Patent Application
20240109852
Chemotherapy remains one of the major approaches in cancer treatment with small molecules still dominating the market. These small organic compounds target diverse pathways, causing cell cycle arrest and death of cancer cells. Due to genetic instability, tumors become more heterogeneous during the progression of the disease, leading to cells with distinct molecular signatures. When this diverse population is subjected to chemotherapeutic agents, drug resistance can emerge due to chemotherapy acting as an evolutionary pressure to select for cells that can grow in the presence of the drug. Indeed, clinically, there is a negative correlation between the diversity of the tumor and therapeutic outcome. Despite being extensively studied, drug resistance remains a major impediment in cancer treatment. Combinatorial treatment approaches are adopted to decrease the chances of drug resistance and increase the chances of tumor eradication. In this approach, chemotherapy can be combined with radiotherapy or surgery, or in the alternative, a combination of two or more drugs can be used to target different cell survival pathways. More than 370 drug combinations have been approved by the food and drug administration FDA.
Combination therapy was first conceptualized by showing the benefits of combining methotrexate, 6-mercaptopurine, vincristine, and prednisone (POMP regimen) to treat pediatric patients with acute lymphocytic leukemia. Since then, numerous drug combination regimens with synergistic or additive effects have been established, allowing reduced dosage requirements and, therefore, fewer side effects. Combining drugs is a common practice due to the advantages of drug combinations over monotherapy. However, the combined drugs remain different molecular entities with different pharmacological properties. Differences in biodistribution at both the cellular level and the organism level can hinder the successful administration of drug combinations. Thus, combinatorial therapy works best when drugs demonstrate similar pharmacokinetic profiles, which limits the available options.
An alternative to drug combinations is the rational design of multi-targeted hybrid molecules which ensure homogenous spatiotemporal biodistribution of the individual active entities. In this approach, pharmacophoric features from the drugs that are to be combined are incorporated into a single scaffold which maintains the pharmacodynamic effects of the individual drugs. The hybrid molecule ensures that the required activities are uniformly distributed in space and time. However, a potential drawback of hybrid molecules is the limitation of a fixed equimolar ratio of the two components. In addition, the design of hybrid molecules is extremely challenging because many pharmacophores do not tolerate significant structural changes.
One class of drugs useful for the multi-targeted hybrid molecules is histone deacetylase inhibitors (HDACis). HDACis act as epigenetic regulators by inhibiting histone deacetylases. This class of enzymes, in combination with histone acetyl transferases (HATs), control chromatin remodeling by regulating the acetylation levels of histones. HDACs also deacetylate numerous non-histone proteins contributing to the effects of HDAC inhibitors on a plethora of diverse cellular functions such as proliferation, cell death, metastasis, autophagy, metabolism, and ciliary expression. Based on phylogenetic comparison with yeast homologues, HDAC proteins are classified into four classes. Class I includes HDAC-1, HDAC-2, HDAC-3, and HDAC-8. Class 1 HDAC proteins use Zn2+ as a co-factor and mainly localize in the nucleus with strong deacetylase activity towards histones. Class II HDACs use Zn2+ as a co-factor as well, and are further divided into two subclasses, class IIa, which includes HDAC-4, HDAC-5, HDAC-7, and HDAC-9, and class IIb, which includes HDAC-6 and HDAC-10. Subclass IIa HDACs are found in both the nucleus and the cytoplasm and control the activities of several non-histone proteins like myocyte enhancer factor-2 (MEF2), while subclass IIb HDACs are found mainly in the cytoplasm with deacetylase activities against several interesting targets like tubulin deacetylation by HDAC-6 which regulates microtubule stability. Class III HDACs are NADtdependent enzymes that do not use Zn2+ as a co-factor and are referred to as sirtuins (SIRT 1-7). Class IV contains only HDAC-11, which uses Zn2+ as a co-factor and has similarities with both class I and class II HDACs. Very little is known about the biochemical function of HDAC-11, though it is believed to have a role in immune activation and tumorigenesis.
Elevated levels of several HDAC isoforms are associated with tumor survival and progression. For example, prostate cancers have elevated levels of HDAC1, while gastric, colorectal carcinomas, cervical, and endometrial cancers all overexpress HDAC2, when compared to the corresponding normal cells. These observations make HDACis possible drug candidates. Four HDACis have already gained FDA approval and are important clinically used drugs. However, the use of HDACis is currently limited to hematological malignancies, and clinical trials are underway to use them for solid tumors in combination with other drugs.
A typical HDACi pharmacophore consists of a zinc-binding group (ZBG), a short planar aliphatic or aromatic linker, and a cap group (
Provided is a composition comprising a hybrid molecule having both a ferroptotic pharmacophore and a histone deacetylase (HDAC) inhibitor pharmacophore.
In certain embodiments, the composition further comprises a pharmaceutically acceptable carrier, diluent, or adjuvant.
In certain embodiments, the ferroptotic pharmacophore comprises a terminal alkyne attached to a thiazole. In certain embodiments, the HDAC inhibitor pharmacophore comprises a hydroxamic acid metal-binding group.
In certain embodiments, the hybrid molecule comprises a zinc-binding group (ZBG) connected to a linker, and a cap group connected to the linker. In particular embodiments, the ZBG comprises a hydroxamate. In particular embodiments, the linker comprises an aliphatic chain. In particular embodiments, the ZBG comprises a hydroxxamate, and the linker comprises an aliphatic chain. In particular embodiments, the cap group comprises a terminal alkyne attached to a thiazole. In particular embodiments, the cap group comprises a terminal alkyne at the 2-position of a thiazole ring. In particular embodiments, the cap group further comprises an amide.
In certain embodiments, the ZBG comprises a hydroxamate, the linker comprises an aliphatic chain, and the hydroxamate comprises a terminal alkyne attached to a thiazole. In particular embodiments, the cap group further comprises an amide.
In certain embodiments, the hybrid molecule has Formula A:
wherein R is alkyl, alkenyl, amidoalkyl, amidoalkenyl, arylalkyl, arylalkenyl, or amidoarylalkenyl. Also provided are salts, stereoisomers, racemates, solvates, hydrates, and polymorphs of Formula A.
In certain embodiments, R is (C1-C6)alkyl or (C1-C6)alkenyl. In certain embodiments, R is ethyl or ethenyl. In certain embodiments, R includes an aliphatic chain of from 4 to 6 carbons. In particular embodiments, R further includes either an alkenyl group or an amido group.
In certain embodiments, the hybrid molecule is HY-1:
In certain embodiments, the hybrid molecule is HY-2:
In certain embodiments, the hybrid molecule is HY-3:
In certain embodiments, the hybrid molecule is HY-4:
In certain embodiments, the hybrid molecule is HY-5:
Further provided is a method of killing cancer cells, the method comprising contacting cancer cells with an effective amount of a composition comprising a hybrid molecule described herein, and killing the cancer cells.
In certain embodiments, the cancer is triple negative breast cancer.
In certain embodiments, the cancer is renal cancer, leukemia, colon cancer, ovarian cancer, breast cancer, lung cancer, melanoma, or CNS cancer, and the composition comprises HY-1.
In certain embodiments, the cancer is renal cancer, leukemia, ovarian cancer, breast cancer, lung cancer, melanoma, or CNS cancer, and the composition comprises HY-2.
In certain embodiments, the cancer is renal cancer, leukemia, ovarian cancer, lung cancer, melanoma, or CNS cancer, and the composition comprises HY-3.
In certain embodiments, the cancer is renal cancer, leukemia, ovarian cancer, breast cancer, lung cancer, melanoma, or CNS cancer, and the composition comprises HY-5.
Further provided is a method of treating a cancer, the method comprising administering an effective amount of a composition comprising a hybrid molecule described herein to a subject having a cancer, and treating the cancer.
Further provided is a composition comprising a ferroptotic inducer having Formula B:
where R1 is alkyl, alkenyl, amidoalkyl, amidoalkenyl, arylalkyl, arylalkenyl, or amidoarylalkenyl; and R2 is alkyl. Also provided are salts, stereoisomers, racemates, solvates, hydrates, and polymorphs of Formula B. In certain embodiments, the composition further comprises a pharmaceutically acceptable carrier, diluent, or adjuvant.
In certain embodiments, R2 is methyl or ethyl. In certain embodiments, R1 is (C1-C6)alkyl or (C1-C6)alkenyl. In certain embodiments, R1 is ethyl or ethenyl. In certain embodiments, R1 includes an aliphatic chain of from 4 to 6 carbons. In particular embodiments, R1 further includes either an alkenyl group or an amido group.
In certain embodiments, the ferroptotic inducer is FC-1:
In certain embodiments, the ferroptotic inducer is FC-2:
In certain embodiments, the ferroptotic inducer is FC-3:
In certain embodiments, the ferroptotic inducer is FC-4:
In certain embodiments, the ferroptotic inducer is FC-5:
Further provided is a method of killing cancer cells, the method comprising contacting cancer cells with an effective amount of a composition comprising a ferroptotic inducer described herein, and killing the cancer cells.
In certain embodiments, the cancer cells are neuroblastoma cells. In certain embodiments, cancer cells are neuroblastoma cells, and the ferroptotic inducer is FC-1.
Further provided is a method of treating a cancer, the method comprising administering to a subject having cancer an effective amount of a composition comprising a ferroptotic inducer described herein, and treating the cancer.
Further provided is a method of inducing ferroptosis in a cell, the method comprising contacting a cell with an effective amount of a composition comprising a ferroptotic inducer described herein, and inducing ferroptosis in the cell
Further provided is a composition comprising a histone deacetylase (HDAC) inhibitor having Formula C:
where X is a halide, and R is an alkyl, alkenyl, alkynyl, amidoalkyl, amidoalkenyl, arylalkyl, arylalkenyl, or amidoarylalkenyl group. Also provided are salts, stereoisomers, racemates, solvates, hydrates, and polymorphs of Formula C. In certain embodiments, the composition further comprises a pharmaceutically acceptable carrier, diluent, or adjuvant.
In certain embodiments, X is Br. In certain embodiments, X is Br, and R includes an aliphatic chain of from 4 to 6 carbons. In certain embodiments, X is Br, and R includes an alkenyl group.
In certain embodiments, wherein the HDAC inhibitor is HC-1:
In certain embodiments, wherein the HDAC inhibitor is HC-2:
In certain embodiments, wherein the HDAC inhibitor is HC-3:
In certain embodiments, wherein the HDAC inhibitor is HC-4:
In certain embodiments, wherein the HDAC inhibitor is HC-5:
Further provided is a method of killing cancer cells, the method comprising contacting cancer cells with an effective amount of a composition comprising a HDAC inhibitor described herein, and killing the cancer cells. In certain embodiments, the cancer cells are leukemia cells.
Further provided is method of treating a cancer, the method comprising administering to a subject having cancer an effective amount of a composition comprising an HDAC inhibitor described herein, and treating the cancer.
Further provided is a method of inhibiting histone deacetylase (HDAC) in a subject, the method comprising administering to the subject an effective amount of a composition comprising an HDAC inhibitor described herein, and inhibiting HDAC in the subject.
Further provided is a method of making an anticancer agent, the method comprising combining a ferroptosis inducing pharmacophore with a HDAC inhibitor pharmacophore to produce an anticancer agent comprising a ferroptotic inducing HDAC inhibitor hybrid molecule.
Further provided is a method of killing cancer cells, the method comprising contacting cancer cells with an effective amount of a composition comprising Formula A, Formula B, or Formula C, and killing the cancer cells:
wherein R is alkyl, alkenyl, amidoalkyl, amidoalkenyl, arylalkyl, arylalkenyl, or amidoarylalkenyl; X is a halide; R1 is alkyl, alkenyl, amidoalkyl, amidoalkenyl, arylalkyl, arylalkenyl, or amidoarylalkenyl; and R2 is alkyl. In certain embodiments, the cancer is triple negative breast cancer. In certain embodiments, the cancer is renal cancer, leukemia, colon cancer, ovarian cancer, breast cancer, lung cancer, melanoma, or CNS cancer.
Further provided is a method of treating a cancer, the method comprising administering to a subject having cancer an effective amount of a composition comprising Formula A or Formula C, and treating the cancer:
wherein R is alkyl, alkenyl, amidoalkyl, amidoalkenyl, arylalkyl, arylalkenyl, or amidoarylalkenyl; and X is a halide.
Further provided is a method of inhibiting histone deacetylase (HDAC) in a subject, the method comprising administering to the subject an effective amount of a composition comprising Formula A or Formula C, and inhibiting HDAC in the subject:
wherein R is alkyl, alkenyl, amidoalkyl, amidoalkenyl, arylalkyl, arylalkenyl, or amidoarylalkenyl; and X is a halide.
Further provided is a method of making an anticancer agent, the method comprising combining a ferroptosis inducing pharmacophore with a HDAC inhibitor pharmacophore to produce an anticancer agent comprising a ferroptotic inducing HDAC inhibitor hybrid molecule.
The patent or application file contains at least one drawings executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Throughout this disclosure, various publications, patents, and published patent specifications are referenced by an identifying citation. The disclosures of these publications, patents, and published patent specifications are hereby incorporated by reference into the present disclosure in their entirety to more fully describe the state of the art to which this invention pertains.
The lack of diversity in activating different cell death mechanisms is a major disadvantage of conventional hybrids molecules, because many cancer cells either have defective apoptosis pathways, or can dysregulate different steps in these pathways leading to drug resistance. Accordingly, the design and synthesis of hybrid molecules that combine apoptosis with other cell death machinery is an attractive alternative. In particular, combinations using drugs to sensitize cancer progenitor cells which are insensitive to standard therapies may be especially useful in improving the clinical outcome of chemotherapy.
One non-apoptotic cell death mechanism is known as ferroptosis. The hallmark of ferroptosis is iron-dependent lipid peroxidation, which, in combination with defective lipid peroxide repair mechanisms, leads to programmed cell death without requiring caspase activity. Ferroptosis is a nonapoptotic cell death mechanism characterized by a rapid increase in ROS leading to membrane lipid peroxidation. There are currently no ferroptosis inducers in clinical use.
Synthetic agents can induce ferroptosis by inhibiting cellular components that are crucial for maintaining an intracellular reductive environment such as system Xc− (erastin, sorefinib) or GPX4 (RSL3, ML210). In addition, several other processes such as ferritinophagy, epithelial-to-mesenchymal transition (EMT), and glutamine and iron metabolism modulate ferroptotic cell death. One important and unique feature of ferroptosis that makes it attractive for drug development is the enhanced sensitivity of mesenchymal cells to ferroptotic agents due to their high dependency on pathways that lead to lipid peroxidation quenching. The mesenchymal state has been associated with drug resistance and cell migration and, thus, enhanced and selective killing of this subpopulation of cells will lead to reduced drug resistance and tumor metastasis, especially when combined with another cell death mechanism such as apoptosis.
The combined effects of HDACi and ferroptosis inducers are highly useful with respect to cancer treatment and reduced neurotoxicity. For example, HDACi increase the sensitivity of cells to ferroptosis, leading to synergetic killing of cancer cells. In addition, the neuroprotective effects of HDACi can be an added benefit of such drug combinations by attenuating the neurotoxic effects of ferroptotic agents. Expression of distinct HDAC isoforms in neurons versus cancer cells is believed to explain this difference. Although the exact mechanisms by which HDAC inhibitors enhance ferroptosis in cancer cells is yet not fully understood, it is beleived that HDAC inhibition induces EMT and alters cellular iron homeostasis.
Combination therapies using a mixture of two or more anticancer agents are used to overcome the limitations of monotherapy, including drug resistance. However, differences in pharmacokinetic properties and spatio-temporal biodistbution of the drugs used limit the scope of combination therapies. Provided herein are hybrid molecules which act as dual-mechanism anticancer agents to overcome the limitations of conventional combination therapies. The hybrid molecules incorporate pharmacophores from different drugs, some acting by apoptotic and nonapoptotic mechanisms. Advantageously, the hybrid molecules may maintain the pharmacodynamic profiles of individual drugs while ensuring their uniform spatiotemporal distribution.
Provided herein are hybrid molecules that are highly potent anticancer agents and which incorporate the pharmacophores of a ferroptosis inducer and a histone deacetylase (HDAC) inhibitor. These hybrid molecules may be referred to as ferroptosis-HDAC inhibitor hybrids, or ferroptotic HDACis.
A ferroptotic agent has the ability to kill cancer stem cells responsible for tumor metastasis and therefore prevent tumor metastasis. An HDAC inhibitor is not effective on solid tumors. However, the hybrid molecules have the ability to extend application to solid tumors. Combination of ferroptosis with the apoptotic cell death mechanism of HDAC inhibitors have the ability reduce drug resistance and tumor metastasis. The hybrid molecules retain the pharmacodynamic profiles of the individual drugs while ensuring their uniform spatiotemporal distribution.
In accordance with the present disclosure, provided are hybrid molecules that are capable of inducing ferroptosis in cancer cells while maintaining HDAC inhibitory activity. In general, the hybrid molecules include a zinc-binding group (ZBG) attached to a linker, and a cap group attached to the linker. The ZBG group includes a hydroxamic acid or hydroxamate. However, other ZBGs are possible and encompassed within the scope of the present disclosure. The linker may be, or may include, a short aliphatic chain, such as from about 3 carbons to about 6 carbons. However, other linkers are possible, as described in more detail below, and encompassed within the scope of the present disclosure. The cap group of the hybrid molecules may include a terminal alkyne bonded to a thiazole, or more specifically a terminal alkyne at the 2-position of a thiazole ring, which is also referred to as a CETZOLE. The cap group may further include additional functional groups or moieties, such as an amide.
In some embodiments, the hybrid molecules have the general structural formula of Formula A:
where R is an alkyl, alkenyl, amidoalkyl, amidoalkenyl, arylalkyl, arylalkenyl, or amidoarylalkenyl group. For example, R may be a (C1-C6) alkyl or (C1-C6) alkenyl. As another example, R may be an amidohexyl. In some examples, R includes an aliphatic chain of from 4 to 6 carbons, and may further include either an alkenyl group or an amido group. Non-limiting example hybrid molecules are HY-1, HY-2, HY-3, HY-4, and HY-5, which are depicted in
As demonstrated in the examples herein, the hybrid molecules are useful as anticancer agents. Certain hybrid molecules have significant activity and selectivity against a wide range of cancers. For example, HY-1 is cytotoxic to renal cancer, colon cancer, leukemia, ovarian cancer, breast cancer, lung cancer, melanoma, and CNS cancer. (
In some embodiments, the hybrid molecules are more active than SAHA (Vorinostat). The hybrid molecules kill cancer cells by ferroptosis (nonapoptotic) and HDAC inhibition (apoptoic) mechanisms, and therefore can prevent drug resistance. In some embodiments, the hybrid molecules are effective on cancer stem cells, and therefore can prevent cancer metastasis.
As noted above, hybrid molecules combine the benefits of combinatorial treatment with homogeneous spatiotemporal distribution. HDAC inhibitors are an attractive class of cytotoxic agents for the design of hybrid molecules. Several HDAC hybrids have emerged over the years but none combines HDAC inhibition with ferroptosis, a combination which leads to enhanced cytotoxicity and attenuated neuronal toxicity. In accordance with the present disclosure, the pharmacophores of an HDAC inhibitor and a ferroptosis inducer have been combined to design dual-mechanism hybrid molecules which induce ferroptosis and inhibit HDAC proteins. As described in the examples herein, the involvement of both mechanisms in cytotoxicity was confirmed by a series of biological assays where hallmarks of both mechanisms were investigated. The cytotoxic effects were evaluated in a series of cancer and neuronal cell lines. In these examples, analog HY-1 demonstrated the best cytotoxic profile with GI50 values as low as 20 nM.
Further provided are ferroptotic inducers which include the CETZOLE cap group like the hybrid molecules, and similar linkers, but do not include the same ZBG group. The ferroptotic inducers, which may also be referred to as ferroptosis inducers, have the general structural formula of Formula B:
where R1 is an alkyl, alkenyl, amidoalkyl, amidoalkenyl, arylalkyl, arylalkenyl, or amidoarylalkenyl group; and R2 is alkyl. Thus, the ferroptosis inducers include an ester in the ZBG group. Non-limiting examples of ferroptotic inducers include FC-1, FC-2, FC-3, FC-4, and FC-5, which are depicted in
As demonstrated in the examples herein, the ferroptotic inducers are useful against certain cancers. For example, as shown in
Further provided are HDAC inhibitors that include a hydroxamate ZBG like the hybrid molecules, and a similar linker connected to a thiazole, but do not include the terminal alkyne that the hybrid molecules include. The HDAC inhibitors have the general structural formula of Formula C:
where X is a halide, and R is an alkyl, alkenyl, alkynyl, amidoalkyl, amidoalkenyl, arylalkyl, arylalkenyl, or amidoarylalkenyl group. In some embodiments, X is Br. R may be, for example, a (C1-C6) alkyl or (C1-C6) alkenyl. As another example, R may be an amidohexyl. In some examples, R includes an aliphatic chain of from 4 to 6 carbons, and may further include either an alkenyl group or an amido group. Non-limiting examples of HDAC inhibitors are HC-1, HC-2, HC-3, HC-4, and HC-5, depicted in
Pharmaceutical compositions of the present disclosure may comprise an effective amount of a hybrid molecule, ferroptotic inducer, or HDAC inhibitor (an “active compound” or “active ingredient”), or combination thereof, optionally with additional agents, dissolved or dispersed in a pharmaceutically acceptable carrier, optionally with an additional cancer therapeutic drug. The preparation of a pharmaceutical composition that contains at least one compound or additional active ingredient will be known to those of skill in the art in light of the present disclosure, as exemplified by Remington's Pharmaceutical Sciences, 2003, incorporated herein by reference. Moreover, for animal (e.g., human) administration, it is understood that preparations should meet sterility, pyrogenicity, general safety, and purity standards as required by FDA Office of Biological Standards.
A composition disclosed herein may comprise different types of carriers depending on whether it is to be administered in solid, liquid or aerosol form, and whether it need to be sterile for such routes of administration as injection. Compositions disclosed herein can be administered intravenously, intradermally, transdermally, intrathecally, intraarterially, intraperitoneally, intranasally, intravaginally, intrarectally, intraosseously, periprosthetically, topically, intramuscularly, subcutaneously, mucosally, intraosseosly, periprosthetically, in utero, orally, topically, locally, via inhalation (e.g., aerosol inhalation), by injection, by infusion, by continuous infusion, by localized perfusion bathing target cells directly, via a catheter, via a lavage, in cremes, in lipid compositions (e.g., liposomes), or by other method or any combination of the forgoing as would be known to one of ordinary skill in the art (see, for example, Remington's Pharmaceutical Sciences, 2003, incorporated herein by reference).
The actual dosage amount of a composition disclosed herein administered to an animal or human patient can be determined by physical and physiological factors such as body weight, severity of condition, the type of disease being treated, previous or concurrent therapeutic interventions, idiopathy of the patient and on the route of administration. Depending upon the dosage and the route of administration, the number of administrations of a preferred dosage and/or an effective amount may vary according to the response of the subject. The practitioner responsible for administration will, in any event, determine the concentration of active ingredient(s) in a composition and appropriate dose(s) for the individual subject.
In certain embodiments, pharmaceutical compositions may comprise, for example, at least about 0.1% of an active compound. In other embodiments, an active compound may comprise between about 2% to about 75% of the weight of the unit, or between about 25% to about 60%, for example, and any range derivable therein. Naturally, the amount of active compound(s) in each therapeutically useful composition may be prepared is such a way that a suitable dosage will be obtained in any given unit dose of the compound. Factors such as solubility, bioavailability, biological half-life, route of administration, product shelf life, as well as other pharmacological considerations will be contemplated by one skilled in the art of preparing such pharmaceutical formulations, and as such, a variety of dosages and treatment regimens may be desirable.
In other non-limiting examples, a dose may also comprise from about 1 microgram/kg/body weight, about 5 microgram/kg/body weight, about 10 microgram/kg/body weight, about 50 microgram/kg/body weight, about 100 microgram/kg/body weight, about 200 microgram/kg/body weight, about 350 microgram/kg/body weight, about 500 microgram/kg/body weight, about 1 milligram/kg/body weight, about 5 milligram/kg/body weight, about 10 milligram/kg/body weight, about 50 milligram/kg/body weight, about 100 milligram/kg/body weight, about 200 milligram/kg/body weight, about 350 milligram/kg/body weight, about 500 milligram/kg/body weight, to about 1000 mg/kg/body weight or more per administration, and any range derivable therein. In non-limiting examples of a derivable range from the numbers listed herein, a range of about 5 mg/kg/body weight to about 100 mg/kg/body weight, about 5 microgram/kg/body weight to about 500 milligram/kg/body weight, etc., can be administered, based on the numbers described above.
In certain embodiments, a composition herein and/or additional agent is formulated to be administered via an alimentary route Alimentary routes include all possible routes of administration in which the composition is in direct contact with the alimentary tract. Specifically, the pharmaceutical compositions disclosed herein may be administered orally, buccally, rectally, or sublingually. As such, these compositions may be formulated with an inert diluent or with an assimilable edible carrier, or they may be enclosed in hard- or soft-shell gelatin capsules, they may be compressed into tablets, or they may be incorporated directly with the food of the diet.
In further embodiments, a composition described herein may be administered via a parenteral route. As used herein, the term “parenteral” includes routes that bypass the alimentary tract. Specifically, the pharmaceutical compositions disclosed herein may be administered, for example but not limited to, intravenously, intradermally, intramuscularly, intraarterially, intrathecally, subcutaneous, or intraperitoneally (U.S. Pat. Nos. 6,753,514, 6,613,308, 5,466,468, 5,543,158; 5,641,515, and 5,399,363 are each specifically incorporated herein by reference in their entirety).
Solutions of the compositions disclosed herein as free bases or pharmacologically acceptable salts may be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions may also be prepared in glycerol, liquid polyethylene glycols and mixtures thereof, and in oils. Under ordinary conditions of storage and use, these preparations may contain a preservative to prevent the growth of microorganisms. The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions (U.S. Pat. No. 5,466,468, specifically incorporated herein by reference in its entirety). In some cases, the form must be sterile and must be fluid to the extent that easy injectability exists. It should be stable under the conditions of manufacture and storage and should be preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (i.e., glycerol, propylene glycol, liquid polyethylene glycol, and the like), suitable mixtures thereof, and/or vegetable oils. Proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion, and/or by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, such as, but not limited to, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption such as, for example, aluminum monostearate or gelatin.
For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous, and intraperitoneal administration. In this connection, sterile aqueous media that can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage may be dissolved in 1 mL of isotonic NaCl solution and either added to 1000 mL of hypodermoclysis fluid or injected at the proposed site of infusion, (see for example, “Remington's Pharmaceutical Sciences” 15th Edition, pages 1035-1038 and 1570-1580). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject.
Sterile injectable solutions are prepared by incorporating the compositions in the required amount in the appropriate solvent with various other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized compositions into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, some methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. A powdered composition is combined with a liquid carrier such as, but not limited to, water or a saline solution, with or without a stabilizing agent.
In other embodiments, the compositions may be formulated for administration via various miscellaneous routes, for example, topical (i.e., transdermal) administration, mucosal administration (intranasal, vaginal, etc.) and/or via inhalation.
Pharmaceutical compositions for topical administration may include the compositions formulated for a medicated application such as an ointment, paste, cream, or powder. Ointments include all oleaginous, adsorption, emulsion, and water-soluble based compositions for topical application, while creams and lotions are those compositions that include an emulsion base only. Topically administered medications may contain a penetration enhancer to facilitate adsorption of the active ingredients through the skin. Suitable penetration enhancers include glycerin, alcohols, alkyl methyl sulfoxides, pyrrolidones, and luarocapram. Possible bases for compositions for topical application include polyethylene glycol, lanolin, cold cream, and petrolatum, as well as any other suitable absorption, emulsion, or water-soluble ointment base. Topical preparations may also include emulsifiers, gelling agents, and antimicrobial preservatives as necessary to preserve the composition and provide for a homogenous mixture. Transdermal administration of the compositions may also comprise the use of a “patch.” For example, the patch may supply one or more compositions at a predetermined rate and in a continuous manner over a fixed period of time.
In certain embodiments, the compositions may be delivered by eye drops, intranasal sprays, inhalation, and/or other aerosol delivery vehicles. Methods for delivering compositions directly to the lungs via nasal aerosol sprays has been described in U.S. Pat. Nos. 5,756,353 and 5,804,212 (each specifically incorporated herein by reference in their entirety). Likewise, the delivery of drugs using intranasal microparticle resins (Takenaga et al., 1998) and lysophosphatidyl-glycerol compounds (U.S. Pat. No. 5,725,871, specifically incorporated herein by reference in its entirety) are also well-known in the pharmaceutical arts and could be employed to deliver the compositions described herein. Likewise, transmucosal drug delivery in the form of a polytetrafluoroetheylene support matrix is described in U.S. Pat. No. 5,780,045 (specifically incorporated herein by reference in its entirety), and could be employed to deliver the compositions described herein.
It is further envisioned the compositions disclosed herein may be delivered via an aerosol. The term aerosol refers to a colloidal system of finely divided solid or liquid particles dispersed in a liquefied or pressurized gas propellant. The typical aerosol for inhalation consists of a suspension of active ingredients in liquid propellant or a mixture of liquid propellant and a suitable solvent. Suitable propellants include hydrocarbons and hydrocarbon ethers. Suitable containers will vary according to the pressure requirements of the propellant. Administration of the aerosol will vary according to subject's age, weight, and the severity and response of the symptoms.
In particular embodiments, the compounds and compositions described herein are useful for treating cancers or killing cancer cells. As described herein, the compounds and compositions herein can be used in combination therapies. That is, the compounds and compositions can be administered concurrently with, prior to, or subsequent to one or more other desired therapeutic or medical procedures or drugs. The particular combination of therapies and procedures in the combination regimen will take into account compatibility of the therapies and/or procedures and the desired therapeutic effect to be achieved. Combination therapies include sequential, simultaneous, and separate administration of the active compound in a way that the therapeutic effects of the first administered procedure or drug is not entirely disappeared when the subsequent procedure or drug is administered.
In some embodiments, the hybrid molecule, ferroptotic inducer, or HDAC inhibitor is part of a combination therapy with a chemotherapeutic agent. Suitable chemotherapeutic agents include, but are not limited to: taxane compounds, such as paclitaxel; platinum coordination compounds; topoisomerase I inhibitors, such as camptothecin compounds; topoisomerase II inhibitors, such as anti-tumor podophyllotoxin derivatives; anti-tumor vinca alkaloids; anti-tumor nucleoside derivatives; alkylating agents; anti-tumor anthracycline derivatives; HER2 antibodies; estrogen receptor antagonists or selective estrogen receptor modulators; aromatase inhibitors; differentiating agents, such as retinoids, and retinoic acid metabolism blocking agents (RAMBA); DNA methyl transferase inhibitors; kinase inhibitors; farnesyltransferase inhibitors; HDAC inhibitors, or other inhibitors of the ubiquitin-proteasome pathway; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, triethylenephosphoramide, triethylenethiophosphoramide, and trimethylomelamine; acetogenins; camptothecins, such as the synthetic analog topotecan; cryptophycins; nitrogen mustards, such as chlorambucil; nitrosoureas; bisphosphonates; mitomycins; epothilones; maytansinoids; trichothecenes; retinoids, such as retinoic acid; pharmaceutically acceptable salts, acids and derivatives of any of the above; and combinations thereof. Non-limiting examples of specific chemotherapeutic agents include erlotinib (TARCEVA®, Genentech/OSI Pharm.), docetaxel (TAXOTERE®, Sanofi-Aventis), 5-FU (fluorouracil, 5-fluorouracil, CAS No. 51-21-8), gemcitabine (GEMZAR®, Lilly), PD-0325901 (CAS No. 391210-10-9, Pfizer), cisplatin (cis-diamine, dichloroplatinum(II), CAS No. 15663-27-1), carboplatin (CAS No. 41575-94-4), paclitaxel (TAXOL®, Bristol-Myers Squibb Oncology), temozolomide (4-methyl-5-oxo-2,3,4,6,8-pentazabicyclo[4.3.0]nona-2,7,9-triene-9-carboxamide, CAS No. 85622-93-1, TEMODAR®, TEMODAL®, Schering Plough), tamoxifen ((Z)-2-[4-(1,2-diphenylbut-1-enyl)phenoxy]-N,N-dimethyl-ethanamine, NOLVADEX®, ISTUBAL®, VALODEX®), doxorubicin (ADRIAMYCIN®), Akti-1/2, HPPD, rapamycin, lapatinib (TYKERB®, Glaxo SmithKline), oxaliplatin (ELOXATIN®, Sanofi), bortezomib (VELCADE®, Millennium Pharm.), sutent (SUNITINIB CD, SU11248, Pfizer), letrozole (FEMARA®, Novartis), imatinib mesylate (GLEEVEC®, Novartis), XL-518 (MEK inhibitor, Exelixis, WO 2007/044515), ARRY-886 (MEK inhibitor, AZD6244, Array BioPharma, Astra Zeneca), SF-1126 (PI3K inhibitor, Semafore Pharmaceuticals), BEZ-235 (PI3K inhibitor, Novartis), XL-147 (PI3K inhibitor, Exelixis), ABT-869 (multi-targeted inhibitor of VEGF and PDGF family receptor tyrosine kinases, Abbott Laboratories and Genentech), ABT-263 (Bcl-2/Bcl-xL inhibitor, Abbott Laboratories and Genentech), PTK787/ZK 222584 (Novartis), fulvestrant (FASLODEX®, AstraZeneca), leucovorin (folinic acid), lonafamib (SARASAR™, SCH 66336, Schering Plough), sorafenib (NEXAVAR®, BAY43-9006, Bayer Labs), gefitinib (IRESSA®, AstraZeneca), irinotecan (CAMPTOSAR®, CPT-11, Pfizer), tipifamib (ZARNESTRA™, Johnson & Johnson), capecitabine (XELODA®, Roche), ABRAXANE™ (Cremophor-free), albumin-engineered nanoparticle formulations of paclitaxel (American Pharmaceutical Partners, Schaumberg, Ill.), vandetanib (rINN, ZD6474, ZACTIMA®, AstraZeneca), chloranmbucil, AG1478, AG1571 (SU 5271; Sugen), temsirolimus (TORISEL®, Wyeth), pazopanib (GlaxoSmithKline), canfosfamide (TELCYTA®, Telik), thioTepa and cyclosphosphamide (CYTOXAN®, NEOSAR®), bullatacin, bullatacinone, bryostatin, callystatin, CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogs), cryptophycin 1, cryptophycin 8, dolastatin, duocarmycin (including the synthetic analogs, KW-2189 and CB1-TM1), leutherobin, pancratistatin, sarcodictyin, spongistatin, chlomaphazine, chlorophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard, carmustine, chlorozotocin, fotemustine, lomustine, nimustine, ranimnustine, clodronate, esperamicin, neocarzinostatin chromophore and related chromoprotein enediyne antibiotic chromophores, aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, porfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin, methotrexate, 5-fluorouracil (5-FU), denopterin, methotrexate, pteropterin, trimetrexate, fludarabine, 6-mercaptopurine, thiamiprine, thioguanine, ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine, calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone, aminoglutethimide, mitotane, trilostane, frolinic acid, aceglatone, aldophosphamide glycoside, aminolevulinic acid, eniluracil, amsacrine, bestrabucil, bisantrene, edatraxate, defofamine, demecolcine, diaziquone, elformithine, elliptinium acetate, etoglucid, gallium nitrate, hydroxyurea, lentinan, lonidainine, maytansine, ansamitocins, mitoguazone, mitoxantrone, mopidanmol, nitraerine, pentostatin, phenamet, pirarubicin, losoxantrone, podophyllinic acid, 2-ethylhydrazide, procarbazine, PSK® polysaccharide complex (JHS Natural Products, Eugene, Oreg.), razoxane, rhizoxin, sizofuran, spirogermanium, tenuazonic acid, triaziquone, 2,2′,2″-trichlorotriethylamine, T-2 toxin, verracurin A, roridin A, anguidine, urethane, vindesine, dacarbazine, mannomustine, mitobronitol, mitolactol, pipobroman, gacytosine, arabinoside (“Ara-C”), cyclophosphamide, thioTepa, 6-thioguanine, mercaptopurine, vinblastine, etoposide (VP-16), ifosfamide, mitoxantrone, vincristine, vinorelbine (NAVELBINE®), novantrone, teniposide, edatrexate, daunomycin, aminopterin, ibandronate, CPT-11, topoisomerase inhibitor RFS 2000, and difluoromethylomithine (DMFO), paclitaxel, 5-fluorouracil, abraxane (paclitaxel albumin-stabilized nanoparticle formulation), afinitor (everolimus), erlotinib hydrochloride, everolimus, gemcitabine hydrochloride, oxaliplatin (eloxatin), capecitabine (xeloda), cisplatin, irinotecan (camptosar), colinic acid (leucovorin), folfox (folinic acid, 5-fluorouracil, and oxaliplatin), folfirinox (folinic acid, 5-fluorouracil, irinotecan, and oxaliplatin), nab-paclitaxel with gemcitabine, metformin, digoxin, and simvastatin.
In some embodiments, the hybrid molecule, ferroptotic inducer, or HDAC inhibitor is part of a combination therapy with an immunotherapeutic agents. Non-limiting examples of immunotherapeutic agents include nivolumab, pembrolizumab, rituximab, durvalumab, cemiplimab, and combinations thereof.
In some embodiments, the hybrid molecule, ferroptotic inducer, or HDAC inhibitor is part of a combination therapy with a hormonal therapeutic agent. Non-limiting examples of hormonal therapeutic agents include anastrozole, exemestane, letrozole, tamoxifen, raloxifene, fulvestrant, toremifene, gosrelin, leuprolide, triptorelin, apalutamide, enzalutamide, darolutamide, bicalutamide, flutamide, nilutamide, abiraterone, ketoconazole, degarelix, medroxyprogesterone acetate, megestrol acetate, mitotane, and combinations thereof.
These examples describe the design, general synthetic route, in silico, in vitro, and cellular evaluation of the hybrid molecules described herein.
The design of HDACi was dictated by the characteristics of the active site (
Twenty compounds were designed based on this pharmacophore, as summarized in
The amide analogs were synthesized as shown in Scheme 1 (
For the synthesis of the non-amide olefinic congeners, a Wittig reaction of 2-bromothiazole-4-carbaldehyde (3) (synthesized in situ) with ethyl 7-(triphenyl-λ5-phosphaneylidene)heptanoate (11) resulted in a mixture of both (E) and (Z) isomers NC-2-M (_1:1 E/Z ratio). Slow column chromatography separation on silica allowed the separation of a small amount of pure (Z) analog (NC-2), while the rest was obtained as an E/Z mixture (1:1 ratio) (NC-2-M). Analogues were synthesized using both the pure (Z) analog as well as the E/Z mixture, using similar synthetic procedures (Scheme 2,
To access the doubly unsaturated linker, the stabilized phosphonate carbanion (15) formed in situ was reacted with 2-bromothiazole-4-carbaldehyde (3) to yield predominantly the E-analog NC-4, followed by a similar synthetic route to access the rest of the analogs of the series (Scheme 3,
Similarly, reaction of compound (3) with methyl 3-(triphenyl-15-phosphaneylidene)propanoate (19) gave the short unsaturated analogs NC-5, FC-5, HC-5, and HY-5 (Scheme 4,
As shown in Table 1,
The Wittig reaction has the inherent tendency to provide mainly the Z-isomer as the faster formed kinetic product. The nature of the counter ion of the base used can have an effect on the stereochemical outcome of the reaction. The smaller and harder Lewis acidic Li+ions result in mostly the E-isomer and softer counter ions such as Na lead to equimolar E/Z mixtures. Indeed, using LiOH as the base resulted in mixtures enriched with E-analogue (2.5:1 E/Z ratio), allowing for its partial separation and purification. Although the Horner—Wadsworth—Emmons reaction would be a good alternative, it was not undertaken due to success in obtaining the E-isomer by counter ion control.
The cytotoxic effects of the compounds was first investigated using two cell lines: NCI-H522 (non-small lung cancer) and HCT116 (human colon carcinoma). Previous studies have shown that NCI-H552 cells undergo ferroptosis, while the HCT116 cells were insensitive to ferroptosis induced by CETZOLEs, sulfasalazine, or simple cystine deprivation. The HCT116 cells are killed by erastin, however, this is only partially explained by ferroptosis, with erastin likely having other targets in this cell line. Comparing effects in NCI-H522 and HCT116 made it possible to delineate the HDAC inhibitory and ferroptotic effects. The negative control (NC) analogs were inactive against both cell lines. The compounds that were designed to induce only ferroptosis (ferroptosis control) showed low mM activity only on the NCI-H522 cell line (2-13 mM IC50), but were inactive against HCT116 cells, except for analog FC-5, which showed some activity on HCT116 (13.73 mM IC50) (Table 1). To investigate if this effect is due to ferroptosis or some other activity, the cells were co-treated with the ferroptosis inhibitor Liproxstatin-1 (0.25 mM), which rescued the cells (
Driven by the demonstrated antiproliferative activity of HY-1, (Table 1 and
In
A salient property of a successful chemotherapeutic agent is the ability to discriminate between normal cells and cancer cells. Lack of selectivity is usually the cause of severe side effects. To investigate the ability of the hybrid molecules to selectively kill cancer cells over normal cells, the cytotoxicity of one of the most potent hybrid analog, HY-1, was tested on WI-38 cells (normal human lung fibroblasts) and hTERT-immortalized RPE cells (retinal pigment epithelial cells) (
Neuronal cells are inherently more sensitive to ferroptosis, as they have higher levels of polyunsaturated fatty acids (PUFAs), which serve as precursors for lipid peroxidation. In addition, due to their high metabolic activity, brain cells are particularly vulnerable to oxidative stress. Indeed, ferroptosis plays an important role in a series of neurodegenerative diseases, and CNS-related toxic effects can explain the failure of ferroptotic agents in clinical applications as potent anticancer agents. Thus, there is a need to find strategies to attenuate their neurotoxic effects while retaining the beneficial anticancer effects. Most ferroptosis inhibitors are capable of inhibiting ferroptosis in both neuronal and cancer cells, but class I histone deacetylase (HDAC) inhibitors selectively protect neurons, while enhancing ferroptosis in cancer cells. Although the pathways that lead to ferroptosis-mediated neuronal and cancer cell death are the same, they are differently regulated by HDACs. Thus, the hybrid molecule HY-1 and its corresponding negative controls were tested on the SH-SYSY cell line (human neuroblastoma), which can serve as a model for neurodegenerative diseases. As shown in
Next, key biomarkers were investigated to directly assess ferroptosis and HDAC inhibition by the hybrid molecules. To measure ferroptosis, lipid peroxidation was first investigated. The fluorescent dye C11-BODIPY581/591 is an established system for the quantification of oxidation processes in membranes of living cells that lead to accumulation of lipid peroxides. Fluorescent measurements in the green area of the spectra can provide information on the levels of the oxidized form of the dye, which are proportional to the lipid peroxide levels. Liproxstatin-1 has previously been identified as a potent small molecule that suppresses ferroptosis in cells and inhibits lipid peroxidation by acting as a radical trapping antioxidant selectively on lipid bilayers. Flow cytometry data (
Next, whether the hybrid molecules inhibit HDAC proteins was investigated by measuring hyperacetylation of the HDAC substrates, histones for class I inhibition and tubulin for class II (HDAC-6) (
Activation of the ferroptotic pathway by hybrid molecules was also indicated by increased levels of transferrin receptor, which has been identified as a selective marker for ferroptosis. Hybrid molecules also increased caspase-3 cleavage, indicating activation of the apoptotic pathway, possibly as a result of HDAC inhibition. However, the pan-caspase inhibitor Z-VAD-FMK did not rescue cells from HDACi SAHA and had no effect on hybrid-induced death (
In contrast, HDAC inhibition has a slower mechanism of action, which through epigenetic regulation of histones, or hyper-acetylation of other proteins, arrests cells in G1 and/or G2/M, eventually leading to cell death. The observations in these examples with SAHA, CETZOLE-1, and the hybrid molecule HY-1 were consistent with these ideas (
Molecular docking studies of the designed analogs were performed to estimate their potential to bind to HDAC proteins. The docking study was focused on class I and class II HADCs using Maestro v10.6 computational software. Initially, a library of 22 compounds, including the 20 analogs shown in
The docking scores indicated that the hybrid molecules as well as the HDACi controls have the ability to bind to the HDAC enzymes in a similar way as SAHA (
The cytotoxicity of the hybrid analogs was additionally evaluated in the NCI-60 human tumor cell lines screen by the National Cancer Institute (NCI) through the development therapeutics program (DTP), initially at a single dose of 10 mM to determine mean inhibition (
Analogs that demonstrated promising cytotoxicity in the one dose assay were tested in the 5-dose assay to determine the GI50 values (
In these examples, dual mechanism hybrid molecules capable of inducing ferroptosis and inhibiting HDAC proteins simultaneously are demonstrated. The HDAC inhibitory component of the hybrid molecules was based on a SAHA-like model in which hydroxamates were used as the ZBG, while a short aliphatic chain constituted the linker. A 2-alkynyl thiazole moiety, which is the warhead of CETZOLE ferroptosis inducers, was used as the cap group. The design of the first-generation hybrid molecules focused mainly on the length and the nature of the linker. Hybrid molecules that lacked either the hydroxamate ZBG or ferroptosis-inducing thiazole moiety or both were used as appropriate controls. A SAR study was performed focusing on the length of the linker as well as the unsaturation levels. The results proved the double bond to be a poor bioisosteric change for the amide in the case of the HDAC inhibitors because it provided analogs with attenuated cytotoxicity. In silico studies indicated that the hybrid molecules are capable of binding to HDAC proteins in a similar binding motif as SAHA, with the ZBG occupying the active site and chelating with the zinc ion, and the cap group occupying the outer rim of the proteins. The cytotoxicity of the library of analogues was initially determined on two cell lines; the ferroptosis-sensitive NCI-H522 and the ferroptosis “resistant” HCT-116 cell lines. This combination allowed the delineation of the HDAC inhibitory and ferroptosis-inducing potential of the molecules. Most of the hybrid molecules showed enhanced cytotoxicity on the NCI-H522 cell line when compared to SAHA, CETZOLE-1, or the corresponding HDAC and ferroptosis controls, indicating synergism by the combination of the two mechanisms. In addition, hybrid molecules showed attenuated neurotoxicity. At concentrations capable of showing cytotoxic effects on the NCI-H522 cell line, hybrid molecules showed minimal effect on the neuronal cell line SH-SY5Y, in contrast to the enhanced neuronal toxicity of the ferroptosis inducers and the moderate effects of HDAC controls. These data indicate the ability to use these hybrid molecules as anticancer agents capable of inducing ferroptosis with minimized neuronal side effects. HY-1 demonstrated the best cytotoxicity profile with low nM GI50 values on many cancer cell lines. The first-generation hybrid molecules incorporated a pan-HDAC inhibitor component which demonstrated no isoform selectivity.
All chemicals and solvents were purchased from commercial sources and used without further purification, unless stated otherwise. Anhydrous tetrahydrofuran was freshly distilled from sodium and benzophenone before use. 1H and 13C NMR spectra were recorded on Brucker Avance 600 MHz, INOVA 600 MHz, and Varian VXRS 400 MHz NMR spectrometers in deuterated solvents using residual undeuterated solvents as internal standard. High-resolution mass spectra (HRMS) were recorded on a Waters Synapt high definition mass spectrometer (HDMS) equipped with nano-ESI source. Melting points were determined using a Fisher-Johns melting point apparatus. Purification of crude products was performed by either flash chromatography on silica gel (40-63 μ) from Sorbent Technologies or on a Teledyne ISCO CombiFlash Companion chromatography system on RediSep prepacked silica cartridges. Thin layer chromatography (TLC) plates (20 cm×20 cm) were purchased from Sorbent Technologies (catalog #4115126) and were viewed under Model UVG-54 mineral light lamp UV-254 nm. A Shimadzu Prominence HPLC with an LCT2OAT solvent delivery system coupled to a Shimadzu Prominence SPD 20AV Dual wavelength UV/Vis absorbance Detector, a Shimadzu C18 column (1.9 m, 2.1 mm×50 m) and HPLC grade solvents (MeOH, H2O with 0.1% formic acid) were used to determine the purity of compounds by HPLC. All compounds were >95% pure by HPLC analysis.
A mixture of the corresponding thiazole-bromide, TMS-acetylene (1.5 equiv.), PdCl2 (PPh3)2 (5 mol %), CuI (6 mol %), Et3N (2 equiv.), and DCE (5 mL/mmol) was heated under reflux at 83 ° C. for 1 h. The reaction was quenched by the addition of brine, followed by DCM. The organic layer was dried over anhydrous Na2SO4, filtered, and concentrated under reduced pressure. The product was purified by flash chromatography on silica in EtOAC/hexanes (0->100% EtOAc) to yield the pure product.
To a solution of the corresponding ester in freshly distilled THF (2 mL/mmol) and H2O (1 mL/mmol) was added LiOH (3 equiv.). The resulting mixture was stirred for 2 h at r.t. Most of the THF was removed under reduced pressure, and the remaining aqueous solution was washed with EtOAc, acidified with conc. HCl, and extracted with EtOAc. The organic extract was dried over Na2SO4, filtered, and concentrated under reduced pressure to yield the pure product.
To a stirred suspension of the corresponding carboxylic acid in anhydrous DCM (3 mL/mmol) was added EDC-HCl (1.5 equiv.), followed by the addition of THP-O-NH2 (1.1 equiv.). The resulting mixture was stirred for 8 h at r.t. The reaction mixture was diluted with brine and extracted with EtOAc. The organic layer was dried over anhydrous Na2SO4, filtered, and concentrated under reduced pressure. The crude product was purified by flash chromatography on silica in EtOAC/DCM (0->100% EtOAc) to yield the pure compound.
To a stirred solution of corresponding THP protected hydroxamic acid in MeOH (3 mL/mmol) was added 1 M HCl (4 equiv.), and the resulting mixture was stirred at r.t. for 3 h. After removal of most of the MeOH under reduced pressure, the residue was diluted with brine and extracted with EtOAC. The organic layer was dried over anhydrous Na2SO4, filtered, and concentrated under reduced pressure. The crude product was purified by flash chromatography on silica in DCM/MeOH (0->7% MeOH) to yield pure compound.
Synthesized according to general hydrolysis conditions. (10 mmol scale, 96% yield). 1H NMR (600 MHz, DMSO-d6) δ 13.33 (br, 1H), 8.47 (s, 1H). 13C NMR (151 MHz, DMSO-d6) δ 161.35, 147.58, 137.10, 133.57.
To a stirred solution of 7-aminoheptanoic acid (1.45 g, 10 mmol) in MeOH (30 mL) at 0° C. was added SOCl2 (7 mL). The resulting mixture was allowed to warm to r.t and stirred at that temperature for 3 hr. The volatiles were removed under reduced pressure to yield the pure product (30) (1.96 g, 100%) as a white solid which was directly used in the next step without any purification. 1H NMR (600 MHz, DMSO-d6) δ 8.11 (br, 3H), 3.58 (s, 3H), 2.72 (t, J=7.2 Hz, 2H), 2.30 (t, J=7.4 Hz, 2H), 1.59 -1.46 (m, 4H), 1.34-1.19 (m, 4H). 13C NMR (151 MHz, DMSO-d6) δ 173.80, 51.67, 39.06, 33.57, 28.36, 27.18, 25.97, 24.65.
To a stirred suspension of 2-bromothiazole-5-carboxylic acid (5) (416 mg, 2 mmol) in anhydrous DCM (10 mL) were added EDC-HCl (575 mg, 3 mmol, 1.5 equiv.) and DMAP (10 mol %), followed by methyl 7-aminoheptanoate hydrochloric salt (7) (391 mg, 2 mmol, 1 equiv.) and Et3 N (0.28 mL, 2 mmol, 1 equiv.). The resulting mixture was stirred overnight at r.t, after which it was diluted with brine and DCM. The two layers were separated, and the organic layer was dried over anhydrous Na2SO4, filtered, and concentrated under reduced pressure. The crude product was purified by flash chromatography on silica in EtOAC/hexanes (0->100% EtOAc) to yield the pure product (NC-1) (435 mg, 1.24 mmol, 62%) as a colorless oil. 1H NMR (600 MHz, CDCl3) δ 8.05 (s, 1H), 7.22 (br, 1H), 3.67 (s, 3H), 3.42 (dt, J=7.2, 3.6 Hz, 2H), 2.31 (t, J=7.5 Hz, 2H), 1.68-1.55 (m, 4H), 1.42-1.33 (m, 4H). 13C NMR (151 MHz, CDCl3) δ 174.16, 159.59, 150.11, 135.72, 126.62, 51.47, 39.37, 33.98, 29.43, 28.75, 26.61, 24.87, 28.75, 26.61 , 24.87. HRMS calcd for C12H17BrN2 NaO3 S (M+Na) 371.0040; found 371.0041.
Synthesized according to general Sonogashira coupling conditions (1 mmol scale, 65% yield). 1H NMR (600 MHz, CDCl3) δ 8.13 (s, 1H), 7.33 (br, 1H), 3.67 (s, 3H), 3.56 (s, 1H), 3.44 (dd, J=13.4, 7.0 Hz, 2H), 2.31 (t, J=7.5 Hz, 2H), 1.68-1.58 (m, 4H), 1.45-1.32 (m, 4H). 13C NMR (151 MHz, CDCl3) δ 174.16, 160.17, 150.73, 147.18, 124.93, 83.06, 75.72, 51.50, 39.34, 33.97, 29.43, 28.78, 26.58, 24.79. HRMS calcd for C14H18N2NaO3S (M+Na) 317.0935; found 317.0934.
Synthesized according to general hydrolysis conditions. (0.27 mmol scale, 93% yield). 1H NMR (600 MHz, DMSO-d6) δ 11.98 (br, 1H), 8.51 (t, J=5.7 Hz, (NH), 1H), 8.25 (s, 1H), 3.21 (dd, J=13.7, 6.6 Hz, 2H), 2.19 (t, J=7.4 Hz, 2H), 1.53-1.44 (m, 4H), 1.30-1.24 (m, 4H). 13C NMR (151 MHz, DMSO-d6) δ 174.96, 159.57, 150.40, 136.64, 128.74, 39.19, 34.08, 29.43, 28.74, 26.61, 24.91.
Synthesized according to the general NH2 OTHP coupling conditions (1.85 mmol scale, 85% yield). 1H NMR (600 MHz, acetone-d6) δ 10.22 (br, 1H), 8.23 (s, 1H), 7.96 (br, 1H), 4.93 (s, 1H), 3.97 (t, J=10.6 Hz, 1H), 3.42 (dd, J=13.6, 6.7 Hz, 2H), 2.10 (t, J=7.1 Hz, 2H), 1.78-1.47 (m, 10H), 1.38 (d, J=3.0 Hz, 4H). 13C NMR (151 MHz, acetone-d6) δ 169.54, 159.29, 150.58, 135.59, 127.42, 101.26, 61.40, 38.99, 32.56, 29.45, 28.59, 27.98, 26.44, 25.25, 25.06, 18.42.
Synthesized according to the general THP deprotection conditions (0.23 mmol scale, 68% yield). 1H NMR (600 MHz, DMSO-d6) δ 10.34 (s, 1H), 8.67 (s, 1H), 8.51 (t, J=5.8 Hz, 1H), 8.25 (s, 1H), 3.21 (dd, J=13.6, 6.7 Hz, 2H), 1.93 (t, J=7.4 Hz, 2H), 1.52-1.44 (m, 4H), 1.30-1.18 (m, 4H). 13C NMR (151 MHz, DMSO-d6) δ 169.55, 159.58, 150.39, 136.66, 128.75, 39.07, 32.69, 29.48, 28.79, 26.61, 25.56. HRMS (ESI) cald for C11H16BrN3NaO3S (M+Na) 371.9993; found 371.9991.
Synthesized according to general Sonogashira coupling conditions. (0.5 mmol scale, 60% yield). 1H NMR (600 MHz, acetone-d6) δ 10.10 (br, 1H), 8.27 (s, 1H), 7.94 (br, 1H), 4.92 (s, 1H), 4.43 (s, 1H), 3.96 (t, J=10.6 Hz, 1H), 3.51 (d, J=11.0 Hz, 1H), 3.43 (dd, J=13.6, 6.7 Hz, 2H), 2.13-2.04 (m, J=8.9, 6.3, 4.4 Hz, 3H), 1.79-1.46 (m, 10H), 1.44-1.34 (m, J=3.1 Hz, 4H). 13C NMR (151 MHz, acetone-d6) δ 169.40, 159.70, 151.36, 147.11, 125.20, 101.24, 84.25, 75.68, 61.38, 38.88, 32.51, 29.44, 27.97, 26.40, 25.21, 25.04, 18.41.
Synthesized according to the general THP deprotection conditions (0.26 mmol scale, 61% yield). 1H NMR (600 MHz, acetone-d6) δ 10.01 (br, 1H), 8.27 (s, 1H), 8.16 (br, J=28.9, 17.3 Hz, 1H), 7.94 (br, 1H), 4.43 (s, 1H), 3.42 (dd, J=13.6, 6.8 Hz, 2H), 2.11 (dd, J=10.3, 4.4 Hz, 2H), 1.67-1.58 (m, 4H), 1.44-1.33 (m, 4H). 13C NMR (151 MHz, acetone-d6) δ 169.81, 159.69, 151.34, 147.11, 125.20, 84.20, 75.71, 38.87, 32.23, 29.41, 26.39, 25.13. HRMS (ESI) calculated for C13H17N3NaO3S (M+Na) 318.0888, found 318.0889.
To a round bottom flask containing ethyl 7-bromoheptanoate (S23) (6 g, 35.3 mmol) and triphenyl phosphine (6.6 gr, 25.3 mmol, 1 equiv.) was added toluene (55 mL). The resulting mixture was refluxed for 24 h. Toluene was evaporated under reduced pressure and the residue was washed with hexanes and diethyl ether and dried under vacuum to obtain the phosphonium bromide salt (S24), which was used in the next step without further purification.
To a stirred solution of 2-bromothiazole-4-carbaldehyde (2) (prepared as shown in Scheme 1,
Some fractions with E/Z mixture (1.3 g, 3.9 mmol, 30%) were obtained as well and were used to obtain a mixture of E/Z analogs.
Synthesized according to general Sonogashira coupling conditions (2 mmol scale, 62.5% yield). 1H NMR (600 MHz, CDCl3) δ 7.12 (s, 1H), 6.45 (dt, J=11.7, 1.7 Hz, 1H), 5.81 (dt, J=11.7, 7.2 Hz, 1H), 4.14 (q, J=7.1 Hz, 2H), 2.57 (qd, J=7.4, 1.7 Hz, 2H), 2.32 (t, J=7.5 Hz, 2H), 1.67 (dt, J=15.2, 7.6 Hz, 2H), 1.52 (dd, J=15.1, 7.6 Hz, 2H), 1.45-1.38 (m, 2H), 1.27 (t, J=7.1 Hz, 3H). 13C NMR (151 MHz, CDCl3) δ 173.84, 154.20, 146.21, 135.70, 121.49, 117.89, 81.82, 76.68, 60.22, 34.31, 29.15, 28.95, 28.80, 24.85, 14.28.
Synthesized according to the general THP deprotection conditions (0.1 mmol scale, 76% yield). 1H NMR (600 MHz, acetone-d6) δ 9.94 (s, 1H), 7.86 (s, 1H), 7.46 (s, 1H), 6.38 (d, J=11.7 Hz, 2H), 5.80-5.74 (m, 1H), 2.61 (q, J=7.4 Hz, 2H), 2.11 (t, J=7.3 Hz, 2H), 1.64 (dt, J=14.9, 7.5 Hz, 2H), 1.50 (dt, J=14.9, 7.3 Hz, 2H), 1.39 (dt, J=15.2, 7.6 Hz, 2H). 13 C NMR (151 MHz, acetone-d6) δ 169.59, 153.97, 134.93, 134.30, 122.34, 120.92, 32.26, 29.49, 29.04, 28.55, 25.16. HRMS (ESI) calcd for C11H16BrN2O2S (M+H) 319.0115 found 319.0122.
Synthesized according to the general THP deprotection conditions (0.1 mmol scale, 75% yield). 1H NMR (600 MHz, acetone-d6) δ 9.96 (s, 1H), 8.01 (s, 1H), 7.53 (s, 1H), 6.44 (d, J=11.7 Hz, 1H), 5.80 (dt, J=11.7, 7.3 Hz, 1H), 4.30 (s, 1H), 2.64 (dd, J=13.8, 7.1 Hz, 2H), 2.11 (t, J=7.3 Hz, 2H), 1.67-1.61 (m, 2H), 1.50 (dt, J=15.1, 7.5 Hz, 2H), 1.38 (dd, J=14.9, 7.0 Hz, 2H). 13C NMR (151 MHz, acetone-d6) δ 169.69, 154.36, 146.10, 135.08, 121.22, 119.13, 83.04, 76.56, 32.26, 29.05, 28.84, 28.72, 25.20. HRMS (ESI) calcd for C13H17N2O2S (M+H) 265.1010, found 265.1017.
To a round bottom flask containing methyl (E)-4-bromobut-2-enoate (S28) (3.8 g, 21.7 mmol, 1 equiv.) was added triethyl phosphite (3.77 mL, 21.7 mmol, 1 equiv). The resulting mixture was heated at 160° C. for 30 min, after which point it was allowed to cool to room temperature. The prepared methyl (E)-4-(diethoxyphosphoryl)but-2-enoate (S29) was added to a stirred solution of 2-bromothiazole-4-carbaldehyde (4.1 gr, 21.7 mmol) in DME (50 mL), followed by the dropwise addition of freshly prepared 1 M MeONa in MeOH (21.7 mL, 1 equiv.). The resulting mixture was stirred at r.t. for 30 min, transferred to a flask containing iced water, and stirred for an additional 15 min. EtOAc was added and the organic layer was collected, dried over anhydrous Na2SO4, filtered, and concentrated under reduced pressure. The crude product mixture was purified by silica gel chromatography in EtOAc/hexanes (0->100% EtOAc) to yield pure compound (NC-4) (3.7 g, 13.4 mmol, 62%). 1H NMR (600 MHz, CDCl3) δ 7.42 (ddd, J=15.2, 11.5, 0.5 Hz, 1H), 7.24-7.19 (m, 1H), 7.19 (s, 1H), 6.78 (d, J=9.3 Hz, 1H), 6.07 (d, J=15.3 Hz, 1H), 3.79 (s, 3H). 13C NMR (151 MHz, CDCl3) δ 167.18, 153.10, 143.70, 136.79, 130.48, 129.82, 122.92, 120.84, 51.76.
Synthesized according to general Sonogashira coupling conditions (0.66 mmol scale, 60% yield). 1H NMR (600 MHz, CDCl3) δ 7.49-7.40 (m, 1H), 7.33-7.25 (m, 2H), 6.85 (d, J=15.2 Hz, 1H), 6.08 (d, J=15.2 Hz, 1H), 3.80 (s, 3H), 3.53 (s, 1H). 13C NMR (151 MHz, CDCl3) δ 167.37, 153.60, 147.90, 143.86, 130.93, 130.09, 122.70, 119.76, 82.82, 76.22, 51.68. HRMS (ESI) calcd for C11H10NO2S (M+H) 220.0432, found 220.0441.
Synthesized according to general hydrolysis conditions. (0.11 mmol scale, 88% yield). 1 H NMR (600 MHz, DMSO d6) δ 12.37 (s, 1H), 7.81 (s, 1H), 7.32 (dd, J=15.1, 11.3 Hz, 1H), 7.14 (dd, J=15.1, 11.3 Hz, 1H), 7.03 (d, J=15.1 Hz, 1H), 6.11 (d, J=15.2 Hz, 1H). 13C NMR (151 MHz, DMSO d6) δ 167.91, 153.21, 143.86, 137.53, 131.41, 129.53, 124.46, 124.11.
Synthesized according to the general NH2 OTHP coupling conditions (0.1 mmol scale, 93% yield). 1H NMR (600 MHz, acetone d6) δ 10.38 (s, 1H), 7.66 (s, 1H), 7.40-7.34 (m, 1H), 7.18 (t, J=12.3 Hz, 1H), 6.97 (d, J=15.0 Hz, 1H), 6.20 (d, J=15.0 Hz, 1H), 4.99 (s, 1H), 4.00 (t, J=10.5 Hz, 1H), 3.54 (d, J=10.9 Hz, 1H), 1.88-1.65 (m, 3H), 1.66-1.48 (m, 3H). 13C NMR (151 MHz, acetone d6) δ 153.70, 139.47, 136.21, 129.75, 123.20, 122.25, 101.49, 61.51, 27.98, 25.01, 18.42.
Synthesized according to the general THP deprotection conditions (0.07 mmol scale, 50% yield). 1H NMR (600 MHz, MeOD-d4) δ 7.54 (s,1H), 7.36-7.30 (m, J=14.5 Hz, 1H), 7.19-7.13 (m, J=14.8, 11.5 Hz, 1H), 6.92-6.85 (m, J=15.1 Hz, 1H), 6.09-6.03 (m, J=12.8 Hz, 1H). 13C NMR (151 MHz, MeOD d4) δ 164.86, 153.52, 139.46, 136.77, 129.58, 129.40, 121.84. HRMS (ESI) calcd for C8H8BrN2O2S (M+H) 274.9489, found 274.9479.
Synthesized according to general Sonogashira coupling conditions (0.35 mmol scale, 70% yield). 1H NMR (600 MHz, CDCl3) δ 8.82 (br, 1H), 7.55-7.42 (m, 1H), 7.30-7.27 (m, 1H), 6.83 (d, J=15.1 Hz, 1H), 5.94 (br, J=69.6 Hz, 1H), 5.01 (s, 1H), 4.05-3.94 (m, 1H), 3.79-3.74 (m, 1H), 3.66 (ddd, J=11.1, 5.5, 4.1 Hz, 1H), 1.87-1.82 (m, 3H), 1.67-1.61 (m, 3H). 13C NMR (151 MHz, CDCl3) δ 207.71, 157.04, 153.28, 152.99, 147.83, 130.54, 130.15, 127.52, 121.34, 119.54, 100.81, 82.50, 76.24, 62.66, 28.07, 24.69, 18.66.
Synthesized according to the general THP deprotection conditions (0.063 mmol scale, 63% yield) using TFA/DCM instead of HCl/MeOH. 1H NMR (600 MHz, acetone d6) δ 10.36 (s, 1H), 8.11 (s, 1H), 7.73 (s, 1H), 7.35 (t, J=13.3 Hz, 1H), 7.27-7.21 (m, 1H), 7.00 (d, J=14.9 Hz, 1H), 6.18 (d, J=14.7 Hz, 1H), 4.37 (s, 1H). 13C NMR (151 MHz, acetone d6) δ 163.23, 153.99, 147.41, 138.92, 130.03, 129.88, 122.58, 120.15, 83.64, 76.23. HRMS (ESI) calcd for C10H9N2O2S (M+H) 221.0384, found 221.0962.
To a stirred solution of triphenyl phosphine (2.3 g, 9 mmol, 1.05 equiv.) in EtOAc (14 mL) was slowly added a solution of bromomethyl acetate (S30) (1.3 g, 8.5 mmol) in EtOAc (2.5 mL). The resulting mixture was stirred at r.t for 12 h. The precipitated white solid was collected by filtration, washed with diethyl ether, and air-dried overnight. It was resuspended in 1 N NaOH (16 mL) and stirred for 20 min, at which point DCM was added. The organic layer was washed with brine, dried over anhydrous Na2SO4, filtered, and concentrated under vacuum to provide ylide (19), which was used in the next step without further purification.
The ylide (19) synthesized as described above (9 mmol) and 2-bromothiazole-4-carbaldehyde (2) (1.7 g, 9 mmol, 1 equiv) were dissolved in THF (52 mL) and stirred at r.t for 12 h. Brine and DCM were added and the organic layer was separated and dried over anhydrous Na2SO4, filtered, and concentrated under vacuum. The crude product was purified by silica gel chromatography in EtOAc/Hexanes (0->100% EtOAc) to provide the pure product (NC-5) (2 g, 8.1 mmol, 90%). 1H NMR (600 MHz, CDCl3) δ 7.55-7.49 (m, 1H), 7.37 (s, 1H), 6.77 (d, J=15.5 Hz, 1H), 3.80 (s, 3H). 13C NMR (151 MHz, CDCl3) δ 167.19, 151.69, 137.37, 134.50, 124.78, 121.49, 52.42. HRMS (ESI) calcd for C7H7BrNO2S (M+H) 247.9380, found 247.9382.
Synthesized according to general Sonogashira coupling conditions (0.415 mmol scale, 83% yield). 1H NMR (600 MHz, CDCl3) δ 7.60 (d, J=15.6 Hz, 1H), 7.46 (s, 1H), 6.84 (d, J=15.6 Hz, 1H), 3.82 (s, 3H), 3.54 (s, 1H). 13C NMR (151 MHz, CDCl3) δ 167.34, 152.04, 148.16, 135.40, 122.77, 121.61, 82.79, 75.98, 51.77. HRMS (ESI) calcd for C9H8NO2S (M+H) 194.0275, found 194.0279.
Synthesized according to general hydrolysis conditions. (2.17 mmol scale, 99% yield). 1H NMR (600 MHz, DMSO-d6) δ 12.54 (s, 1H), 8.10 (s, 1H), 7.53 (d, J=15.5 Hz, 1H), 6.48 (d, J=15.5 Hz, 1H). 13C NMR (151 MHz, DMSO-d6) δ 167.75, 151.43, 138.01, 135.71, 128.28, 121.84.
Synthesized according to the general NH2 OTHP coupling conditions (2.11 mmol scale, 88% yield). 1H NMR (600 MHz, acetone d6) δ 10.42 (s, 1H), 7.86 (s, 1H), 7.53 (d, J=15.3 Hz, 1H), 6.79 (t, J=13.7 Hz, 1H), 5.02 (s, 1H), 4.02 (t, J=10.5 Hz, 1H), 3.58-3.54 (m, 1H), 1.81-1.74 (m, 3H), 1.63-1.56 (m, 3H). 13C NMR (151 MHz, acetone d6) δ 162.64, 152.48, 136.59, 133.36, 131.35, 101.43, 67.43, 61.48, 27.94, 27.32, 25.04, 25.00, 22.77, 18.35.
Synthesized according to the general THP deprotection conditions (0.29 mmol scale, 97% yield). 1H NMR (600 MHz, DMSO-d6) δ 10.83 (S, 1H), 9.12 (d, J=1.7 Hz, 1H), 7.95 (s, 1H), 7.40 (d, J=15.3 Hz, 1H), 6.63 (d, J=15.3 Hz, 1H). 13C NMR (151 MHz, DMSO-d6) δ 162.61, 151.88, 137.57, 130.78, 126.63, 121.85. HRMS (ESI) calcd for C6H6BrN2O2S (M+H) 248.9333, found 248.9345.
Synthesized according to general Sonogashira coupling conditions (1.16 mmol scale, 83% yield). 1H NMR (600 MHz, acetone d6) δ 10.45 (s, 1H), 7.96 (s, 1H), 7.61 (d, J=15.8 Hz, 2H), 6.90 (d, J=15.8 Hz, 1H), 5.05 (s, 1H), 4.41 (s, 1H), 4.06 (s, 1H), 3.59 (s, 1H), 1.80 (m, 3H), 1.62 (m, 3H). 13C NMR (151 MHz, acetone d6) δ 162.60, 152.64, 147.77, 131.74, 128.57, 123.06, 121.73, 101.50, 83.89, 76.11, 61.50, 27.99, 25.05, 18.39.
Synthesized according to the general THP deprotection conditions (0.29 mmol scale, 96% yield). 1H NMR (600 MHz, DMSO-d6) δ 10.85 (s, 1H), 9.12 (s, 1H), 8.05 (s, 1H), 7.44 (d, J=15.3, 6.9 Hz, 1H), 6.68 (d, J=15.3 Hz, 1H), 5.02 (s, 1H). 13C NMR (151 MHz, DMSO-d6) δ 162.79, 152.45, 147.73, 131.00, 124.14, 122.28, 87.09, 76.58. HRMS (ESI) calcd for C8H7N2O2S (M+H) 195.0228, found 195.0222.
Synthesized as previously described for the synthesis of compound (14) using LiOH as the base instead of NaOH (1.41 mmol scale, 70% yield). 1H NMR (600 MHz, CDCl3) δ 6.88 (s, 1H), 6.63-6.56 (m, 1H), 6.31 (d, J=14.6 Hz, 1H), 4.17-4.11 (m, 2H), 2.35-2.28 (m, 2H), 2.26-2.17 (m, 2H), 1.70-1.62 (m, J=6.9 Hz, 2H), 1.54-1.47 (m, 2H), 1.42-1.35 (m, 2H), 1.30-1.24 (m, 3H). 13C NMR (151 MHz, CDCl3) δ 173.80, 154.76, 135.84, 135.27, 121.98, 116.28, 60.24, 34.29, 32.43, 28.66, 28.60, 24.80, 14.27. HRMS (ESI) calcd for C13H19BrNO2S (M+H) 334.0319, found 334.0311.
Synthesized according to general Sonogashira coupling conditions (0.268 mmol scale, 67% yield). 1H NMR (600 MHz, CDCl3) δ 6.99 (s, 1H), 6.68-6.62 (m, 1H), 6.39 (dd, J=15.6, 1.4 Hz, 1H), 4.17-4.12 (m, 2H), 3.47 (s, 1H), 2.31 (dd, J=9.7, 5.4 Hz, 2H), 2.26-2.22 (m, 2H), 1.66 (dt, J=15.4, 7.6 Hz, 2H), 1.51 (dt, J=15.2, 7.6 Hz, 2H), 1.44-1.36 (m, 3H), 1.27 (t, J=7.1 Hz, 3H). 13 C NMR (151 MHz, CDCl3) δ 173.82, 155.04, 147.05, 135.40, 122.29, 114.94, 81.92, 76.61, 60.22, 34.30, 32.53, 29.71, 28.67, 28.61, 24.81, 14.26. HRMS (ESI) calcd for C15H20NO2S (M+H) 278.1214, found 278.1242.
Synthesized according to the general THP deprotection conditions (0.04 mmol scale, 77% yield). 1H NMR (600 MHz, MeOH-d4) δ 7.22 (s, 1H), 6.58-6.51 (m, 1H), 6.38 (d, J=15.6 Hz, 1H), 3.66 (s, 1H), 2.25 (q, J=6.9 Hz, 2H), 2.12 (t, J=7.4 Hz, 2H), 1.67 (dt, J=15.0, 7.5 Hz, 3H), 1.52 (dd, J=15.0, 7.5 Hz, 2H), 1.41 (dd, J=15.3, 8.3 Hz, 3H), 0.92 (t, J=6.8 Hz, 2H). 13 C NMR (151 MHz, MeOH d4) δ 171.53, 154.59, 135.81, 134.41, 121.96, 117.06, 32.28, 32.02, 28.40, 28.23, 25.19. HRMS (ESI) calcd for C11H16BrN2O2S (M+H) 319.0115, found 319.0122.
Synthesized according to the general THP deprotection conditions (0.105 mmol scale, 75% yield). 1H NMR (600 MHz, acetone-d6) δ 9.95 (s, 1H), 7.86 (s, 1H), 7.42 (s, 1H), 6.66-6.61 (m, 2H), 6.48 (d, J=15.6 Hz, 2H), 4.29 (s, 1H), 2.24 (q, J=6.9 Hz, 3H), 2.12 (dd, J=12.0, 4.6 Hz, 3H), 1.64 (dt, J=15.1, 7.5 Hz, 4H), 1.50 (dd, J=15.0, 7.5 Hz, 4H), 1.38 (dt, J=15.0, 7.6 Hz, 4H). 13C NMR (151 MHz, acetone-d6) δ 169.58, 155.07, 146.68, 134.76, 122.64, 115.78, 82.96, 76.54, 32.22, 28.57, 28.49, 25.12. HRMS (ESI) calcd for C13H17N2O2S (M+H) 265.1010, found 265.1034.
Synthesized following similar protocol for the synthesis of compound (7). 100% yield. 1H NMR (600 MHz, DMSO) δ 7.99 (s, 3H), 3.58 (s, 3H), 2.75 (s, 2H), 2.34 (s, 2H), 1.56 (s, 4H). 13C NMR (151 MHz, DMSO) δ 173.56, 51.75, 38.80, 33.11, 26.82, 21.82.
Synthesized following similar protocol for the synthesis of (NC-1). 36% yield. 1H NMR (600 MHz, CDCl3) δ 8.03 (s, 1H), 7.24 (d, J=5.6 Hz, 1H), 3.67 (s, 3H), 3.44 (dd, J=13.1, 6.8 Hz, 2H), 2.36 (t, J=7.3 Hz, 2H), 1.75-1.60 (m, 4H). 13C NMR (151 MHz, CDCl3) δ 173.81, 159.71, 150.01, 135.82, 126.70, 51.63, 39.01, 33.56, 29.06, 22.21.
Synthesized according to general hydrolysis conditions. 92% yield. 1H NMR (600 MHz, DMSO) δ 8.54 (t, J=6.0 Hz, 1H), 8.20 (s, 1H), 3.26-3.18 (m, 2H), 2.21 (t, J=6.9 Hz, 2H), 1.50-1.45 (m, 4H). 13C NMR (151 MHz, DMSO) δ 175.31, 160.00, 149.95, 136.92, 128.84, 38.82, 33.71, 28.88, 22.23.
Synthesized according to the general NH2 OTHP coupling conditions. 72% yield. 1HNMR (600 MHz, CDCl3) δ 9.19 (s, 1H), 8.07 (s, 1H), 7.38 (s, 1H), 4.97 (s, 1H), 3.97 (t, J=9.9 Hz, 1H), 3.65-3.58 (m, 1H), 3.45 (dd, J=12.8, 6.3 Hz, 2H), 2.23 (dd, J=20.5, 13.0 Hz, 2H), 1.84-1.66 (m, 10H). 13C NMR (151 MHz, CDCl3) δ 170.29, 160.01, 149.80, 135.95, 126.96, 102.36, 94.50, 62.44, 38.67, 32.46, 28.84, 27.99, 25.02, 22.51, 18.53.
Synthesized according to general Sonogashira coupling conditions. 58% yield. 1H NMR (400 MHz, CDCl3) δ 8.81 (s, 1H), 8.10 (s, 1H), 7.40 (s, 1H), 4.94 (s, 1H), 3.94 (t, J=9.6 Hz, 1H), 3.65-3.55 (m, 1H), 3.53 (s, 1H), 3.49-3.37 (m, 4H), 1.81-1.58 (m, 10H). 13C NMR (151 MHz, CDCl3) δ 170.24, 160.46, 150.47, 147.24, 125.08, 102.33, 83.16, 75.65, 62.40, 38.60, 32.52, 29.70, 28.87, 27.98, 25.02, 22.56, 18.41.
Compound S7 was synthesized using the general THP deprotection conditions. 14% yield. 1H NMR (600 MHz, acetone-d6) δ 10.04 (s, 1H), 8.27 (s, 1H), 8.23 (s, 1H), 7.95 (s, 1H), 4.43 (s, 1H), 3.47-3.41 (m, 2H), 2.17 (t, J=6.9 Hz, 2H), 1.73-1.60 (m, 4H). 13C NMR (151 MHz, acetone-d6) δ 169.79, 159.80, 151.24, 147.14, 125.30, 84.24, 75.69, 38.49, 31.90, 29.02, 22.62.
Synthesized following similar protocol for the synthesis of compound (7). 100% yield. 1H NMR (600 MHz, DMSO) δ 8.11 (s, 3H), 3.58 (s, 3H), 2.76-2.67 (m, 2H), 2.34-2.22 (m, 2H), 1.61-1.45 (m, 4H), 1.34-1.25 (m, 2H). 13C NMR (151 MHz, DMSO) δ 173.27, 51.28, 38.49, 33.06, 26.59, 25.33, 23.92.
Synthesized following similar protocol for the synthesis of (NC-1). 53% yield. 1H NMR (600 MHz, CDCl3) δ 8.03 (s, 1H), 7.22 (s, J=10.8 Hz, 1H), 3.66 (s, 3H), 3.43 (dd, J=13.6, 6.8 Hz, 2H), 2.32 (t, J=7.5 Hz, 2H), 1.71-1.65 (m, 2H), 1.65-1.59 (m, 2H), 1.44-1.37 (m, 2H). 13C NMR (151 MHz, CDCl3) δ 174.16, 159.79, 150.19, 135.91, 126.80, 51.68, 39.37, 34.02, 29.44, 26.54, 24.68.
Synthesized according to general hydrolysis conditions. 92% yield. 1H NMR (600 MHz, DMSO) δ 11.99 (s, 1H), 8.51 (t, J=5.8 Hz, 1H), 8.25 (s, 1H), 3.21 (dd, J=13.5, 6.7 Hz, 2H), 2.19 (t, J=7.4 Hz, 2H), 1.54-1.45 (m, 4H), 1.30-1.23 (m, 2H). 13C NMR (151 MHz, DMSO) δ 174.95, 159.58, 150.38, 136.66, 128.76, 39.08, 34.04, 29.31, 26.39, 24.69.
Synthesized according to the general NH2 OTHP coupling conditions. 79% yield. 1H NMR (600 MHz, CDCl3) δ 9.20 (s, 1H), 8.04 (s, 1H), 7.31 (s, 1H), 4.93 (s, 1H), 3.93 (t, J=9.8 Hz, 1H), 3.57 (d, J=11.1 Hz, 1H), 3.38 (dd, J=13.2, 6.6 Hz, 2H), 2.10 (s, J=6.5 Hz, 2H), 1.80-1.54 (m, 12H). 13C NMR (151 MHz, CDCl3) δ 170.43, 159.83, 149.93, 135.88, 126.90, 102.35, 62.43, 39.28, 33.04, 29.24, 28.00, 25.01, 18.57.
Synthesized according to general Sonogashira coupling conditions. 55% yield. 1H NMR (400 MHz, CDCl3) δ 9.21 (s, 1H), 8.11 (s, 1H), 7.39 (s, 1H), 4.92 (s, 1H), 3.92 (t, J=9.0 Hz, 1H), 3.59-3.52 (m, 2H), 3.38 (dd, J=13.2, 6.6 Hz, 2H), 2.10 (s, 2H), 1.77-1.51 (m, 12H). 13C NMR (151 MHz, CDCl3) δ 170.46, 160.33, 150.49, 147.28, 125.18, 102.20, 83.46, 75.63, 62.27, 39.27, 32.99, 29.23, 27.98, 26.37, 25.00, 18.53.
Compound S14 was synthesized using the general THP deprotection conditions. 24% yield. 1H NMR (600 MHz, acetone-d6) δ 10.02 (s, 1H), 8.27 (s, 1H), 8.27 (s, 1H), 7.95 (s, 1H), 4.43 (s, 1H), 3.42 (dd, J=13.5, 6.7 Hz, 2H), 2.13 (t, J=7.3 Hz, 2H), 1.71-1.59 (m, 4H), 1.45-1.36 (m, 2H). 13 C NMR (151 MHz, acetone-d6) δ 169.75, 159.72, 151.31, 147.12, 125.24, 84.23, 75.70, 38.83, 32.24, 26.24, 25.00.
Synthesized following similar protocol for the synthesis of compound (7). 100% yield. 1 H NMR (600 MHz, DMSO) δ 7.80 (s, 3H), 3.58 (s, 3H), 2.76-2.72 (m, 2H), 2.31-2.27 (m, 2H), 1.56-1.46 (m, 4H), 1.31-1.21 (m, 6H). 13C NMR (151 MHz, DMSO) δ 173.84, 51.67, 39.19, 33.68, 28.70, 28.62, 27.38, 26.09, 24.76.
Synthesized following similar protocol for the synthesis of NC-1. 40% yield. 11H NMR (600 MHz, CDCl3) δ 8.03 (s, J=1.0 Hz, 1H), 7.20 (s, 1H), 3.66 (s, 3H), 3.41 (dd, J=13.5, 6.9 Hz, 2H), 2.30 (t, J=7.5 Hz, 2H), 1.66-1.55 (m, 4H), 1.41-1.27 (m, 6H). 13C NMR (151 MHz, CDCl3) δ 174.28, 159.64, 150.14, 135.76, 126.62, 51.51, 39.47, 34.05, 29.54, 29.01, 28.93, 26.75, 24.86.
Synthesized according to general hydrolysis conditions. 83% yield. 11H NMR (600 MHz, DMSO) δ 8.50 (t, J=5.9 Hz, 1H), 8.23 (s, 1H), 3.20 (dd, J=13.6, 6.7 Hz, 2H), 2.17 (t, J=7.4 Hz, 2H), 1.50-1.43 (m, 4H), 1.25 (s, J=2.1 Hz, 6H). 13C NMR (151 MHz, DMSO) δ 175.06, 159.64, 150.33, 136.69, 128.74, 39.20, 34.11, 29.48, 28.95, 28.90, 26.71, 24.91.
Synthesized according to the general NH2 OTHP coupling conditions. 72% yield. 11H NMR (600 MHz, CDCl3) δ 8.88 (s, 1H), 8.08 (t, J=15.9 Hz, 1H), 7.26 (s, J=14.1 Hz, 1H), 4.94 (s, 1H), 3.94 (s, 1H), 3.62-3.59 (m, 1H), 3.44-3.38 (m, 2H), 2.13 (m, 2H), 1.85-1.76 (m, 4H), 1.66-1.45 (m, 12H). 13C NMR (151 MHz, CDCl3) δ 170.67, 159.84, 149.97, 135.86, 102.52, 62.60, 39.21, 38.82, 29.39, 28.52, 28.03, 27.79, 24.93, 18.66.
Synthesized according to general Sonogashira coupling conditions. 34% yield. 11H NMR (600 MHz, CDCl3) δ 8.70 (s, 1H), 8.16 (s, 1H), 7.34 (s, 1H), 4.95 (s, 1H), 3.95 (t, J=9.0 Hz, 1H), 3.61 (ddd, J=9.8, 4.8, 3.5 Hz, 1H), 3.54 (s, 1H), 3.43 (dd, J=13.4, 6.8 Hz, 2H), 2.10 (s, 2H), 1.84-1.54 (m, 10H), 1.34 (s, 6H). 13C NMR (151 MHz, CDCl3) δ 160.31, 150.65, 147.23, 125.11, 102.52, 83.08, 75.70, 62.61, 39.13, 33.08, 29.42, 28.65, 28.35, 28.03, 26.37, 25.03, 18.66.
Compound (S21) was synthesized using the general THP deprotection conditions. 62% yield. 11H NMR (600 MHz, acetone-d6) δ 10.07 (s, 1H), 8.40 (s, 1H), 8.29 (s, 1H), 7.96 (s, 1H), 4.43 (s, 1H), 3.43 (dd, J=13.4, 6.8 Hz, 2H), 2.11 (dd, J=9.4, 5.3 Hz, 2H), 1.67-1.56 (m, 4H), 1.42-1.25 (m, 6H). 13C NMR (151 MHz, acetone-d6) δ 169.98, 159.77, 151.29, 147.13, 125.27, 84.25, 75.70, 38.87, 38.74, 32.24, 29.47, 28.77, 28.67, 26.54, 25.21.
Synthesized according to general hydrolysis conditions. (0.27 mmol scale, 92% yield.) 1H NMR (600 MHz, acetone-d 6) δ 10.47 (br, 1H), 7.46 (s, 1H), 6.38 (dt, J=11.7, 1.5 Hz, 1H), 5.81-5.75 (m, 1H), 2.65-2.60 (m, 2H), 2.33-2.28 (m, 2H), 1.68-1.61 (m, 2H), 1.55-1.49 (m, 2H), 1.46-1.40 (m, 2H). 13C NMR (151 MHz, acetone-d 6) δ 173.67, 153.95, 134.90, 134.24, 120.92, 33.24, 29.02, 28.64, 28.57, 24.62.
Synthesized according to the general NH2 OTHP coupling conditions (0.9 mmol scale, 90% yield). 1H NMR (600 MHz, CDCl3) δ 8.53 (s, 1H), 7.02 (s, 1H), 6.36 (d, J=11.7 Hz, 1H), 5.75 (dt, J=11.8, 7.3 Hz, 1H), 4.96 (s, 1H), 3.95 (d, J=8.8 Hz, 1H), 3.63 (dtd, J=11.2, 4.2, 1.6 Hz, 2H), 2.52 (q, J=6.8 Hz, 3H), 2.20-2.02 (m, 2H), 1.87-1.76 (m, 4H), 1.73-1.56 (m, 9H), 1.50 (dt, J=14.5, 7.2 Hz, 4H), 1.42 (dt, J=13.1, 6.5 Hz, 4H). 13C NMR (151 MHz, CDCl3) δ 170.58, 153.82, 135.50, 134.75, 121.17, 119.43, 102.53, 62.58, 33.32, 29.09, 28.76, 28.00, 25.19, 25.02, 18.60.
Synthesized according to general Sonogashira coupling conditions (0.06 mmol scale, 65% yield). 1H NMR (600 MHz, CDCl3) δ 8.38 (s, 1H), 7.12 (s, 1H), 6.44 (d, J=11.7 Hz, 1H), 5.80 (dt, J=11.7, 7.3 Hz, 1H), 4.96 (s, 1H), 3.98-3.93 (m, 1H), 3.66-3.62 (m, 1H), 2.55 (q, J=6.9 Hz, 2H), 2.16-2.11 (m, 2H), 1.87-1.77 (m, 2H), 1.73-1.58 (m, 6H), 1.51 (dd, J=14.7, 7.4 Hz, 2H), 1.42 (dd, J=14.6, 7.5 Hz, 2H). 13C NMR (151 MHz, CDCl3) δ 170.59, 154.17, 146.24, 135.65, 121.49, 117.99, 102.52, 81.88, 76.69, 62.56, 33.33, 29.04, 28.88, 28.75, 27.99, 25.16, 25.01, 18.58.
Synthesized according to general hydrolysis conditions. (1.3 mmol scale, 92% yield). 1 H NMR (600 MHz, MeOH-d4) δ 7.22 (s, 1H), 6.58-6.51 (m, 1H), 6.38 (dt, J=15.5, 1.3 Hz, 1H), 2.32 (t, J=7.4 Hz, 2H), 2.24 (tt, J=7.0, 3.4 Hz, 2H), 1.65 (dt, J=15.1, 7.5 Hz, 2H), 1.53 (dt, J=14.9, 7.4 Hz, 2H), 1.44 -1.39 (m, 2H). 13C NMR (151 MHz, MeOH d4) δ 176.24, 154.60, 135.80, 134.46, 121.93, 117.04, 33.48, 32.05, 28.47, 28.36, 24.53.
Synthesized according to the general NH 2 OTHP coupling conditions (530 mg, 1.27 mmol, 90%). 1H NMR (600 MHz, CDCl3) δ 8.26 (s, 1H), 6.90 (s, 1H), 6.62-6.55 (m, 1H), 6.32 (d, J=15.5 Hz, 1H), 4.96 (s, 1H), 3.99-3.92 (m, 1H), 3.65 (m, 1H), 2.23 (q, J=7.0 Hz, 2H), 2.12 (S, 2H), 1.88-1.80 (m, 4H), 1.71-1.62 (m, 6H), 1.53-1.48 (m, 2H), 1.42-1.38 (m, 2H). 13C NMR (151 MHz, CDCl3) δ 156.74, 154.70, 135.84, 122.10, 116.33, 100.51, 33.35, 32.40, 29.12, 28.60, 27.97, 25.28, 25.01, 20.31, 18.56.
Synthesized according to general Sonogashira coupling conditions (0.167 mmol scale, 67% yield). 11H NMR (600 MHz, CDCl3) δ 8.23 (br, J=20.4 Hz, 1H), 7.00 (s, 1H), 6.64 (dt, J=14.4, 7.0 Hz, 1H), 6.39 (d, J=15.6, 1.3 Hz, 1H), 4.96 (s, 1H), 3.95 (t, J=7.5 Hz, 1H), 3.67-3.63 (m, 1H), 2.24 (dd, J=13.9, 6.9 Hz, 2H), 2.12 (s, 2H), 1.87-1.78 (m, 4H), 1.71-1.59 (m, 6H), 1.51 (dt, J=14.7, 7.2 Hz, 2H), 1.44-1.37 (m, 2H). 13C NMR (151 MHz, CDCl3) δ 170.55, 155.01, 147.07, 135.34, 122.35, 114.99, 102.53, 81.95, 76.61, 62.57, 33.38, 32.49, 29.72, 28.66, 27.96, 25.19, 25.01, 18.54.
The docking analysis was accomplished using Glide tool on maestro version 10.6. A library of the compounds was generated utilizing the ligand prep tool allowing possible ionization states at pH=7±2. Protein structures were obtained from protein data bank (PDB) and their structures were prepared using the protein preparation wizard. The prepared protein structures were used to generate the receptor grid using the receptor grid generation tool. The active site was determined by utilizing the co-crystalized ligand. Metal coordination to the zinc ion was implemented as a constraint. Rotation of amino acid side chains was allowed only within the determined active site. Then the library of the compounds was screened with the obtained receptors utilizing the ligand docking tool using extra precision and OPLS3 force field. The results were analyzed with the xp visualizer tool and pose analysis was performed with the pose viewer tool. For the pose analysis the Maestro version 13.1 for academic use was used.
HCT116 human colorectal carcinoma cells, NCI-H522 human lung cancer cells, WI38 diploid human cell line, and human retinal pigment epithelial RPE cells were maintained in Dulbecco's Modified Eagle's medium (Mediatech, Inc.) supplemented with 10% calf serum (Atlanta Biologicals) or 10% fetal bovine serum (Gemini Bio-Products # 100-106) and 1000 U/ml of both Penicillin and Streptomycin (Mediatech, Inc.) at 37° C. with 5% CO2. Cell viability was assessed using methylene blue staining: cells were plated at 5000/well in 96 well plates (n=3) respectively and treated the next day. Three days after treatment cells were fixed/stained in methylene blue saturated in 50% ethanol for 30 min at RT. Plates were washed with excess water to wash off extra dye. Retained dye was dissolved in 0.1 N HCl and absorbance was measured at 668 nm.
Human neuroblastoma cells (SH-SY5Y) were grown on poly-D-lysine coated plates and cultured in DMEM/F12 medium (HyClone, Thermo Scientific) containing 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were maintained in a 37° C. incubator with a 5% CO2 atmosphere. Cells were seeded at a density of 15,000 cells in 96 well plates for 36 hr before treatment of drugs.
Cell viability was assessed using the MTT reagent 3-[4,5 dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (MTT, Promega Corporation USA, Ref no. G4102) according to the manufacturer's instructions. Cells were treated with amide series analogs for 24 hrs. Briefly, the cells were incubated with MTT reagent for 2 h at 37° C. incubator. Then, the solubilization/stop solution was added to solubilize the formazan products, incubated for 1 hr, and absorbance at 570 was measured using micro-plate reader (SynergyH1, BioTek, USA). DMSO was used a vehicle control. The experimental data represent the means±SD (*P<0.05) of triplicates from three separate experiments. The statistical significance was determined by one-way ANOVA and significant differences P<0.05, P<0.01, P<0.001, and P<0.0001 are symbolized as *, **, ***, and ****, respectively.
Pheochromocytoma (PC-12) cells were grown on poly-D-lysine coated plates and cultured in DMEM/F12 medium (HyClone, Thermo Scientific) containing 5% fetal bovine serum, 5% horse serum, and 1% penicillin-streptomycin. Cells were maintained in a 37° C. incubator with a 5% CO2 atmosphere. Cells were seeded at a density of 15,000 cells per well in 96 well plates for 36 hr before treatment with the test compounds. The MTT assay was performed after 24 hr of treatment.
Pheochromocytoma (PC-12) cells were seeded on poly-D-lysine coated plates containing neuron differentiation medium (100 ng nerve growth factor, DMEM/F12, 5% fetal bovine serum, 5% horse serum, and 1% penicillin-streptomycin) and grown for 5 days to differentiate to neurons. Cells were maintained in a 37° C. incubator with a 5% CO2 atmosphere. Cells were trypsinized, and seeded at a density of 15,000 cells/well in 96 well plates with neuron differentiation medium for 36 hr before treatment with the test compounds. The MTT assay was performed after 24 hr of treatment.
For time lapse imaging, NCI-H522 cells were plated at ˜70% density and left overnight to adhere and pre-equilibrate to 10% CO2. The next day cells were treated with DMSO or inhibitors, and the flask was maintained sealed. Flasks were placed on a 37° C. heated stage on an inverted microscope. Images were captured every 12 min and for a total of 300 images using a ×40 microscope objective and an Olympus C740 digital camera controlled by AmScope software. Image analysis was done using Image J. For the Kaplan-Maier graphs at least 100 cells were counted and the event of cell death was measured on a time frame of either 1 h or 0.2 h.
NCI-H522 cells (˜70% density) were plated on 7 cm dishes and let overnight to adhere. The next day cells were treated with DMSO, Inhibitors (10 mM) [with (0.25 mM) or without Liproxstatin-1]. Bodipy 581/591 C11 (1 μM) (ThermoFischer) was added at the time of treatment. After 6 h, cells were washed with 1×PBS and collected by trypsinization and centrifugation. The cells were washed once with 1×PBS and resuspended in PBS containing 2% FBS. Cells were analyzed using a BD LSR Fortessa FACScanner and FlowJo software. For each sample 20×103 cells were analyzed.
NCI-H522 cells (5*105 cells per condition) were plated on 7 cm dishes and left overnight to adhere. After 12 h, 24 h, or 48 h of treatment with DMSO or inhibitors (in presence of Liproxstatin-1 0.25 mM), floating and attached cells were collected by trypsinization and centrifugation. Cells were then washed once with 1×PBS and fixed by pre-chilled ethanol (70% final concentration). After fixation, cells were collected by centrifugation and resuspended in PBS, followed by treatment with RNase H (10 μg/ml) for 30 min at 37° C. Cells again were collected by centrifugation and resuspended in PBS containing 2% FBS and propidium iodide. Cells were analyzed using a BD LSR Fortessa FACScanner and FlowJo software. For each sample 20×103 cells were analyzed.
NCI-H522 cell pellets obtained after the corresponding treatment conditions were lysed using lysis buffer containing 50 mM Tris (pH 7.4), 150 mM NaCl, 0.5% NP-40, (supplemented with 1 μg/ml aprotinin, 2 μg/ml leupeptin, 1 μg/ml pepstatin A, 1 mM DTT, and 0.1 M PMSF) for 30 minutes on ice and centrifuged at 13×103 g for 25 minutes at 4° C. The protein levels of the obtained lysates were normalized using BCA Protein Assay Kit (Pierce) and separated by SDS-polyacrylamide gel electrophoresis (12.5% acrylamide). Transfer to polyvinylidene difluoride membranes (Millipore) was followed by blocking of membranes with blocking buffer containing 5% (w/v) non-fat dry milk dissolved in PBST [1×PBS containing 0.05% (v/v) Tween 20] for 1 hour at room temperature. Membranes were then incubated with corresponding primary antibodies overnight at 4° C. The membranes were then washed (3×15 min each) with PBST and incubated with secondary antibodies conjugated to horse-radish peroxidase, obtained from Biorad and used at a dilution of 1:10,000. Bound antibodies were detected using enhanced chemiluminescence (Biorad).
Inhibitor testing with HDAC class I, IIa, and IIb: In a half-area 96-well white opaque plate (Corning), recombinant HDAC1 (1 μL; 3 ng/μL, BPS Bioscience), HDAC2 (1 μL; 1 ng/μL, BPS Bioscience), HDAC3 (1 μL; 30 ng/μL, BPS Bioscience), HDAC6 (1 μL; 35 ng/μL, BPS Bioscience), and HDAC8 (1 μL; 70 ng/μL, BPS Bioscience) were added to HDAC-Glo™ buffer (43 μL) provided by the manufacturer (Promega). In the case of HDAC4, recombinant HDAC4 (1 μL; 2 ng/μL, BPS Bioscience) was added to HDAC-Glo IIa™ buffer (43 μL) provided by Promega. For negative controls, either the HDAC-Glo™ or the HDAC-Glo™ IIa buffer (44 μL) alone was used. Serial dilutions or single concentrations of inhibitors (1 μL in DMSO, concentrations shown in Tables S4-9) or DMSO alone (1 μL) were added to the enzyme solution, followed by 3 hr. incubation at room temperature. For HDAC1, 2, 3, 6, and 8, the HDAC-Glo™ reagent was prepared using the pre-measured lyophilized HDAC-Glo I/II Substrate (Promega) and dissolving in the buffer provided (10 mL). To activate the HDAC-Glo I/II Substrate, the developer reagent was added (1 μL for every 1 mL of HDAC-Glo I/II Substrate solution). For HDAC4, the HDAC-Glo IIa™ reagent was prepared using the pre-measured lyophilized HDAC-Glo Ha luciferase (Promega) and dissolving in the HDAC-Glo IIa buffer provided (10 mL). To activate, the HDAC-Glo IIa substrate (7 μL for every 1 mL of buffer luciferase solution) was added to the luciferase buffer solution and incubated at 37° C. for 1 hour. The developer reagent was added (1 μL for every 1 mL of HDAC-Glo IIa substrate/luciferase solution). The HDAC-Glo™ reagent (5 μL) was added to each reaction containing HDAC1, 2, 3, 5, and 8, whereas the HDAC-Glo™ IIa reagent (5 μL) was added to each reactions containing HDAC4. Luminescent signal was measured every 3 minutes over the course of 30 minutes using an M-Plex Infinite 200 Pro (Tecan). To determine IC50, the luminescent signal at peak reading was first background corrected with the signal from a background control reaction where HDAC was excluded. The background corrected luminescence signal of each inhibitor-containing reaction was divided by the signal of the reaction without inhibitor for each HDAC enzyme to generate a percent deacetylase activity remaining value. IC50 values were calculated by fitting the percent deacetylase activity remaining as a function of inhibitor concentration to a sigmoidal dose-response curve (y=100/(1+(x/IC50)z), where y=percent deacetylase activity and x=inhibitor concentration) using non-linear regression with KaleidaGraph 4.1.3 software.
BDR, bromodomain; CD, Catalytic Domain; CDK, cyclin dependent kinases; CNS, central nervous system; d, doublet (spectral); DCM, dichloromethane; EMT, epithelial to mesenchymal transition; ESI, electrospray ionization; FC, ferroptosis control; FDA, Food and Drug Administration; GPX4, glutathione peroxidase 4; HAT, histone acetyl transferase; HC, HDAC control; HDAC, histone deacetylase; HDACi, histone deacetylase inhibitor; HPLC, high performance liquid chromatography; HRMS, high-resolution mass spectra; HY, hybrid molecules ; MEF2, myocyte enhancer factor-2; NAD, nicotinamide adenine dinucleotide; NC, negative control; NCI, National Cancer Institute; NMR, nuclear magnetic resonance; PDB, protein data bank ; PI, propidium iodide; PUFAs, polyunsaturated fatty acids; q, quartet (spectral); ROS, reactive oxygen species; RPE, retinal pigment epithelial; RPE, retinal pigment epithelial; s, singlet (spectral); SAR, structure activity relationship; SD, standard deviation; t, triplet (spectral); THP, tetrahydropyran; THP, tetrahydropyran-2-yl; TLC, thin layer chromatography; TMS, trimethylsilyl; TNBC, triple-negative breast cancer; Topo, topoisomerase ; UV, ultraviolet; ZBG, zinc binding group; Z-VAD-FMK, N-benzyloxycarbonyl-Val-Ala-Asp(O-Me) fluoromethyl ketone.
Certain embodiments of the compositions and methods disclosed herein are defined in the above examples. It should be understood that these examples, while indicating particular embodiments of the invention, are given by way of illustration only. From the above discussion and these examples, one skilled in the art can ascertain the essential characteristics of this disclosure, and without departing from the spirit and scope thereof, can make various changes and modifications to adapt the compositions and methods described herein to various usages and conditions. Various changes may be made and equivalents may be substituted for elements thereof without departing from the essential scope of the disclosure. In addition, many modifications may be made to adapt a particular situation or material to the teachings of the disclosure without departing from the essential scope thereof.
This application claims priority to U.S. Provisional Application No. 63/401,893 filed under 35 U.S.C. § 111(b) on Aug. 29, 2022, the disclosure of which is incorporated herein by reference in its entirety.
This invention was made with government support under Grant Number 1R15CA213185-01A1 awarded by the National Institutes of Health. The government has certain rights in this invention.
| Number | Date | Country | |
|---|---|---|---|
| 63401893 | Aug 2022 | US |
