and 5 mg/kg doses. Tails are then rapidly transected and bleeding time onto an absorbent pad was determined.

Example 34
In Vivo Neutralization of Fondaparinux in the Rat

Compounds are selected to test fondaparinux neutralization in vivo. Rats are pre-treated with fondaparinux administered by IV injection at 0.5 mg/kg. The rats are treated with a single IV injection of saline, protamine or the compound. Blood is collected via the orbital sinus from three rats per group at the following time points: pre-dose, 1, 3, 10, 30 and 60 minutes. Plasma samples are prepared for analysis of anti-factor Xa activity using an AMEX Destiny Plus Coagulation Analyzer.

Example 35
Mitigation of Hemodynamic Responses in the Anesthetized Rat

Reduction in blood pressure shortly after administration is a safety issue for cationic compounds. To address this hemodynamic issue, a medicinal chemistry strategy with literature precedence of introducing carboxylic acid functionality is applied. Surgically prepared animals are purchased from Charles River Laboratories, Raleigh, N.C. Animals are anesthetized on the day of experiment with isoflurane (1.8-4%). Blood pressure and heart rate data are collected on a Grass Polygraph recorder. The compounds, vehicle or protamine dosing preparations are administered once to each rat by a 10 minute intravenous infusion three minutes following a single intravenous injection of heparin (50 U/kg). Each animal receives a dose volume of 2.0 mL/kg. Blood pressure is recorded prior to treatment for approximately 1 minute and immediately following heparin, immediately following vehicle, test articles or protamine and at 5, 15, 30, and 60 minutes following dosing. The doses of test agent are either 8 mg/kg or 16 mg/kg.

Example 36
FXa Chromogenic Assay (Absence of Plasma)

Human antithrombin is mixed with an anticoagulant agent (a LMWH or fondaparinux); final concentrations are 0.22 μg/mL for the LMWHs and 0.07 μg/mL for fondaparinux. Different concentrations of a test compound are added (typically 0.07 to 9 μg/mL range) followed by factor Xa and substrate (S-2765). Absorbance is read every 30 seconds over a 4 minute period in a SpectraMax 250 instrument (Molecular Devices, Inc.). EC₅₀values are determined by a curve-fit program (SoftMax Pro) using the following formula:

P(C_p)=1/[1+(K/C_p)ⁿ]

Example 37
FIIa (Thrombin) Chromogenic Assay (Absence of Plasma)

The procedure for measuring anti-FIIa activity is similar to that for the anti-FXa assay except FIIa and S-2238 are used in place of FXa and S-2765, respectively.

Example 38
Clotting and Amidolytic Assays in Presence of Human Plasma

Eight parts of pooled human plasma is supplemented with 1 part LMWH or UFH at final concentrations of 4 μg/mL, or fondarinux at a final concentration of 1.25 μg/mL. One μL sample of test agent is then added to 9 μL of supplemented plasma (test agent concentration ranges=0.156 to 20 μg/mL) and mixed. The supplemented plasmas are analyzed immediately in clotting and amidolytic assays as described below. All samples are performed in duplicate.

aPTT Clotting Assay.

Supplemented plasma is added to aPTT reagent (activated partial thromboplastin time reagent) (activator) in fibrometer. Clotting is initiated by addition of CaCl₂and time to clot was recorded.

HepTest Clotting Assay.

Factor Xa is added to supplemented plasma in a fibrometer and incubated for 120 seconds. Recalmix is added and time to clot was recorded.

Thrombin Time (TT) Clotting Assay.

Human thrombin is added to supplemented plasma in a fibrometer and time to clot was recorded.

FXa Amidolytic Assay:

Bovine factor Xa is added to supplemented plasma and incubated for 5 minutes at 37° C. Spectrozyme FXa substrate is added and the optical density change at 405 nm is measured for 30 seconds. % factor Xa inhibition is calculated using the following equation:

% Inhibition=[(OD_baseline−OD_sample)/OD_baseline]×100.

FXa Amidolytic Assay:

LMWH (enoxaparin or tinzaparin) at final concentrations of 0.1 μg/mL, UFH at final concentrations of 0.03 units/mL, or fondaparinux at a final concentration of 0.02 μg/mL (or concentration which fully inhibits factor Xa) is combined with human antithrombin at a final concentration of 0.036 units/mL. Two μl of test agent are added (range between 0.01 and 23 μg/mL) and incubated for 5 minutes at 23° C. Bovine Factor Xa was added to a final concentration of 0.636 nkat/mL and incubated for a further 10 minutes at 23° C. Using a SpectraMax 250 (Molecular Devices, Inc.) and SoftMax Pro V.5 software, the plate is read every 30 seconds for 4 minutes, with a 10 second shaking before first read and maximum interval shaking. Fit curve to report an EC₅₀(50% reversal of anticoagulant effects) value for each compound: P(C_p)=1/[1+(K/C_p)ⁿ].

FIIa Amidolytic Assay.

Human thrombin is added to supplemented plasma and incubated for 1 minute at 37° C. Spectrozyme TH substrate is added and the optical density change at 405 nm is measured for 30 seconds in a SpectraMax 250 instrument. % factor IIa inhibition is calculated using the following equation:

% Inhibition=[(OD_baseline−OD_sample)/OD_baseline]×100.

Example 39
Heparin-Binding Activity

The heparin (unfractionated) preparations are tyramine end-labeled and radiolabeled with ¹²⁵Iodine to a specific activity of 1-2.5×10⁷cpm/μg. Increasing concentrations of a test agent (protamine or an exemplary compound provided herein) are added to individual wells across a 1% agarose gel in 125 mM sodium acetate, 50 mM MOPSO (3-(n-morpholino)-2-hydroxypropanesulfonic acid), pH 7.0). The radio-labeled heparin is added to a closely neighboring upper well and electrophoresed through the test agent wells. Heparin binding is visualized on the dried gel using a Phosphorimager. The dissociation constant (Kd) is calculated from the test agent concentration (n=3) at which the polysaccharide is half-shifted between its fully mobile position at low concentrations of test agent and its fully retarded position at saturating concentrations of test agent according to the methods of Lee and Lander (See Lee, M. K. and Lander, A. D., “Analysis of affinity and structural selectivity in the binding of proteins to glycosaminoglycans: development of a sensitive electrophoretic approach” Proc. Natl. Acad. Sci. USA, 1991, 88, 2768-2772).

Example 40
In Vivo Neutralization of Unfractionated Heparain in the Rat

The male Sprague-Dawley rats used in this study are obtained from Charles River Laboratories, Raleigh. They are nine-weeks-old at the start of the study and their weights range from 279-334 g. Rats are pre-treated with UFH administered by IV injection in a tail vein at 100 U/kg in a dose volume of 1 mL/kg. The rats are then treated with a single IV injection of saline, protamine or the appropriate test compound at doses of 0.25, 0.5 and 1.0 mg/kg. All treatments are dosed in a volume of 1 mL/kg. Blood is collected via the orbital sinus from three rats per group at the following time points after treatment: predose, 1, 3, 10, 30 and 60. At each time point, 1 mL of blood is collected from each animal into a single tube. The blood is analyzed using an AMEX Destiny Plus Coagulation Analyzer for activated partial thromboplastintime (APTT) and anti-Factor Xa.

Example 41
In Vivo Neutralization of Enoxaparin in the Rat

Example 42
Normalization of Enoxaparin-Extended Bleeding Times in a Rat Tail Transection Model

Male Sprague Dawley rats (Charles River) are administered 2 mg/kg enoxaparin by IV injection in the tail vein, followed 3 minutes later by test agent (IV, tail vein) at 2 and 5 mg/kg doses. Tails are then rapidly transected and bleeding time onto an absorbant pad is determined.

Example 43
In Vivo Neutralization of Fondaparinux in the Rat

Compounds are selected to test fondaparinux neutralization in vivo. Rats are pre-treated with fondaparinux administered by IV injection at 0.5 mg/kg. The rats are then treated with a single IV injection of saline, protamine or the compound. Blood is collected via the orbital sinus from three rats per group at the following time points: pre-dose, 1, 3, 10, 30 and 60 min. Plasma samples are prepared for analysis of anti-factor Xa activity using an AMEX Destiny Plus Coagulation Analyzer.

Example 44
Anti-Factor Xa Inhibition

The following example illustrates the effects of compounds of the present disclosure on anti-Factor Xa inhibition. To determine the anti-heparin activity of the compounds, an assay measuring the percent inhibition using a fixed concentration of compound or concentrations of compounds causing lysis of 50% of human red blood cells is used.

10 IU of anti-thrombin is dissolved in 10 mL of buffer, resulting in a 1 IU/mL stock solution (250×) of the anti-thrombin. The 1 IU/mL (250×) stock solution of anti-thrombin and a 336 mM stock solution of NaCl are diluted into a total volume of 50 μl buffer so that the final anti-thrombin concentration is 0.004 IU/sample well and the NaCl is 150 mM/sample well. 1 μl of the compound to be tested, final concentration 10 μg/mL (corresponding to 0.5 logarithmic antagonist dilution) is added to the sample well. The samples are mixed and allowed to incubate at room temperature for 20 minutes. 50 μl of factor Xa dissolved in buffer is added to the sample well to a final concentration of 0.14 knat/well (2 μl of the 7.1 knat/mL stock solution to a final sample well buffer volume of 100 μl). The samples are mixed and further incubated at room temperature for 10 minutes. 10 μl of a 4 mM stock solution of the substrate S-2765 is added to each sample well for a final concentration of 0.4 mM in each sample well. The samples are mixed and hydrolyses of the chromogenic substrate Z-D-Arg-Gly-Arg-pNA (S-2765), thus liberating the chromophoric group pNA (p-nitroaniline), is monitored at 405 nm. The samples are mixed every 30 seconds to maintain a uniform mixture. ThermoLabsystems Multiskan Spectrum spectrophotometer is used to measure the absorbance spectrums. The increase in absorbance is proportional to the enzyme (factor Xa) activity. The % inhibition of factor Xa is determined using a standard curve.

Anti-Factor Xa Inhibition: EC50. To determine the concentration of polycationic compound that causes about 50% lysis of human red blood cells, fixed heparin concentrations are used and different amounts of heparin antagonists are added.

Example 45
Breast Cancer Cells

Compounds are tested for effectiveness against two human breast cancer cell lines, MCF-7 (ATCC HTB-22) and TMX2-28, and one non-tumorigenic breast cell line, MCF-10A (ATCC CRL-10317). MCF-7 and TMX2-28 cells are grown in DC₅cell growth media while the MCF-10A cells are grown in MEGM, both supplemented with 5% bovine growth serum. The cells are grown using standard techniques. Cell cultures at 50% confluence are harvested with trypsin, seeded onto sterile 96 well plates at a density of 10,000 cells/well and allowed to grow overnight to 50% confluence. Compounds are then added to the growth medium and allowed to further incubate for 48 hours. Viable cells are quantitated using an XTT assay (purchased from Roche).

Example 46
Methodology for the NCI-60 DTP Human Tumor Cell Line Screen

Several compounds are tested at single concentrations (10 μM) against 59 different human tumor cell lines, representing leukemia, melanoma and cancers of the lung, colon, brain, ovary, breast, prostate, and kidney (see, Table 3). The human tumor cell lines of the cancer screening panel are grown in RPMI 1640 medium containing 5% fetal bovine serum and 2 mM L-glutamine. For a typical screening experiment, cells are inoculated into 96 well microtiter plates in 100 μL at plating densities ranging from 5,000 to 40,000 cells/well depending on the doubling time of individual cell lines. After cell inoculation, the microtiter plates are incubated at 37° C., 5% CO₂, 95% air and 100% relative humidity for 24 hours prior to addition of the compounds.

After 24 hours, two plates of each cell line are fixed in situ with TCA, to represent a measurement of the cell population for each cell line at the time of drug addition (Tz). Compounds are solubilized in dimethyl sulfoxide at 400-fold the desired final maximum test concentration and stored frozen prior to use. At the time of drug addition, an aliquot of frozen concentrate is thawed and diluted to twice the desired final maximum test concentration with complete medium containing 50 μg/mL gentamicin. Additional four, 10-fold or ½ log serial dilutions are made to provide a total of five compound concentrations plus control. Aliquots of 100 μL of these different drug dilutions are added to the appropriate microtiter wells already containing 100 μL of medium, resulting in the required final compound concentrations.

Following drug addition, the plates are incubated for an additional 48 hours at 37° C., 5% CO₂, 95% air, and 100% relative humidity. For adherent cells, the assay is terminated by the addition of cold TCA. Cells are fixed in situ by gentle addition of 50 μL of cold 50% (w/v) TCA (final concentration, 10% TCA) and incubated for 60 minutes at 4° C. The supernatant is discarded, and the plates are washed five times with tap water and air dried. Sulforhodamine B (SRB) solution (100 μL) at 0.4% (w/v) in 1% acetic acid is added to each well, and plates are incubated for 10 minutes at room temperature. After staining, unbound dye is removed by washing five times with 1% acetic acid and the plates are air dried. Bound stain is subsequently solubilized with 10 mM trizma base, and the absorbance is read on an automated plate reader at a wavelength of 515 nm. For suspension cells, the methodology is the same except that the assay is terminated by fixing settled cells at the bottom of the wells by gently adding 50 μL of 80% TCA (final concentration, 16% TCA). Using the seven absorbance measurements (time zero, (Tz), control growth, (C), and test growth in the presence of drug at the five concentration levels (Ti)), the percentage growth is calculated at each of the compound concentrations levels. Percentage growth inhibition is calculated as:

[(Ti−Tz)/(C−Tz)]×100 for concentrations for which Ti>/=Tz

[(Ti−Tz)/Tz]×100 for concentrations for which Ti<Tz.

Three dose response parameters are calculated for each compound. Growth inhibition of 50% (GI50) is calculated from [(Ti−Tz)/(C−Tz)]×100=50, which is the compound concentration resulting in a 50% reduction in the net protein increase (as measured by SRB staining) in control cells during the compound incubation. The compound concentration resulting in total growth inhibition (TGI) is calculated from Ti=Tz. The LC50 (concentration of compound resulting in a 50% reduction in the measured protein at the end of the compound treatment as compared to that at the beginning) indicating a net loss of cells following treatment is calculated from [(Ti−Tz)/Tz]×100=−50. Values are calculated for each of these three parameters if the level of activity is reached; however, if the effect is not reached or is exceeded, the value for that parameter is expressed as greater or less than the maximum or minimum concentration tested.

TABLE 3

List of tumor cell lines

Panel Name
Cell Name

1.
Leukemia
CCRF-CEM

2.
Leukemia
HL-60(TB)

3.
Leukemia
K-562

4.
Leukemia
MOLT-4

5.
Leukemia
RPMI-8226

6.
Leukemia
SR

7.
Non-Small Cell Lung Cancer
A549/ATCC

8.
Non-Small Cell Lung Cancer
EKVX

9.
Non-Small Cell Lung Cancer
HOP-62

10.
Non-Small Cell Lung Cancer
HOP-92

11.
Non-Small Cell Lung Cancer
NCI-H226

12.
Non-Small Cell Lung Cancer
NCI-H23

13.
Non-Small Cell Lung Cancer
NCI-H322M

14.
Non-Small Cell Lung Cancer
NCI-H460

15.
Non-Small Cell Lung Cancer
NCI-H522

16.
Colon Cancer
COLO 205

17.
Colon Cancer
HCC-2998

18.
Colon Cancer
HCT-116

19.
Colon Cancer
HCT-15

20.
Colon Cancer
HT29

21.
Colon Cancer
KM12

22.
Colon Cancer
SW-620

23.
CNS Cancer
SF-268

24.
CNS Cancer
SF-295

25.
CNS Cancer
SF-539

26.
CNS Cancer
SNB-19

27.
CNS Cancer
SNB-75

28.
CNS Cancer
U251

29.
Melanoma
LOX IMVI

30.
Melanoma
MALME-3M

31.
Melanoma
MDA-MB-435

32.
Melanoma
SK-MEL-2

33.
Melanoma
SK-MEL-28

34.
Melanoma
SK-MEL-5

35.
Melanoma
UACC-257

36.
Melanoma
UACC-62

37.
Ovarian Cancer
IGROV1

38.
Ovarian Cancer
OVCAR-3

39.
Ovarian Cancer
OVCAR-4

40.
Ovarian Cancer
OVCAR-5

41.
Ovarian Cancer
OVCAR-8

42.
Ovarian Cancer
NCI/ADR-RES

43.
Ovarian Cancer
SK-OV-3

44.
Renal Cancer
786-0

45.
Renal Cancer
A498

46.
Renal Cancer
ACHN

47.
Renal Cancer
CAKI-1

48.
Renal Cancer
RXF 393

49.
Renal Cancer
SN12C

50.
Renal Cancer
TK-10

51.
Renal Cancer
UO-31

52.
Prostate Cancer
PC-3

53.
Prostate Cancer
DU-145

54.
Breast Cancer
MCF7

55.
Breast Cancer
MDA-MB-31/ATCC

56.
Breast Cancer
HS 578T

57.
Breast Cancer
BT-549

58.
Breast Cancer
T-47D

59.
Breast Cancer
MDA-MB-468

Example 47
Irradiated Hamster Cheek Pouch Model of Oral Mucositis

In the irradiated hamster cheek pouch model of oral mucositis, the hamster cheek pouch is everted and irradiated to produce a localized mucositis. The progression and resolution of mucositis in the hamster model is very similar to that observed in the human condition and the model has been validated clinically with respect to dosing schedules of therapeutic agents (Murphy et al., Clin. Cancer Res., 2008, 14, 4292-4297; Alvarez et al., Clin. Cancer Res., 2003, 9, 3454-3461; and Schuster et al., J. Clin. Oncol., 2006, 24, 6537). Briefly, on day 0, all animals are given an acute radiation dose directed to their left buccal cheek pouch. Test articles are applied topically to the left pouch three times per day from day 0 to day 20 and mucositis is evaluated clinically starting on day 6, and continued on alternate days until day 20. Study endpoints are mucositis score, weight change and survival. Mucositis is scored visually by comparison to a validated photographic scale. The scale ranges from 0 for normal, to 5 for severe ulceration. The clinical mucositis score of 3 in hamsters indicates the presence of an ulcer. In terms of the syndrome, it is believed that the dose-limiting chemotherapeutic- or radiation-induced pain is associated with frank ulceration; therefore a compound that prevents ulceration in the model might have utility in the clinical setting.

To evaluate mucositis severity, animals are anesthetized with an inhalation anesthetic, and the left cheek pouch everted. Mucositis is scored visually by comparison to a validated photographic scale. The scale ranges from 0 for normal, to 5 for severe ulceration. In descriptive terms, this scale is defined as follows:

Mucositis Scoring

Score:
Description:

0
Pouch completely healthy. No erythema or vasodilation.

1
Light to severe erythema and vasodilation. No erosion of

mucosa.

2
Severe erythema and vasodilation. Erosion of superficial aspects

of mucosa leaving denuded areas. Decreased stippling of

mucosa.

3
Formation of off-white ulcers in one or more places. Ulcers may

have a yellow/gray appearance due to pseudomembrane

formation.

Cumulative size of ulcers should equal about ¼ of the pouch.

Severe erythema and vasodilation.

4
Cumulative size of ulcers should equal about ½ of the pouch.

Loss of pliability. Severe erythema and vasodilation.

5
Virtually all of pouch is ulcerated. Loss of pliability (pouch can

only partially be extracted from mouth.

A score of 1-2 is considered to represent a mild stage of injury, whereas a score of 3-5 is considered to indicate moderate to severe mucositis. In terms of the syndrome, it is believed that the dose-limiting chemotherapeutic- or radiation-induced pain is associated with frank ulceration; therefore a compound that prevents ulceration in the model might have utility in the clinical setting. In the hamster model, a clinical mucositis score of 3 indicates the presence of an ulcer and the duration of scores of 3 or greater is used as a primary measurement of efficacy in mucositis treatment. Ulceration is the point in the development of mucositis where the physical integrity of the oral mucosa is breached. In the clinic, a patient presenting with severe oral ulcerations may require hospitalization for analgesic, narcotic and/or antibiotic therapies or fluid support.

On day 0, all animals are given an acute radiation dose directed to their left buccal cheek pouch. This is accomplished by anesthetizing the animals and everting the left buccal pouch, while protecting the rest of the animals with a lead shield. Test agents are applied topically to the left buccal pouch three times per day from day 0 to day 20. Mucositis is evaluated clinically starting on day 6, and continued on alternate days until day 28. Study endpoints are mucositis score, weight change and survival. Mucositis is scored visually by comparison to a validated photographic scale.

Alternately, ulcerative severity differences between control and treatment groups are assessed by the comparison of the number of days with an ulcer (i.e., a score of 3 or higher) using a chi-squared (χ2) test.

Example 48
Cytokine and Inflammation Assays

Growth medium from stimulated cultures is collected either by aspiration (from keratinocytes) or after centrifugation at 1000 rpm for 15 minutes (for THP-1 cells). Cell debris is removed by centrifugation at 8,000 g (12,000 rpm) for 10 minutes at 4° C. To quantify IL-8 levels, the Human IL-8 Single Analyte ELISArray Kit (SA bioscience, MD) is used according to the manufacturer's protocol. The Cellular Activation of Signaling ELISA kit IKBα (SA bioscience, MD) is used to quantify both phosphorylated and whole IkBα levels in OKF6/TERT cells grown in a 96-well plate. All assays are performed in duplicate.

Example 49
PCR

Total cellular RNA is isolated from cultures using QIAshredder and RNeasy Mini Kit (Qiagen Valencia, Calif.). Total RNA is reversed transcribed using Superscript II reverse transcriptase kit as described by the manufacturer (Invitrogen, CA). Quantitative PCR (qPCR) is carried out using SYBR Green in a MyiQ iCycler (Bio-Rad). A total of 1 μl of cDNA (described above) is analyzed using final concentration of 100 nM of primers, 2×SYBR Green PCR Master Mix (Applied Biosystems, Foster City, Calif., USA) in volume of 20 μl. Prmer sequences are:

hBD-2:

Forward

(SEQ ID NO: 1)

5′-GATGCCTCTTCCAGGTGTTTTTGG-3′

Reverse

(SEQ ID NO: 2)

5′-TTG TTCCAGGACCACAGGTG-3′

IL-8:

Forward

(SEQ ID NO: 3)

5′-GCAGCTCTGTGTGAAGGTGCAGTTTTGC-3′

Reverse

(SEQ ID NO: 4)

5′-TTTCTGTGTTGGCGCAGTGTGGTCC-3′

b-2-microgloublin (control):

Forward

(SEQ ID NO: 5)

5′-CTCCGTGGCCTTAGCTGTG-3′

Reverse

(SEQ ID NO: 6)

5′-TTGGAGTACGCTGGATAGCCT-3′

Amplification is carried out for 50 cycles (95° C., 15 seconds; 60° C., 60 seconds). The relative for mRNA expression in each sample is calculated based on its Ct value comparison to Ct of a housekeeping gene. The data are presented as 2^-DDCt, an arbitrary unit. RTQ-PCR is performed in triplicates for each sample. This procedure is conducted in at least three independent experiments.

Example 50
Activity Against A. actinomycetemcomitans and P. gingivalis

To quantify the activity of compounds on biofilms, the activity against two bacterial species associated with periodontitis, A. actinomycetemcomitans and P. gingivalis is measured under conditions that lead to biofilm formation (Kaplan et al., J. Bacteriol. 2003, 185, 1399-1404; Davey, Periodontol 2000, 2006, 42, 27-35). The MIC of mPE against these species in planktonic form is 0.4 μg/mL for A. actinomycetemcomitans and 2.5 μg/mL for P. gingivalis (Beckloff et al., Antimicrob. Agents Chemother., 2007, 51, 4125-4132). Aa strain IDH781 is grown in AAGM in 96-well plates until complete confluence. To assess the activity against A. actinomycetemcomitans biofilms, mPE is added at decreasing concentrations in two-fold dilutions as in a standard MIC assay. After 24 hours, the growth medium is replaced with RPMI (without Phenol Red) and an XTT assay is carried out to quantify the metabolic activity. Metabolic activity is quantified by measuring the OD at 450 nm and 600 nm. Results are shown as % reduction in the A450-A600 from untreated cultures.

To test the activity against P. gingivalis biofilms, strain 381 is grown in 96-well plates under conditions (i.e., grown in a 96-well plate for 21 days in an anaerobic chamber in Brain Heart Infusion (BHI) medium) that favor biofilm formation (Davey, Periodontol 2000, 2006, 42, 27-35). mPE is added in serial dilutions, incubated anaerobically for 24 hours, and the medium is replaced with XTT in RPMI. Metabolic activity is quantified as above. To confirm the ability of XTT to measure activity in the biofilm, the growth medium is removed, and biomass is quantified by crystal violet staining, followed by destaining and quantification of the optical density. Staining is quantified by reading A600.

Example 51
The Effect of mPE on Inflammatory Response

To examine the effect of mPE on the inflammatory response, gingival epithelial cells (the OKF6/TERT cell line) and the monocytic cell line, THP-1, are treated with rhIL-1β (100 ng/mL) in the presence of increasing concentrations (0, 2, or 5 μg/mL) of mPE. Secreted levels of IL-8 are measured by ELISA. The experiment is carried out in quadruplicate; error bars represent±SD.

OKF6/TERT cells are treated with mPE as above in the presence or absence of IL-1β. Total mRNA is isolated and IL-8 and hBD-2 mRNA levels are quantified by QPCR normalized to β2-Microglobulin. Gingival epithelial cells are treated with mPE in the presence or absence of 100 ng/mL IL-1β, and IκB phosphorylation levels are quantified using the CASE assay (SA Biosciences, MD), and quantified relative to total IκB levels). In particular, OKF6/TERT cells are grown in 96-well plates, treated with 100 ng/mL IL-1β for 2 or 4 hours in the presence of 0, 2 or 5 μg/mL mPE. Reductions in pIκB/total IκB are significant at p<0.002.

Various modifications of the disclosure, in addition to those described herein, will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims. Each reference (including, but not limited to, journal articles, U.S. and non-U.S. patents, patent application publications, international patent application publications, gene bank accession numbers, and the like) cited in the present application is incorporated herein by reference in its entirety.

	Number	Date	Country
	61735105	Dec 2012	US
	61764605	Feb 2013	US

Polymeric Compounds And Methods Of Making And Using The Same

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