Patent Application
20200190083
The present document relates to the field of medicinal chemistry. More particularly, it relates to novel pyridine-containing macrocyclic compounds and libraries that are useful as research tools for drug discovery efforts. The present disclosure also relates to methods of preparing these compounds and libraries and methods of using these libraries, such as in high throughput screening. In particular, these libraries are useful for evaluation of bioactivity at existing and newly identified pharmacologically relevant targets, including G protein-coupled receptors, nuclear receptors, enzymes, ion channels, transporters, transcription factors, protein-protein interactions and nucleic acid-protein interactions. As such, these libraries can be applied to the search for new pharmaceutical agents for the treatment and prevention of a range of medical conditions.
From its start in the 1990's, high throughput screening (HTS) of chemical compound libraries has become an essential part of the drug discovery process with the successful generation of many lead molecules, clinical candidates and marketed pharmaceuticals (Curr. Opin. Chem. Biol. 2001, 5, 273-284; Curr. Opin. Chem. Biol. 2003, 7, 308-325; J. Biomol. Screen. 2006, 11, 864-869; Drug Disc. Today 2006, 11, 277-279; Nat. Rev. Drug Disc. 2011, 10, 188-195). Current collections of molecules for HTS, however, often are overpopulated by compounds related to known pharmaceutical agents, with a continuing need to expand chemical diversity and improve the content of screening collections (Curr. Opin. Chem. Biol. 2010, 14, 289-298; Drug Disc. Today 2013, 18, 298-304). Indeed, the diversity of molecular structures available in the library collections utilized for HTS has been identified as an area that needs to be dramatically improved (Biochem. Pharmacol. 2009, 78, 217-223; Curr. Med. Chem. 2009, 16, 4374-4381; Curr. Opin. Chem. Biol. 2010, 14, 289-298). Whereas the initial efforts at building screening libraries focused primarily on numbers of compounds, the focus has shifted to providing higher quality molecules (Fut. Med. Chem. 2014, 6, 497-502) that permit more complete sampling of “chemical space”. Fortunately, given the estimated vastness of this space (J. Chem. Info. Model. 2007, 47, 342-353), significant opportunity exists for creating and exploring new or underexplored compound classes for desirable biological activity.
As an additional consideration, HTS has traditionally varied considerably in success rate depending on the type of target being interrogated, with certain target classes identified as being particularly challenging, for example protein-protein interactions (PPI). To effectively address such intractable targets, a wider range of compounds and chemotypes will need to be explored. This situation has been exacerbated as advances in genomics and proteomics have led to the identification and characterization of large numbers of new potential pharmacological targets (Nat. Rev. Drug Disc. 2002, 1, 727-730; Drug Disc. Today 2005, 10, 1607-1610; Nat. Biotechnol. 2006, 24, 805-815), many of which fall into these difficult classes.
Recently, macrocycles have been identified as an underexplored class of biologically relevant synthetic molecules that possess properties considered to be amenable to these more difficult targets (Nat. Rev. Drug Disc. 2008, 7, 608-624; J. Med. Chem. 2011, 54, 1961-2004; Fut. Med. Chem. 2012, 4, 1409-1438; Molecules 2013, 18, 6230-6268; J. Med. Chem. 2014, 57, 278-295; Eur. J. Med. Chem. 2015, 94, 471-479; Curr. Pharm. Design 2016, 22, 4086-4093; Biochem. J. 2017, 474, 1109-1125; Chimia 2017, 71, 678-702). Although macrocyclic structures are widespread in bioactive natural products, considerable challenges of synthetic accessibility have to date limited their presence in screening collections.
The interest in macrocycles originates in part from their ability to bridge the gap between traditional small molecules and biomolecules such as proteins, nucleotides and antibodies. They are considered as filling an intermediate chemical space between these two broad classes, but possessing favorable features of each: the high potency and exceptional selectivity of biomolecules with the ease of administration, manufacturing and formulation, favorable drug-like properties and attractive cost-of-goods of small molecules. Hence, macrocycles provide a novel approach to addressing targets on which existing screening collections have not proven effective.
Indeed, macrocycles display dense functionality in a rather compact structural framework, but still occupy a sufficiently large topological surface area and have sufficient flexibility to enable interaction at the disparate binding sites often present in PPI and other difficult targets. In addition, macrocycles possess defined conformations, which can preorganize interacting functionality into appropriate regions of three-dimensional space, thereby permitting high selectivity and potency to be achieved even in early stage hits. Interestingly, spatial or shape diversity in the design of libraries has been identified as an important factor for broad biological activity (J. Chem. Info. Comput. Sci. 2003, 43, 987-1003).
Although cyclic peptide libraries of both synthetic and biosynthetic origin have been prepared and studied in some depth (J. Comput. Aided. Mol. Des. 2002, 16, 415-430; Curr. Opin. Struct. Biol. 2013, 23, 571-580; Drug Discov Today. 2014, 19, 388-399; J. Biomol. Screen. 2015, 20, 563-576; Curr. Opin. Chem. Biol. 2015, 24, 131-138), libraries of macrocyclic non-peptidic or semi-peptidic structures remain more problematic to construct synthetically and their bioactivity has only begun to be investigated (J. Med. Chem. 2011, 54, 1961-2004; J. Med. Chem. 2011, 54, 8305-8320; Macrocycles in Drug Discovery, J. Levin, ed., RSC Publishing, 2014, pp 398-486, ISBN 978-1-84973-701-2; J. Med. Chem. 2015, 58, 2855-2861).
Therefore, methods that combine the heterocyclic structural motifs found in the majority of traditional small molecule pharmaceutical agents with the multiple advantages provided by the macrocycle framework, and further extend to the preparation of libraries of such structures, would be of interest in the effort to create collections of new classes of compounds within which to search for pharmacological potential. As one example, Intl. Pat. Publ. WO 2017/049383 describes macrocyclic libraries containing the five-membered ring heteroaromatic oxazole, thiazole and imidazole groups for this purpose.
Pyridine, pyridine-fused heterocycles and derivatives are recognized for their importance in medicinal chemistry applications (J. Drug Design Med. Chem. 2015, 1, 1-11; Curr. Top. Med. Chem. 2016, 16, 3274-3302). Indeed, the presence of this ring structure in medicinal natural products and in essential nutrients (niacin, nicotinamide) has suggested that pyridines should be considered a privileged scaffold for certain pharmaceutical purposes (Mini-Rev. Med. Chem. 2017, 17, 869-901).
Among the limited examples of pyridine-containing macrocycles is the clinical stage kinase inhibitor, lorlatinib, that is particularly noteworthy for its ability to cross the blood-brain barrier and exert its pharmacological action (J. Med. Chem. 2014, 57, 4720-4744; Proc. Nat. Acad, Sci. USA 2015, 112, 11, 3493-3498; Eur. J. Med. Chem. 2017, 134, 348-356; Lancet Oncol. 2017, 18, 1590-1599). Indeed, much of the interest to date in this hybrid-type structure has been in the kinase area. Macrocyclic pyridyl-pyrimidine derivatives are taught as inhibitors of cyclin-dependent protein kinases CDK2 and CDK5 (Intl. Pat. Publ. WO 04/078682). As a related example, substituted macrocylic pyridyl-pyrimidine derivatives with eukaryotic elongation factor 2 kinase (EF2K) and optional Vps34 kinase inhibitory activity have been reported in Intl. Pat. Publ. WO 2015/150557. In addition, Intl. Pat. Appl. Publ. WO 2014/182839 describes symmetrical macrocyclic compounds comprising a 2,6-disubstituted pyridine ring along with two cysteine components that possess antifungal and antimicrobial activities.
However, the pyridine-containing macrocyclic compounds and libraries of the disclosure provide distinct structural scaffolds from those previously known. In that manner, they satisfy a significant need in the art for novel compounds and libraries that are useful in the search for new therapeutic agents for the prevention or treatment of a wide variety of disease states.
According to one aspect, there are provided libraries of two or more macrocyclic compounds chosen from compounds of formula (I) and their salts as defined in the present disclosure.
According to a additional aspect, there are provided libraries comprising from two (2) to ten thousand (10,000) macrocyclic compounds chosen from compounds of formula (I) and their salts as defined in the present disclosure.
According to other aspects, there are provided libraries comprising discrete macrocyclic compounds chosen from compounds of formula (I) and their salts as defined in the present disclosure and libraries comprising mixtures of macrocyclic compounds chosen from compounds of formula (I) and their salts as defined in the present disclosure.
According to a further aspect, it was found that such libraries can be useful for the identification of macrocyclic compounds that modulate a biological target.
According to still other aspects, there are provided libraries of two or more macrocyclic compounds chosen from compounds of formula (I) and their salts as defined in the present disclosure, dissolved in a solvent and libraries of two or more macrocyclic compounds chosen from compounds of formula (I) and their salts as defined in the present disclosure, distributed in one or more multiple sample holders.
According to a further aspect, there are provided macrocyclic compounds chosen from compounds of formula (I) and their salts as defined in the present disclosure.
According to yet another aspect, there are provided kits comprising the libraries as defined in the present disclosure or compounds as defined in the present disclosure and one or more multiple sample holders.
According to a further aspect, there is provided a method of using the library according to the present disclosure or the compounds of the present disclosure, the method comprises contacting any compound described in the present disclosure with a biological target so as to obtain identification of compound(s) that modulate(s) the biological target.
According to one more aspect, there is provided a process for preparing macrocyclic compounds and libraries thereof as defined in the present disclosure.
It was found that such libraries of macrocyclic compounds are useful as research tools in drug discovery efforts for new therapeutic agents to treat or prevent a range of diseases.
There are provided new macrocyclic compounds and libraries thereof that are useful as research tools for the discovery of new pharmaceutical agents for a range of diseases. Processes for preparing these compounds and libraries, as well as methods of using the libraries, have also been developed and comprise part of this disclosure.
Therefore, in a first aspect, the disclosure relates to libraries comprising at least two macrocyclic compounds selected from the group consisting of compounds of formula (I) and salts thereof.
In a specific embodiment, Q1 is selected from the group consisting of C═O and CH2.
In a further embodiment, Y1 is selected from the group consisting of:
In still another embodiment, A1 is selected from the group consisting of:
In another specific embodiment, V1 is a covalent bond,
In an analogous embodiment, V1 is (B2)—B3-(Q1);
In another similar embodiment, V1 is (B2)—B3—B4-(Q1);
In an additional embodiment, V1 is (B2)—B3—B4—B6-(Q1);
In a further embodiment, at least one of B1, B2, B3, B4, and B5 is selected from the group consisting of:
In yet another embodiment, R2a, R2b, R6a, R6b, R14a, R14b, R22a, R22b, R30a, R30b, and R38 are independently selected from the group consisting of:
In more embodiments, n12b is 1-4 and R6a is amino, n21b is 1-4 and R14a is amino, n30b is 1-4 and R22a is amino, n39b is 1-4 and R30a is amino, or n48b is 1-4 and R48 is amino.
In a further embodiment, the libraries of the present disclosure may comprise as few as two (2) to more than ten thousand (10,000) such macrocyclic compounds.
In an additional embodiment, the library is comprised of macrocyclic compounds chosen from those with structures 4201-4825 as defined herein.
In a preferred embodiment, the library can be synthesized as discrete individual macrocyclic compounds utilizing techniques as described herein.
In still another embodiment, the library is synthesized as mixtures of at least two macrocyclic compounds.
In further embodiments, the macrocyclic compounds in the library are provided as solids (powders, salts, crystals, amorphous material and so on), syrups or oils as they are obtained from the preparation methods described in the disclosure.
In a different embodiment, the macrocyclic compounds in the library are provided dissolved in an appropriate organic, aqueous or mixed solvent, solvent system or buffer.
In another preferred embodiment, the organic solvent used to dissolve the macrocyclic compounds in the library is DMSO. The resulting concentration of the compound in DMSO may be between 0.001 and 100 mM.
In an embodiment relating to the use of the libraries, the macrocyclic compounds are distributed into at least one multiple sample holder, such as a microtiter plate or a miniaturized chip. For most uses, this distribution is done in an array format compatible with the automated systems used in HTS.
In a related embodiment, this distribution may be done as single, discrete compounds in each sample of the at least one multiple sample holder or as mixtures in each sample of the at least one multiple sample holder.
In a further embodiment, the at least one multiple sample holder is a microtiter plate containing 96, 384, 1536, 3456, 6144 or 9600 wells, which includes the sizes typically used in HTS, although other numbers of wells may be utilized for specialized assays or equipment.
In another aspect, the disclosure relates to kits comprising a library of macrocyclic compounds as described herein and at least one multiple sample holder.
In an embodiment, the one multiple sample holder in the kit is a microtiter plate containing 96, 384, 1536, 3456, 6144 or 9600 wells or a miniaturized chip.
In other embodiments, the library in the kit is distributed as individual compounds in each sample of the at least one multiple sample holder or as more than one compound in each sample of the at least one multiple sample holder.
In an additional aspect, the disclosure relates to macrocyclic compounds represented by formula (I) and salts thereof.
In particular embodiments, macrocyclic compounds with structures 4201-4825 as defined in the disclosure and their pharmaceutically acceptable salts are provided.
In a further aspect, the disclosure relates to methods of using the libraries of macrocyclic compounds of formula (I) and their salts for the identification of specific compounds that modulate a biological target by contacting the compounds of the libraries with said target. This is most often done using HTS assays, but may also be done in low or medium throughput assays. The libraries of the disclosure may be tested in these assays in whole or in part and may be tested separately or at the same time as tests of other compounds and libraries.
In an embodiment, the biological target is selected from any known class of pharmacological targets, including, but not limited to, enzymes, G protein-coupled receptors (GPCR), nuclear receptors, ion channels, transporters, transcription factors, protein-protein interactions and nucleic acid-protein interactions. Enzymes include, but are not limited to, proteases, kinases, esterases, amidases, dehydrogenases, endonucleases, hydrolases, lipases, phosphatases, convertases, synthetases and transferases. Since HTS assays have been developed for all of these target classes, the nature of the target is not a limiting factor in the use of the libraries of the present disclosure. Further, given this level of experience, it is within the scope of those skilled in the art to develop such assays for new targets that are identified and characterized for use in drug discovery programs.
In a further embodiment, the modulation in the method of using the libraries is agonism, antagonism, inverse agonism, activation, inhibition or partial variants of each of these types of activities as may be of interest depending on the specific target and the associated disease state.
In other embodiments, the modulation and biological target being investigated in the method of using the libraries may have relevance for the treatment and prevention of a broad range of medical conditions. As such, the libraries of the present disclosure have wide applicability to the discovery of new pharmaceutical agents.
In an additional aspect, the disclosure provides a process for preparing the macrocyclic compounds of formula (I) and libraries of such macrocyclic compounds.
In a particular embodiment, the process involves the following steps:
In another embodiment applicable to libraries, the process further comprises distribution of the final macrocycle compounds into a format suitable for screening.
In an additional embodiment, one or more of the above steps are performed on the solid phase. In particular, the assembly of the building blocks is preferentially conducted on the solid phase.
In further embodiments, the attachment of each individual building block is performed using a reaction independently selected from amide bond formation, reductive amination, Mitsunobu reaction and its variants, such as the Fukuyama-Mitsunobu reaction, nucleophilic substitution and metal- or organometallic-mediated coupling.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs.
The term “alkyl” refers to straight or branched chain saturated or partially unsaturated hydrocarbon groups having from 1 to 20 carbon atoms, in some instances 1 to 8 carbon atoms. Examples of alkyl groups include, but are not limited to, methyl, ethyl, isopropyl, tert-butyl, 3-hexenyl, and 2-butynyl. By “unsaturated” is meant the presence of 1, 2 or 3 double or triple bonds, or a combination of the two. Such alkyl groups may also be optionally substituted as described below.
When a subscript is used with reference to an alkyl or other hydrocarbon group defined herein, the subscript refers to the number of carbon atoms that the group may contain. For example, “C2-C4 alkyl” indicates an alkyl group with 2, 3 or 4 carbon atoms.
The term “cycloalkyl” refers to saturated or partially unsaturated cyclic hydrocarbon groups having from 3 to 15 carbon atoms in the ring, in some instances 3 to 7, and to alkyl groups containing said cyclic hydrocarbon groups. Examples of cycloalkyl groups include, but are not limited to, cyclopropyl, cyclopropylmethyl, cyclopentyl, cyclohexyl, 2-(cyclohexyl)ethyl, cycloheptyl, and cyclohexenyl. Cycloalkyl as defined herein also includes groups with multiple carbon rings, each of which may be saturated or partially unsaturated, for example decalinyl, [2.2.1]-bicycloheptanyl or adamantanyl. All such cycloalkyl groups may also be optionally substituted as described below.
The term “aromatic” refers to an unsaturated cyclic hydrocarbon group having a conjugated pi electron system that contains 4n+2 electrons where n is an integer greater than or equal to 1. Aromatic molecules are typically stable and are depicted as a planar ring of atoms with resonance structures that consist of alternating double and single bonds, for example benzene or naphthalene.
The term “aryl” refers to an aromatic group in a single or fused carbocyclic ring system having from 6 to 15 ring atoms, in some instances 6 to 10, and to alkyl groups containing said aromatic groups. Examples of aryl groups include, but are not limited to, phenyl, 1-naphthyl, 2-naphthyl and benzyl. Aryl as defined herein also includes groups with multiple aryl rings which may be fused, as in naphthyl and anthracenyl, or unfused, as in biphenyl and terphenyl. Aryl also refers to bicyclic or tricyclic carbon rings, where one of the rings is aromatic and the others of which may be saturated, partially unsaturated or aromatic, for example, indanyl or tetrahydronaphthyl (tetralinyl). All such aryl groups may also be optionally substituted as described below.
The term “heterocycle” or “heterocyclic” refers to non-aromatic saturated or partially unsaturated rings or ring systems having from 3 to 15 atoms, in some instances 3 to 7, with at least one heteroatom in at least one of the rings, said heteroatom being selected from O, S or N. Each ring of the heterocyclic group can contain one or two O atoms, one or two S atoms, one to four N atoms, provided that the total number of heteroatoms in each ring is four or less and each ring contains at least one carbon atom. The fused rings completing the heterocyclic groups may contain only carbon atoms and may be saturated or partially unsaturated. The N and S atoms may optionally be oxidized and the N atoms may optionally be quaternized. Examples of non-aromatic heterocycle groups include, in a non-limitative manner, pyrrolidinyl, tetrahydrofuranyl, morpholinyl, thiomorpholinyl, piperidinyl, piperazinyl, thiazolidinyl, isothiazolidinyl, and imidazolidinyl. All such heterocyclic groups may also be optionally substituted as described below.
The term “heteroaryl” refers to an aromatic group in a single or fused ring system having from 5 to 15 ring atoms, in some instances 5 to 10, which have at least one heteroatom in at least one of the rings, said heteroatom being selected from O, S or N. Each ring of the heteroaryl group can contain one or two O atoms, one or two S atoms, one to four N atoms, provided that the total number of heteroatoms in each ring is four or less and each ring contains at least one carbon atom. The fused rings completing the bicyclic or tricyclic groups may contain only carbon atoms and may be saturated, partially unsaturated or aromatic. In structures where the lone pair of electrons of a nitrogen atom is not involved in completing the aromatic pi electron system, the N atoms may optionally be quaternized or oxidized to the N-oxide. Heteroaryl also refers to alkyl groups containing said cyclic groups. Examples of monocyclic heteroaryl groups include, but are not limited to pyrrolyl, pyrazolyl, pyrazolinyl, imidazolyl, oxazolyl, isoxazolyl, thiazolyl, thiadiazolyl, isothiazolyl, furanyl, thienyl, oxadiazolyl, pyridyl, pyrazinyl, pyrimidinyl, pyridazinyl, and triazinyl. Examples of bicyclic heteroaryl groups include, but are not limited to indolyl, benzothiazolyl, benzoxazolyl, benzothienyl, quinolinyl, tetrahydroisoquinolinyl, isoquinolinyl, benzimidazolyl, benzopyranyl, indolizinyl, benzofuranyl, isobenzofuranyl, chromonyl, coumarinyl, benzopyranyl, cinnolinyl, quinoxalinyl, indazolyl, purinyl, pyrrolopyridinyl, furopyridinyl, thienopyridinyl, dihydroisoindolyl, and tetrahydroquinolinyl. Examples of tricyclic heteroaryl groups include, but are not limited to carbazolyl, benzindolyl, phenanthrollinyl, acridinyl, phenanthridinyl, and xanthenyl. All such heteroaryl groups may also be optionally substituted as described below.
The term “alkoxy” or “alkoxyl” refers to the group —ORa, wherein Ra is alkyl, cycloalkyl or heterocyclic. Examples include, but are not limited to methoxy, ethoxy, tert-butoxy, cyclohexyloxy and tetrahydropyranyloxy.
The term “aryloxy” refers to the group —ORb wherein Rb is aryl or heteroaryl. Examples include, but are not limited to phenoxy, benzyloxy and 2-naphthyloxy.
The term “acyl” refers to the group —C(═O)—Rc wherein Rc is alkyl, cycloalkyl, heterocyclic, aryl or heteroaryl. Examples include, but are not limited to, acetyl, benzoyl and furoyl.
The term “amino acyl” indicates an acyl group that is derived from an amino acid as later defined.
The term “amino” refers to an —NRdRe group wherein Rd and Re are independently selected from the group consisting of hydrogen, alkyl, cycloalkyl, heterocyclic, aryl and heteroaryl. Alternatively, Rd and Re together form a heterocyclic ring of 3 to 8 members, optionally substituted with unsubstituted alkyl, unsubstituted cycloalkyl, unsubstituted heterocyclic, unsubstituted aryl, unsubstituted heteroaryl, hydroxy, alkoxy, aryloxy, acyl, amino, amido, carboxy, carboxyalkyl, carboxyaryl, mercapto, sulfinyl, sulfonyl, sulfonamido, amidino, carbamoyl, guanidino or ureido, and optionally containing one to three additional heteroatoms selected from O, S or N.
The term “amido” refers to the group —C(═O)—NRfRg wherein Rf and Rg are independently selected from the group consisting of hydrogen, alkyl, cycloalkyl, heterocyclic, aryl and heteroaryl. Alternatively, Rf and Rg together form a heterocyclic ring of 3 to 8 members, optionally substituted with unsubstituted alkyl, unsubstituted cycloalkyl, unsubstituted heterocyclic, unsubstituted aryl, unsubstituted heteroaryl, hydroxy, alkoxy, aryloxy, acyl, amino, amido, carboxy, carboxyalkyl, carboxyaryl, mercapto, sulfinyl, sulfonyl, sulfonamido, amidino, carbamoyl, guanidino or ureido, and optionally containing one to three additional heteroatoms selected from O, S or N.
The term “amidino” refers to the group —C(═NRh)NRiRj wherein Rh is selected from the group consisting of hydrogen, alkyl, cycloalkyl, heterocyclic, aryl and heteroaryl; and Ri and Rj are independently selected from the group consisting of hydrogen, alkyl, cycloalkyl, heterocyclic, aryl and heteroaryl. Alternatively, Ri and Rj together form a heterocyclic ring of 3 to 8 members, optionally substituted with unsubstituted alkyl, unsubstituted cycloalkyl, unsubstituted heterocyclic, unsubstituted aryl, unsubstituted heteroaryl, hydroxy, alkoxy, aryloxy, acyl, amino, amido, carboxy, carboxyalkyl, carboxyaryl, mercapto, sulfinyl, sulfonyl, sulfonamido, amidino, carbamoyl, guanidino or ureido, and optionally containing one to three additional heteroatoms selected from O, S or N.
The term “carboxyalkyl” refers to the group —CO2Rk, wherein Rk is alkyl, cycloalkyl or heterocyclic.
The term “carboxyaryl” refers to the group —CO2Rm, wherein Rm is aryl or heteroaryl.
The term “oxo” refers to the bivalent group ═O, which is substituted in place of two hydrogen atoms on the same carbon to form a carbonyl group.
The term “mercapto” refers to the group —SRn wherein Rn is hydrogen, alkyl, cycloalkyl, heterocyclic, aryl or heteroaryl.
The term “sulfinyl” refers to the group —S(═O)Rp wherein Rp is alkyl, cycloalkyl, heterocyclic, aryl or heteroaryl.
The term “sulfonyl” refers to the group —S(═O)2—Rq1 wherein Rq1 is alkyl, cycloalkyl, heterocyclic, aryl or heteroaryl.
The term “aminosulfonyl” refers to the group —NRq2—S(═O)2—Rq3 wherein Rq2 is hydrogen, alkyl, cycloalkyl, heterocyclic, aryl or heteroaryl; and Rq3 is alkyl, cycloalkyl, heterocyclic, aryl or heteroaryl.
The term “sulfonamido” refers to the group —S(═O)2—NRrRs wherein Rr and Rs are independently selected from the group consisting of hydrogen, alkyl, cycloalkyl, heterocyclic, aryl or heteroaryl. Alternatively, Rr and Rs together form a heterocyclic ring of 3 to 8 members, optionally substituted with unsubstituted alkyl, unsubstituted cycloalkyl, unsubstituted heterocyclic, unsubstituted aryl, unsubstituted heteroaryl, hydroxy, alkoxy, aryloxy, acyl, amino, amido, carboxy, carboxyalkyl, carboxyaryl, mercapto, sulfinyl, sulfonyl, sulfonamido, amidino, carbamoyl, guanidino or ureido, and optionally containing one to three additional heteroatoms selected from O, S or N.
The term “carbamoyl” refers to a group of the formula —N(Rt)—C(═O)—ORu wherein Rt is selected from hydrogen, alkyl, cycloalkyl, heterocyclic, aryl or heteroaryl; and Ru is selected from alkyl, cycloalkyl, heterocylic, aryl or heteroaryl.
The term “guanidino” refers to a group of the formula —N(Rv)—C(═NRw)—NRxRy wherein Rv, Rw, Rx and Ry are independently selected from hydrogen, alkyl, cycloalkyl, heterocyclic, aryl or heteroaryl. Alternatively, Rx and Ry together form a heterocyclic ring or 3 to 8 members, optionally substituted with unsubstituted alkyl, unsubstituted cycloalkyl, unsubstituted heterocyclic, unsubstituted aryl, unsubstituted heteroaryl, hydroxy, alkoxy, aryloxy, acyl, amino, amido, carboxy, carboxyalkyl, carboxyaryl, mercapto, sulfinyl, sulfonyl, sulfonamido, amidino, carbamoyl, guanidino or ureido, and optionally containing one to three additional heteroatoms selected from O, S or N.
The term “ureido” refers to a group of the formula —N(Rz)—C(═O)—NRaaRbb wherein Rz, Raa and Rbb are independently selected from hydrogen, alkyl, cycloalkyl, heterocyclic, aryl or heteroaryl. Alternatively, Raa and Rbb together form a heterocyclic ring of 3 to 8 members, optionally substituted with unsubstituted alkyl, unsubstituted cycloalkyl, unsubstituted heterocyclic, unsubstituted aryl, unsubstituted heteroaryl, hydroxy, alkoxy, aryloxy, acyl, amino, amido, carboxy, carboxyalkyl, carboxyaryl, mercapto, sulfinyl, sulfonyl, sulfonamido, amidino, carbamoyl, guanidino or ureido, and optionally containing one to three additional heteroatoms selected from O, S or N.
The expression “optionally substituted” is intended to indicate that the specified group is unsubstituted or substituted by one or more suitable substituents, unless the optional substituents are expressly specified, in which case the term indicates that the group is unsubstituted or substituted with the specified substituents. As defined above, various groups may be unsubstituted or substituted (i.e., they are optionally substituted) unless indicated otherwise herein (e.g., by indicating that the specified group is unsubstituted).
The term “substituted” when used with the terms alkyl, cycloalkyl, heterocyclic, aryl and heteroaryl refers to an alkyl, cycloalkyl, heterocyclic, aryl or heteroaryl group having one or more of the hydrogen atoms of the group replaced by substituents independently selected from unsubstituted alkyl, unsubstituted cycloalkyl, unsubstituted heterocyclic, unsubstituted aryl, unsubstituted heteroaryl, hydroxy, alkoxy, aryloxy, acyl, amino, amido, carboxy, carboxyalkyl, carboxyaryl, halo, oxo, mercapto, sulfinyl, sulfonyl, sulfonamido, amidino, carbamoyl, guanidino, ureido and groups of the formulas —NRccC(═O)Rdd, —NReeC(═NRff)Rgg, —OC(═O)NRhhRii, —OC(═O)Rjj, —OC(═O)ORkk, —NRmmSO2Rnn, or —NRppSO2NRqqRrr wherein Rcc, Rdd, Ree, Rff, Rgg, Rhh, Rii, Rjj, Rmm, Rpp, Rqq and Rrr are independently selected from hydrogen, unsubstituted alkyl, unsubstituted cycloalkyl, unsubstituted heterocyclic, unsubstituted aryl or unsubstituted heteroaryl; and wherein Rkk and Rnn are independently selected from unsubstituted alkyl, unsubstituted cycloalkyl, unsubstituted heterocyclic, unsubstituted aryl or unsubstituted heteroaryl. Alternatively, Rgg and Rnn, Rjj and Rkk or Rpp and Rqq together form a heterocyclic ring of 3 to 8 members, optionally substituted with unsubstituted alkyl, unsubstituted cycloalkyl, unsubstituted heterocyclic, unsubstituted aryl, unsubstituted heteroaryl, hydroxy, alkoxy, aryloxy, acyl, amino, amido, carboxy, carboxyalkyl, carboxyaryl, mercapto, sulfinyl, sulfonyl, sulfonamido, amidino, carbamoyl, guanidino or ureido, and optionally containing one to three additional heteroatoms selected from O, S or N. In addition, the term “substituted” for aryl and heteroaryl groups includes as an option having one of the hydrogen atoms of the group replaced by cyano, nitro or trifluoromethyl.
A substitution is made provided that any atom's normal valency is not exceeded and that the substitution results in a stable compound. Generally, when a substituted form of a group is present, such substituted group is preferably not further substituted or, if substituted, the substituent comprises only a limited number of substituted groups, in some instances 1, 2, 3 or 4 such substituents.
When any variable occurs more than one time in any constituent or in any formula herein, its definition on each occurrence is independent of its definition at every other occurrence. Also, combinations of substituents and/or variables are permissible only if such combinations result in stable compounds.
A “stable compound” or “stable structure” refers to a compound that is sufficiently robust to survive isolation to a useful degree of purity and formulation into an efficacious therapeutic agent.
The term “amino acid” refers to the common natural (genetically encoded) or non-natural, synthetic amino acids and common derivatives thereof, known to those skilled in the art. When applied to amino acids, “standard” or “proteinogenic” refers to the genetically encoded 20 amino acids in their natural configuration. Similarly, when applied to amino acids, “non-standard,” “unnatural” or “unusual” refers to the wide selection of non-natural, rare or synthetic amino acids such as those described in Hunt, S. in Chemistry and Biochemistry of the Amino Acids, Barrett, G. C., ed., Chapman and Hall: New York, 1985; Ann. NY Acad. Sci. 1992, 672, 510-527; Acc. Chem. Res. 2003, 36, 342-351; Mini-Rev. Med. Chem. 2006, 6, 293-304; Curr. Org. Chem. 2007, 11, 801-832; Methods Enzymol. 2009, 462, 1-264; Mini-Rev. Med. Chem. 2012, 12, 277-300; Ann. Rev. Pharm. Tox. 2013, 53, 211-221; J. Org. Chem. 2013, 78, 12288-12313; Bioorg. Med. Chem. Lett. 2014, 24, 5349-5356; J. Med. Chem. 2016, 59, 10807-10836.
The term “amino acid side chain” refers to any side chain from a standard or unnatural amino acid, and is denoted RAA. For example, the side chain of alanine is methyl, the side chain of valine is isopropyl and the side chain of tryptophan is 3-indolylmethyl.
The term “activator” refers to a compound that increases the normal activity of a protein, receptor, enzyme, interaction, or the like.
The term “agonist” refers to a compound that duplicates at least some of the effect of the endogenous ligand of a protein, receptor, enzyme, interaction, or the like.
The term “antagonist” refers to a compound that reduces at least some of the effect of the endogenous ligand of a protein, receptor, enzyme, interaction, or the like.
The term “inhibitor” refers to a compound that reduces the normal activity of a protein, receptor, enzyme, interaction, or the like.
The term “inverse agonist” refers to a compound that reduces the activity of a constitutively-active receptor below its basal level.
The term “library” refers to a collection of two or more chemical compounds.
The term “modulator” refers to a compound that imparts an effect on a biological or chemical process or mechanism. For example, a modulator may increase, facilitate, upregulate, activate, inhibit, decrease, block, prevent, delay, desensitize, deactivate, downregulate, or the like, a biological or chemical process or mechanism. Accordingly, a modulator can be an “agonist” or an “antagonist.” In addition, a modulator can be an “inhibitor” or an “inverse agonist.” Exemplary biological processes or mechanisms affected by a modulator include, but are not limited to, enzyme binding, receptor binding, protein-protein interactions, protein-nucleic acid interactions and hormone release or secretion. Exemplary chemical processes or mechanisms affected by a modulator include, but are not limited to, catalysis and hydrolysis.
The term “peptide” refers to a chemical compound comprising at least two amino acids covalently bonded together using amide bonds. The related term “peptidic” refers to compounds that possess the structural characteristics of a peptide.
The term “peptidomimetic” refers to a chemical compound designed to mimic a peptide, but which contains structural differences through the addition or replacement of one of more functional groups of the peptide in order to modulate its activity or modify other properties, such as solubility, metabolic stability, oral bioavailability, lipophilicity, permeability, etc. This can include replacement of the peptide bond, side chain modifications, truncations, additions of functional groups, etc. When the chemical structure is not derived from the peptide, but mimics its activity, it is often referred to as a “non-peptide peptidomimetic.”
The term “peptide bond” refers to the amide [—C(═O)—NH—] functionality with which individual amino acids are typically covalently bonded to each other in a peptide.
The term “protecting group” or “protective group” refers to any chemical compound that may be used to prevent a potentially reactive functional group, such as an amine, a hydroxyl or a carboxylic acid, on a molecule from undergoing a chemical reaction while chemical change occurs elsewhere in the molecule. A number of such protecting groups are known to those skilled in the art and examples can be found in Greene's Protective Groups in Organic Synthesis, P. G. Wuts, ed., John Wiley & Sons, New York, 5th edition, 2014, 1400 pp, ISBN 978-1-118-05748-3. Examples of amino protecting groups include, but are not limited to, phthalimido, trichloroacetyl, benzyloxycarbonyl, tert butoxycarbonyl, and adamantyl-oxycarbonyl. In some embodiments, amino protecting groups are carbamate amino protecting groups, which are defined as an amino protecting group that when bound to an amino group forms a carbamate. In other embodiments, amino carbamate protecting groups are allyloxycarbonyl (Alloc), benzyloxycarbonyl (Cbz), 9 fluorenylmethoxycarbonyl (Fmoc), tert-butoxycarbonyl (Boc) and α,α dimethyl-3,5 dimethoxybenzyloxycarbonyl (Ddz). For an additional discussion of certain nitrogen protecting groups, see: Tetrahedron 2000, 56, 2339-2358. Examples of hydroxyl protecting groups include, but are not limited to, acetyl, tert-butyldimethylsilyl (TBDMS), trityl (Trt), tert-butyl, and tetrahydropyranyl (THP). Examples of carboxyl protecting groups include, but are not limited to, methyl ester, tert-butyl ester, benzyl ester, trimethylsilylethyl ester, and 2,2,2-trichloroethyl ester. A protecting group is herein designated as PG, with a subscript if more than one is present in the same molecule or if multiple protecting groups are utilized in a particular reaction scheme. In the latter case only, different PGi designations in the scheme may refer to the same protecting group.
The term “orthogonal,” when applied to a protecting group, refers to one that can be selectively deprotected in the presence of one or more other protecting groups, even if they are protecting the same type of chemical functional group. For example, an allyl ester can be removed in the presence of other ester protecting groups through the treatment with homogeneous Pd(0) complexes.
The term “solid phase chemistry” refers to the conduct of chemical reactions where one component of the reaction is covalently bonded to a polymeric material (solid support as defined below). Reaction methods for performing chemistry on solid phase have become more widely known and established outside the traditional fields of peptide and oligonucleotide chemistry (Solid Phase Organic Synthesis, K. Burgess, ed., Wiley-Interscience, 1999, 296 pp, ISBN: 978-0471318255; Solid-Phase Synthesis: A Practical Guide, F. Albericio, ed., CRC Press, 2000, 848 pp, ISBN: 978-0824703592; Organic Synthesis on Solid Phase, 2nd edition, Florencio Zaragoza Dörwald, Wiley-VCH, 2002, 530 pp, ISBN: 3-527-30603-9; Solid-Phase Organic Synthesis: Concepts, Strategies, and Applications, P. H. Toy, Y. Lam, eds., Wiley, 2012, 568 pp, ISBN: 978-0470599143).
The term “solid support,” “solid phase,” “resin” or “resin support” refers to a mechanically and chemically stable polymeric matrix utilized to conduct solid phase chemistry. This is denoted by “Resin,” “P-” or the following symbol:
For a discussion of the use of resins in organic synthesis, see J. Comb. Chem 2000, 2, 579-596.
Examples of appropriate polymeric materials for solid phase chemistry include, but are not limited to, polystyrene, polyethylene, polyethylene glycol (PEG, including, but not limited to, ChemMatrix® (Matrix Innovation, Quebec, Quebec, Canada; J. Comb. Chem. 2006, 8, 213-220)), polyethylene glycol grafted or covalently bonded to polystyrene (also termed PEG-polystyrene, TentaGel™, Rapp, W.; Zhang, L.; Bayer, E. In Innovations and Perspectives in Solid Phase Synthesis. Peptides, Polypeptides and Oligonucleotides; Epton, R., ed.; SPCC Ltd.: Birmingham, UK; p 205), polystyrene-oligo(oxyethylene) copolymer (ACS Comb. Sci. 2014, 16, 367-374), polyacrylate (CLEAR™, J. Am. Chem. Soc. 1996, 118, 7083-7093, polyacrylamide, polyurethane, PEGA [polyethyleneglycol poly(N,N dimethyl-acrylamide) co-polymer, Tetrahedron Lett. 1992, 33, 3077-3080], cellulose, etc. These materials can optionally contain additional chemical agents to form cross-linked bonds to mechanically stabilize the structure, for example polystyrene cross-linked with divinylbenezene (DVB, usually 0.1-5%, preferably 0.5-2%). This solid support can include, as non-limiting examples, aminomethyl polystyrene, hydroxymethyl polystyrene, benzhydrylamine polystyrene (BHA), methylbenzhydrylamine (MBNA) polystyrene, and other polymeric backbones containing free chemical functional groups, most typically, NH2 or —OH, but also halogens like —Cl, for further derivatization or reaction. The term is also meant to include “Ultraresins” with a high proportion (“loading”) of these functional groups such as those prepared from polyethyleneimines and cross-linking molecules (J. Comb. Chem. 2004, 6, 340-349). At the conclusion of the synthesis, resins are typically discarded, although they have been demonstrated to be able to be recycled (Tetrahedron Lett. 1975, 16, 3055).
In general, the materials used as resins are insoluble polymers, but certain polymers have differential solubility depending on solvent and can also be employed for solid phase chemistry. For example, polyethylene glycol can be utilized in this manner since it is soluble in many organic solvents in which chemical reactions can be conducted, but it is insoluble in others, such as diethyl ether. Hence, reactions can be conducted homogeneously in solution, then the product on the polymer precipitated through the addition of diethyl ether and processed as a solid. This has been termed “liquid-phase” chemistry.
The term “linker” when used in reference to solid phase chemistry refers to a chemical group that is bonded covalently to a solid support and is attached between the support and the substrate, typically in order to permit the release (cleavage) of the substrate from the solid support. However, it can also be used to impart stability to the bond to the solid support or merely as a spacer element. Many solid supports are available commercially with linkers already attached. Also see: Curr. Opin. Chem. Biol. 1997, 1, 86-93; Tetrahedron, 1999, 55, 16, 4855-4946; Chem. Rev. 2000, 100, 2091-2158; Linker Strategies in Solid-Phase Organic Synthesis, P. Scott, ed., Wiley, 2009, 706 pp, ISBN: 978-0-470-51116-9
Abbreviations used for amino acids and designation of peptides follow the rules of the IUPAC-IUB Commission of Biochemical Nomenclature in J. Biol. Chem. 1972, 247, 977-983. This document has been updated: Biochem. J., 1984, 219, 345-373; Eur. J. Biochem., 1984, 138, 9-37; 1985, 152, 1; Int. J. Pept. Prot. Res., 1984, 24, following p 84; J. Biol. Chem., 1985, 260, 14-42; Pure Appl. Chem. 1984, 56, 595-624; Amino Acids and Peptides, 1985, 16, 387-410; and in Biochemical Nomenclature and Related Documents, 2nd edition, Portland Press, 1992, pp 39-67. Extensions to the rules were published in the JCBN/NC-IUB Newsletter 1985, 1986, 1989; see Biochemical Nomenclature and Related Documents, 2nd edition, Portland Press, 1992, pp 68-69.
The expression “compound(s) and/or composition(s) of the present disclosure” as used in the present document refers to compounds of formulas (I) presented in the disclosure, isomers thereof, such as stereoisomers (for example, enantiomers, diastereoisomers, including racemic mixtures) or tautomers, or to pharmaceutically acceptable salts, solvates, hydrates and/or prodrugs of these compounds, isomers of these latter compounds, or racemic mixtures of these latter compounds, and/or to composition(s) made with such compound(s) as previously indicated in the present disclosure. The expression “compound(s) of the present disclosure” also refers to mixtures of the various compounds or variants mentioned in the present paragraph. The expression “library(ies) of the present disclosure” refers to a collection of two or more individual compounds of the present disclosure, or a collection of two or more mixtures of compounds of the present disclosure.
It is to be clear that the present disclosure includes isomers, racemic mixtures, pharmaceutically acceptable salts, solvates, hydrates and prodrugs of compounds described therein and mixtures comprising at least two of such entities.
The macrocyclic compounds comprising the libraries of the disclosure may have at least one asymmetric center. Where the compounds according to the present document possess more than one asymmetric center, they may exist as diastereomers. It is to be understood that all such isomers and mixtures thereof in any proportion are encompassed within the scope of the present disclosure. It is to be understood that while the stereochemistry of the compounds of the present disclosure may be as provided for in any given compound listed herein, such compounds of the disclosure may also contain certain amounts (for example less than 30%, less than 20%, less than 10%, or less than 5%) of compounds of the present disclosure having alternate stereochemistry.
The expression “pharmaceutically acceptable” means compatible with the treatment of subjects such as animals or humans.
The expression “pharmaceutically acceptable salt” means an acid addition salt or basic addition salt which is suitable for or compatible with the treatment of subjects such as animals or humans.
The expression “pharmaceutically acceptable acid addition salt” as used herein means any non-toxic organic or inorganic salt of any compound of the present disclosure, or any of its intermediates. Acidic compounds of the disclosure that may form a basic addition salt include, for example, where —NH2 is a functional group. Illustrative inorganic acids which form suitable salts include hydrochloric, hydrobromic, sulfuric and phosphoric acids, as well as metal salts such as sodium monohydrogen orthophosphate and potassium hydrogen sulfate. Illustrative organic acids that form suitable salts include mono-, di-, and tricarboxylic acids such as glycolic, lactic, pyruvic, malonic, succinic, glutaric, fumaric, malic, tartaric, citric, ascorbic, maleic, benzoic, phenylacetic, cinnamic and salicylic acids, as well as sulfonic acids such as p-toluenesulfonic and methanesulfonic acids. Either the mono or di-acid salts can be formed, and such salts may exist in either a hydrated, solvated or substantially anhydrous form. In general, the acid addition salts of the compounds of the present disclosure are more soluble in water and various hydrophilic organic solvents, and generally demonstrate higher melting points in comparison to their free base forms. The selection of the appropriate salt will be known to one skilled in the art. Other non-pharmaceutically acceptable salts, e.g. oxalates, may be used, for example, in the isolation of the compounds of the present disclosure, for laboratory use, or for subsequent conversion to a pharmaceutically acceptable acid addition salt.
The term “pharmaceutically acceptable basic addition salt” as used herein means any non-toxic organic or inorganic base addition salt of any acid compound of the disclosure, or any of its intermediates. Acidic compounds of the disclosure that may form a basic addition salt include, for example, where CO2H is a functional group. Illustrative inorganic bases which form suitable salts include lithium, sodium, potassium, calcium, magnesium or barium hydroxide. Illustrative organic bases which form suitable salts include aliphatic, alicyclic or aromatic organic amines such as methylamine, trimethylamine and picoline or ammonia. The selection of the appropriate salt will be known to a person skilled in the art. Other non-pharmaceutically acceptable basic addition salts, may be used, for example, in the isolation of the compounds of the disclosure, for laboratory use, or for subsequent conversion to a pharmaceutically acceptable acid addition salt.
The formation of a desired compound salt is achieved using standard techniques. For example, the neutral compound is treated with an acid or base in a suitable solvent and the formed salt is isolated by filtration, extraction or any other suitable method.
The term “solvate” as used herein means a compound of the present disclosure, wherein molecules of a suitable solvent are incorporated in the crystal lattice. A suitable solvent is physiologically tolerable at the dosage administered. Examples of suitable solvents are ethanol, water and the like. When water is the solvent, the molecule is referred to as a “hydrate”. The formation of solvates of the compounds of the present disclosure will vary depending on the compound and the solvate. In general, solvates are formed by dissolving the compound in the appropriate solvent and isolating the solvate by cooling or using an antisolvent. The solvate is typically dried or azeotroped under ambient conditions.
The terms “appropriate” and “suitable” mean that the selection of the particular group or conditions would depend on the specific synthetic manipulation to be performed and the identity of the molecule, but the selection would be well within the skill of a person trained in the art. All process steps described herein are to be conducted under conditions suitable to provide the product shown. A person skilled in the art would understand that all reaction conditions, including, for example, reaction solvent, reaction time, reaction temperature, reaction pressure, reactant ratio and whether or not the reaction should be performed under an anhydrous or inert atmosphere, can be varied to optimize the yield of the desired product and it is within their skill to do so.
Compounds of the present disclosure include prodrugs. In general, such prodrugs will be functional derivatives of these compounds which are readily convertible in vivo into the compound from which it is notionally derived. Prodrugs of the compounds of the present disclosure may be conventional esters formed with available hydroxy, or amino group. For example, an available OH or nitrogen in a compound of the present disclosure may be acylated using an activated acid in the presence of a base, and optionally, in inert solvent (e.g. an acid chloride in pyridine). Some common esters which have been utilized as prodrugs are phenyl esters, aliphatic (C8-C24) esters, acyloxymethyl esters, carbamates and amino acid esters. In certain instances, the prodrugs of the compounds of the present disclosure are those in which one or more of the hydroxy groups in the compounds is masked as groups which can be converted to hydroxy groups in vivo. Conventional procedures for the selection and preparation of suitable prodrugs are described, for example, in Design of Prodrugs, ed. H. Bundgaard, Elsevier Science Ltd., 1985, 370 pp, ISBN 978-0444806758.
Compounds of the present disclosure include stable isotope and radiolabeled forms, for example, compounds labeled by incorporation within the structure 2H, 3H, 14C, 15N, or a radioactive halogen such as 125I. A radiolabeled compound of the compounds of the present disclosure may be prepared using standard methods known in the art.
The term “subject” as used herein includes all members of the animal kingdom including human.
The expression a “therapeutically effective amount”, “effective amount” or a “sufficient amount” of a compound or composition of the present disclosure is a quantity sufficient to, when administered to the subject, including a mammal, for example a human, effect beneficial or desired results, including clinical results, and, as such, an “effective amount” or synonym thereto depends upon the context in which it is being applied. For example, in the context of treating cancer, for example, it is an amount of the compound or composition sufficient to achieve such treatment of the cancer as compared to the response obtained without administration of the compound or composition. The amount of a given compound or composition of the present disclosure that will correspond to an effective amount will vary depending upon various factors, such as the given drug or compound, the pharmaceutical formulation, the route of administration, the type of disease or disorder, the identity of the subject or host being treated, and the like, but can nevertheless be routinely determined by one skilled in the art. Also, as used herein, a “therapeutically effective amount,” “effective amount” or a “sufficient amount” of a compound or composition of the present disclosure is an amount which inhibits, suppresses or reduces a cancer (e.g., as determined by clinical symptoms or the amount of cancerous cells) in a subject as compared to a control.
As used herein, and as well understood in the art, “treatment” or “treating” is an approach for obtaining beneficial or desired results, including clinical results. Beneficial or desired clinical results can include, but are not limited to, alleviation or amelioration of one or more symptoms or conditions, diminishment of extent of disease, stabilized (i.e. not worsening) state of disease, preventing spread of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable. “Treatment” or “treating” can also mean prolonging survival as compared to expected survival if not receiving treatment.
“Palliating” a disease or disorder, means that the extent and/or undesirable clinical manifestations of a disorder or a disease state are lessened and/or time course of the progression is slowed or lengthened, as compared to not treating the disorder.
The expression “derivative thereof” as used herein when referring to a compound means a derivative of the compound that has a similar reactivity and that could be used as an alternative to the compound in order to obtain the same desired result.
In understanding the scope of the present disclosure, the term “comprising” and its derivatives, as used herein, are intended to be open ended terms that specify the presence of the stated features, elements, components, groups, integers, and/or steps, but do not exclude the presence of other unstated features, elements, components, groups, integers and/or steps. The foregoing also applies to words having similar meanings such as the terms, “including”, “having” and their derivatives. Finally, terms of degree such as “substantially”, “about” and “approximately” as used herein mean a reasonable amount of deviation of the modified term such that the end result is not significantly changed. These terms of degree should be construed as including a deviation of at least ±5% of the modified term if this deviation would not negate the meaning of the word it modifies.
Further features and advantages of the macrocyclic compounds and libraries of the present disclosure will become more readily apparent from the following description of synthetic methods, analytical procedures and methods of use.
Reagents and solvents were of reagent quality or better and were used as obtained from various commercial suppliers unless otherwise noted. For certain reagents, a source may be indicated if the number of suppliers is limited. Solvents, such as DMF, DCM, DME and THF, are of DriSolv®, OmniSolv® (EMD Millipore, Darmstadt, Germany), or an equivalent synthesis grade quality except for (i) deprotection, (ii) resin capping reactions and (iii) washing. NMP used for coupling reactions is of analytical grade. DMF was adequately degassed by placing under vacuum for a minimum of 30 min prior to use. Ether refers to diethyl ether. Amino acids, Boc-, Fmoc- and Alloc-protected and side chain-protected derivatives, including those of N-methyl and unnatural amino acids, were obtained from commercial suppliers, including AAPPTec (Louisville, Ky., USA), Advanced ChemTech (part of CreoSalus, Louisville, Ky., USA), Anaspec (Fremont, Calif., USA), AstaTech (Bristol, Pa., USA), Bachem (Bubendorf, Switzerland), Biopeptek (Malvern, Pa., USA), Chem-Impex International (Wood Dale, Ill., USA), Iris Biotech (Marktredwitz, Germany), Matrix Scientific (Columbia, S.C., USA), Novabiochem (EMD Millipore), PepTech (Bedford, Mass., USA), or synthesized through standard methodologies known to those in the art. Amino alcohols were obtained commercially or synthesized from the corresponding amino acids or amino esters using established procedures from the literature (for example Tet. Lett. 1992, 33, 5517-5518; J. Org. Chem. 1993, 58, 3568-3571; Lett. Pept. Sci. 2003, 10, 79-82; Ind. J. Chem. 2006, 45B, 1880-1886; Synth. Comm. 2011, 41, 1276-1281). Hydroxy acids were obtained from commercial suppliers or synthesized from the corresponding amino acids as described in the literature (Tetrahedron 1989, 45, 1639-1646; Tetrahedron 1990, 46, 6623-6632; J. Org. Chem. 1992, 57, 6239-6256.; J. Am. Chem. Soc. 1999, 121, 6197-6205; Org. Lett. 2004, 6, 497-500; Chem. Comm. 2015, 51, 2828-2831). Resins for solid phase synthesis were obtained from commercial suppliers, including AAPTech, Novabiochem and Rapp Polymere (Tübingen, Germany). Analytical TLC was performed on pre-coated plates of silica gel, for example 60F254 (0.25 mm thickness) containing a fluorescent indicator.
NMR spectra were recorded on a Bruker 400 MHz or 500 MHz spectrometer, or comparable instrument, and are referenced internally with respect to the residual proton signals of the solvent. Additional structural information or insight about the conformation of the molecules in solution can be obtained utilizing appropriate two-dimensional NMR techniques known to those skilled in the art.
HPLC analyses were performed on a Waters Alliance system running at 1 mL/min using a Zorbax SB-C18 (4.6 mm×30 mm, 2.5 μm), an Xterra MS C18 column (4.6 mm×50 mm, 3.5 μm), or comparable. A Waters 996 PDA provided UV data for purity assessment. Data was captured and processed utilizing the instrument software package. MS spectra were recorded on a Waters ZQ or Platform II system.
Preparative HPLC purifications were performed on deprotected macrocycles using the following instrumentation configuration (or comparable): Waters 2767 Sample Manager, Waters 2545 Binary Gradient Module, Waters 515 HPLC Pumps (2), Waters Flow Splitter, 30-100 mL, 5000:1, Waters 2996 Photodiode Detector, Waters Micromass ZQ., on an Atlantis Prep C18 OBD (19×100 mm, 5 μm) or an XTerra MS C18 column (19×100 mm, 5 μm). The mass spectrometer, HPLC, and mass-directed fraction collection are controlled via MassLynx software version 4.0 with FractionLynx. Fractions shown by MS analysis to contain the desired pure product were evaporated under reduced pressure, usually on a centrifugal evaporator system [Genevac (SP Scientific), SpeedVac™ (Thermo Scientific, Savant) or comparable] or, alternatively, lyophilized. Compounds were then analyzed by LC-MS-UV analysis for purity assessment and identity confirmation. Automated medium pressure chromatographic purifications were performed on a Biotage Isolera system with disposable silica or C18 cartridges. Solid phase extraction was performed utilizing PoraPak™ [Waters, Milford, Mass., USA or Sigma-Aldrich (Supelco), St. Louis, Mo., USA], SiliaSep, SiliaPrep™ and SiliaPrepX™ (SiliCycle, Quebec, QC, Canada) or comparable columns, cartridges, plates or media as appropriate for the compound being purified.
The expression “concentrated/evaporated/removed under reduced pressure” or “concentrated/evaporated/removed in vacuo” indicates evaporation utilizing a rotary evaporator under either water aspirator pressure or the stronger vacuum provided by a mechanical oil vacuum pump as appropriate for the solvent being removed or, for multiple samples simultaneously, evaporation of solvent utilizing a centrifugal evaporator system. “Flash chromatography” refers to the method described as such in the literature (J. Org. Chem. 1978, 43, 2923-2925.) and is applied to chromatography on silica gel (230-400 mesh, EMD Millipore or equivalent) used to remove impurities, some of which may be close in Rf to the desired material.
The majority of the synthetic procedures described herein are for the solid phase (i.e. on resin), since this is more appropriate for creating the libraries of the present disclosure, but it will be appreciated by those in the art that these same transformations can also be modified to be applicable to traditional solution phase processes as well. The major modifications are the substitution of a standard aqueous organic work-up process for the successive resin washing steps and the use of a lower number of equivalents for reagents versus the solid phase.
The following synthetic methods will be referenced elsewhere in the disclosure by using the number 1 followed by the letter referring to the method or procedure, i.e. Method 1F for Fmoc deprotection.
Different synthetic strategies, including solution and solid phase techniques, are employed to prepare the libraries of macrocyclic compounds of the disclosure. An outline of the general strategy for the synthesis of the libraries of compounds of the disclosure is provided in Scheme 1. It will be appreciated by those skilled in the art that for the synthesis of larger libraries, the use of solid phase procedures typically will be preferable and more efficient. Further, the macrocyclic compounds can be made in mixtures or, preferably, as discrete compounds. In either case, the utilization of specific strategies for tracking the synthesis can be advantageous, such as the use of tagging methodologies (i.e. radiofrequency, color-coding or specific chemical functionality, for a review, see J. Receptor Signal Transduction Res. 2001, 21, 409445) and sequestration of resin containing a single compound using a polypropylene mesh “tea” bag (Proc. Natl. Acad. Sci. USA 1985, 82, 5131-5135) or flow-through capsule (MiniKan, Biotechnol. Bioengineer. 2000, 71, 44-50), which permit the simultaneous transformation of multiple different individual compounds in the same reaction vessel. For mixtures, such tags can also be effectively used to facilitate “deconvolution” or the identification of the active structure(s) from a mixture that was found to be a hit during screening.
The construction of the macrocyclic compounds of the library involves the following steps: (i) synthesis of the individual multifunctional, appropriately protected, building blocks, including elements for interaction at biological targets and fragments for control and definition of conformation, as well as moieties that can perform both functions; (ii) assembly of the building blocks, typically in a sequential manner with cycles of selective deprotection and attachment, although this step could also be performed in a convergent manner, utilizing standard chemical transformations as well as those described in more detail in the General/Standard Procedures and Examples herein, such as amide bond formation, reductive amination, Mitsunobu reaction and its variants, nucleophilic substitution reactions and metal- and organometallic-catalyzed coupling; (iii) optionally, selective removal of one or more side chain protecting groups can be performed, either during the building block assembly or after assembly is completed, then the molecule further reacted with one or more additional building blocks to extend the structure at the selectively unprotected functional group(s); (iv) selective deprotection of two functional groups followed by cyclization of the assembled linear intermediate compounds, which can involve one or more steps, to form the macrocyclic structures; and (v) removal of all remaining protecting groups, if necessary, and, optionally, purification to provide the desired final macrocycles.
The assembly reactions require protection of functional groups to avoid side reactions. Even though amino acids are only one of the types of building blocks employed, the well-established strategies of peptide chemistry have utility for the macrocyclic compounds and libraries of the disclosure as well (Meth. Mol. Biol. 2005, 298, 3-24). In particular, these include the Fmoc/tBu strategy (Int. J. Pept. Prot. Res. 1990, 35, 161-214) and the Boc/Bzl strategy (Meth. Mol. Biol. 2013, 1047, 65-80), although those in the art will appreciate that other orthogonal strategies may be necessary to enable selective reaction at a particular site in multi-functional building blocks, for example the use of allyl-based protecting groups.
For solid phase processes, the cyclization can be conducted with the linear precursor on the resin after the two reacting groups are selectively deprotected and the appropriate reagents for cyclization added. This is followed by cleavage from the resin, which may also remove the side chain protecting groups with the use of appropriate conditions. However, it is also possible to cyclize concomitant with resin cleavage if a special linker that facilitates this so-called “cyclization-release” process (Comb. Chem. HTS 1998, 1, 185-214) is utilized. Alternatively, the assembled linear precursor can be cleaved from the resin and then cyclized in solution. This requires the use of a resin that permits removal of the bound substrate without concomitant protecting group deprotection. For Fmoc strategies, 2-chlorotrityl resin (Tetrahedron Lett. 1989, 30, 3943-3946; Tetrahedron Lett. 1989, 30, 3947-3950) and derivatives are effective for this purpose, while for Boc approaches, an oxime resin has been similarly utilized (J. Org. Chem. 1980, 45, 1295-1300). Alternatively, a resin can be used that is specially activated for facile cleavage only after precursor assembly, but is otherwise quite stable, termed a “safety-catch” linker or resin (Bioorg. Med. Chem. 2005, 13, 585-599). For cyclization in solution phase, the assembled linear precursor is selectively deprotected at the two reacting functional groups, then subjected to appropriate reaction conditions for cyclization. Typically, side chain protecting groups are removed at the end of the synthesis regardless of the method utilized prior to purification or any biological testing. However, in some cases, purification prior to removal of the side chain protection may be performed, for example, if separation from side products and reagents is more easily achieved than at the fully deprotected stage.
Upon isolation and characterization, the library compounds can be stored individually in the form thus obtained (solids, syrups, liquids) or dissolved in an appropriate solvent, for example DMSO. If in solution, the compounds can also be distributed into an appropriate array format for ease of use in automated screening assays, such as in microplates or on miniaturized chips. Prior to use, the library compounds, as either solids or solutions, are typically stored at low temperature to ensure the integrity of the compounds is maintained over time. As an example, libraries are stored at or below −70° C. as 10 mM solutions in 100% DMSO, allowed to warm to ambient temperature and diluted with buffer, first to a working stock solution, then further to appropriate test concentrations for use in HTS or other assays.
These methods can be equally well applied for the combinatorial synthesis of mixtures of compounds or the parallel synthesis of multiple individual compounds to provide the libraries of macrocyclic compounds of the present disclosure. In the event of combinatorial synthesis of mixtures, it is necessary to include some type of encoding or tracking mechanism in order to deconvolute the data obtained from HTS of the libraries so that the identity of the active compound obtained can be ascertained (Curr. Opin. Biotechnol. 1995, 6, 632-639; Curr. Opin. Drug Discov. Develop. 2002, 5, 580-593; Curr. Opin. Chem. Biol. 2003, 7, 374-379).
For solid phase chemistry, the solvent choice is important not just to solubilize reactants as in solution chemistry, but also to swell the resin to be able to access all the reactive sites thereon. Certain solvents interact differently with the polymer matrix depending on its nature and can affect this swelling property. As an example, polystyrene (with DVB cross-links) swells best in nonpolar solvents such as DCM and toluene, while shrinking when exposed to polar solvents like alcohols. In contrast, other resins such as PEG (for example, ChemMatrix®) and PEG-grafted ones (for example, TentaGel®), maintain their swelling even in polar solvents. For the reactions of the present disclosure, appropriate choices can be made by one skilled in the art. In general, polystyrene-DVB resins are employed with DMF, DCM and NMP as common solvents. The volume of the reaction solvent required is generally 3-5 mL per 100 mg resin. When the term “appropriate amount of solvent” is used in the synthesis methods, it refers to this quantity. Reaction stoichiometry was determined based upon the “loading” (represents the number of active functional sites, provided by the supplier, typically as mmol/g) of the starting resin. The recommended quantity of solvent roughly amounts to a 0.2 M solution of building blocks (amino acids, hydroxy acids, amino alcohols, diacids, diamines, and derivatives thereof, typically used at 5 eq. relative to the initial loading of the resin).
The reaction can be conducted in any appropriate vessel, for example round bottom flasks, solid phase reaction vessels equipped with a fritted filter and stopcock, or Teflon-capped jars. The vessel size should be such that there is adequate space for the solvent, and that there is sufficient room for the resin to be effectively agitated taking into account that certain resins can swell significantly when treated with organic solvents. Hence, the solvent/resin mixture should typically fill about 60% of the vessel. Agitations for solid phase chemistry can be performed manually or with an orbital shaker (for example, Thermo Scientific, Forma Models 416 or 430) at 150-200 rpm, except for those reactions where scale makes use of mild mechanical stirring more suitable to ensure adequate mixing, a factor which is generally accepted in the art as important for a successful chemical reaction on resin.
The volume of solvent used for the resin wash is a minimum of the same volume as used for the reaction, although more solvent is generally used to ensure complete removal of excess reagents and other soluble residual by-products (minimally 0.05 mL/mg resin). Each of the resin washes specified in the General/Standard Procedures and Examples should be performed for a duration of at least 5 min with agitation (unless otherwise specified) in the order listed. The number of washings is denoted by “nx” together with the solvent or solution, where n is an integer. In the case of mixed solvent washing systems, they are listed together and denoted solvent 1/solvent 2. After washing, the expression “dried in the usual manner” and analogous expressions mean that the resin is dried first in a stream of air or nitrogen (or other inert gas like argon) for 20 min to 1 h, using the latter if there is concern over oxidation of the substrate on the resin, and subsequently under vacuum (oil pump usually) until full dryness is attained (minimum 2 h to overnight (o/n)).
The general and specific synthetic methods and procedures utilized for representative macrocyclic compounds disclosed and utilized herein are presented below. Although the methods described may indicate a specific protecting group, other suitable protection known in the art may also be employed.
Certain resins can be obtained with the first building block (BB1), in particular standard amino acid building blocks, already attached. For other cases on the solid support, the building blocks can be attached using methods known in the art. As an example, the following procedure is followed for adding the first protected building block to 2-chlorotrityl chloride resin.
Prewash the resin with DCM (2×), then dry in the usual manner. In a suitable reaction vessel, dissolve Fmoc-BBi (2.5 eq) in DCM (0.04 mL/mg resin) and add DIPEA (5 eq.), agitate briefly, then add the resin. Agitate o/n on an orbital shaker, remove the solvent, wash with DMF (2×), then, cap any remaining reactive sites using MeOH/DIPEA/DCM (2:1:17) (3×). The resin is washed sequentially with DCM (1×), iPrOH (1×), DCM (2×), ether (1×), then dried in the usual manner.
In the case of solution phase chemistry, the first building block is typically used as a suitably protected derivative with one functional group free for subsequent reaction.
Since methods usually employed for monitoring reaction progress (TLC, direct GC or HPLC) are not directly available for solid phase reactions, it is necessary to perform cleavage of a small amount of material from the support in order to determine the progress of a transformation, such as described in the following representative procedure for 2-chlorotrityl resin.
A small amount of resin (a few beads are usually sufficient) is removed from the reaction vessel, then washed successively with DMF (2×), iPrOH (1×), DCM (2×), ether (1×), dried, then treated with 200 μL 20% hexafluoroisopropanol (HFIP)/DCM, for 10-20 min, and concentrated with a stream of air or nitrogen. To the crude residue obtained, add 200-400 μL MeOH (or use DMSO or THF to solubilize fully protected intermediate compounds), filter through a 45 μm HPLC filter, or a plug of cotton, and analyze the filtrate by HPLC or HPLC-MS.
It is also possible to monitor the progress of solid phase reactions involving amines using a variety of other tests, including the Kaiser (ninhydrin) test for primary amines (Anal. Biochem. 1970, 34, 595-598; Meth. Enzymol. 1997, 289, 54), the 2,4,6-trinitrobenzene-sulphonic acid test (Anal. Biochem. 1976, 71, 260-264), the bromophenol blue test (Collect. Czech. Chem. Commun. 1988, 53, 2541-2548), the isatin test for proline (Meth. Enzymol. 1997, 289, 54-55), and the chloroanil test for secondary amines (Pept. Res. 1995, 8, 236-237).
In an appropriate vessel, a solution of 20% piperidine (Pip) in DMF (0.04 mL/mg resin) was prepared. The resin was added to the solution and the mixture agitated for 30 min. The reaction solution was removed, then this treatment repeated. After this, the resin was washed sequentially with: DMF (2×), iPrOH (1×), DMF (1×), iPrOH (1×), DCM (2×), ether (1×), then the resin dried in the usual manner.
Note that when N-alkylated-amino acids are present in the BBi position, to minimize the potential of diketopiperazine formation, 50% Pip/DMF is used for Fmoc-deprotection of BB2 and the procedure modified as follows: Add the solution to the resin and agitate for only 5-7 min, remove the solvent, add DMF, agitate quickly and remove the solvent, then resume the remaining washes as described above.
An analgous procedure is performed in solution to remove the Fmoc group. The N-Fmoc protected compound is dissolved in a solution of 20% piperidine in DMF, stirred for 30 min at rt, then concentrated in vacuo. The residue is typically used as obtained in the next chemical reaction step, but also can be purified by crystallization either as the free base or salt, aqueous-organic extraction or flash chromatography as appropriate for the structure.
To an appropriate reaction vessel, add the acid building block (2.5-3.5 eq), coupling agent (2.5-3.5 eq) and NMP (0.04 mL/mg resin), followed by DIPEA (5-7 eq). Agitate the mixture vigorously for a few seconds and then add the amine-containing resin. Alternatively, separately prepare a solution of the coupling agent (3.5 eq) in NMP, then add this solution to the acid building block (2.5-3.5 eq) and agitate vigorously. Add DIPEA (5-7 eq), agitate a few seconds, then add the resin. HATU (1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxid hexafluoro-phosphate) and DEPBT (3-(diethoxyphosphoryloxy)-1,2,3-benzotriazin-4(3H)-one) are two typical coupling agents employed, although many other suitable ones are known and could also be utilized (Chem. Rev. 2011, 111, 6557-6602). Agitate the reaction mixture o/n, remove the solution and, if deprotection will be done immediately, wash the resin sequentially with: DMF (2×), iPrOH (1×), DMF (2×), then dry. If deprotection will not be performed immediately, wash sequentially with DMF (2×); iPrOH (1×); DMF (1×); iPrOH (1×), DCM (2×), ether (1×), then dry in the usual manner. With DEPBT, colored side products typically require a modified wash procedure: DMF (3×); iPrOH (1×); DMF (1×); iPrOH (1×), DMF (1×); iPrOH (1×), THF (1×); iPrOH (1×), DCM (2×), ether (1×), then dry in the usual manner.
For attachment of BB3 and beyond, utilize 5 eq. of acid building block and 5 eq. of coupling agent with 10 eq of DIPEA. If the acid building block is one known to require repeated treatment for optimal results, for example N-alkylated and other hindered amino acids, use half of the indicated equivalents for each of the two treatments.
With the pyridine-containing building blocks, DEPBT is used as the preferred coupling agent, although HATU and others may also be employed.
Although the above describes the amine on resin and the acid as the new building block added, it will be appreciated by those in the art that the reverse can also be performed in a similar manner, with the acid component on the solid phase and the amine being the added component.
In addition to the use of acids as building blocks, it is also possible to utilize Fmoc acid fluorides (formed from the acid using cyanuric fluoride, J. Am. Chem. Soc. 1990, 112, 9651-9652) and Fmoc acid chlorides (formed from the acid using triphosgene, J. Org. Chem. 1986, 51, 3732-3734) as alternatives for particularly difficult attachments.
A number of different oxidation methods can be utilized to convert alcohols to aldehydes for use in the attachment of building blocks by reductive amination. The following lists the most appropriate methods for the compounds of the present disclosure, and the types of building blocks on which they are typically applied,
The following are structures of representative aldehyde building blocks of the present disclosure formed by oxidation of the corresponding alcohols using these general procedures or prepared as described in the Examples.
The products are characterized by 1H NMR (using the aldehyde CHO as a diagnostic tool) and LC-MS.
The N-protected aldehyde (1.5 eq) was dissolved in MeOH/DCM/TMOF (trimethyl orthoformate) (2:1:1) or MeOH/TMOF (3:1) (0.04 mL/mg resin) and the resulting solution added to the resin and agitated for 0.5-1 h. If solubility is a problem, THF can be substituted for DCM in the first solvent mixture. Add borane-pyridine complex (BAP, 3 eq) and agitate for 15 min, then carefully release built-up pressure and continue agitation o/n. If the reaction is not complete, add more BAP (2 eq) and agitate again o/n. After removal of the solvent, the resin was washed sequentially with DMF (2×), THF (1×), iPrOH (1×), DCM (1×), THF/MeOH (3:1, 1×), DCM/MeOH (3:1, 1×), DCM (2×), ether (1×), then dried in the usual manner.
For alkyl aldehydes, the quantity of reactants can be adjusted slightly to 1.4-1.5 eq of aldehyde and 2-3 eq of BAP in MeOH/DCM/TMOF (2:1:1). However, note that the reaction often does require up to 3 eq of reducing agent to go to completion with hindered amines. For benzylic aldehydes, add 3 eq of BAP in a mixture of 3:1 MeOH/TMOF. If the reaction is not complete, add another 2 eq of BAP and agitate again o/n. Certain amino acids, such as Gly, undergo double alkylation easily (for such cases use Nos-Gly and attach the building block using Method 1 L), while hindered amino acids such as Aib (2-aminoisobutyric acid) do not proceed to completion. In the latter instance, monitor reaction closely before proceeding to Fmoc deprotection and, if not complete, perform a second treatment.
J. General Procedure for Attachment of Building Blocks by Reductive Amination using Sodium Triacetoxyborohydride
As an alternative method, found particularly useful for benzylic aldehydes, sodium triacetoxyborohydride can be employed in the reductive amination process as follows: Dissolve 1.5-3 eq of the aldehyde in DCM (0.4 mL/mg resin), add the amine-containing resin, then agitate for 2 h. To the mixture, add NaBH(OAc)3 (4-5 eq) and agitate o/n. Once the reaction is complete, remove the solvent, then wash the resin sequentially with DMF (2×), THF (1×), iPrOH (1×), DCM (1×), THF/MeOH (3:1, 1×), DCM/MeOH (3:1, 1×), DCM (2×), ether (1×) and dry in the usual manner. Please note that if the reductive amination is not complete, such as is often encountered with Pro or N-alkyl amino acids, additional aldehyde must be included as part of the second treatment.
K. General Procedure for Attachment of Building Blocks by Reductive Amination using Sequential Sodium Cyanoborohydride and BAP Treatment.
For certain benzylic aldehydes, a sequential Borch and BAP reduction process can be beneficial as described in the following. In the first step, the Fmoc-protected aldehyde (3 eq) in NMP/TMOF (1:1) containing 0.5% glacial acetic acid) (0.4 mL/mg resin) is added to the resin in an appropriate reaction vessel and agitate for 30 min. To the mixture, add NaBH3CN (10 eq), agitate for 10 min, then release pressure and continue agitation o/n. Remove the solvent and wash the resin sequentially with: DMF (2×), iPrOH (1×), DMF (1×), iPrOH (1×), DCM (2×), ether (1×). If in-process QC (Method 1E) shows incomplete reaction, proceed to suspend the resin in MeOH/DCM/TMOF (2:1:1), add BAP (2-3 eq) and agitate for 4 h. Remove the solvent and wash the resin sequentially with: DMF (2×), THF (1×), iPrOH (1×), DCM (1×), THF/MeOH (3:1, 1×), DCM/MeOH (3:1, 1×), DCM (2×), ether (1×), then dry in the usual manner. For building blocks containing a pyridine moiety, use MeOH/DCM (1:1), no TMOF, for the second treatment.
Reductive amination conditions and reagents for representative building blocks are collated in Table K-1:
Although the above procedures for reductive amination describe the amine being the resin component and the aldehyde as the new building block added, it will be appreciated by those in the art that the reverse can also be performed in a similar manner, with the aldehyde component on the solid phase and the amine being the added component.
L. Standard Procedure for Building Block Attachment using Mitsunobu Reaction.
The procedure below specifically describes the building block being attached as its 2-nitrobenzenesulfonyl-derivative (Nos, nosyl) with Fukuyama-Mitsunobu reaction conditions (Tet. Lett. 1995, 36, 6373-6374), then being used for attachment of the next building block.
Step 1L-1.
Prepare a solution of HATU (5 eq), or other appropriate coupling agent, in NMP (0.04 mL/mg resin), monitoring the pH and adjusting to maintain around pH 8, then add to the nosyl-containing building block (5 eq, see Method 1M below) and agitate vigorously. To this solution, add DIPEA (10 eq), agitate briefly, then add to resin and agitate o/n. Use 50% of the indicated quantities if a repeat treatment is planned or anticipated. Upon completion, if the next step will be conducted immediately, wash the resin sequentially with DMF (2×), i-PrOH (1×), DMF (2×), then proceed. Otherwise, wash with DMF (2×); i-PrOH (1×); DMF (1×); DCM (2×), the last wash cycle can be alternatively done as DCM (1×), ether (1×), then dry the resin in the usual manner.
Step 1L-2.
Dissolve the reactant hydroxy component (alcohol, phenol) (5 eq) in THF (0.04 mL/mg resin, 0.2 M) and add PPh3-DIAD adduct (5 eq, see Method 10 below) and very briefly agitate (10-15 sec). Alternatively, prepare a solution of PPh3 (5 eq) and alcohol (5 eq) in THF, cool to 0° C. and add DIAD (5 eq) dropwise. Stir for 15 min at 0° C., add nosyl-containing resin and agitate o/n. Filter the resin and wash sequentially with: THF (2×), toluene (1×), EtOH (1×), toluene (1×), THF (1×), iPrOH (1×), THF (1×), THF/MeOH (3:1, 1×), DCM/MeOH (3:1, 1×), DCM (2×), then dry the resin in the usual manner. Note that the order of addition is generally important for best results.
The Mitsunobu reaction procedure is used preferentially to attach the following building blocks (note that for best conversion, incorporation of these may require being subjected to a second treatment with the building block and reagents): PG-S7, PG-S8, PG-S9, PG-S10, PG-S13, PG-S15.
Alternatively, the building block can also be attached first as its Fmoc, Boc or other N-protected derivative. In those cases, that protection must first be removed using the appropriate method, then the nosyl group installed and the alkyation executed as described in more detail in Method 1P below. Other sulfonamides containing electron-withdrawing substituents can also be utilized for this transformation, including, but not limited to, the 4-nitrobenzenesulfonyl, 2,4-dinitrobenzenesulfonyl (Tet. Lett. 1997, 38, 5831-5834), 4-cyanobenzenesulfonyl (J. Org. Chem. 2017, 82, 4550-4560) and Bts (benzothiazolylsulfonyl) (J. Am. Chem. Soc. 1996, 118, 9796-9797; Bioorg. Med. Chem. Lett. 2008, 18, 4731-4735) groups.
Further, although the above procedure describes the nosylated amine being on the resin and the hydroxy/phenol-containing component being present on the new building block added, it will be appreciated by those in the art that the reverse arrangement can also be utilized in an analogous manner, with the hydroxy/phenol-containing component on the solid phase and the nosylated amine being present on the added building block.
Additionally, a procedure has been described that does not require the activation of the amine component in order to utilize a Mitsunobu reaction in the formation of C—N bonds. Rather, N-heterocyclic phosphine-butane (NHP-butane, L3) is employed along with 1,1′-(azodicarbonyl)dipiperidine (ADDP) to provide the product (L4) (J. Org. Chem. 2017, 82, 6604-6614).
The amino acid substrate was added to a solution of 2-nitrobenzenesulfonyl chloride (Nos-CI, 4 eq) and 2,4,6-collidine (10 eq) in NMP (0.04 mL/mg resin), then the reaction agitated for 1-2 h. The solution was removed and the resin washed sequentially with: DMF (2×), iPrOH (1×), DMF (1×), iPrOH (1×), DMF (2×), iPrOH (1×), DCM (2×), ether (1×). For protection of primary amines, Nos-CI (1-1.2 eq) and 2,4,6-collidine (2.5 eq) in NMP (0.04 mL/mg resin) were used with agitation for 30-45 min. With more hindered amines, a second treatment might be required. Analogous procedures are utilized to conduct this reaction in solution.
A solution of 2-mercaptoethanol (10 eq), DBU (1,8-diaza-bicyclo[5.4.0]undec-7-ene, 5 eq) in NMP (0.04 mL/mg resin) was prepared and added to the resin, then the mixture agitated for 8-15 min. The longer reaction time will be required typically for more hindered substrates. The resin was filtered and washed with NMP, then the treatment repeated. The resin was again filtered and washed sequentially with: DMF (2×), iPrOH (1×), DMF (1×), iPrOH (1×), DMF (1×), DCM (1×), iPrOH (1×), DCM (2×), ether (1×).
This reagent was prepared in a manner essentially as described in Intl. Pat. Publ. No. WO 2004/111077. In a round bottom flask under nitrogen, DIAD (1 eq) was added dropwise to a solution of PPh3 (1 eq) in THF (0.4 M) at 0° C., then the reaction stirred for 30 min at that temperature. The solid precipitate was collected on a medium porosity glass-fritted filter, the solid washed with cold THF (DriSolv grade or equivalent) to remove any color, then with anhydrous ether. The resulting white powder was dried under vacuum and stored under nitrogen in the freezer. It is removed shortly before an intended use.
If the building block is attached as its Fmoc (depicted), Boc or other N-protected derivative, first remove that protecting group using the appropriate deprotection method, and perform installation of the nosyl group using Method 1M. With the Nos group in place, use the procedure of Step 1L-2 above to alkylate the nitrogen under Fukuyama-Mitsunobu conditions (Tet. Lett. 1995, 36, 6373-6374) with an alcohol (R—OH). This procedure can be utilized for preparing N-methyl and other N-alkyl components for which the respective individual building block is commercially unavailable or otherwise difficult to access. Methylation can also be conducted using diazomethane with the nosyl substrate on resin (J Org Chem. 2007, 72, 3723-3728). The nosyl group is removed using Method 1N, then the next building block is added or, if the building block assembly is concluded, the precursor is cleaved from the resin (or the appropriate functionality on the first building block is deprotected if solution phase) and subjected to the macrocyclization reaction (Method 1R).
Alternatively, as can be appreciated by those in the art, in the case that other functionality in the molecule is used for the next building block reaction, it may be advantageous to leave the N-Nos group installed and delay its cleavage until the end of the building block assembly or even until after the macrocyclization, since it essentially provides protection of the backbone amide and prevents side reactions at that site (J. Pept. Res. 1997, 49, 273-279).
Q. General Procedure for Cleavage from 2-Chlorotrityl Resin.
Add a solution of 20% HFIP (hexafluoro-2-propanol) in DCM (0.03 mL/mg resin) to the resin and agitate for 2 h. Filter the resin and wash it with 20% HFIP in DCM (0.01 mL/mg resin, 2×) and DCM (0.01 mL/mg resin, 1×). The filtrate is evaporated to dryness under vacuum.
A solution of DEPBT (1.0-1.2 eq) and DIPEA (2.0-2.4 eq) in 25% NMP/THF (0.03 mL/mg original resin) is prepared and added to the residue from the previous step. In certain cases where compounds may be poorly soluble, dissolve the residue first in NMP, then add DEPBT and DIPEA in THF to the solution. The crude reaction mixture is filtered through one or more solid phase extraction (SPE) cartridges (for example PoraPak, PS-Trisamine, Si-Triamine, Si-Carbonate), then further purified by flash chromatography or preparative HPLC.
The method of deprotection depends on the nature of the protecting groups on the side chains of the macrocycle(s) being deprotected using the following guidelines.
Using orthogonal protecting groups on side chain reactive functionalities permits selective deprotection and reaction of the liberated group(s) in order to further diversify the library of macrocyclic compounds through the addition of pendant building blocks. Representative groups that can be derivatized with one or more of the procedures below are amines, alcohols, phenols and carboxylic acids. This is typically performed while the structure is still bound to the resin and prior to cyclization, although may also be conducted at other appropriate times as will be understood by those in the art. The following are representative types of transformations that can be performed:
1) Amines, Alcohols and Phenols with Acid Chlorides
Prepare a solution of acid chloride (3.5 eq) in THF, 2,4,6-collidine (5 eq) and add the substrate on resin, agitate at rt o/n. The reaction mixture becomes milky after about 5 min. After o/n, remove the solution and wash the resin with: DMF (2×), DCM (1×), iPrOH (1×), DMF (1×), DCM (2×), ether (1×), then dry in the usual manner.
2) Amines with Sulfonyl Chlorides
Add the sulfonyl chloride (4 eq for aryl sulfonyl chlorides and 8 eq for alkyl sulfonyl chlorides) to the suspension of the resin and 2,4,6-collidine (2.5× sulfonyl chloride eq) in NMP, then agitate for 1-2 h. Remove the solution, wash the resin sequentially with DMF (2×), iPrOH (1×), DMF (1×), DCM (2×), ether (1×), then dry the resin in the usual manner.
3) Amines, Alcohols and Phenols with Carboxylic Acids
To a solution of carboxylic acid (5 eq), DIPEA (10 eq), HATU (5 eq) in NMP, add the resin and agitate o/n. Remove the solution, wash the resin sequentially with DMF (2×), iPrOH (1×), DMF (1×), DCM (2×), ether (1×), then dry the resin in the usual manner.
The standard procedures (Methods 1I, 1J and 1K) described above are employed for reductive amination, except only 1 eq of the aldehyde is used to avoid double alkylation side products.
5) Carboxylic Acids with Amines
Prepare a solution of 6-Cl-HOBt (1 eq), EDAC (3-(((ethylimino)-methylene)amino)-N,N-dimethylpropan-1-amine hydrochloride, 5 eq.), and DIPEA (1 eq) in NMP. Add the resin and agitate for 15 min. To this is added the amine (5 eq) and the reaction mixture agitated o/n. Remove the solutions and wash the resin sequentially with DMF (2×); iPrOH (1×); DMF (1×); DCM (2×), ether (1×), then dry in the usual manner.
6) Amines and Phenols with Alcohols
Suspend the resin containing the phenol or nosylated amine in THF (0.04 mL/mg resin, 0.2 M) and add PPh3-DIAD adduct (5 eq, see Method 10 below) and very briefly agitate (10-15 sec). Alternatively, prepare a solution of PPh3 (5 eq) and alcohol (5 eq) in THF, cool to 0° C. and add DIAD (5 eq) dropwise. In either case, stir for 15 min at 0° C., then agitate o/n. Filter the resin and wash sequentially with: THF (2×), toluene (1×), EtOH (1×), toluene (1×), THF (1×), iPrOH (1×), THF (1×), THF/MeOH (3:1, 1×), DCM/MeOH (3:1, 1×), DCM (2×), then dry in the usual manner. Note that the order of addition is generally important for best results.
The following are structures of representative reagent building blocks that can be utilized for the above transformations in the preparation of macrocyclic compounds and libraries of the disclosure.
The following non-limiting reaction schemes illustrate these transformations in conjunction with particular orthogonal protecting groups [R in the schemes contains one or more protected moieties that are not affected by the selective deprotection of allyl (Methods 1 BB and 1 CC), Alloc (Methods 1AA) or Fmoc (Method 1F)] for derivatization of selected functional groups on the macrocyclic compounds of the disclosure.
Di-tert-butyl dicarbonate (Boc2O, 5 eq) was added to the amine substrate on resin and triethylamine (5 eq) in DCM (0.04 mL/mg resin), then the mixture agitated for 4 h. Alternative organic amine bases, sodium carbonate or potassium carbonate can also be used. The solvent was removed and the resin washed sequentially with DMF (2×), iPrOH (1×), DMF (1×), DCM (2×), ether (1×), then dried the resin in the usual manner. An analogous method can be utilized in solution phase.
The Boc-containing substrate on resin was treated with 25% TFA in DCM (0.04 mL/mg resin) and agitated for 30 min. The resin was washed sequentially with DMF (2×); iPrOH (1×); DMF (1×); DCM (2×), ether (1×), then dried in the usual manner. A similar procedure is applied for removal of the Boc group in solution, although typically using a lower concentration of TFA (1-10%).
The free amine or amino acid is dissolved in water and NaHCO3(2 eq) added. To the resulting stirred solution at 0° C. is slowly added Fmoc-OSu or Fmoc-Cl (1.5 eq) in dioxane. The reaction mixture is maintained at 0° for 1 h, then allowed to warm to room temperature overnight. Water is added and the aqueous layer extracted with EtOAc (2×). The organic layer is extracted with saturated NaHCO3(aq) (2×). The combined aqueous layers are acidified to pH 1 with 10% HCl, then extracted with EtOAc (3×). The combined organic layers are dried (anhydrous MgSO4 or Na2SO4) and concentrated in vacuo. The resulting residue is then purified by crystallization or flash chromatography as appropriate. An analogous procedure without the extractive work-up, but with the addition of a standard resin washing process, can be used on solid phase.
The amine is dissolved in water and Na2CO3 (2.7 eq) added with stirring. The resulting solution is cooled to 0° and a cooled solution of allyl chloroformate (1.5 eq) in dioxane added dropwise. The resulting mixture is stirred at 0° for 1 h then allowed to warm to room temperature while stirring overnight. Water is then added and the aqueous layer extracted with EtOAc (2×). The organic layer is extracted with saturated NaHCO3(aq) (2×). The combined aqueous layers are acidified to pH 1 through the addition of 10% HCl, then extracted with EtOAc (3×). The combined organic layers are dried (MgSO4) and concentrated in vacuo. The resulting residue is then purified by flash chromatography or crystallization. An analogous procedure without the extractive work-up, but with the addition of a standard resin washing process, can be used on solid phase. With acid sensitive solid supports, like 2-chlorotrityl resin, however, care must be exercised to maintain a neutral or slightly basic reaction medium during this process.
The carboxylic acid is dissolved in dry DCM and allyl alcohol (1.1 eq) added with stirring. The mixture is cooled to at 0° C. under an inert atmosphere and dicyclohexylcarbodiimide (DCC, 1 eq) added followed by DMAP (0.05 eq). The reaction is allowed to warm to room temperature until complete as indicated by TLC (typically 24-48 h). EtOAc is added and the resulting precipitate removed by filtration and the solid washed with additional EtOAc. The filtrate is concentrated in vacuo and the residue purified by flash chromatography or crystallization as necessary.
Prepare a solution of PPh3 (1.5 eq) and allyl alcohol (1.2 eq) in THF, cool to 0° C. and add DIAD (1.5 eq) dropwise. Stir for 15 min at 0° C., add the phenol component (for example Boc-Tyr-OBut, 1 eq) and allow the reaction mixture to warm to room temperature over 3 h. Alternatively, dissolve the phenol (1 eq) in THF (0.2 M) and add PPh3-DIAD adduct (1.5 eq, Method 10) with stirring. Ether (equal volume to THF) is added and the precipitated solid removed by filtration, washed with ether, then the combined filtrate and washings washed with H2O and saturated NaCl (aq). The organic layer is dried over anhydrous MgSO4, then the dessicant removed and the solvent evaporated under reduced pressure. The residue is purified by flash chromatography to give the protected product.
Suspend the resin in DCM and bubble nitrogen gas through the mixture for 10 min, then add phenylsilane (PhSiH3) (10-24 eq) and bubble nitrogen through the suspension again for 5 min. Add Pd(PPh3)4 (0.1 eq) and maintain the nitrogen flow for a further 5 min, then agitate the reaction for 4 h protected from light. Remove the solvent and wash the resin sequentially with: DMF (2×), iPrOH (1×), DCM (1×), DMF (1×), 0.5% sodium diethylthiocarbamate in DMF (3×), DMF (1×), iPrOH (1×), DMF (1×), DCM (2×), ether (1×), then dry in the usual manner. A similar process can be applied in solution along with the addition of an appropriate extractive work-up procedure followed by crystallization or flash chromatography purification.
Bubble nitrogen through the resin in DCM for 5 min, then evacuate and flush with nitrogen (3×) and bubble nitrogen through for a further 5 min. Add phenylsilane (10-24 eq), bubble nitrogen for 5 min, then add Pd(PPh3)4 (0.1 eq) and keep bubbling nitrogen through for a further 5 min. Close the reaction vessel, and agitate for 5 h protected from light. Remove the solution and wash the resin sequentially with: DMF (2×); iPrOH (1×); DCM (1×); DMF (1×); 0.5% sodium diethylthiocarbamate in DMF (3×); DMF (1×); iPrOH (1×); DMF (1×); DCM (2×); ether (1×) and dry in the usual manner. A similar process can be applied in solution along with the addition of an appropriate extractive work-up procedure followed by crystallization or flash chromatography purification.
Bubble nitrogen through the resin in DCM for 5 min, then evacuate and flush with nitrogen (3×) and bubble nitrogen through for a further 5 min. Add phenylsilane (24 eq), bubble nitrogen for 5 min, then add Pd(PPh3)4 (0.10-0.25 eq) and keep bubbling nitrogen through for a further 5 min, close the reaction vessel and agitate at rt for 16 h (o/n) protected from light. Remove the solution and wash the resin sequentially with: DMF (2×); iPrOH (1×); DCM (1×); DMF (1×); 0.5% sodium diethylthiocarbamate in DMF (3×); DMF (1×); iPrOH (1×); DMF (1×); DCM (2×); ether (1×), then dry in the usual manner. A similar process can be applied in solution along with the addition of an appropriate extractive work-up procedure followed by crystallization or flash chromatography purification.
1) From Diamines
A suspension of the pyridine carboxylic acid (DD-1, 10.0 mmol), the protected bifunctional reagent with a free amine (DD-A, 10.0 mmol), and anhydrous potassium carbonate (25.0 mmol) in DMA-dioxane (3:2, 25 mL) was heated to at least 90° C. under a positive nitrogen pressure and the reaction monitored by TLC or LC/MS. When the reaction was complete or no longer progressing, heating was removed and the mixture cooled. Water and diethyl ether were added, and the mixture agitated until an almost homogeneous solution was obtained. The ether layer was separated and back-extracted with water. Any insoluble material was removed by filtration, and the aqueous layer was extracted with ether (2×). The aqueous layer was cooled to 0° C. and acidified (pH 4) slowly and carefully with concentrated HCl. This acidified aqueous layer was saturated with solid NaCl, and extracted with 10% MeOH/DCM (3-4×). The combined extracts were washed with saturated brine, dried over MgSO4, then filtered, concentrated under reduced pressure, and the residue dried under vacuum o/n. The resulting residual material was triturated 2-3 times with an appropriate solvent, each time with agitation, using a sonicating bath if necessary, allowed to settle, and the supernatant was decanted. The solid product (DD-2) was dried under reduced pressure to a constant weight and, generally, was of sufficient purity to be used in macrocycle construction. If not, purification by flash chromatography or crystallization is performed.
For this nucleophilic aromatic substitution (SNAr) process, the requisite DD-1 substrates containing all possible substitution patterns of halide and carboxylic acid are commercially available with either chloro (X═Cl) or bromo (X═Br) substituents (PA1-PA20, Table DD-1).
Those skilled in the art will recognize that the pyridine ring, particularly possessing an electron-withdrawing substituent such as a carboxylic acid, is reactive for SNAr processes. This reactivity is particularly facilitated for the case of halide leaving groups in the 4-position and, slightly less so, in the 2- and 6-positions. Likewise, it will be appreciated by those in the art that the typically lower reactivity for halides in the 3- and 5-position may require higher reaction temperatures, different solvents and longer reaction times in order to effect efficient conversion to the desired product.
Note that because of the conditions required in assembly, it is preferable to make the pyridine building blocks prior to their incorporation into the macrocyclic synthetic sequence.
For the nucleophilic component in the procedure, the partially protected diamine building block element DD-A, a number of compounds can be utilized, some of which are depicted below.
Protected derivatives for many of these are accessible either commercially or through straightforward or established synthetic procedures (see Method 1EE). Due to the strongly basic conditions utilized for the transformation, Boc, Cbz and Alloc protection are appropriate for the non-reacting amine moiety of the diamine, but then may need to be converted to another protecting group, such as the corresponding Fmoc derivative, for use in macrocycle construction (see Example 1T) or other solid phase processes. Table DD-2 compiles a representative selection, not meant to be limiting, of commercially available protected derivatives which can be employed as DD-A in this standard procedure.
To illustrate the array of different pyridine building blocks that can be constructed from the various components described above, the following structures illustrate the compounds PG-PY1(n)(PG′), PG-PY2(n)(PG′), PG-PY3(n), PG-PY4(n), PG-PY5, PG-PY6, PG-PY7, PG-PY8, PG-PY9, PG-PY10, PG-PY11, PG-PY12, PG-PY13, PG-PY14, PG-PY15, PG-PY16, PG-PY17, PG-PY18, PG-PY19, PG-PY20, PG-PY21, PG-PY22, PG-PY23(OPG′), PG-PY24(OPG′), PG-PY25(OPG′), PG-PY26(OPG′), prepared from the reaction of pyridine PA1 or PA2 with protected diamines PG-DA1(n), PG-DA2(n), PG-DA3(n), PG-DA4(n), PG-DA5, PG-DA6, PG-DA7, PG-DA8, PG-DA9, PG-DA10, PG-DA11, PG-DA12, PG-DA13, PG-DA14, PG-DA15, PG-DA16, PG-DA17, PG-DA18, PG-DA19, PG-DA20, PG-DA21, PG-DA22, PG-DA23(OPG′), PG-DA24(OPG′), PG-DA25(OPG′), PG-DA26(OPG′), respectively. Note that the secondary amine functionality of PG-PY1(n) and PG-PY2(n), must be protected with an orthogonal protecting group to PG to prevent potential side reactions at that site in any subsequent transformations. Thus, the actual building block becomes PG-PY1(n)(PG′) and PG-PY2(n)(PG′), which are the structures employed for macrocycle synthesis.
As an additional illustration of the diverse building blocks that can be prepared, the following structures [PG-PY27(n)(PG′), PG-PY28(n)(PG′), PG-PY29(n), PG-PY30(n), PG-PY31, PG-PY32, PG-PY33, PG-PY34, PG-PY35, PG-PY36, PG-PY37, PG-PY38, PG-PY39, PG-PY40, PG-PY41, PG-PY42, PG-PY43, PG-PY44, PG-PY45, PG-PY46, PG-PY47, PG-PY48, PG-PY49(OPG′), PG-PY50(OPG′), PG-PY51(OPG′), PG-PY52(OPG′)] can be synthesized from prepared from the reaction of pyridine PA3 or PA4 with protected diamines PG-DA1(n), PG-DA2(n), PG-DA3(n), PG-DA4(n), PG-DA5, PG-DA6, PG-DA7, PG-DA8, PG-DA9, PG-DA10, PG-DA11, PG-DA12, PG-DA13, PG-DA14, PG-DA15, PG-DA16, PG-DA17, PG-DA18, PG-DA19, PG-DA20, PG-DA21, PG-DA22, PG-DA23(OPG′), PG-DA24(OPG′), PG-DA25(OPG′), PG-DA26(OPG′), respectively. As in the previous example, the secondary amines of PG-PY27(n) and PG-PY28(n) are subsequently protected with an orthogonal protecting group to PG to form PG-PY27(n)(PG′) and PG-PY28(n)(PG′) as shown.
And as a further illustration of the building blocks that can be synthesized via this procedure, PG-PY53(n)(PG′), PG-PY54(n)(PG′), PG-PY557(n), PG-PY56(n), PG-PY57, PG-PY58, PG-PY59, PG-PY60, PG-PY61, PG-PY62, PG-PY63, PG-PY64, PG-PY65, PG-PY66, PG-PY67, PG-PY68, PG-PY69, PG-PY70, PG-PY71, PG-PY72, PG-PY73, PG-PY74, PG-PY75(OPG′), PG-PY76(OPG′), PG-PY77(OPG′), PG-PY78(OPG′)] are prepared from the reaction of pyridine PA5 or PA6 with protected diamines PG-DA1(n), PG-DA2(n), PG-DA3(n), PG-DA4(n), PG-DA5, PG-DA6, PG-DA7, PG-DA8, PG-DA9, PG-DA10, PG-DA11, PG-DA12, PG-DA13, PG-DA14, PG-DA15, PG-DA16, PG-DA17, PG-DA18, PG-DA19, PG-DA20, PG-DA21, PG-DA22, PG-DA23(OPG′), PG-DA24(OPG′), PG-DA25(OPG′), PG-DA26(OPG′), respectively. Similar to the prior examples, the secondary amines of PG-PY53(n) and PG-PY54(n) are subsequently protected with a protecting group orthogonal to PG to form PG-PY53(n)(PG′) and PG-PY54(n)(PG′) as shown.
Of course, reaction at either one of the two amine groups in the diamine building blocks DA5, DA6, DA7, DA8, DA9, DA10, DA11, DA12, DA14, DA15, DA16, DA19, DA20, DA21, DA22, DA23, DA24, DA25, DA26 is possible in the context of this standard procedure. Only one of the protection sites, typically on a side chain amine moiety, was illustrated previously, which enables reaction to occur at the other amine, which is typically part of the ring. Appropriately protected derivatives for reaction on the side chain moiety (see following) are commercially available for most of these building blocks and, when they are, have been included in the previous listing. Note that for DA1(n), DA4(n), DA13, DA17, DA18 reaction at the two amines form equivalent products, whereas PG-DA2(n) is equivalent to DA3(n)(PG) and DA2(n)(PG) is equivalent to PG-DA3(n).
It will be recognized by those in the art that exchange of protecting groups or additional protection-deprotection steps may need to be performed using standard methods in order to arrive at the most appropriate protection strategy in order to access a desired target structure. As an example, from the commercial compound DA14(Fmoc), the free primary amine can be protected with a Boc moiety to provide the orthogonally protected diamine Boc-DA14(Fmoc). The Fmoc moiety can then by selectively deprotected using Method 1F to yield Boc-DA14. This compound is then employed in the standard procedure for reaction with the halogenated pyridine derivative PA6 to give the building block Boc-PY66.
In addition to those just described, other mono-protected diamines such as can be derived for S50, S51, S52, S57, S58, S59, S60, S61, S62, S63 and S64 prepared in the Examples, also can be employed in the standard procedure.
A suspension of the pyridine carboxylic acid (DD-1, 5.0 mmol), the protected amino carboxylic acid (DD-B(PG), 5.0 mmol), and anhydrous potassium carbonate (12.5 mmol) in DMA-dioxane (3:2, 15 mL) was heated to at least 90° C. under a positive nitrogen pressure and the reaction monitored by TLC or LC-MS. When the reaction was complete or no longer progressing, heating was removed and the mixture cooled. Water and ether were added, and the mixture agitated until an essentially homogeneous solution was obtained. The ether layer was separated and back-extracted with water. Any insoluble material was removed by filtration, and the aqueous layer was extracted with ether (2×). The aqueous layer was cooled to 0° C. and acidified (pH 4) slowly and carefully with concentrated HCl. This acidified aqueous layer was saturated with solid NaCl, and extracted with 10% MeOH/DCM (3-4×). The combined extracts were washed with saturated brine, dried over MgSO4, then filtered, concentrated under reduced pressure, and the residue dried under vacuum o/n. The resulting residual material was triturated 2-3 times with an appropriate solvent, each time with agitation, using a sonicating bath if necessary, allowed to settle, and the supernatant was decanted. The product (DD-3(PG)) was dried under reduced pressure to a constant weight and, generally, was of sufficient purity to be used in macrocycle construction. If not, purification by flash chromatography or crystallization is performed.
A suspension of the pyridine carboxylic acid (DD-1, 1.0 mmol), the bifunctional reagent with a free alcohol (DD-C, 1.0 mmol), and anhydrous potassium carbonate (2.5 mmol) in DMA-dioxane (3:2, 5 mL) was heated to 90° C. or higher under a positive nitrogen pressure and the reaction monitored by TLC or LC/MS. When the reaction was complete or no longer progressing, heating was removed and the mixture cooled. Water and ether were added, and the mixture agitated until almost a homogeneous solution was obtained. The ether layer was separated and back-extracted with water. Any insoluble material was removed by filtration, and the aqueous layer was extracted with ether (2×). The aqueous layer was cooled to 0° C. and acidified (pH 4) slowly and carefully with concentrated HCl. This acidified aqueous layer was saturated with solid NaCl, and extracted with 10% MeOH/DCM (3-4×). The combined extracts were washed with saturated brine, dried over MgSO4, then filtered, concentrated under reduced pressure, and the residue dried under vacuum o/n. The resulting residual material was triturated 2-3 times with an appropriate solvent, each time with agitation, using a sonicating bath if necessary, allowed to settle, and the supernatant was decanted. The product (DD-4) was dried under reduced pressure to a constant weight and, generally, was of sufficient purity to be used in macrocycle construction. If not, purification by flash chromatography or crystallization is performed.
In addition to the commercially accessible materials, some of which are compiled in Table DD-2, methodologies for the monoprotection of diamines are known in the literature. As an example, an approach applicable to Boc, Cbz, Alloc protection is the use of the corresponding alkyl phenyl carbonate as the electrophilic reagent, which gave 50-97% yield for mono-protection of symmetrical and unsymmetrical diamines and polyamines (Synthesis 2002, 15, 2195-2202; Org. Synth. 2007, 84, 209). Additional such strategies include (a) reaction of linear α,ω-alkanediamines with Boc2O in dioxane giving 75-90% yield of the mono-Boc derivative (Synth. Commun. 1990, 20, 2559-2564); (b) the use of 1 mol of HCl followed by one mol of Boc2O (Synth. Commun. 2007, 37, 737-742), which is effective for both symmetrical and unsymmetrical diamines (64-95%). A secondary amine can be protected with Boc in the presence of a primary amine through initial formation of an intermediate imine from the primary amine and benzaldehyde, protection of the secondary amine, then hydrolysis of the imine (Synth. Commun. 1992, 22, 2357-2360). This procedure would be applicable for PG-DA2(n) or analogous structures for example. Other routes to monoprotected diamines have also been developed, such as protection of an w-halo-alkylamine (Boc2O, Et3N, MeOH), followed by displacement of the halide under typical SN2 conditions (RNH2, KI, EtOH) to yield mono-Boc-protected unsymmetrical diamines (Org. Prep. Proc. Intl. 2009, 41, 301-307). Such procedures are applicable to the construction of PG-DA1(n), PG-DA2(n), PG-DA3(n), PG-DA4(n), PG-DA17, PG-DA18 from the corresponding commercially available free diamines (see Table EE-1 for selections of these materials, some of which can be utilized to access more than one derivative). As well, Example 1P describes methods for the synthesis of these mono-protected derivatives for simple α,ω-diaminoalkanes.
FF. Standard Procedures for the Synthesis of Diamines from Amino Acids
In addition to the commercially available diamines and protected derivatives such as those In Tables DD-1 and EE-1, diamine building blocks such as FF5 are accessible from the protected amino acids FF1 using the synthetic sequence shown below.
Reduction of FF1 is performed through the intermediate mixed anhydride formed with isobutyl chloroformate to provide the alcohol FF2 (Synthesis 1990, 299-301). Some of the FF2 derivatives are also available commercially. Using any number of known methods (e.g. MsCl, Et3N, DCM, 0° C., TsCl, DIPEA, DCM, 0° C.->rt or Tf2O, pyr, DCM, 0° C.->rt), the alcohol can be converted into a good leaving group (LG). Nucleophilic substitution with azide in an aprotic polar solvent gives FF4, which is then reduced to the amine (FF5) via the Staudinger reaction or, alternatively, through hydrogenation if compatible with the rest of the molecule. Protecting group manipulation would permit the alternative derivative FF6 with the protection on the other amine to be prepared. Both FF5 and FF6 can be reacted with PA1 using Method 1DD to yield the pyridine building blocks PG-FF12 and PG′-FF13, respectively.
In addition to these derivatives from α-amino acids, analogous transformations can be applied to enable the preparation of additional homologous building blocks, such as FF8 from β2-amino acids (FF7) and FF10, FF11 from β3-amino acids (FF9). The two amines in FF8 are equivalent, so an alternative protected derivative is not relevant in this instance.
Again for these derivatives, reaction with PA1 according to Method 1DD gives pyridine building blocks PG-FF14, PG-FF15 and PG-FF16 from FF8, FF10 and FF11 respectively.
Apart from the acids prepared as in Method 1DD, additional pyridine building blocks can be accessed from the pyridine carboxylic acids of Table DD-1. In particular, alcohols can be obtained by reduction, although this usually does require protection of the acid moiety prior to the nucleophilic substitution reaction for best efficiency. Reduction of the acid DD-2 directly can result in low yields of the corresponding alcohol. Alternatively, conversion of DD-1 to the ester GG-1 using standard conditions, followed by SNAr in the same manner as Method 1DD, except that a slightly weaker base (potassium bicarbonate) was employed to minimize the potential for ester hydrolysis, gave the coupled product GG-2.
Subsequent reduction of the ester provided the alcohol GG-3. In addition, to the borohydride reagents, other reducing agents, including borane and low temperature LiAlH4, can be utilized to effect this conversion The corresponding aldehyde (GG-4) can then be synthesized from the alcohol by oxidation using one of the reagent options presented in Method 1H, with MnO2 somewhat preferred.
The following representative methods for qualitative and quantitative analysis and characterization of the macrocyclic compounds comprising the libraries of the disclosure are routinely performed both for monitoring reaction progress as well as to assess the final products obtained. These analytical methods will be referenced elsewhere in the disclosure by using the number 2 followed by the letter referring to the method or procedure, i.e. Method 2B for preparative purification.
Column: Zorbax SB-C18, 4.6 mm×30 mm, 2.5 μm
Solvent A: Water+0.1% TFA
Solvent B: CH3CN+0.1% TFA
UV Monitoring at λ=220, 254, 280 nm
Gradient Method A1
Gradient Method A2
The following representative methods are employed for preparative HPLC purification of the macrocyclic compounds comprising the libraries of the disclosure.
Column: Atlantis Prep C18 OBD, 19 mm×100 mm, 5 μm
Solvent A: Aqueous Buffer (10 mM ammonium formate, pH 4)
Solvent B: MeOH
Gradient Method P1
Gradient Method P2
Gradient Method P3
Gradient Method P4
Gradient Method P5
Gradient Method P6
Gradient Method P7
Gradient Method P8
Gradient Method P9
Gradient Method P10
Typically, methods P5, P6, P7, P8, P9 and P10 are used if a sample requires additional purification after the initial purification run.
Note that lower flow rates (i.e. 20-25 mL/min) can be utilized with concomitant lengthening of the gradient run time.
The use of ammonium formate buffer results in the macrocyclic compounds, typically, being obtained as their formate salt forms.
3. Methods of Use
The libraries of macrocyclic compounds of the present disclosure are useful for application in high throughput screening (HTS) on a wide variety of targets of therapeutic interest. The design and development of appropriate HTS assays for known, as well as newly identified, targets is a process well-established in the art (Methods Mol. Biol. 2009, 565, 1-32; Mol. Biotechnol. 2011, 47, 270-285) and such assays have been found to be applicable to the interrogation of targets from any pharmacological target class. These include G protein-coupled receptors (GPCR), nuclear receptors, enzymes, ion channels, transporters, transcription factors, protein-protein interactions and nucleic acid-protein interactions. Methods for HTS of these target classes are known to those skilled in the art (High Throughput Screening in Drug Discovery, J. Hüser, ed., Wiley-VCH, 2006, pp 343, ISBN 978-3-52731-283-2; High Throughput Screening: Methods and Protocols, 2nd edition, W. P. Janzen, P. Bernasconi, eds., Springer, 2009, pp 268, ISBN: 978-1-60327-257-5; Cell-Based Assays for High-Throughput Screening: Methods and Protocols, P. A. Clemons, N. J. Tolliday, B. K. Wagner, eds., Springer, 2009, pp 211, ISBN 978-1-60327-545-3). These methods can be utilized to identify modulators of any type, including agonists, activators, inhibitors, antagonists, and inverse agonists. The Examples describe representative HTS assays in which libraries of the present disclosure are useful. The exemplified targets include an enzyme, a G protein-coupled receptor and a protein-protein interaction. Prior to use, the libraries are typically stored at or below −70° C. as 10 mM stock solutions in 100% DMSO (frozen), allowed to warm to rt, then aliquots diluted, typically serially, to an appropriate test concentration, for example 10 μM in buffer.
The libraries of compounds of the present disclosure are thus used as research tools for the identification of bioactive hits from HTS that in turn serve to initiate drug discovery efforts directed towards new therapeutic agents for the prevention and treatment of a range of medical conditions. As used herein, treatment” is not necessarily meant to imply cure or complete abolition of the disorder or symptoms associated therewith.
Further embodiments of the present disclosure will now be described with reference to the following Examples. It should be appreciated that these Examples are for the purposes of illustrating embodiments of the present disclosure, and do not limit the scope of the disclosure.
When not obtained from commercial vendors, protected building blocks S1, S2, (S)-S3, (R)-S3, (S)-S4, (R)-S4, S5, S6, S7, S8, (S)-S53, (R)-S53 were prepared by N-protection of the readily commercially available materials 2-aminoethanol, 2-methylaminoethanol, L-alaninol, D-alaninol, L-leucinol, D-leucinol, 3-aminopropan-1-ol, 4-aminobutan-1-ol, 5-aminopentan-1-ol, 6-aminohexan-1-ol, L-valinol and D-valinol, respectively, with methods and conditions known to those in the art, for example Boc2O and K2CO3 for N-Boc derivatives (Method 1U), and Fmoc-OSu (Method 1W, Example 1A) or Fmoc-C1 and NaHCO3for N-Fmoc derivatives or allyl chloroformate and Na2CO3 (see Method 1×) for N-Alloc derivatives. Similarly, protected derivatives of S9, S11, S12, S13, S14, S23, S24 and S28 can be prepared directly from the commercially available starting materials indicated below:
Fmoc-OSu (38.6 g, 115 mmol) was added to a solution of [3-(amino-methyl)phenyl]methanol (S14, 16.5 g, 121 mmol) in THF (150 mL), water (75 mL) and sodium bicarbonate (20.3 g, 241 mmol) at room temperature (rt) and the reaction stirred overnight (o/n). At that point, a small sample was diluted with MeOH, acidified with a drop of HOAc, and analyzed by LC-MS, which showed the desired product with no Fmoc-OSu reagent. The reaction was acidified with 1M HCl, diluted with ethyl acetate (EtOAc), and stirred for 2 h. The white solid was filtered off, washed well with water, then EtOAc, and air dried for 3 h until a constant weight was attained. The product thus obtained, Fmoc-S14 (15.3 g), was found by LC-MS to be free of identifiable organic impurities. The aqueous layer was extracted with EtOAc (2×). The combined organic layers were washed with H2O (2×) and brine, then dried over anhydrous MgSO4. The dessicant was removed by filtration and the filtrate concentrated under reduced pressure to give additional amounts of the desired product as a white solid (34.1 g). The combined solids were triturated with ethyl acetate at reflux for a few minutes, then o/n at rt to give Fmoc-S14 in 88% yield (38.1 g).
Similarly, Fmoc-protected derivatives of the unnatural amino acids, 3-azetidine carboxylic acid (3-Azi), 4-piperidine carboxylic acid (4-Pip, isonipecotic acid) and cis-4-aminocyclohexane-1-carboxylic acid (cis-4-Ach) are prepared utilizing this method.
Protected materials are also available commercially: Fmoc-3-Azi (Chem-Impex, Cat. No. 07330; Matrix Scientific Cat. No. 059921), Fmoc-4-Pip (Chem-Impex, Cat. No, 04987, Anaspec, Cat. No. AS-26202), Fmoc-4-cis-Ach, (Chem-Impex, Cat. No, 11954, Anaspec, Cat. No. AS-26385).
Conversion of 3-bromobenzaldehyde (14-1) to the nitrile was accomplished through nucleophilic aromatic substitution with copper(I) cyanide. Subsequent reduction of both the carbonyl and nitrile with lithium aluminum hydride (LAH) provided the amino alcohol after appropriate work-up, which was then protected with Fmoc using standard conditions (Method 1W, Example 1A). The corresponding Boc derivative is accessed by substituting Boc2O and K2CO3 in the last step of the scheme.
Analogous procedures are utilized to access protected derivatives of S15 and S16 starting, respectively, from 2-(2-aminoethyl)benzoic acid (15-1, Ark Pharm, Cat. No. AK-32693) and 3-(2-aminoethyl)benzoic acid (16-1, Ark Pharm, Cat. No. AK-34290). The amine is protected with Boc (Method 1U) or Fmoc (Method 1W, Example 1A) in the standard manner to provide 15-2 and 16-2. The acid was then reduced to the alcohol through the mixed anhydride (see Example 11) to yield PG-S15 and PG-S16.
An identical strategy is employed for the preparation of the protected building blocks of S17 and S19. The former begins from 2-(2-aminomethyl)-phenol (Combi-Blocks, Cat. No. A-3525, as HCl salt), while the latter proceeds from 2-(2-aminoethyl)phenol (Ark Pharm, Cat. No. 114741). The amine of each is protected with Boc in the usual manner (Method 1V) to give 17-1 and 19-1, respectively. The free phenols are then derivatized using a Mitsunobu reaction with triphenylphosphine and diisopropylazodicarboxylate (DIAD) along with the mono-t-butyldimethylsilyl (TBDMS) ether of ethylene glycol (17-A), followed by removal of the silyl protection with tetrabutylammonium fluoride (TBAF, 1 M in THF) to give Boc-S17 and Boc-S19. These can be converted into the corresponding Fmoc analogues through the deprotection-protection sequence shown.
As an alternative approach to these two molecules, the phenol can be alkylated via a substitution reaction utilizing base (for example K2CO3, NaH) and a suitable derivative of 17-A containing a leaving group (i.e. halide, mesylate, tosylate, triflate) in place of the hydroxyl, which can be prepared from 17-A using procedures known to those in the art.
An essentially identical strategy is utilized for the synthesis of the protected building blocks S18 and S20. The former starts from methyl salicylate (18-1), while the latter initiates from methyl 2-(2-hydroxyphenyl)acetate (20-1, Ark Pharm Cat. No. AK-76378). Reaction of the phenol of these two materials with Boc-2-aminoethanol (Boc-S1) under Mitsunobu conditions gives 18-2 and 20-2, respectively. Reduction of the ester group with diisobutylaluminum hydride (DIBAL) provides the Boc-protected target compounds. Conversion of the protecting group from Boc to Fmoc can be effected as already shown in Example 1D to give Fmoc-S18 and Fmoc-S20.
The two phenols of catechol (22-1) or resorcinol (27-1) were sequentially reacted under Mitsunobu conditions, first with 1 eq of the mono-protected diol 17-A, followed by 1 eq of an appropriate N-protected-2-amino-ethanol (PG-S1). Material that does not react fully can be extracted with aqueous base (hence, the PG chosen must be compatible with such conditions). Standard deprotection of the silyl ether with 1 M TBAF in THF provides PG-S22 and PG-527. The N-protecting group can be interchanged as already described if necessary.
To a solution of 3-hydroxybenzaldehyde (25-1, 100 mg, 0.819 mmol), Ph3P (215 mg, 0.819 mmol) and Fmoc-3-amino-1-propanol (Fmoc-S5, 256 mg, 0.860 mmol) in THF (30 mL) at rt was added dropwise DIAD (0.159 mL, 0.819 mmol). The mixture was stirred at rt for 2 d, then evaporated in vacuo and the residue purified by flash chromatography (hexanes:EtOAc: 95:5 to 50:50 over 14 min). Product-containing fractions were concentrated under reduced pressure to leave the desired coupled product, Fmoc-S45, as a white solid, 1H NMR and MS consistent with structure. Reduction of the aldehyde with sodium borohydride under standard conditions provided Fmoc-S25.
In a manner analogous to that described above for PG-S22 and PG-527, the two phenol moieties of 4-fluoro-catechol (26-1, Fluorochem (Hadfield, United Kingdom, Cat. No. 306910) were sequentially reacted under Mitsunobu conditions, first with 17-A, then with PG-S1. Although the initial conversion is regioselective for the phenol para to the fluorine substituent, the first reaction uses only a single equivalent of 17-A to minimize formation of side products. Standard deprotection of the silyl ether with 1 M TBAF in THF provides PG-526.
For the transformation of amino acid building blocks (I-1) to the corresponding amino alcohol (I-2) components, a solution of the protected amino acid (I-1, 15 mmol) in THF (100 mL) under nitrogen was cooled in an ice-salt bath, then isobutyl chloroformate (IBCF, 1.96 mL, 15.0 mmol) and 4-methylmorpholine (NMM, 1.64 mL, 15.0 mmol) added dropwise simultaneously via syringes over 5 min. The mixture was stirred at 0° C. for 30 min, then at rt for another 30 min. The white precipitate that formed was filtered into a 500 mL flask through a pre-washed Celite® pad and rinsed with anhydrous ether (70 mL). The flask was placed under nitrogen in an ice-bath, and a mixture of sodium borohydride (0.85 g, 22.5 mmol) in water (10 mL) added in one shot with the neck of the flask left open. Significant gas evolution was observed and the reaction mixture formed a suspension. More water (20 mL) was added, the ice-bath removed, and the reaction stirred rapidly with monitoring by LC-MS and TLC. After 1 h at ambient temperature, LC-MS analysis indicated that the reaction was complete. More water was then added and the organic layer extracted with EtOAc (2×150 mL). The combined organic layers were washed sequentially with 1 M citric acid, NaHCO3 (sat.), water, brine, and dried over anhydrous MgSO4. The mixture was filtered and the filtrate concentrated under reduced pressure to give 1-2 in 60-80% yield. The product thus obtained was sufficiently pure to be used without further purification for subsequent reactions.
The following procedure is provided for the transformation of Fmoc-protected amino alcohol building blocks such as 1-2 to the corresponding amino aldehyde components (J-1) for use in a reductive amination attachment procedure. In a 250 mL round-bottomed flask was dissolved 1-2 (10 mmol) in CH2C12 (46.3 mL) and DMSO (10 mL). Triethylamine (TEA, 5.58 mL, 40 mmol) was added and the solution cooled to 0° C. under nitrogen. Pyridine sulfur trioxide complex (pyr.SO3, 4.77 g, 30 mmol) was added as a solution in DMSO (16.3 mL) over 20 min and the reaction monitored by TLC and LC-MS until complete. After 4 h, the reaction was cooled to 0° C. in an ice-bath, EtOAc/ether (1:1, 150 mL) was added, and the organic layer washed with saturated NaHCO3 (1×150 mL). More water was added as necessary to dissolve any insoluble material. The aqueous layer was extracted with EtOAc/ether (1:1, 3×150 mL). The organic extracts were combined and washed sequentially with 1M KHSO4 (1×150 mL), saturated NH4Cl (2×120 mL), water (200 mL), brine (2×200 mL), dried over anhydrous MgSO4, filtered and the filtrate concentrated under reduced pressure to give J-1 typically in excellent 90-95% yields. The product thus obtained was acceptable for use in subsequent transformations without further purification.
K. Representative Procedure for the Oxidation of Building Blocks to Aldehydes with Manganese Dioxide
Fmoc-S14 (38 g, 106 mmol) was suspended in DCM (151 mL) and THF (151 mL). Manganese dioxide (Strem (Newburyport, Mass., USA) Cat. No. 25-1360, 92 g, 1.06 mol) was added and the reaction agitated o/n on an orbital shaker at 200 rpm. A small sample was filtered through MgSO4 with THF and analyzed by LC-MS, which indicated 87% conversion. More MnO2 (23.0 g, 264 mmol) was added and the reaction agitated for 16 h more, at which time the reaction was found to have progressed to 90% conversion. Another quantity of MnO2 (23.0 g, 264 mmol) was added and agitation continued for another 16 h, after which LC-MS indicated complete reaction. The reaction mixture was filtered through MgSO4 with filter-paper on top, and the trapped solids rinsed with THF. The residual MnO2 was agitated with THF, filtered and washed with THF. The filtrate was passed again through MgSO4 and several layers of filter-paper and the filtrate was pale yellow with no MnO2. Evaporation of the filtrate under reduced pressure left a light yellow solid. The solid was triturated with ether, heated to reflux and allowed to cool slowly with stirring. After stirring for 4 h, the white solid that formed was filtered to give Fmoc-S37 as a white solid (28.6 g, 80 mmol, 76.0% yield). 1H-NMR and LC-MS were consistent with the expected product. The MnO2 was washed again with THF (300 mL) with agitation o/n, followed by filtration and concentration of the filtrate in vacuo to give 1.0 g of crude product which was combined with 2.0 g recovered from the mother liquor of the above trituration and this combined solid triturated with ether. A second crop of the desired product was isolated as an off white solid (1.60 g, 4.48 mmol, 4.2% additional yield).
Step S50-1.
To a solution of 2-hydroxybenzaldehyde (50-1, 10.0 g, 82 mmol) in MeOH (100 mL) at rt was added 7 N ammonium hydroxide (29.2 mL, 205 mmol) in MeOH. The solution turned yellow in color. The homogeneous solution was stirred at rt for 3 h at which time TLC showed a new, more polar product. Solid sodium borohydride (1.73 g, 45.7 mmol) was added to the reaction in small portions and stirring continued at rt for 2 h. The reaction was quenched with 10% NaOH, then the methanol evaporated in vacuo. The resulting aqueous solution was diluted with EtOAc (50 mL) and the layers separated. The organic layer was washed with 10% HCl (3×). The aqueous washes were combined with the original aqueous layer and the pH adjusted to 9 with 10% NaOH. A white solid formed, which was isolated by filtration, washed and dried in air. This material was treated with Boc2O (19.0 mL, 82.0 mmol) in DCM and stirred at rt for 24 h. The reaction mixture was diluted with water, extracted with EtOAc, the organic layers dried over MgSO4, filtered, then evaporated in vacuo to leave an oil that was purified by flash chromatography (hexanes:EtOAc, 9:1 to 1:1) to give 50-2 as a colorless oil (65% yield).
Step S50-2.
To a solution of 50-2 (3.86 g, 17.29 mmol) and Alloc-S1 (3.76 g, 25.9 mmol) in THF (200 mL) at rt was added Ph3P (6.80 g, 25.9 mmol), then DIAD (5.04 mL, 25.9 mmol). The mixture was stirred at rt o/n at which point TLC indicated reaction completion. The solvent was evaporated in vacuo and the residue purified by flash chromatography (100 g silica, hexanes:EtOAc: 90:10 to 70:30 over 13 min) to give two fractions. The main fraction contained primarily the desired product, while the minor fraction was contaminated with a significant amount of solid hydrazine by-product. The minor fraction was triturated with an ether/hexane mixture, then filtered. The residue from concentration in vacuo of the mother liquors from this filtration were combined with the major fraction and subjected to a second flash chromatography (hexanes:EtOAc: 90:10 to 60:40 over 14 min) to give the diprotected product, Alloc-S50(Boc), as a colorless oil (46% yield). This was treated with 1% TFA to remove the Boc group, which provided Alloc-550.
To 2-hydroxybenzaldehyde (50-1, 605 mg, 4.96 mmol) and (9H-fluoren-9-yl)methyl carbamate (593 mg, 2.48 mmol) in toluene (30 mL) was added TFA (0.955 mL, 12.4 mmol). The mixture was stirred at 80° C. for 2 d, then allowed to cool to rt, evaporated in vacuo and the residue purified by flash chromatography (hexanes:EtOAc: 95:5 to 50:50 over 14 min). Product-containing fractions were concentrated under reduced pressure to leave 50-3 as a solid, 1H NMR and LC-MS consistent with structure, 0.39 mg, estimated 46% yield.
As another alternative, 2-(aminomethyl) phenol is commercially available (Matrix Scientific Cat. No. 009264; Apollo Scientific Cat. No. OR12317; Oakwood Cat. No. 023454) and can be protected with Fmoc using standard methods (Method 1W, Example 1A).
Analogously as described for 50-2, 50-3 can be converted into Alloc-S50 by a reaction sequence involving Mitsunobu coupling followed by standard Fmoc deprotection (Method 1F).
To a solution of 2-(2-hydroxyphenyl)acetamide (51-1, Fluorochem, Cat. No. 375417, 50.0 mg, 0.331 mmol), Ph3P (104 mg, 0.397 mmol) and Fmoc-2-aminoethanol (Fmoc-S1, 122 mg, 0.430 mmol) in THF (4 mL) at rt was added DIAD (0.077 ml, 0.397 mmol) dropwise. The mixture was stirred at rt overnight, then evaporated in vacuo and the residue purified by flash chroatography. The intermediate amide 51-2 was then treated with borane-dimethyl sulfide at 0° C. for 2 h, then quenched carefully with water, followed by dilute acid. The product Fmoc-S51 was isolated after standard work-up. Use of other appropriate nitrogen protecting groups on 2-aminoethanol provides alternative protected derivatives of S51.
In a similar manner, various protected derivatives of S50 can be accessed starting from salicylamide (50-3) as an alternative route to these materials.
Boc-L-phenylalaninamide ((S)-52-1), purchased from commercial suppliers or prepared from the unprotected precursor (Alfa Aesar, Cat. No. H65506) by treatment with Boc2O under standard conditions (Method 1U), was reduced with borane-dimethyl sulfide to give the mono-protected diamine (S)-S52(Boc). The primary amine was protected in the usual manner (Method 1×) with an Alloc group, then the Boc group removed using standard conditions to yield Alloc-(S)-S52. The enantiomer, Alloc-(R)-S52, is synthesized similarly from D-phenylalaninamide. Such a procedure is also applicable to the synthesis of other diamines from α-N-protected amino acid amides.
Linear diamines (P-1, n=0-4) are monoprotected with Boc under standard conditions using literature methods (Synth. Comm. 1990, 20, 2559-2564; Synth. Comm. 2007, 37, 737-742; Org. Lett. 2015, 17, 422-425). The products (P-2) thus obtained are reacted with allyl chloroformate in the presence of base to install the Alloc protecting group. The now differentially diprotected amines are treated with acid to cleave the Boc group and provide the desired Alloc-protected diamines [P-3: Alloc-S57 (n=0), Alloc-S58 (n=1), Alloc-S59 (n=2), Alloc-S61 (n=3), Alloc-S62 (n=4)].
Alternatively, Boc-monoprotected diamines (P-2) are commercially available: n=0 (Alfa Aesar, Cat. No. L19974); n=1 (Aldrich, Cat. No. 436992); n=2 (Aldrich, Cat. No. 15404); n=3 (Aldrich, Cat. No. 15406); n=4 (Aldrich, Cat. No. 79229).
The (S) and (R)-isomers of Q-1 are commercially available [Key Organics (Camelford, United Kingdom) Cat. No. GS-0920, Ark Pharm, Cat. No. AK-77631, respectively]. The latter portion of the method just described to prepare Alloc-monoprotected 1,ω diamines, is applied to (S)- and (R)-Q-1 to provide both isomers of the differentially protected diamine Q-2. Selective removal of the Boc group provides the enantiomers of Alloc-560.
To 3-hydroxybenzaldehyde (25-1, 1.99 g, 16.3 mmol) and (9H-fluoren-9-yl)methyl carbamate (2.44 g, 10.2 mmol) in toluene (100 mL) was added TFA (2.36 mL, 30.6 mmol). The mixture was stirred at 80° C. for 2 d, then allowed to cool to rt, evaporated in vacuo and the residue purified by flash chromatography (hexanes:EtOAc: 95:5 to 50:50 over 14 min). Product-containing fractions were concentrated under reduced pressure to leave 63-2 as a white solid, 1H NMR and LC-MS (M+H+346) consistent with structure, 2.50 g, 71% yield.
Alternatively, 3-(aminomethyl) phenol is commercially available (Matrix Scientific Cat. No. 009265; Alfa Aesar Cat. No. H35708) and is protected with Fmoc using Method 1W/Example 1A.
In a manner similar to that already described for S50, the phenol is reacted with Alloc-S1 under Mitsunobu conditions to yield Alloc-S63(Fmoc), from which the Fmoc is cleaved to provide the desired product, Alloc-563.
Commerically available 3-(2-aminoethyl) phenol (3-hydroxyphenethyl-amine, AstaTech, Cat. No. 51439; Ark Pharm, Cat. No. AK-41280) is protected with Boc using standard methods (Method 1U) to provide 64-1. Fmoc protection can also be employed (Method 1W, Example 1A). In a manner analogous to that already described for S50 and S63, the phenol is reacted with Alloc-S1 under Mitsunobu conditions to give Alloc-S64(Boc), which is then subjected to acid treatment for removal of the Boc to yield the desired product, Alloc-564.
A suspension of 2-chloronicotinic acid (PA3, 11.0 g, 70.0 mmol), Boc-DA12 (15.0 g, 70.0 mmol), and anhydrous potassium carbonate (24.2 g, 175 mmol) in DMA (55 mL), and dioxane (25 mL) under a positive pressure of nitrogen, was placed in an oil-bath at 90° C. and the progress of the reaction was monitored by LC/MS. After 6-days the reaction did not progress to completion, therefore water and ether were added, and the mixture was sonicated until almost all was soluble. The ether layer was separated, and back extracted with water. The insoluble material was removed, and the aqueous layer was extracted twice more with ether to remove the by-products. LC/MS showed very little desired product in the ether extract. The aqueous layer was cooled in ice and acidified slowly with conc. HCl, until pH 4. The acidified aqueous layer was saturated with solid NaCl, and extracted with 10% MeOH/DCM (4×), and the extracts were washed with brine, dried over MgSO4, filtered and concentrated under reduced pressure, and the residue was dried under vacuum. The residual material was triturated from heptane and a small amount of ether and the suspension was sonicated, allowed to settle, and the solvents were decanted. This process was repeated 3×. The solid material was then dried under reduced pressure. The decanted solvents had mainly PA3 and DMA with very little of the desired product. The material, Boc-PY38, as obtained was sufficiently pure to be utilized directly for the next step.
Boc-PY38 (18.8 g, 56 mmol) was cooled in an ice-bath and treated with a 50% TFA/49% DCM/1% TIPS solution. The progress of the reaction was followed by LC/MS. After completion of Boc-deprotection was indicated, the reaction was reduced to dryness under reduced pressure. DCM and toluene were added to the residue, then the mixture again concentrated in vacuo to remove residual TFA. This process was continued until a constant weight (56.0 g) was achieved. The material thus obtained was dissolved in THF (80 mL) and H2O (80 mL), cooled in an ice-bath, then the pH adjusted to 8 by slow addition of NaOH pellets (11.4 g). To this, potassium carbonate (4.2 g), followed by Fmoc-OSu (18.9 g, 56.0 mmol), were added portionwise, then the mixture stirred at room temperature for 16 h. Water was added to the reaction solution and the resulting basic mixture transferred to a separatory funnel, and extracted with ether (3×), then the combined organic extracts back-extracted with saturated NaHCO3 (aq, 2×) until the ether layer showed no evidence of product (TLC or LC-MS). The NaHCO3 extracts were combined with the main basic aqueous layer. The combined aqueous basic layer was cooled to 0° C., acidified to pH 4-5 and extracted with 10% MeOH/DCM. The acidic aqueous layer was saturated with solid NaCl and extracted with additional 10% MeOH/DCM (2×). The combined organic extracts were washed twice with saturated brine, dried over MgSO4, filtered and concentrated in vacuo to give 37.0 g of a solid. This material was triturated with ether, collected by filtration, then washed with ether and allowed to air dry o/n. This gave 23.0 g (72%) of the product, Fmoc-PY38. Analysis by HPLC/MS showed a single peak (100% purity).
The yields for synthesis of other representative Fmoc-protected pyridine building blocks from PA3 and the monoBoc-protected diamine nucleophiles (Boc-DA3(1), Boc-DAS, Boc-DA6, Boc-DA7, Boc-DA8, Boc-DA9, Boc-DA10, Boc-DA11, respectively) using this procedure are shown below:
As an example of the use of Method 1GG to access alternative pyridine-containing building blocks, Boc-PY79 was prepared in 20% overall yield from PA3. After exchange of protecting groups using standard chemistry, the corresponding aldehyde (Fmoc-PY80) was then synthesized from the alcohol by oxidation using DMP, one of the options in Method 1H.
The following describe the procedures that are utilized for attachment of the pyridine-containing building blocks at various points using different methodologies during the synthesis of macrocyclic compounds.
Scheme 2 presents the synthetic route to a representative library of macrocyclic compounds of formula (I) containing four building blocks, which was followed to prepare the library of compounds 4201-4520 on solid support. The pyridine-containing building block (BB1) was loaded onto the resin (Method 1D), then the next two building blocks (BB2, BB3) sequentially attached utilizing amide coupling (Method 1G) after removal of the Fmoc protection (Method 1F) on the preceding building block. The final building block (BB4) was attached using reductive amination (Methods 1I or 1J), amide coupling (Method 1G) or Mitsunobu-Fukuyama reaction (Method 1P, not shown in Scheme). This was followed by selective N-terminal deprotection (Method 1F), cleavage from the solid support (Method 1Q) and macrocyclization (Method 1R). The side chain protecting groups were then removed (Method 1S) and the resulting crude product purified by preparative HPLC (Method 2B). The amounts of each macrocycle obtained, confirmation of their identity by mass spectrometry (MS), and their HPLC purity (UV or MS) are provided in Table 1A. The individual structures of the compounds thus prepared are presented in Table 1B.
1All syntheses were carried out on the solid phase starting from 70-80 mg of 2-chlorotrityl chloride resin (typical loading 1.0 mmol/g).
2Purity is determined by analysis with LC-UV at 220 nm, except for compounds 4502, 4517, 4518 where it was estimated from the MS.
For all compounds in Table 1B, m=0, R1═H, R3═H, R5═H and R7═H.
Scheme 3 presents the synthetic route to another representative library of macrocyclic compounds of formula (I) containing four building blocks, which was followed to prepare the library of macrocyclic compounds 4521-4772 on solid support. The first building block (BB1) was loaded onto the resin (Method 1D), then, after removal of the Fmoc group (Method 1F), the pyridine building block (BB2) added using amide bond formation (Method 1G). Fmoc deprotection (Method 1F) was followed by the addition of the next building component (BB3) again utilizing amide coupling (Method 1G). The final building block (BB4) was then attached using amide coupling (Method 1G), reductive amination (Methods 1I or 1J) or Mitsunobu-Fukuyama reaction (Method 1P, not shown in Scheme). The sequence was concluded by sequential N-terminal deprotection (Method 1F), cleavage from the resin support (Method 1Q), cyclization (Method 1R), and acidic deprotection of the side chain protecting groups (Method 1S). The crude products were then purified by preparative HPLC (Method 2B). The amounts of each macrocycle obtained, confirmation of their identity by mass spectrometry (MS), and their HPLC purity (UV or MS) are provided in Table 2A. The individual structures of the compounds thus prepared are presented in Table 2B.
1All syntheses were carried out on the solid phase starting from 70-80 mg of 2-chlorotrityl chloride resin (typical loading 1.0 mmol/g).
2Purity is determined by analysis with LC-UV at 220 nm, except for compounds 4756, 4757, 4759, 4760, 4761, 4762, 4763, 4765 where it was estimated from the MS.
For all compounds in Table 2B, m=0, R2═H, R3═H, R5═H and R7═H.
Scheme 4 presents the synthetic route to another representative library of macrocyclic compounds of formula (I) containing four building blocks, which was followed to prepare the library of macrocyclic compounds 4773-4779 on solid support. The first building block (BB1) was attached directly to the resin using the standard procedure (Method 1D). After removal of the Fmoc group (Method 1F), the second building block (BB2) was added using amide bond formation (Method 1G). Deprotection (Method 1F) was followed by the addition of the pyridine building block (BB3) using amide bond coupling (Method 1G). The final building block (BB4) was then attached using reductive amination (Methods 1I or 1J), amide coupling (Method 1G) or Mitsunobu-Fukuyama reaction (Method 1P, not shown in Scheme). Next, N-terminal Fmoc deprotection (Method 1F), cleavage from the resin support (Method 1Q), macrocyclization via amide bond formation (Method 1R), and final deprotection of the side chain protecting groups (Method 1S) were sequentially performed. The crude products thus obtained were purified by preparative HPLC (Method 2B). The amounts of each macrocycle obtained, the HPLC purity (UV) determined and their identity confirmation by mass spectrometry (MS) are provided in Table 3A. The individual structures of the compounds thus prepared are presented in Table 3B.
Compound 4779 originates from the same synthetic process as compound 4775 from reductive amination with two molecules of Fmoc-(S)-31 on the terminal amine of BB3 to give the additional substitution shown as R5 in Table 3B.
1All syntheses were carried out on the solid phase starting from 70-80 mg of 2-chlorotrityl chloride resin (typical loading 1.0 mmol/g).
2Purity is determined by analysis with LC-UV at 220 nm.
For all compounds in Table 3B, m=0, n=0, R2═H, R4═H and R7═H, except for those compounds (4774 and 4777) in which BB3 is Fmoc-PY39 wherein (N)R5 and Y are part of a six-membered ring, including the nitrogen atom, as shown for Y—R5 in Table 3B.
Scheme 5 presents the synthetic route to another representative library of macrocyclic compounds of formula (I) containing four building blocks, which was followed to prepare the library of macrocyclic compounds 4780-4785 on resin. The initial building block (BB1) was loaded directly to the solid support in the usual manner (Method 1D). The Fmoc protecting group was removed (Method 1F), then the second building block (BB2) attached using amide coupling (Method 1G). Deprotection of the Fmoc (Method 1F) was followed by the addition of the third building block (BB3) also employing amide bond formation (Method 1G). The pyridine building block (BB4) was then likewise attached with an amide coupling protocol (Method 1G). To complete the macrocycle construction, selective removal of the N-terminal Fmoc protection (Method 1F) was followed by cleavage from the support (Method 1Q), then macrocyclization (Method 1R). After final deprotection of the side chain protecting groups (Method 1S), the crude products obtained were purified by preparative HPLC (Method 2B). In Table 4A are presented the amounts obtained of each macrocycle, the HPLC purity determined and confirmation of identity by mass spectrometry (MS), while the structures of the individual compounds prepared are in Table 4B.
1All syntheses were carried out on the solid phase starting from 70-80 mg of 2-chlorotrityl chloride resin (typical loading 1.0 mmol/g).
2Purity is determined by analysis with LC-UV at 220 nm.
For all compounds in Table 4B, m=1, n=1, p=1, R2═H, R4═H and R6═H. For compounds 4780, 4781 and 4782, Q1 is CH2, while for compounds 4783, 474 and 4785, Q1 is C═O.
Scheme 6 presents the synthetic route to a representative library of macrocyclic compounds of formula (I) containing three building blocks, which was followed to prepare the library of macrocyclic compounds 4786-4807 on solid support. The initial pyridine-containing building unit (BB1) was loaded directly onto the resin (Method 1D). The Fmoc group was removed (Method 1F), then the second building block (BB2) attached using amide bond formation (Method 1G). Deprotection of the Fmoc (Method 1F) of BB2 was followed by the addition of the third building block (BB3) utilizing reductive amination (Method 1I or 1J). Selective N-terminal Fmoc deprotection (Method 1F), cleavage from the resin (Method 1Q), macrocyclization (Method 1R), and final deprotection of the side chain protecting groups (Method 1S) gave the crude products. These were then purified by preparative HPLC (Method 2B). The amounts of each macrocycle obtained, their HPLC purities and confirmation of their identities by mass spectrometry (MS) are provided in Table 5A, with the individual compound structures presented in Table 5B.
Compounds 4804, 4805, 4806 and 4807 originate from the same synthetic process as compounds 4786, 4787, 4789 and 4794, respectively, via reductive amination with two molecules of Fmoc-(R)-31 on the terminal amine of BB2 to give the substitution shown as R3 in Table 5B.
1All syntheses were carried out on the solid phase starting from 70-80 mg of 2-chlorotrityl chloride resin (typical loading 1.0 mmol/g).
2Purity is determined by analysis with LC-UV at 220 nm.
For all compounds in Table 5B, R1═H and R5═H.
Scheme 7 presents the synthetic route to another representative library of macrocyclic compounds of formula (I) containing three building blocks, which was followed to prepare the library of macrocyclic compounds 4808-4815 on solid support. The standard method was employed to load the first building block (BB1) directly onto the resin (Method 1D). The Fmoc protecting group was removed (Method 1F), then the pyridine building block (BB2) attached utilizing amide coupling (Method 1G). After deprotection of the Fmoc (Method 1F), the third building block (BB3) was added using reductive amination (Method 1I or 1J). Sequential N-terminal deprotection (Method 1F), cleavage from the support (Method 1Q), and cyclization via intramolecular amide bond formation (Method 1R), was followed by deprotection of the side chain protecting groups (Method 1S). The crude products were then purified by preparative HPLC (Method 2B). The amounts of each macrocycle obtained, their HPLC purity and confirmation of their identity by mass spectrometry (MS) are provided in Table 6A. The individual structures of the compounds thus prepared are presented in Table 6B.
1All syntheses were carried out on the solid phase starting from 70-80 mg of 2-chlorotrityl chloride resin (typical loading 1.0 mmol/g).
2Purity is determined by analysis with LC-UV at 220 nm.
For all compounds in Table 6B, R2═H and R5═H.
Scheme 8 presents the synthetic route to another representative library of macrocyclic compounds of formula (I) containing three building blocks, which was followed to prepare the library of macrocyclic compounds 4816-4825 on solid support. The first building block (BB1) was loaded directly onto the resin (Method 1D), then the Fmoc group removed (Method 1F). The second building block (BB2) was attached via amide bond formation (Method 1G). After deprotection of the Fmoc (Method 1F) on BB2, the pyridine building block (BB3) was the last added, again using amide coupling (Method 1G). Selective N-terminal deprotection (Method 1F), then cleavage from the support (Method 1Q), was followed by macrocyclization (Method 1R) and removal of the side chain protecting groups (Method 1S). The crude products obtained were purified by preparative HPLC (Method 2B). The amount of each macrocycle obtained, their HPLC purity and their identity confirmation by mass spectrometry (MS) are provided in Table 7A. The individual compound structures prepared are presented in Table 7B.
1All syntheses were carried out on the solid phase starting from 70-80 mg of 2-chlorotrityl chloride resin (typical loading 1.0 mmol/g).
2Purity is determined by analysis with LC-UV at 220 nm.
For all compounds in Table 7B, m=0, R2═H, R4═H and R5═H.
Infection with hepatitis C virus (HCV) is a major global health concern causing chronic hepatitis, liver cirrhosis and hepatocellular carcinoma. The non-structural viral proteins are cleaved from a precursor protein by the HCV NS3 serine protease that requires the adjacent NS4A cofactor. The NS3 protease plays a vital role in protein processing as it directs proteolytic cleavages at the NS3/4A, NS4A/4B, NS4B/5A, and NS5A/5B junctions and is thus essential for replication and infectivity of the virus.
To identify new HCV NS3 protease inhibitors, a scintillation proximity assay (SPA) optimized for HTS is conducted as described in the literature (J. Biomol. Screen. 2000, 5, 153-158). The buffer used for the assay is 62.5 mM HEPES (pH 7.5), 30 mM dithiothreitol, 18.75% (v/v) glycerol, 0.062% (v/v) Triton X-100. HCV NS3 protease is activated by incubation with the NS4A cofactor (1000:1 cofactor:protease ratio) in assay buffer for 5 min at ambient temperature with mild agitation. Assays are conducted in 96 or 384-well microtiter plates with 50 μL assay buffer, 15 nM dual biotin and tritium-labelled protease substrate (biotin-DRMEECASHLPYK[propionyl-3H]-NH2), 6 mM biotinyl-protease substrate, 25 nM HCV NS3 protease, 25 μM NS4A cofactor peptide (HKKKGSVVIVGRIILSG-NH2), and library test compound in 2.5 μL DMSO. Reaction is initiated by the addition of 10 μL of the enzyme and cofactor. The plates are incubated for 30 min at ambient temperature with gentle agitation, then stopped by the addition of 100 μL of an appropriate stop solution (for example, streptavidin-coated YSi-SPA beads in PBS). Measurement of the radioactivity bound to the SPA beads is performed with an appropriate microplate scintillation counter (typically using a 1 min count time). Data thus obtained are analyzed using an appropriate software package, for example GraphPad Prism (La Jolla, Calif.).
The majority of clinically important antipsychotic agents have been found, in addition to their antagonistic action at dopamine D2 receptors, to be potent inverse agonists at the 5-HT2A receptor. For the identification of new such CNS therapeutic agents, the receptor selection and amplification assay as described in the literature (J. Pharm. Exp. Ther. 2001, 299, 268-276) is conducted.
In preparation for the assay, appropriate cells (NIH-3T3 or other) are grown to 70-80% confluence in roller bottles or standard 96-well tissue culture plates in Dulbecco's modified essential media (DMEM) supplemented with 10% calf serum and 1% PSG (penicillin/streptomycin/glutamine. Transfection of cells with plasmid DNAs (cloned receptor) using standard methods for 12-16 h (o/n) followed. Co-expression of Gq was used to augment 5-HT2A receptor constitutive activity. If in plates, assays are performed with 1 to 50 ng/well cloned receptor and 20 ng/well β-galactosidase plasmid DNA. To assist with the 5-HT2A constitutive activity, 4-20 ng/well of Gq protein were also added. After transfection in roller bottles, the cells were trypsinized, harvested and frozen, or could be immediately used in the assay.
For the assay, cells were placed (or rapidly thawed, if previously forzen) in DMEM with 0.5% calf serum and 2% cyto-sf3 (Kemp Biotechnologies, Frederick, Md., USA), then added to the assay plates (typically 96- or 384-well) containing test compounds from the library, negative controls or positive controls (ritanserin). Alternatively, after the o/n transfection in plates, medium was replaced with serum-free DMEM containing 2% cyto-sf3 and 1% PSG and one (or more) concentrations of test library compounds or controls. In all cases, cells were grown in a humidified atmosphere with 5% ambient CO2 for 4-6 d. After removal of the medium, β-galactosidase activity in the plates is measured using standard methods, for example adding o-nitrophenyl β-D-galactopyranoside in phosphate buffered saline. The resulting colorimetric reaction was then measured using a spectrophotometric plate reader at the wavelength appropriate for the β-galactosidase method employed (420 nm for the example). Analysis of data is done using an appropriate software package, for example GraphPad Prism.
The p53 transcription factor is a potent tumor suppressor that regulates expression of a variety of genes responsible for DNA repair, differentiation, cell cycle inhibition and apoptosis. The function of p53 is suppressed by the MDM2 oncoprotein through direct inhibition of its transcriptional activity and also enhancement of its degradation via the ubiquitin-proteosome pathway. Many human tumors overexpress MDM2 and effectively impair p53-mediated apoptosis. Hence, stabilization of p53 through inhibiting the p53-MDM2 interaction offers an approach for cancer chemotherapy. For the identification of such inhibitors, the validated cell-based assay as described in the literature is employed (J. Biomol. Screen. 2011, 16, 450-456). This is based upon mammalian two-hybrid technology utilizing a dual luciferase reporter system to eliminate false hits from cytotoxicity to the compounds.
Appropriate cells (for example HEK293, U2OS, MDA-MB-435) were obtained from ATCC (Manassas, Va., USA) and maintained in DMEM with 10% fetal bovine serum (FBS), 100 mg/L penicillin, and 100 mg/L streptomycin at 37° C. in a humidified atmosphere of 5% CO2. About 1×106 cells were combined with plasmids (2-4 pg) in transfection buffer (200 μL), and electroporation executed for transient transfection.
A mammalian two-hybrid system (Stratagene, La Jolla, Calif.) was utilized for the cell-based assay developed for assessing the p53-MDM2 interaction. To effect this strategy, full-length p53 or MDM2 were inserted at the C-terminus of the DNA binding domain (BD) of GAL4 or the transcriptional activation domain (AD) of NFκB. Interaction of p53 and MDM2 brings the two domains (BD and AD) into proximity and thereby activates the downstream firefly luciferase reporter gene. Specifically, into the pCMV-AD and pCMV-BD vectors were cloned full-length cDNAs encoding human p53 and MDM2 in-frame with AD or BD at the N terminus. For single-luciferase analysis, cells were co-transfected with pCMV-AD-MDM2 (or -p53), pCMV-BD-p53 (or-MDM2), and the pFR-Luc firefly luciferase reporter plasmid at an equivalent ratio of 1:1:1. While for dual-luciferase analysis, an internal control, the pRL-TK plasmid encoding a renilla luciferase, was included. After transfection, seeding of cells is performed at a density of approximately 3×104 cells per well onto microplate (96 wells). The library test compounds at various concentrations are added 16 h post-transfection. Luciferase activities were measured after an additional 24 h using the Dual-Glo Luciferase system (Promega, Madison, Wis., USA) and an appropriate multiplate reader. Compounds are typically initially screened at a single concentration of 10 μM, 20 μM or 50 μM, then a dose-response curve obtained for those compounds found to be hits as defined below. In each 96-well plate, eight wells were used as positive controls (10 μM known inhibitor, for example nutilin-3, in 1% DMSO) and another eight wells as negative controls (1% DMSO). The luciferase activity was normalized to 100% and 0 in the wells treated with DMSO and known inhibitor, respectively. The compounds causing the luciferase activity to reduce to less than 30% could be considered as “hits” in the primary screening, although other values can also be selected. GraphPad Prism software, or other appropriate package, is used to analyze data and perform nonlinear regression analyses to generate dose-response curves and calculate IC50 values.
While the disclosure has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the disclosure following, in general, the principles of the disclosure and including such departures from the present disclosure as come within known or customary practice within the art to which the disclosure pertains and as may be applied to the essential features hereinbefore set forth, and as follows in the scope of the appended claims.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2018010147131-0 | Feb 2018 | CN | national |
The present application claims priority to U.S. application No. 62/523,575 filed on Jun. 22, 2017. This document is hereby incorporated by reference in its entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CA2018/050749 | 6/20/2018 | WO | 00 |
