Selective TC-PTP degraders for cancer immunotherapy
Selective TC-PTP degraders using PROTAC technology effectively address the challenges of existing inhibitors by achieving specific and potent degradation of TC-PTP, enhancing immunotherapy efficacy with minimal side effects.
Patent Information
- Application Number
- PCT/US2024/049380
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2023-10-06
- Filing Date
- 2024-10-01
- Publication Date
- 2025-04-10
AI Technical Summary
Current TC-PTP inhibitors face challenges due to limited specificity and bioavailability, and simultaneous targeting of TC-PTP and PTP IB can lead to significant side effects.
Development of selective TC-PTP degraders using PROTAC technology, which comprises a targeting ligand for TC-PTP, a ligand for an E3 ligase, and a chemical linker to tether the ligands, facilitating the degradation of TC-PTP through the ubiquitination-proteasome pathway.
The selective TC-PTP degraders achieve potent and specific degradation of TC-PTP with low nanomolar DC50 values and >110-fold selectivity over PTP1B, enhancing IFN-y signaling, antigen presentation, and T-cell activation, thereby offering a promising approach for cancer immunotherapy.
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Abstract
Description
SELECTIVE TC-PTP DEGRADERS FOR CANCER IMMUNOTHERAPYCROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority to U.S. provisional patent application no. 63 / 542,825 which was filed October 6, 2023, and which is hereby incorporated by reference in its entirety.STATEMENT OF GOVERNMENT SUPPORT
[0002] This invention was made with government support under CA 069202 and CA 023168 awarded by the National Institutes of Health. The government has certain rights in the invention.TECHNICAL FIELD
[0003] The present disclosure relates to T-cell protein tyrosine phosphatase (TC-PTP) protein degraders, pharmaceutical compositions comprising the same, and their use in the treatment of cancer and other diseases.BACKGROUND
[0004] This section introduces aspects that may help facilitate a better understanding of the disclosure. Accordingly, these statements are to be read in this light and are not to be construed as admissions about what is or is not prior art.
[0005] Protein tyrosine phosphorylation is a crucial post-translational modification controlled by protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs) and plays a key role in regulating essential cellular functions. Given that numerous human diseases are associated with aberrant protein tyrosine phosphorylation, both PTKs and PTPs are highly sought-after targets for drug discovery. Among members of the PTP family, protein-tyrosine phosphatase IB (PTP1B, also called PTPN1) and T-cell protein tyrosine phosphatase (TC-PTP, also called PTPN2) are the two most closely related cytosolic PTPs sharing over 72% amino acid sequence identity between their catalytic domains. TC-PTP is a non-receptor type PTP ubiquitously expressed in all tissues, with the highest expression in hematopoietic cells.
[0006] The studies disclose that TC-PTP deletion in B16 melanoma murine tumor cells promotes tumor cell antigen presentation and growth inhibition by amplifying the effects of interferongamma (IFN-y) (Nature, 2017, 547, 413-418), while loss of TC-PTP in T-cells enhances T-cell receptor (TCR) signaling and stimulates cell proliferation and activation. Thus, TC-PTP is a promising target for cancer immunotherapy. Most of the TC-PTP inhibitors encounter limitedspecificity and bioavailability due to the highly conserved and positively charged nature of PTP active sites. The development of highly potent and subtype-selective TC-PTP inhibitors remains a challenge due to the prevalent similarity between the active sites of TC-PTP and PTP IB (Molecular and Cellular Biology, 2001, 21, 7117-7136; Biochemical Journal, 2007, 402, 1-15.) Simultaneously targeting of TC-PTP and PTP IB can also lead to considerable side effects as PTP IB is a major negative regulator of insulin and leptin signaling and a critical positive regulator of microglia activation and neuroinflammation (Proceedings of the National Academy Sciences U.S.A., 2009, 106, 9368-9372; Cancer Discovery, 2022, 12, 752-773).
[0007] Thus, there is an unmet need for a compound that degrades TC-PTP protein selectively, provides effective immunotherapy in cancer, and is used for treating other TC-PTP -mediated diseases. It is an object of the present disclosure to provide such compounds. This and the other objects and advantages, as well as inventive feaures, will be apparent from the detailed description.SUMMARY
[0008] Provided is a compound of formula (I), or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof:wherein L is a linker selected from:wherein x is 1-15, w is 1-5, and each a and b is independently 0-3; a bond designated with "" is attached to E; and represents the point of attachment of the linker; andE is an E3 ligase ligand selected from Ei and E2, whereinEi is represented by a structure:wherein X is CO or CEE;Ri is fluoro, hydrogen, or deuterium; and a bond designated with represents the point of attachment of linker L; andE2 is represented by a structure:wherein R4 is methyl, hydrogen, or deuterium; and a bond designated with" is attached to the linker.
[0009] In some embodiments, the ligase ligand E is Ei.
[0010] In some embodiments, the linker L is:wherein x is 1-15, w is 1-5, and each a and b is independently 0-3; a bond designated with "" is attached to E; and represents the point of attachment of the linker.
[0011] In some embodiments, the compound of formula (I) is:or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof.
[0012] Provided is a pharmaceutical composition comprising a compound of formula (I), or a pharmaceutically acceptable salt, hydrate, tautomer, and stereoisomer thereof, and a pharmaceutically acceptable carrier, excipient, or diluent.
[0013] Provided is a method of inhibiting cancer in a patient, wherein the method comprises administering to the patient an effective amount of a compound of formula (I), or a pharmaceutically acceptable salt, hydrate, tautomer, and stereoisomer thereof, or a pharmaceutical composition comprising the same, whereupon cancer in the patient is inhibited.
[0014] Provided is a method of treating or preventing cancer, wherein the method comprises administering to a patient in need thereof an effective amount of a compound of formula (I), or a pharmaceutically acceptable salt, hydrate, tautomer, and stereoisomer thereof, or a pharmaceutical composition comprising the compound and a pharmaceutically acceptable carrier, excipient, or diluent.
[0015] In some embodiments, the cancer is colon cancer, lung adenocarcinoma, squamous cell carcinoma, and melanoma. The compound can be administered orally.
[0016] Further provided is a method of degrading T-cell protein tyrosine phosphatase (TC-PTP) proteins in a patient, wherein the method comprises administering to the patient an effective amount of a compound of formula (I), or a pharmaceutically acceptable salt, hydrate, tautomer,and stereoisomer thereof, or a pharmaceutical composition comprising the same, whereupon TC- PTP in the patient is degraded. In some embodiments, the patient has cancer. In some embodiments, the patient has type-II diabetes. In some embodiments, the patient is obese.
[0017] Still further provided is a method of treating or preventing type-II diabetes, wherein the method comprises degrading TC-PTP by administering to a patient in need thereof an effective amount of a compound of formula (I), or a pharmaceutically acceptable salt, hydrate, tautomer, and stereoisomer thereof, or a pharmaceutical composition comprising the same.
[0018] Still further provided is a method of treating or preventing obesity, wherein the method comprises degrading TC-PTP by administering to a patient in need thereof an effective amount of a compound of formula (I), or a pharmaceutically acceptable salt, hydrate, tautomer, and stereoisomer thereof, or a pharmaceutical composition comprising the same.BRIEF DESCRIPTION OF THE DRAWINGS
[0019] The present disclosure will be more readily understood from the detailed description of embodiments presented below considered in conjunction with the attached drawings of which:
[0020] Fig. 1A shows immunoblots of cell lysates from HEK293 treated with compound 12 at indicated concentrations, e.g., 0 nM, 3.9 nM, 7.8 nM, 15.6 nM, 31.2 nM, 62.5 nM, 125 nM, 250 nM, 500 nM, 1000 nM, 2000 nM and 4000 nM for 16 hours.
[0021] Fig. IB shows dose-dependent selective degradation of T-cell protein tyrosine phosphatase (TC-PTP) for compound 12 with DCso of 35.8 ± 1.4 nM.
[0022] Fig. 2A shows immunoblots of cell lysates from HEK293 treated with compound 12 at 1 pM for indicated hours, e.g., 0, 3, 6, 16, and 24 showing time-dependent degradation of TC- PTP.
[0023] Fig. 2B shows compound 12 selectively degrades TC-PTP in HEK293 cells. Treatment of 0.5 pM compound 12 for 16 hours led to substantial degradation of TC-PTP, whereas none of the other PTPs and signaling proteins were affected.
[0024] Fig. 3A shows a mechanistic investigation of TC-PTP degradation induced by compound 12 in HEK293 cells. Cells were pre-treated with the indicated concentration (0.5 pM) of pevonedistat (prevents ubiquitination), MG132 (blocks proteasome activity), or lenalidomide (prevents CRBN binding), followed by six hours of treatment with compound 12 at 0.5 pM showing compound 12 mediated TC-PTP degradation depends on the ubiquitination-proteasome pathway.
[0025] Fig. 3B shows immunofluorescences of TC-PTP and protein-tyrosine phosphatase IB (PTP1B,) with U2OS cells treated with DMSO, 5 pM compound 12 for 3 and 24 hours, showing compound 12 degrades both nucleus and cytoplasm localized TC-PTP. 20 pM MG132 was used along with compound 12 to block PTP1B and TC-PTP degradation in the control group.
[0026] Fig. 3C shows immunofluorescences of TC-PTP and PTP1B with HeLa cells treated with DMSO, 5 pM compound 12 for 3 and 24 hours, showing compound 12 degrades both nucleus and cytoplasm localized TC-PTP. 20 pM MG132 was used along with compound 12 to block PTP1B and TC-PTP degradation in the control group.
[0027] Fig. 4A shows compound 12 selectively enhances IFN-y signaling. It illustrates immunoblots of whole cell lysates from HEK293 cells showed that pJAKl, pJAK3, and pSTATl levels were elevated by compound 12 in a dose-dependent manner, along with TC-PTP degradation upon the treatment with compound 12 for 16 hours and stimulation with 20 ng / ml human IFN-y for 15 mins.
[0028] Fig. 4B shows compound 12 promotes antigen presentation in HEK293. It illustrates immunoblots of cell lysates from wild-type and TC-PTP deleted HEK293 cells that were treated with 0.5 pM compound 12 for 16 hours and stimulated with 20 ng / ml human IFN-y for 15 minutes. Deletion of TC-PTP abolished the compound 12-induced phosphorylation level increase of the TC-PTP substrate JAK1 and STAT1.
[0029] Fig. 5A shows immunofluorescence showing compound 12 dramatically enhanced IFN- y mediated STAT1 phosphorylation and nucleus translocation through degradation of TC-PTP. Wild-type and TC-PTP deleted HEK293 cells were treated with dimethyl sulfoxide (DMSO) or 0.5 pM compound 12 for 16 hours and stimulated with 20 ng / ml IFN-y for 30 minutes. DAPI was used to stain the cell nucleus.
[0030] Fig. 5B shows compound 12 promotes MHC-1 expression in HEK293 cells. Wildtype and TC-PTP knockout HEK293 cells were treated with DMSO or 500 nM compound 12 for 16 hours for TC-PTP degradation, then stimulated with 20 ng / ml mouse IFN-y for 48 hours to induce MHC-I expression. Mouse MHC-I complex was stained with mouse H2K(b) / H2D(b) antibody and measured by flow cytometry.
[0031] Fig. 6A shows that compound 12 elevates pLCK in Jurkat T-cells. It illustrates immunoblots of cell lysates showed that compound 12 dose-dependently degrades TC-PTP and promotes phosphorylation of LCK in Jurkat T cells. Cells were treated with compound 12 at concentrations 0 nM, 8 nM, 40 nM, 200 nM, and 1000 nM for 16 hours and stimulated with 2.5 pg / ml anti-CD3 antibody for 10 mins.
[0032] Fig. 6B shows that compound 12 enhances CAR-T cells killing efficiency in a coculture system. It illustrates immunoblots of cell lysates from KB cells treated with compound 12 at concentrations 0 nM, 62.5 nM, 125 nM, 250 nM, 500 nM, and 1000 nM for 16 hours, showing dose-dependent degradation of TC-PTP and elevation of pSTATl.
[0033] Fig. 7A shows the flow cytometry analysis of CD25 and CD69 and total lysis levels in cell lysates from KB and CAR-T cells with and without treatment of compound 12 with the addition of bivalent molecule EC 17.
[0034] Fig. 7B shows the screening of selective TC-PTP PROTACs by the degradation assay of compounds at 2 pM for 16 hours in HEK293 cells.
[0035] Fig. 8 shows the screening of selective TC-PTP PROTACs by the degradation assay of compounds at 1 pM for 16 hours in HEK293 cells.
[0036] Fig. 9 shows the cell viability assay of compound 12 in HEK 293 cells. No toxicity was observed with compound 12 in cells at up to 20 pM concentration. HEK293 cells were treated with DMSO or compound 12 at the indicated concentration for 48 hours, and the cell viability was measured with cell counting Kit-8 assay and normalized with DMSO control.
[0037] Fig. 10A shows the mice blood concentration of compound 12 overtime after single dose administration of 25 mg kg1compound 12 via intraperitoneal (i.p.) injection which indicates that compound 12 is bioavilable.
[0038] Fig. 10B shows the mice blood concentration of compound 12 over time after single dose administration of 50 mg kg1compound 12 via i.p. injection which indicates that compound 12 is bioavilable.DETAILED DESCRIPTION
[0039] For the purposes of promoting an understanding of the principles of the present disclosure, reference will now be made to the embodiments illustrated in the drawings, and specific language will be used to describe the same. It will nevertheless be understood that no limitation of the scope of the claimed invention is thereby intended.
[0040] The term "TC-PTP degrader" refers to a compound that degrades T-cell protein tyrosine phosphatase (TC-PTP, also called PTPN2; Protein Tyrosine Phosphatase Non-Receptor Type 2; TCELLPTP, T-Cell Protein-Tyrosine Phosphatase) proteins.
[0041] The term "protein degrader" or "proteolysis targeting chimera (PROTAC)" refers to a heterobi functional compound composed of three components: a ligand that binds to a specific target protein meant for degradation, a linker that can remove specific unwanted proteins and aprotein binding moiety that binds E3 ubiquitin ligase ligand. The function of PROTACs requires the formation of a ternary complex of target protein-PROTAC-E3 ligase and protein-protein interactions between the E3 ubiquitin ligase and the target protein, and this mechanism can provide another layer of target selectivity and other distinct benefits, including the extended efficacy and catalytic concentrations.
[0042] The term "cereblon E3 ligand" refers to compounds that bind to ubiquitin ligase cereblon and redirect its ubiquitination activity.
[0043] This disclosure provides a compound that is a protein degrader for TC-PTP. The compound is a PROTAC compound, which comprises a targeting ligand that binds to the target protein TC-PTP selectively, a ligand for an E3 ligase system, and a chemical linker that tethers the first and second ligands.
[0044] Provided is a compound of formula (I):or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof, whereinL is a linker selected from:wherein x is 1-15, w is 1-5, and each a and b is independently 0-3; a bond designated with "" is attached to E; and represents the point of attachment of the linker; andE is an E3 ligase ligand selected from Ei and E2, wherein Ei is represented by a structure:wherein X is CO or CEE;Ri is fluoro, hydrogen, or deuterium; and a bond designated with represents the point of attachment of linker L; and E2 is represented by a structure:wherein R4 is methyl, hydrogen, or deuterium; and a bond designated with" is attached to the linker.
[0045] In some embodiments, the E3 ligase ligand is El, where El is a cereblon ligand.
[0046] In some embodiments, the linker L is:wherein x is 1-15, w is 1-5, and each a and b is independently 0-3;a bond designated with " " is attached to E; and represents the point of attachment of the linker.
[0047] In some embodiments, TC-PTP degraders are heterobifunctional small molecules containing TC-PTP inhibitor moiety, a first ligand that binds TC-PTP targeted protein selectively, a second cereblon ligand that binds an E3 ligase that exploits the cell’s ubiquitin-proteasome system to achieve selective target protein degradation, and a linker that tethers the first and second ligands. They induce the formation of a ternary complex of target protein-protac-E3 ligase by simultaneously binding to an E3 ligase and TC-PTP, thereby bringing the TC-PTP into proximity of the E3 ligase for efficient ubiquitination and subsequent proteasome-mediated degradation. Thus, TC-PTP inhibitor moiety can be converted to potent and selective TC-PTP degrader using such PROTAC technology.
[0048] In some embodiments, the compound of formula (I) is:or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof.
[0049] The compounds of formula (I) and intermediates used for the preparation thereof, are enantiomerically enriched, e.g., the enantiomeric excess or “ee” of the compound is about 5% or more as measured by chiral HPLC.
[0050] In some embodiments, the ee is about 10%. In some embodiments, the ee is about 20%. In some embodiments, the ee is about 30%. In some embodiments, the ee is about 40%. In some embodiments, the ee is about 50%. In some embodiments, the ee is about 60%. In some embodiments, the ee is about 70%. In some embodiments, the ee is about 80%. In some embodiments, the ee is about 85%. In some embodiments, the ee is about 90%. In some embodiments, the ee is about 91%. In some embodiments, the ee is about 92%. In some embodiments, the ee is about 93%. In some embodiments, the ee is about 94%. In someembodiments, the ee is about 95%. In some embodiments, the ee is about 96%. In some embodiments, the ee is about 97%. In some embodiments, the ee is about 98%. In some embodiments, the ee is about 99%.
[0051] In some embodiments, E is the E3 ligase binding moiety of the molecule that can be enantiomerically enriched. In exemplary embodiments, the E3 ligase binding portion of the molecule is racemic. The present disclosure encompasses all possible stereoisomeric compounds, e.g., diastereomeric, forms of compounds of formula (I).
[0052] Provided are pharmaceutically acceptable salts of the above-described compounds and the preparation and use thereof. Salts can be prepared during the final isolation and purification of the compound or separately by reacting the compound with a suitable acid.
[0053] The term "pharmaceutically acceptable salt" refers to salts or zwitterionic forms of compounds of the present disclosure.
[0054] In some embodiments, the salts can be acid addition salts formed with pharmaceutically acceptable acids. Examples of inorganic acids, which can be employed to form pharmaceutically acceptable salts, include, but are not limited to, nitric acid, boric acid, hydrochloric acid, hydrobromic acid, sulfuric acid, and phosphoric acid. Examples of organic acids include, but are not limited to, oxalic acid, maleic acid, succinic acid, and citric acid.
[0055] Examples of the salts of the compounds described herein include, but are not limited to, hydrochloride salt, hydrobromide salt, hydroiodide salt, sulfate salt, bisulfate salt, 2- hydroxyethansulfonate salt, phosphate salt, hydrogen phosphate salt, acetate salt, adipate salt, alginate salt, aspartate salt, benzoate salt, bisulfate salt, butyrate salt, camphorate salt, camphorsulfonate salt, di gluconate salt, glycerolphosphate salt, hemi sulfate salt, heptanoate salt, hexanoate salt, formate salt, succinate salt, fumarate salt, maleate salt, ascorbate salt, isethionate salt, salicylate salt, methanesulfonate salt, mesitylenesulfonate salt, naphthylenesulfonate salt, nicotinate salt, 2-naphthalenesulfonate salt, oxalate salt, pamoate salt, pectinate salt, persulfate salt, 3-phenylproprionate salt, picrate salt, pivalate salt, propionate salt, tri chloroacetate salt, trifluoroacetate salt, phosphate salt, glutamate salt, bicarbonate salt, paratoluenesulfonate salt, undecanoate salt, lactate salt, citrate salt, tartrate salt, gluconate salt, methanesulfonate salt, ethanedi sulfonate salt, benzene sulfonate salt, and p-toluenesulfonate salt.
[0056] The amino groups in the compounds described herein can be quaternized with methyl chloride, ethyl chloride, propyl chloride, butyl chloride; methyl bromide, ethyl bromide, propyl bromide, butyl bromide; methyl iodide, ethyl iodide, propyl iodide, butyl iodide; dimethyl sulfate, diethyl sulfate, dibutyl sulfate, diamyl sulfates; decyl chloride, lauryl chloride, myristyl chloride,steryl chloride; decyl bromide, lauryl bromide, myristyl bromide, steryl bromide; decyl iodide, lauryl iodide, myristyl iodide, steryl iodide; benzyl bromide and phenethyl bromide.
[0057] Provided are hydrates of the compounds and preparation and use thereof. Hydrates typically do not significantly alter the physiological activity or toxicity of the compounds and, as such, may function as pharmacological equivalents.
[0058] Solvated forms of the compounds can be prepared with a pharmaceutically acceptable solvent. Examples of the solvents include, but are not limited to, water, methanol, and ethanol, and it is intended that the disclosure includes both solvated and unsolvated forms of abovedescribed compounds. One type of solvate is a hydrate. A "hydrate" relates to a particular subgroup of solvates where the solvent molecule is water. Solvates typically can function as pharmacological equivalents. The preparation of solvates is known in the art. For example, M. Caira et al., J. Pharmaceut. Sci., 2004, 93(3): 601-611, describes the preparation of solvates of fluconazole with ethyl acetate and with water. Similar preparation of solvates, hemisolvates, hydrates, and the like are described by E.C. van Tender et al., AAPS Pharm. Sci. Tech., 2004, 5(1): Article 12, and A.L. Bingham et al, 200, Chem. Commun., 603-604. Atypical, non-limiting, process of preparing a solvate would involve dissolving a compound in a desired solvent (organic, water, or a mixture thereof) at temperatures above 20 °C to about 25 °C, then cooling the solution at a rate sufficient to form crystals, and isolating the crystals by known methods, e.g., filtration. Analytical techniques, such as infrared spectroscopy, can be used to confirm the presence of the solvate in a crystal of the solvate.
[0059] Any reference compounds of the present disclosure appearing herein are intended to include compounds of the present disclosure as well as pharmaceutically acceptable salts or hydrates thereof.
[0060] The term "substituted" refers to a functional group in which one or more hydrogen atoms contained therein are replaced by one or more non-hydrogen atoms. The term "functional group" or "substituent" refers to a group that can be or is substituted onto a molecule. Examples of substituents or functional groups include, but are not limited to, a halo (e.g., F, Cl, Br, and I); an oxygen atom in groups such as hydroxyl groups, alkoxy groups, aryloxy groups, aralkyloxy groups, oxo(carbonyl) groups, carboxyl groups including carboxylic acids, carboxylates, and carboxylate esters; a sulfur atom in groups such as thiol groups, alkyl and aryl sulfide groups, sulfoxide groups, sulfone groups, sulfonyl groups, and sulfonamide groups; a nitrogen atom in groups such as amines, azides, hydroxylamines, cyano, nitro groups, N-oxides, hydrazides, and enamines; and other heteroatoms in various other groups.
[0061] Non-limiting examples of substituents, which can be bonded to a substituted carbon atom (or other atom, such as nitrogen) include F, Cl, Br, I, OR, OC(O)N(R)2, CN, NO, NO2, ONO2, azido, CF3, OCF3, R, O (oxo), S (thiono), C(O), S(O), methylenedioxy, ethylenedioxy, N(R)2, SR, SOR, SO2R, SO2N(R)2, SO3R, (CH2)O-2P(0)OR2, C(O)R, C(O)C(O)R, C(O)CH2C(O)R, C(S)R, C(O)OR, OC(O)R, C(O)N(R)2, OC(O)N(R)2, C(S)N(R)2, (CH2)O-2N(R)C(0)R, (CH2)O-2N(R)C(O)OR, (CH2)O-2N(R)N(R)2, N(R)N(R)C(O)R, N(R)N(R)C(O)OR, N(R)N(R)CON(R)2, N(R)SO2R, N(R)SO2N(R)2, N(R)C(O)OR, N(R)C(O)R, N(R)C(S)R, N(R)C(O)N(R)2, N(R)C(S)N(R)2, N(COR)COR, N(OR)R, C(=NH)N(R)2, C(O)N(OR)R, and C(=NOR)R wherein R can be hydrogen or a carbon-based moiety, and wherein the carbon-based moiety can itself be further substituted; for example, where R can be hydrogen, alkyl, acyl, cycloalkyl, aryl, aralkyl, heterocyclyl, heteroaryl, or heteroarylalkyl, any alkyl, acyl, cycloalkyl, aryl, aralkyl, heterocyclyl, heteroaryl, or heteroarylalkyl or R can be independently mono- or multi-substituted; or when two R groups bonded to a nitrogen atom or to adjacent nitrogen atoms can, together with the nitrogen atom or atoms to which they are bonded, form a heterocyclyl, the heterocycle can be mono- or independently multi -substituted.
[0062] The term " alkyl" refers to substituted or unsubstituted straight-chain and branched alkyl groups and cycloalkyl groups having from 1 to about 20 carbon atoms (e.g., C1-C20), 1 to 12 carbons (e.g., C1-C12), 1 to 8 carbon atoms (e.g., Ci-Cs), or, in some embodiments, from 1 to 6 carbon atoms (e.g., Ci-Ce). Examples of straight-chain alkyl groups include those with from 1 to 8 carbon atoms such as methyl, ethyl, n-propyl, n-butyl, n-pentyl, n-hexyl, n-heptyl, and n-octyl groups. Examples of branched alkyl groups include, but are not limited to, isopropyl, iso-butyl, sec-butyl, tert-butyl, neopentyl, isopentyl, and 2,2-dimethylpropyl groups. The term "alkyl" encompasses n-alkyl, isoalkyl, and anteisoalkyl groups as well as other branched chain forms of alkyl. Representative substituted alkyl groups can be substituted one or more times with any of the groups listed herein, for example, amino, hydroxy, cyano, carboxy, nitro, thio, alkoxy, carbonyl, and halogen groups.
[0063] The term "alkenyl" refers to substituted or unsubstituted straight-chain and branched divalent alkenyl and cycloalkenyl groups having from 2 to 20 carbon atoms (e.g., C2-C20), 2 to 12 carbons (e.g., C2-C12), 2 to 8 carbon atoms (e.g., C2-C8) or, in some embodiments, from 2 to 4 carbon atoms (e.g., C2-C4) and at least one carbon-carbon double bond. Examples of straight-chain alkenyl groups include those with from 2 to 8 carbon atoms such as -CH=CH-, -CH=CHCH2-, and the like. Examples of branched alkenyl groups include, but are not limited to, -CH=C(CH3)- and the like.
[0064] The term "alkynyl" refers to an unsaturated monovalent chain of carbon atoms, including at least one triple bond, which may be optionally branched. In various embodiments that include alkynyl, illustrative examples include lower alkynyl, such as C2-C6,C2-C4alkynyl, and the like.
[0065] The term "hydroxyalkyl" refers to alkyl groups substituted with at least one hydroxyl (- OH) group.
[0066] The term "cycloalkyl" refers to substituted or unsubstituted cyclic alkyl groups such as, but not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl groups. In some embodiments, the cycloalkyl group can have 3 to about 8-12 ring members, whereas in other embodiments, the number of ring carbon atoms ranges from 3 to 4, 5, 6, or 7. In some embodiments, cycloalkyl groups can have 3 to 6 carbon atoms (e.g., C3-C6). Cycloalkyl groups further include polycyclic cycloalkyl groups such as, but not limited to, norbornyl, adamantyl, bornyl, camphenyl, isocamphenyl, and carenyl groups, and fused rings such as, but not limited to, decalinyl, and the like.
[0067] The term "acyl" refers to a group containing a carbonyl moiety wherein the group is bonded via the carbonyl carbon atom. The carbonyl carbon atom is also bonded to another carbon atom, which can be part of a substituted or unsubstituted alkyl, aryl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, heterocyclylalkyl, heteroaryl, heteroarylalkyl group or the like. In the special case wherein the carbonyl carbon atom is bonded to a hydrogen, the group is a "formyl" group, an acyl group as the term is defined herein. An acyl group can include 0 to about 12-40, 6- 10, 1-5 or 2-5 additional carbon atoms bonded to the carbonyl group. An acryloyl group is an example of an acyl group. An acyl group can also include heteroatoms within the meaning herein. A nicotinoyl group (pyridyl-3-carbonyl) is an example of an acyl group within the meaning herein. Other examples include acetyl, benzoyl, phenylacetyl, pyridylacetyl, cinnamoyl, and cryloyl groups and the like. When the group containing the carbon atom that is bonded to the carbonyl carbon atom contains a halogen, the group is termed a "haloacyl" group. An example is a trifluoroacetyl group.
[0068] The term "aryl" refers to substituted or unsubstituted cyclic aromatic hydrocarbons that do not contain heteroatoms in the ring. Thus aryl groups include, but are not limited to, phenyl, azulenyl, heptalenyl, biphenyl, indacenyl, fluorenyl, phenanthrenyl, triphenylenyl, pyrenyl, naphthacenyl, chrysenyl, biphenylenyl, anthracenyl, and naphthyl groups. In some embodiments, aryl groups contain about 6 to about 14 carbons (e.g., C6-C14) or from 6 to 10 carbon atoms (e.g., C6-C10) in the ring portions of the groups. Aryl groups can be unsubstituted or substituted, as defined herein. Representative substituted aryl groups can be mono-substituted or substituted more than once, such as, but not limited to, 2- substituted phenyl, 3- substituted phenyl, 4-substituted phenyl, 5- substituted phenyl, or 6-substituted phenyl or 2-8 substituted naphthyl groups, which can be substituted with carbon or non-carbon groups such as those listed herein.
[0069] The term "heteroaryl" represents aromatic ring comprising at least one hetero atom such as N, S, O, or Se. Heteroaryl in the present disclosure may be any hetero aryl. Heteroaryl includes, but is not limited to, pyrrolidinyl, azetidinyl, piperidynyl, piperazinyl, morpholinyl, chromanyl, indolinonyl, isoindolinonyl, furanyl, pyrrolidinyl, pyridinyl, pyrazinyl, pyrimidinyl, triazinyl, thiophenyl, tetrahydrofuranyl, pyrrolyl, oxazolyl, oxadiazolyl, imidazolyl, triazyolyl, tetrazolyl, benzoxazolinyl, benzthiazolinyl, benzimidazolinyl groups, or any combination thereof.
[0070] The term "halogen" refers to an atom selected from fluorine, chlorine, bromine, and iodine.
[0071] The term "heterocycloalkyl" refers to a non-aromatic heterocycle where one or more of the ring-forming atoms is / are a heteroatom, such as an O, N, or S atom. Heterocycloalkyl groups can include mono- or polycyclic (e.g., having 2, 3 or 4 fused rings) ring systems as well as spirocycles. Example heterocycloalkyl groups include morpholino, thiomorpholino, piperazinyl, tetrahydrofuranyl, tetrahydrothienyl, 2,3 -dihydrobenzofuryl, 1,3 -benzodi oxole, benzo- 1,4- dioxane, piperidinyl, pyrrolidinyl, isoxazolidinyl, isothiazolidinyl, pyrazolidinyl, oxazolidinyl, thiazolidinyl, imidazolidinyl, and the like. Also included in the definition of heterocycloalkyl are moieties that have one or more aromatic rings fused (i.e., having a bond in common with) to the nonaromatic heterocyclic ring, for example phthalimidyl, naphthalimidyl, and benzo derivatives of heterocycles. A heterocycloalkyl group having one or more fused aromatic rings can be attached though either the aromatic or non-aromatic portion. Also included in the definition of hetero-cycloalkyl are moieties where one or more ring-forming atoms are substituted by 1 or 2 oxo or sulfido groups. In some embodiments, the heterocycloalkyl group has from 1 to about 20 carbon atoms, and in further embodiments from about 3 to about 20 carbon atoms. In some embodiments, the heterocycloalkyl group contains 3 to about 20, 3 to about 14, 3 to about 7, or 5 to 6 ring-forming atoms. In some embodiments, the heterocycloalkyl group has 1 to about 4, 1 to about 3, or 1 to 2 heteroatoms. In some embodiments, the heterocycloalkyl group contains O to 3 double bonds. In some embodiments, the heterocycloalkyl group contains 0 to 2 triple bonds.
[0072] It is understood that each of alkyl, cycloalkyl, alkenyl, cycloalkenyl, alkylene, and heterocycle may be optionally substituted with independently selected groups such as alkyl, haloalkyl, hydroxyalkyl, aminoalkyl, carboxylic acid and derivatives thereof, including esters, amides, and nitrites, hydroxy, alkoxy, acyloxy, amino, alky and dialky-lamino, acylamino, thio, and the like, and combinations thereof.
[0073] The terms "optionally substituted" and "optional substituents" indicate that the groups in question are either unsubstituted or substituted with one or more of the substituents specified. When the groups in question are substituted with more than one substituent, the substituents may be the same or different. When used with the terms "independently", "independently are," and "independently selected from," the groups in question may be the same or different. Certain of the herein defined terms may occur more than once in the structure and, upon such occurrence, each term shall be defined independently of the other.
[0074] The term "amine" refers to primary, secondary, and tertiary amines having, e.g., the formula N(group)3 wherein each group can independently be H or non-H, such as alkyl, aryl, and the like. Amines include, but are not limited to, R-NH2, for example, alkylamines, arylamines, alkylarylamines; R2NH, wherein each R is independently selected, such as dialkylamines, diarylamines, aralkylamines, heterocyclylamines and the like; and R3N, wherein each R is independently selected, such as trialkylamines, dialkylarylamines, alkyldiarylamines, triarylamines, and the like. The term "amine" also includes ammonium ions.
[0075] The term "amino group" refers to a substituent of the form -NH2, -NHR, -NR2, -NR3+, wherein each R is independently selected, and protonated forms of each, except for -NR3+, which cannot be protonated. Accordingly, any compound substituted with an amino group can be viewed as an amine. An "amino group" can be a primary, secondary, tertiary, or quaternary amino group. An "alkylamino" group includes a monoalkylamino, a dialkylamino, and a trialkylamino group.
[0076] The compounds may contain one or more chiral centers, or may otherwise be capable of existing as multiple stereoisomers. In various embodiments, the compounds are not limited to any particular stereochemical requirement, and the compounds, and compositions, methods, uses, and medicaments that include them may be optically pure or any of a variety of stereoisomeric mixtures, including racemic and other mixtures of enantiomers, other mixtures of diastereomers, and the like. Such mixtures of stereoisomers may include a single stereochemical configuration at one or more chiral centers, while including mixtures of stereochemical configuration at one or more other chiral centers.
[0077] Similarly, the compounds described herein may include geometric centers, such as cis, trans, E, and Z double bonds. In various embodiments, the compounds are not limited to any particular geometric isomer requirement, and the compounds, and compositions, methods, uses, and medicaments that include them, may be pure or any of a variety of geometric isomer mixtures. Such mixtures of geometric isomers may include a single configuration at one or more double bonds, while including mixtures of geometry at one or more other double bonds.
[0078] The term "compound" as used herein, is meant to include all stereoisomers, geometric isomers, and tautomers of the structures depicted.
[0079] In some embodiments, the compounds can induce degradation of TC-PTP with low nanomolar DCsos (compound concentration needed to induce target protein degradation by 50 %) and > 110-fold selectivity over PTP1B, which is a close homolog of TC-PTP. Compounds disclosed herein can have DCso values about 0.1 to about 10000 nM, such as about 0.1 to 10000 nM or 0.1 to about 10000 nM or 0.1 to 10000 nM.
[0080] The compounds can selectively degrade TC-PTP protein with % degradation from about less than 5% to about greater than 95%. In some embodiments, TC-PTP protein is reduced by about 50% or less, e.g., 1%, about 2%, about 4%, about 5%, about 9%, about 11%, about 14%, about 20%, about 25%, about 29%, about 35%, about 40%, about 48%. In some embodiments, TC-PTP protein is reduced by about 50% or more, about 51%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 92%, about 94%, about 95%.
[0081] In some embodiments, provided is a pharmaceutical composition comprising a compound of formula (I) or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof, and a pharmaceutically acceptable carrier, excipient, or diluent. Any suitable carrier, excipient, or diluent, as known in the art, can be used. The carrier, excipient, or diluent can vary based on the particular route of administration (see, e.g., Remington's The Science and Practice of Pharmacy, 23rd ed. (2020)).
[0082] In some embodiments, a pharmaceutical composition further comprises at least one additional pharmaceutically active agent. Pharmaceutical compositions can be prepared by combining a compound of formula (I) or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof, with a pharmaceutically acceptable carrier, excipient, or diluent and, optionally, one or more additional pharmaceutically active agents.
[0083] Provided is a pharmaceutical composition comprising (i) one or more compounds of formula (I) or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof, and (ii) one or more other prophylactic or therapeutic agents, and a pharmaceutically acceptable carrier, excipient, or diluent.
[0084] The compound and one or more other prophylactic or therapeutic agents can be administered as two separate compositions, simultaneously or sequentially, in either order by the same or different routes.
[0085] Compounds of the formula (I) or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof can degrade TC-PTP. Thus, they can treat or prevent various diseases and conditions mediated by TC-PTP. In some embodiments, the disease or condition is cancer.
[0086] Provided is a method of treating or preventing cancer. The method comprises administering to a patient in need thereof an effective amount of a compound of formula (I) or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof, or a pharmaceutical composition comprising the same and a pharmaceutically acceptable carrier, excipient, or diluent.
[0087] Further provided is a method of treating or preventing cancer. The method comprises administering to a patient in need thereof an effective amount of (i) a compound of formula (I) or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof, and (ii) one or more other prophylactic or therapeutic agents, optionally as a pharmaceutical composition comprising (i) and (ii) and a pharmaceutically acceptable carrier, excipient, or diluent. The other prophylactic or therapeutic agent can be selected from drugs known to prevent or treat cancer, e.g., a monoclonal antibody useful in treating a particular cancer.
[0088] Further provided is a method of inhibiting cancer in a patient, wherein the method comprises administering to the patient an effective amount of a compound of formula (I) or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof, or a pharmaceutical composition comprising the same, whereupon cancer in the patient is inhibited.
[0089] In some embodiments, the cancer is colon cancer, lung adenocarcinoma, squamous cell carcinoma, and melanoma.
[0090] Further provided is a method of degrading TC-PTP proteins, which method comprises administering to a patient in need thereof an effective amount of a compound of formula (I) or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof.
[0091] In some embodiments, the disease or condition mediated by TC-PTP is type II diabetes or obesity. Further provided is a method of treating or preventing type II diabetes. The method comprises administering to a patient in need thereof an effective amount of a compound of formula (I) or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof, or a pharmaceutical composition comprising the compound and a pharmaceutically acceptable carrier, excipient, or diluent. The effective amount of the compound can be optionally administered with one or more other prophylactic or therapeutic agents. The other prophylactic or therapeutic agent can be selected from drugs known to prevent or treat type II diabetes.
[0092] Further provided is a method of treating or preventing obesity. The method comprises administering to a patient in need thereof an effective amount of a compound of formula (I) or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof, or a pharmaceuticalcomposition comprising the compound and a pharmaceutically acceptable carrier, excipient, or diluent. The effective amount of the compound can be optionally administered with one or more other prophylactic or therapeutic agents. The other prophylactic or therapeutic agent can be selected from drugs known to prevent or treat obesity.
[0093] Since compounds described herein are degraders of TC-PTP protein, a number of diseases and conditions mediated by TC-PTP can be treated (e.g., prophylactically or therapeutically) by employing these compounds.
[0094] Still further provided is a method of treating or preventing a disease or condition responsive to TC-PTP degradation. The method comprises administering to a patient in need thereof an effective amount of an above-described compound, or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof, optionally as a pharmaceutical composition comprising the compound and a pharmaceutically acceptable carrier, excipient, or diluent. The effective amount of the compound can be optionally administered with one or more other prophylactic or therapeutic agents. The other prophylactic or therapeutic agent can be selected from drugs known to prevent or treat the disease or condition.
[0095] The method comprises administering a therapeutically effective amount of a compound of formula (I) as a neat compound or as a pharmaceutical composition. The compound or pharmaceutical composition can be administered during or after the onset of the disease or condition. Typically, the pharmaceutical compositions are sterile and contain no toxic, carcinogenic, or mutagenic compounds, which would cause an adverse reaction when administered.
[0096] Still further provided are kits comprising a compound of formula (I) and, optionally, one or more other therapeutic agents, packaged separately or together, and an insert having instructions for using these active agents.
[0097] The other therapeutic agent(s), including specifically, but not limited to, a compound that can be used in the treatment of a disease or condition wherein degradation of TC-PTP provides a benefit. Examples of the therapeutic agent (s) are not limited to anticancer agents and antidaibetic agents.
[0098] The other therapeutic agent(s) can be administered simultaneously or sequentially, by the same or a different route, to achieve the desired effect. The compound described herein and one or more other prophylactic or therapeutic agents can be administered from a single composition or two separate compositions, such as by the same or different routes. The prophylactic or therapeutic agent can be administered in an amount to provide its desired prophylactic or therapeutic effect. The effective dosage range for each prophylactic or therapeutic agent is well-known in the art or can be determined in accordance with dosage range-determining methods known to those of ordinary skill in the art, and the therapeutic agent can be administered to a patient in need thereof within such established ranges. The compound described herein, and one or more other prophylactic or therapeutic agents can be administered together as a single unit dose or separately as multi-unit doses, wherein the compound can be administered before the other prophylactic or therapeutic agent (s) or vice versa. One or more doses of the compound and / or one or more doses of the second prophylactic or therapeutic agent can be administered.
[0099] An effective amount of the compound is typically formulated in accordance with pharmaceutical practice. The effective amount depends on the individual case, and it is subject to medical assessment (diagnosis) that considers signs, symptoms, and / or malfunctions that are present, the risks of developing particular signs, symptoms, and / or malfunctions, and other factors.
[0100] The term "effective amount" or "effective dose" refers to an amount of the active ingredient(s) that is(are) sufficient, when administered, to deliver efficaciously the active ingredient(s) for the treatment of a disease or condition of interest to a subj ect in need thereof. The prophylactically or therapeutically effective amount of such compound will vary depending upon the patient and the disease or condition being treated, the weight and age of the patient, the severity of the disease or condition, the manner of administration, and the like, which can readily be determined by one of ordinary skill in the art. In the case of a cancer or other proliferative disorder, the prophylactically or therapeutically effective amount of the agent may reduce (z.e., inhibit to some extent or stop) unwanted cellular proliferation; reduce the number of cancer cells; reduce the tumor size; inhibit (or stop) cancer cell infiltration into peripheral organs; inhibit (or stop) tumor metastasis; inhibit, e.g., to some extent, tumor growth; and / or relieve, to some extent, one or more of the signs or symptoms associated with the cancer. To the extent the administered compound or composition prevents growth and / or kills existing cancer cells, it may be cytostatic and / or cytotoxic.
[0101] The compounds can be typically administered in admixture with a pharmaceutical carrier to give a pharmaceutical composition selected with regard to the intended route of administration and standard pharmaceutical practice. Pharmaceutical compositions can be formulated in a conventional manner using one or more physiologically acceptable carriers comprising excipients and / or auxiliaries that facilitate the processing of the compound. The pharmaceutical compositions can be manufactured, for example, by conventional mixing, dissolving, granulating, drageemaking, emulsifying, encapsulating, entrapping, or lyophilizing processes. Proper formulation is dependent upon the route of administration chosen. When a therapeutically effective amount of a compound described herein is administered orally, the composition typically is in the form of atablet, capsule, powder, solution, or elixir. When administered in tablet form, the composition additionally can contain a solid carrier, such as a gelatin or an adjuvant. The tablet, capsule, and powder can contain about 0.01% to about 95%, and preferably from about 1% to about 50%, of the compound. When administered in liquid form, a liquid carrier can be added, such as water, petroleum, or oils of animal or plant origin. The liquid form of the composition can further contain the physiological saline solution, dextrose or other saccharide solutions, or glycols. When administered in liquid form, the composition contains about 0.1% to about 90%, and preferably about 1% to about 50%, by weight, of the compound.
[0102] The compounds can be administered by any suitable route, for example, oral, buccal, inhalation, sublingual, rectal, vaginal, intraci sternal, intrathecal through a lumbar puncture, transurethral, nasal, percutaneous, i.e., transdermal, or parenteral including intravenous, intramuscular, subcutaneous, intracoronary, intradermal, intramammary, intraperitoneal, intraarticular, intrathecal, retrobulbar, intrapulmonary injection and / or surgical implantation at a particular site administration. Parenteral administration can be accomplished using a needle and syringe or using a high-pressure technique.
[0103] For oral administration, the compounds can be formulated readily by combining the active compound(s) with pharmaceutically acceptable carriers, excipients, or diluents well-known in the art. Such carriers, excipients, or diluents enable the compounds to be formulated as tablets, pills, powders, dragees, capsules, liquids, gels, syrups, slurries, suspensions, solutions, and the like for oral ingestion by a subject to be treated.
[0104] The exact formulation, route of administration, and dosage of a pharmaceutical composition comprising an effective amount of the compound are determined by an individual physician in view of the diagnosed condition or disease. The dosage amount and interval can be adjusted individually to provide levels of the compound that are sufficient to maintain a prophylactic or therapeutic effect.
[0105] Toxicity and therapeutic efficacy of the compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the maximum tolerated dose (MTD) of a compound, which is defined as the highest dose that causes no toxicity in animals. The therapeutic index is the dose ratio between the maximum tolerated dose and therapeutic effects (e.g., inhibition of tumor growth). The dosage can vary within this range depending upon the dosage form employed and the route of administration utilized. The determination of a therapeutically effective amount is well within the capability of those ordinarily skilled in the art, especially in light of the detailed disclosure provided herein.
[0106] An effective amount of a compound required for use in therapy varies with the nature of the condition being treated, the length of time that activity is desired, and the age and the condition of the patient, and ultimately is determined by the attendant physician. Dosage amounts and intervals can be adjusted individually to provide plasma levels of the TC-PTP degrader that are sufficient to maintain the desired prophylactic or therapeutic effect. The desired dose can be administered in a single dose or as multiple doses administered at appropriate intervals, for example, as one, two, three, four, or more sub-doses per day. Multiple doses often are desired or required. For example, the compound can be administered at a frequency of four doses delivered as one dose per day at four-day intervals (q4d x 4). Four doses delivered as one dose per day at three-day intervals (q3d x 4); one dose delivered per day at five-day intervals (qd x 5); one dose per week for three weeks (qwk3); five daily doses, with two days rest, and another five daily doses (5 / 2 / 5); or, any dose regimen determined to be appropriate for the circumstance.
[0107] A compound can be administered in an amount of about 0.005 to about 500 milligrams per dose, about 0.05 to about 250 milligrams per dose, or about 0.5 to about 100 milligrams per dose. For example, the compound can be administered, per dose, in an amount of about 0.005, about 0.05, about 0.5, about 5, about 10, about 20, about 30, about 40, about 50, about 100, about 150, about 200, about 250, about 300, about 350, about 400, about 450, or about 500 milligrams, including all doses between 0.005 and 500 milligrams.
[0108] The compositions comprising the compound (s) can be formulated in a unit dosage form, each dosage containing from about 5 to about 1,000 nig (1 g), more usually about 100 mg to about 500 mg, of the active ingredient.
[0109] The dosage of a composition comprising a compound described herein, can range from about 1 mg / kg to about 200 mg / kg, about 1 mg / kg to about 100 mg / kg, or about 1 mg / kg to about 50 mg / kg. The above dosages are exemplary of the average case, but there can be individual instances in which higher or lower dosages are merited, and such are within the scope of this disclosure. In practice, the physician determines the actual dosing regimen that is most suitable for an individual patient, which can vary with the age, weight, and response of the particular patient.
[0110] The term "a disease or condition wherein degradation of TC-PTP provides a benefit" and the like pertains to a disease or condition in which TC-PTP is important or necessary, e.g., for the onset, progress, expression of that disease or condition, or a disease or a condition which is known to be treated by a TC-PTP inhibitor or degrader.
[0111] The term "additional prophylactic or therapeutic agent" refers to a prophylactic or therapeutic agent different from a compound of the disclosure and that is known to treat the disease or condition of interest.
[0112] The term "disease" or "condition" denotes disturbances and / or anomalies that as a rule are regarded as being pathological conditions or functions, and that can manifest themselves in the form of particular signs, symptoms, and / or malfunctions.
[0113] As used herein, the terms "treat," "treating," "treatment," and the like refer to eliminating, reducing, or ameliorating a disease or condition, and / or symptoms associated therewith. Although not precluded, treating a disease or condition does not require that the disease, condition, or symptoms associated therewith be completely eliminated. The term "treat" and synonyms contemplate administering a prophylactic or therapeutically effective amount of a compound described herrein to a subject in need of such treatment. The treatment can be orientated symptomatically, for example, to suppress symptoms. It can be effected over a short period, be oriented over a medium term, or can be a long-term treatment, for example within the context of maintenance therapy.
[0114] The terms "prevent," "preventing," and "prevention" refer to a method of preventing the onset of a disease or condition and / or its attendant symptoms or barring a subject from acquiring a disease. As used herein, "prevent," "preventing," and "prevention" also include delaying the onset of a disease and / or its attendant symptoms and reducing a subject's risk of acquiring a disease. The terms "prevent," "preventing" and "prevention" may include "prophylactic treatment," which refers to reducing the probability of redeveloping a disease or condition, or of a recurrence of a previously- controlled disease or condition, in a subject who does not have, but is at risk of or is susceptible to, redeveloping a disease or condition or a recurrence of the disease or condition.
[0115] The term "therapeutically effective amount" or "effective dose" as used herein refers to an amount of the active ingredient(s) that is(are) sufficient, when administered by a method of the disclosure, to efficaciously deliver the active ingredient(s) for the treatment of condition or disease of interest to a subject in need thereof. In the case of a cancer or other proliferation disorder, the therapeutically effective amount of the agent may reduce (i.e., retard to some extent or stop) unwanted cellular proliferation; reduce the number of cancer cells; reduce the tumor size; inhibit (i.e., retard to some extent or stop) cancer cell infiltration into peripheral organs; inhibit (i.e., retard to some extent or stop) tumor metastasis; inhibit, to some extent, tumor growth; and / or relieve, to some extent, one or more of the symptoms associated with cancer. To the extent the administeredcompound or composition prevents growth and / or kills existing cancer cells, it may be cytostatic and / or cytotoxic.
[0116] As stated above, a compound described herein can be administered in combination with one or more other therapeutically active agents. In some embodiments, the therapeutically active agent (s) is an immune checkpoint inhibitor. Examples of immune checkpoint inhibitors include, but are not limited to, PD-1 inhibitors, PD-L1 inhibitors, CTLA-4 inhibitors, LAG3 inhibitors, TIM3 inhibitors, cd47 inhibitors, and B7-H1 inhibitors.
[0117] In some embodiments, the immune checkpoint inhibitor is a programmed cell death (PD- 1) inhibitor. PD-1 is a T-cell coinhibitory receptor that plays a pivotal role in the ability of tumor cells to evade the host's immune system. Blockage of interactions between PD-1 and PD-L1, a ligand of PD-1, enhances immune function and mediates the antitumor activity. Examples of PD- 1 inhibitors specifically include, but are not limited to, antibodies that specifically bind to PD-1. The anti-PD-1 antibodies selected from the group consisting of nivolumab, pembrolizumab, STI- A1014, and pidilzumab. The availability, methods of production, mechanism of action, and clinical studies of anti-PD-1 antibodies are described in U.S. Pat. Appl. Pub. No. 2013 / 0309250, U.S. Pat. No. 7,595,048, U.S. Pat. No. 8,728,474, U.S. Pat. No. 8,779,105, U.S. Pat. No. 8,952,136, U.S. Pat. No. 8,900,587, U.S. Pat. No. 9,073,994, and U.S. Pat. No. 9,084,776, all of which are hereby specifically incorporated by reference for their teachings regarding same.
[0118] In some embodiments, the immune checkpoint inhibitor is a PD-L1 (also known as B7- H1 or CD274) inhibitor. PD-L1 inhibitors include antibodies that specifically bind to PD-L1. Examples of anti-PD-Ll antibodies include, but are not limited to, avelumab, atezolizumab, durvalumab, and BMS-936559. Anti-PD-Ll antibodies’s availability, methods of production, mechanism of action, and clinical studies are described in U.S. Pat. No. 8,217,149, U.S. Pat. App. Pub. No. 2014 / 0341917, U.S. Pat. App. Pub. No. 2013 / 0071403, Int’l Pat. App. Pub. No. WO 2015036499, and Naido et al., British Journal of Cancer 2014, 777 2214-19, all of which are hereby specifically incorporated by reference for their teachings regarding same.
[0119] In some embodiments, the immune checkpoint inhibitor is a CTLA-4 inhibitor. CTLA-4, also known as cytotoxic T-lymphocyte antigen 4, is a protein receptor that down-regulates the immune system. CTLA-4 is characterized as a "brake" that binds costimulatory molecules on antigen-presenting cells, which prevents interaction with CD28 on T cells and also generates an overtly inhibitory signal that constrains T cell activation. Examples of CTLA-4 inhibitors include antibodies that specifically bind to CTLA-4. Particular anti-CTLA-4 antibodies include, but arenot limited to, ipilimumab and tremelimumab. The availability, methods of production, mechanism of action, and clinical studies of CTLA-4 antibodies are described in U.S. Pat. No. 6,984,720, U.S. Pat. No. 6,207,156, and Naido et al., British Journal of Cancer 2014, 777 2214- 19, all of which are hereby specifically incorporated by reference for their teachings regarding same.
[0120] In some embodiments, the immune checkpoint inhibitor is a LAG-3 inhibitor. LAG-3, Lymphocyte Activation Gene 3, is a negative co-simulatory receptor that modulates T cell homeostatis, proliferation, and activation. In addition, LAG-3 has been reported to participate in regulatory T cells (Tregs) suppressive function. A large proportion of LAG-3 molecules are retained in the cell close to the microtubule organizing center and only induced following antigenspecific T cell activation, (see U.S. Pat. App. Pub. No. 2014 / 0286935). LAG-3 inhibitors include antibodies that specifically bind to LAG-3. Examples of anti -LAG-3 antibodies include, but are not limited to, GSK2831781. For a general discussion of the availability, methods of production, mechanism of action, and studies, see U.S. Pat. App. Pub. No. 2011 / 0150892, U.S. Pat. App. Pub. No. 2014 / 0093511, U.S. Pat. App. Pub. No. 2015 / 0259420, and Huang et al., Immunity, 2004, 21, 503-13, all of which are hereby specifically incorporated by reference for their teachings regarding same.
[0121] In some embodiments, the immune checkpoint inhibitor is a TIM-3 inhibitor. TIM-3, T- cell immunoglobulin and mucin domain 3, is an immune checkpoint receptor that functions to limit the duration and magnitude of TH1 and TCI T-cell responses. The TIM-3 pathway is considered a target for anticancer immunotherapy due to its expression on dysfunctional CD8+ T cells and Tregs, which are two reported immune cell populations that constitute immunosuppression in tumor tissue (Anderson, Cancer Immunology Research 2014, 2, 393-98). Examples of TIM3 inhibitors include antibodies that specifically bind to TIM-3. For a general discussion of the availability, methods of production, mechanism of action, and studies of TIM-3 inhibitors, see U.S. Pat. App. Pub. No. 2015 / 0225457, U.S. Pat. App. Pub. No. 2013 / 0022623, U.S. Pat. No. 8,522,156, Ngiow et al., Cancer Res 201, 7, 6567-71, Ngiow, et al., Cancer Res 201, 7, 3540-51, and Anderson, Cancer Immunology Res., 2014, 2, 393-98, all of which are hereby specifically incorporated by reference for their teachings regarding same.
[0122] In some embodiment, the immune checkpoint inhibitor is a CD47 inhibitor (see Unanue, E.R., PNAS 2013,110: 10886-87, which is specifically incorporated herein by reference for its teachings regarding same).
[0123] The term "antibody" refers to intact monoclonal antibodies, polyclonal antibodies, multispecific antibodies formed from at least two intact antibodies, and antibody fragments, solong as they exhibit the desired biological activity. In some embodiments, "antibody" refers to include soluble receptors that do not possess the Fc portion of the antibody. In some embodiments, the antibodies are humanized monoclonal antibodies and fragments thereof made by means of recombinant genetic engineering.
[0124] Another class of immune checkpoint inhibitors includes polypeptides that bind to and block PD-1 receptors on T-cells without triggering inhibitor signal transduction. U.S. Pat. No. 8,114,845 (specifically incorporated herein by reference for its teachings regarding same) describes such peptides, including B7-DC polypeptides, B7-H1 polypeptides, B7-1 polypeptides, and B7-2 polypeptides, and soluble fragments thereof.
[0125] Another class of immune checkpoint inhibitors includes compounds with peptide moi eties that inhibit PD-1 signaling as disclosed in U.S. Pat. No. 8,907,053, which is specifically incorporated herein by reference for its teachings regarding same.
[0126] Another class of immune checkpoint inhibitors includes inhibitors of certain metabolic enzymes, such as indoleamine 2,3 dioxygenase (IDO), which is expressed by infiltrating myeloid cells and tumor cells. The IDO enzyme inhibits immune responses by depleting amino acids that are necessary for anabolic functions in T cells or through the synthesis of particular natural ligands for cytosolic receptors that are able to alter lymphocyte functions (Lob, Cancer Immunol Immunother, 2009, 58.T53-57). Particular IDO blocking agents include, but are not limited to, levo-1 -methyl typtophan (L-1MT) and 1-methyl-tryptophan (1MT) ( Lob et al., Cancer Immunol Immunother 2009, 58.T53-7; specifically incorporated herein by reference for its teachings regarding same).
[0127] In some embodiments, the immune checkpoint inhibitor is nivolumab, pembrolizumab, pidilizumab, STI-Al l 10, avelumab, atezolizumab, durvalumab, STLA1014, ipilimumab, tremelimumab, GSK2831781, BMS-936559 or MED14736.
[0128] The above-described other prophylactically or therapeutically active agents, one or more of which can be used in combination with a compound of formula (I) are prepared and administered as described in the art.
[0129] It will be appreciated by persons skilled in the art that the present disclosure is not limited by what has been particularly shown and described herein above. Rather the scope of the present disclosure includes both combinations and sub-combinations of the various features described hereinabove as well as variations and modifications which would occur to persons skilled in the art upon reading the specification and which are not in the prior art.EXAMPLES
[0130] The following examples serve to illustrate the present disclosure. The examples are not intended to limit the scope of the claimed invention.
[0131] Cloning, expression, and purification of PTP proteinsThe proteins (TC-PTP, Aa 1-387; PTP IB, Aa 1-321; SHP-2, Aa 224-528; LYP, Aa 1-294; STEP, Aa 258-539; HePTP, Aa 22-360; FAP-1, Aa 2124-2485; PTPa, Aa 173-793; CD45, Aa 620-1236; CDC14A, Aa 1-413; MEG2, Aa 286-582; VHR, Aa 1-185; Larforin, Aa 1-331; LMW-PTP, Aa 1-158.) were cloned into pET-21a(+) vector. Bacterial BL21(DE3) was used as an expression host, and the induction of protein expression was carried out in LB media with 1 mM IPTG at 18 °C overnight. Cell pellets were stored at -80 °C for subsequent protein purification. Protein purification was conducted at 4 °C. Frozen cell pellets were lysed by sonication in 40 ml cold lysis buffer (50 mM Tris-HCl, pH 8.0, 150 mMNaCl, 5 mM imidazole, and 1 mM PMSF) per liter cell pellet. Cell lysates were clarified by centrifugation using a Bechman JA-18 rotor for 15 min at 6,000 rpm. The supernatant was incubated with HisPur Ni-NTA resin for 2 hours, and then packed onto a column and washed with 50 resin volume of buffer A (50 mM Tris-HCl, pH 8.0, 500 mM NaCl, 5 mM imidazole). The HIS-tagged proteins were eluted with Buffer B (50 mM Tris-HCl, pH=8.0, 500 mM NaCl, 300 mM imidazole). Pooled HIS-protein-containing fractions were concentrated, loaded onto a HiLoad 26 / 600 Superdex 75 column, and eluted with storage buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM DTT, 10% glycerol). Proteins used for inhibition assays were purified using Ni-NTA resin followed by size exclusion column chromatography and the purity was determined to be >95% by SDS-PAGE and Coomassie staining. The protein was aliquoted and stored at -80 °C.
[0132] PTP inhibition assay and determination of ICso valuesPTP activity was assayed using p-nitrophenyl phosphate (pNPP) as a substrate in DMG buffer (50 mM dimethylglutarate, pH 7.0, 1 mM EDTA, 150 mM NaCl, 2 mM DTT, 0.1 mg / mL BSA) at 25 °C. The assays were performed in 96-well plates. To determine the IC50 values, the reaction was initiated by the addition of enzyme (for PTP IB and TC-PTP, the final concentration was 0.4 nM, for other PTPs, the final concentration was 10 nM) to a reaction mixture (0.2 mL) containing pNPP (at final concentration close to the Kms of tested enzymes, in specific: 0.05 mM for CDC- 14A; 0.5 mM for FAP-1; 2 mM for TC-PTP, PTP1B, STEP, LWM-PTP, and PTPa; 3 mM for SHP2; 4 mM for Laforin; 5 mM for LYP, CD45, and VHR; 6 mM for MEG2 and HePTP) with various concentrations of inhibitors. The reaction rate was measured using a SpectraMax Plus 384 Microplate Spectrophotometer. Data were fitted using SigmaPlot Enzyme Kinetics Module.Table 1Enzymatic ICsos of PROTAC compounds against PTP1B and TC-PTP
[0133] Cell CultureHEK293, U2OS, HeLa, and KB cells were grown in DMEM, while Jurkat and H358 cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum, penicillin (50 units / mL), and streptomycin (50 pg / mL) in a 37 °C incubator containing 5% CO2. 20 ng / ml human or mouse Interferon-y were used for JAK / STAT pathway stimulation. Human CAR-T cells were generated using a well-known procedure (see Cancer Research 2019, 79 (2), 387-396)
[0134] Generation of TC-PTP deleted cellTC-PTP deleted HEK293 cells were generated by transfecting HEK293 cells with TC-PTP CRISPR Plasmids. Transfection was performed using Lipofectamine 2000. After transfection, cells were selected in growth media containing 1 pg / mL puromycin for 7 days. Single clones were picked and TC-PTP deletion was verified by western blot.
[0135] ImmunoblottingThe antibodies are purchased from Cell Signaling Technology, Abeam, and Invitrogen.Cells were lysed with ice-cold lysis buffer (50 mM Tris (pH 8.0, 150 mM NaCl, 10% Glycerol, 1% Triton-X-100) supplied with phosphatase inhibitor (Bimake) and protease inhibitor mixture. Equal amounts of protein were resolved by SDS-PAGE, transferred to a nitrocellulose membrane, and subjected to immunoblotting. Antibodies used in this study include anti-following proteins: pSTATlTyr701, GAPDH, pJAKlTyrl034 / 1035, pJAK2Tyrl 007 / 1008, TC-PTP, PTP1B, MEG2, PTEN, STAT1, STAT3, STAT5, LCK, AKT, ZAP70, GSK-3a / p, ACTIN, SHP2.
[0136] Imaging and ImmunofluorescenceCells were cultured directly on glass coverslips in 12- or 24-well plates. After experiments, cells were fixed with 4% paraformaldehyde in phosphate-buffered saline (PBS) for 15 min at room temperature, permeabilized with 0.2% Triton X-100 in PBS for 10 min, and blocked with BSA. For immunofluorescence, appropriate antibodies were applied overnight at 4 °C, followed by wash and 1 hour incubation with appropriate secondary antibody. DNA staining (0.5 pg of Hoechst no. 33258 / ml; Sigma) was used to identify cell nuclei. After washing with PBS, the coverslips were mounted with anti-fade mounting solution. Images were obtained with a Nikon Inverted Microscope Eclipse Ti-S. Antibodies used in this study include anti-following proteins: PTP1B, TC-PTP, pSTATlTyr701, Alexa Fluor™ 488 conjugated Goat anti-Rabbit Secondary antibody, Alexa Fluor™ 555 conjugated Goat anti-Mouse Secondary antibody .
[0137] Analysis of cytotoxic activity of anti-FITC CAR T cells in vitroFolate receptor-expressing KB cells were seeded at a density of 104 cells / 100 pL into 96-well plates and grown overnight. Anti-FITC CAR T cells (5 x 104) were added to each well in the absence or presence of the FITC-folate bispecific adaptor small molecule (EC 17) and EC 17 with compound 12. After coincubation for 48 hours, plates were centrifuged at 350 x g for 10 minutes. Supernatants were analyzed for lactate dehydrogenase release (cell death analysis) using cytotoxicity assay kit. T cells in the pellet were collected for flow cytometry to determine T cell activation levels.
[0138] Flow CytometryAfter incubation, as described in the results, HEK293 cells were trypsinized and washed in PBS + 2% FBS, stained with Anti-HLA Class 1 ABC antibody against human MHC-I complex and subsequently with Alexa Fluor™ 488 conjugated Goat anti-Rabbit Secondary antibody and then analysed on an flow cytometry cell analyzer. To measure CAR-T cell activation, CAR-T cells were collected by centrifuge and stained with anti-human CD3 APC antibody, anti-human CD25 FITC Antibody, anti-human CD69 Pacific Blue Antibody 0) and then analysed on an flow cytometry cell analyzer.Results
[0139] Degradation assay results
[0140] A] The in vitro biochemical IC50S of PROTAC compounds with pomalidomide ligand (Table 2) against PTP1B and TC-PTP were determined, and the data showed that they all inhibit TC-PTP with low nanomolar IC50S and 3~5-fold selectivity over PTP1B, indicating that the linker did not disturb the binding affinity and preference to the target protein (Table 1). The compounds’ ability to induce TC-PTP degradation was subsequently evaluated in HEK293 cells by western blot (Table 2, Fig. 7B). Among this series of PROATC candidates, compound 2 with an n- pentane linker presented the highest degradation potency for TC-PTP. After 16 hours of treatment, 2 pM of compound 2 induced the depletion of 48% TC-PTP and only 8% PTP1B. The degradation potency on TC-PTP was significantly reduced when the linker length in compound 2 was increased or decreased by one additional methylene (compound 1, compound 3). Compounds with even longer linkers exhibit trivial (compound 4) or no degradation (compound 5, compound 6). Hence, it was concluded that the n-pentane chain demonstrated the most optimal linker length for inhibitor 3 based CRBN recruiting TC-PTP degrader with a pomalidomide ligand. In addition, the parent inhibitor 3 did not induce any change on the protein level of TC- PTP in this assay.Table 2: Structures and degradation results of first-generation TC-PTP PROTACsa(a) HEK293 cells were treated with 2 |1M PROTAC compounds for 16 hours.
[0141] B] Lenalidomide, another CRBN binding ligand often used in PROTAC development, offers certain advantages compared to pomalidomide. The absence of one phthalimide carbonyl group in lenalidomide leads to reduced TPSA (total polar surface area), improved physicochemical properties, and increased metabolic and chemical stability. Therefore, to explore for more potent and bioavailable TC-PTP selective degraders, we synthesized a set of PROTAC candidate compounds employing lenalidomide as the E3 ligand with a series of linear alkyl chain linkers (Table 3, Fig. 8). These compounds were evaluated in HEK293 cells for their ability to degrade TC-PTP in parallel with the pomalidomide based PROTACs compound 2 and compound 3 at 1 pM. Compound 8 and compound 9 showed improved potency on TC-PTP degradation compared with their counterparts, compound 2 and compound 3, and nearly complete depletion of TC-PTP was achieved. However, degradation of PTP1B was observed with these two compounds. Lenalidomide based PROTAC candidates with either short or long linkers did not show significant degradation under the same conditions (compound 7, compound 10, and compound 11). Besides the linker length, the chemical nature and flexibility of linkers are known to influence the formation and stability of the target protein — PROTAC — E3 ligase ternary complex and thus can alter the degradative efficiency and selectivity. Therefore, a lenalidomidebased PROTAC compound 12 was synthesized and evaluated with an ethoxy ethane linker instead of the alkyl chain in compound 8. The treatment of 1 pM compound 12 resulted in an almost complete degradation of TC-PTP, while the PTP1B level remained unaffected. A PROTAC with a piperidine ring linker was also examined (compound 13), and interestingly, high degradative potency for both TC-PTP and PTP1B was observed. Overall, compound 12 showed optimal potency and selectivity and, therefore, was selected for thorough characterization.Table 3: Structures and degradation results of second-generation TC-PTP PROTACsa(a) HEK293 cells were treated with 1 |1M PROTAC compounds for 16 hours.
[0142] C] TC-PTP degradation with Compound 12Degradation efficacy assessments were conducted using compound 12 across a broad concentration range in HEK293 cells (Fig. la). The DCso (compound concentration needed to induce target protein degradation by 50 %) for compound 12 mediated TC-PTP degradation is35.8 nM in HEK293 cells after 16 hours of treatment, while the level of PTP1B is not significantly changed unless 4 pM compound 12 is applied, demonstrating that this degrader is at least 110- fold selective for TC-PTP over PTP1B in degradation efficiency (Fig. lb). The time course of PTP1B and TC-PTP degradation was then determined by treating HEK293 cells with 1 pM compound 12 for 3, 6, 16, and 24 hours (Fig. 2A). Nearly complete depletion of TC-PTP was observed within 6 hours, and the suppression of protein level was sustained for at least 24 hours. It is noteworthy that the PTP1B protein level did not decrease during the entire period of compound 12 treatment. To investigate the binding affinity of compound 12 to TC-PTP and selectivity towards other PTPs, we determined its enzymatic IC50S against a panel of 14 representative PTP family members, including receptor-like, nonreceptor-like, and dual-specific phosphatases (Table 4). The results indicated that compound 12 showed no significant inhibition on other PTPs except for TC-PTP and PTP1B at 10 pM or lower concentrations. Interestingly, the IC50 on TC-PTP is only 6 times lower than that on PTP IB, implying that the high degree of degradation preference to TC-PTP is presumably due to the favorable tendency of the degrader to form the TC-PTP- compound 12 -CRBN ternary complex over the one with PTP1B. Next, the selectivity of compound 12 as a PROTAC degrader for TC-PTP over other PTP family members and different classes of enzymes was verified (Fig. 2B). Western blots showed that treatment of HEK293 cells with 0.5 pM compound 12 for 16 hours led to substantial degradation of TC-PTP, whereas none of the other PTPs including PTP IB, SHP2, PTP-MEG2, LYP and PRL2 were affected. In addition, under the same conditions, compound 12 did not induce any appreciable degradation of other signaling proteins, including STAT1, STAT3, STAT5, GSK3a, LCK, ACTIN, AKT, and PTEN. Taken together, the above results validated compound 12 as a potent and selective TC-PTP PROTAC degrader.
[0143] Table 4: ICsos of compound 12 for a panel of 14 PTPs
[0144] The mechanism of action of compound 12 in degrading TC-PTP was next investigated in the HEK293 cells by running a series of control experiments (Fig. 3A). The data showed that TC- PTP degradation induced by compound 12 can be effectively blocked by the pretreatment of a NEDD8-activating enzyme (NAE) inhibitor Pevonedistat, a proteasome inhibitor MG132, or the CRBN ligand lenalidomide, indicating that the degradation of TC-PTP requires the recruitment of the E3 ligase and is ubiquitination- and proteasome-dependent. In addition, the compound 12 mediated TC-PTP degradation and proteasome dependency were verified by immunofluorescent imaging (Fig. 3B). In both U2OS and Hela cells, compound 12 selectively degrades TC-PTP in a time-dependent manner, and the proteasome inhibitor MG132 disrupted this process. These mechanistic data provide clear evidence that compound 12 is a bona fide TC-PTP PROTAC.
[0145] 2] INF-y signaling and antigen presentationEvaluated the ability of compound 12 to modulate IFN-y signaling in cells by measuring the phosphorylation levels of JAK1 and STAT1 upon the treatment of compound 12. As shown in Fig. 4A, the pJAKl and pSTATl levels upon IFN-y stimulation were enhanced by compound 12 in a dose-dependent manner, and their ECsos were determined to be 209 nM and 259 nM, respectively. Importantly, the phosphorylation level of JAK2, which is a substrate of PTP1B, was not affected in the presence of compound 12, demonstrating that the degrader was specific to TC- PTP. To further ascertain that compound 12 boosts INF-y signaling through degradation of TC- PTP, we utilized the TC-PTP knockout HEK293 cell line to run a control experiment (Fig. 4B). With the stimulation by IFN-y and 500 nM treatment of compound 12, pJAKl and pSTATl levels were significantly increased in wildtype HEK293 cells, while they are not changed in the TC-PTP knockout cells under the same conditions. As expected, pJAK2 and PTP1B levels were not affected by compound 12 in either cell lines in this experiment.Furthermore, immunofluorescence microscopy also showed that the pSTATl signal in the nucleus is enhanced by treatment of compound 12 in wildtype HEK293 cells, while no change was observed in TC-PTP knockout cells (Fig. 5A). Moreover, in line with the increased activation of upstream IFN-y signaling, itwas observed over 100% increase in the cell surface MHC-I expression in HEK293 cells induced by compound 12 following IFN-y stimulation, while the MHC-1 level in TC-PTP knockout cells was not affected (Fig. 5B). Collectively, we demonstrated that compound 12 efficiently amplifies IFN-y signaling through inhibition of TC-PTP catalyzed tyrosine dephosphorylation of JAK1 and STAT1, resulting in elevated cell surface MHC-I expression, which is crucial for efficient T-cell- mediated tumor cells elimination.
[0146] 3] Jurkat T-cell and CAR-T-cell activation, and augments tumor killing efficacyThe activation and clonal expansion of T cells requires T-cell receptor (TCR) signaling activation, which is mediated by a series of tyrosine phosphorylation events. TC-PTP suppresses TCR signaling by dephosphorylating and inactivating the Src family kinase LCK, which initiates TCR signaling upon recognition of the MHC-I complex, and the deletion of TC-PTP in T-cells significantly enhances anti-tumor immunity. The impact of TC-PTP degradation was assessed induced by compound 12 in T-cells. The phosphorylation level of LCK was elevated by the treatment of compound 12 in Jurkat T-cells followed by the stimulation with anti-CD3 antibody in a dose-dependent manner, while the protein level of TC-PTP was decreased accordingly (Fig. 6A). It is noteworthy that the PTP1B protein level was not changed under the same conditions, indicating that compound 12 is selective in Jurkat T cells.
[0147] To investigate the impact of TC-PTP degrader on CAR-T cell therapy, the effect of compound 12 on an established epidermoid carcinoma KB cell-CAR-T cell coculture system was evaluated. In this system, the folate receptor was overexpressed in KB cells, while CAR-T cells were engineered to recognize fluorescein. Once a FITC-folate bispecific adaptor small molecule (EC 17) has been added to the coculture, the immunologic synapse will be formed in an EC 17 dependent manner therefore triggering CAR-T cell activation and tumor cell destruction. To confirm whether compound 12 mediates efficient TC-PTP degradation in KB cells, KB cells were treated with a series of doses of compound 12 for 16 hours and stimulated with human IFN- y before harvesting the cells. Consistent with the previous results from HEK293 cells, compound 12 treatment efficiently induced dose-dependent TC-PTP degradation and STAT1 phosphorylation, resulting in sensitization of KB cells to IFN-y (Fig. 6B). To evaluate the effect of compound 12 mediated TC-PTP degradation on CAR-T cell activation, the earlier and late T cell activation markers CD69 and CD25 were measured after coculturing KB cells and CAR-T cells for 48 hours. As shown in Fig. 6C, there was a 26% increase in the early activation marker CD69 and over 2-fold increase in the late activation marker CD25 in the presence of compound 12, indicating that CAR-T cells were further activated after TC-PTP degradation. As the result ofenhanced CAR-T cell activation, the killing efficiency of the CAR-T cells were boosted by compound 12 (Fig. 6C).
[0148] Cytotoxicity of compound 12Cytotoxicity of the degrader compound 12 in cells was evaluated. No toxicity was observed when HEK293 cells were treated with compound 12 at up to 20 pM concentration for 48 hours. The cell viability was measured with cell counting kit-8 assay and normalized with DMSO control (Fig- 9)
[0149] Pharmacokinetic studies in miceThe bioavailability of compound 12 as a chemical probe and potential lead compound for drug discovery was examined by performing pharmacokinetic studies in mice. A single dose of compound 12 was administered via intraperitoneal injection, and the plasma levels of the compound were quantified by LCMS (Table 5). The data indicates that the inj ection of compound 12 at 25 and 50 mg / kg achieved a peak plasma concentration (Cmax) of 0.83 ± 0.15 and 3.75 ± 0.52 pM with half-lives of 4.2 ± 0.9 and 2.3 ± 0.6 hours, respectively (Figs. 10A and 10B). At both doses, the plasma concentrations of compound 12 were maintained well above its effective concentration for TC-PTP degradation (DCso = 35.79 nM) for at least 8 hours. Thus, compound 12 possesses acceptable pharmacokinetic properties, allowing for in vivo applications.Table 5. Plasma concentrations of compound 12 (pM) in pharmacokinetic studiesGeneral Information
[0150] Unless otherwise noted, all reagents were purchased from commercial suppliers and used without further purification. Thin-layer chromatography was performed using glass precoated Merck silica gel 60 F254 plates. Flash column chromatography was performed on Biotage prepacked columns using the automated flash chromatography system Biotage Isolera One.Normal phase column chromatography was performed using KP-SIL silica gel, and reverse phase column chromatography was performed using Teledyne Isco RediSepRf Gold columns. HPLC purification was performed using column: C18 5 pm 150 x 21.2 mm; Eluent A: water + 0.1% trifluoroacetic acid (99%), Eluent B: methanol; DAD scan: 210-400 nm.
[0151] TheJH and13C NMR spectra were recorded on a Bruker AVANCE 500 MHz spectrometer using chloroform-D (CDCh) or dimethyl sulfoxide (DMSO-d6) as the solvents. Chemical shifts are expressed in ppm (5 scale) and referenced to the residual protonated solvent. Peak multiplicities are reported using the following abbreviations: s (singlet), d (doublet), t (triplet), q (quartet), m (multiplet), or br (broad singlet). Mass spectra and purity data were obtained using an Agilent Technologies 6470 series, triple quadrupole LC-MS. The purity of all final tested compounds was determined to be >95% (UV, X = 254 nm). High-resolution mass analysis was performed on an Agilent 6550 iFunnel Q-TOF mass LC-MS. pNPP was purchased from Thermo Scientific.Abbreviations used: r.t.-room temperature; HPLC-high-performance liquid chromatography; LC / MS-liquid chromatography-mass spectrometry;EtOAc - ehtyl acetate, DCM - dichloromethane; DMF - dimethylformamide; NMM- N-methyl morpholine; DIPEA - N,N-diisopropylethylamine; EDTA - ethylenediaminetetraacetic acid; DTT - dithiothreitol; BSA - bis(trimethylsilyl)acetamide; HATU- hexafluorophosphate Azabenzotriazol-tetramethyluronium; TFA-trifluoroacetic acid; DMSO - dimethyl sulfoxide; AcOH - acetic acid; HO AT - 1 -hydroxy-7- azabenzotriazole; LiOH - lithium hydroxide
[0152] Preparation of TC-PTP ligand Intermediate 11
[0153] Synthesis of Intermediate 4Scheme 1
[0154] Benzyl (5)-2-((tert-butoxycarbonyl)amino)-3-(4-iodophenyl)propanoate (Intermediate 2)To a stirred mixture of (5)-2-((tert-butoxycarbonyl)amino)-3-(4-iodophenyl)propanoic acid (10.00 g, 25.6 mmol, 1.0 eq.) and K2CO3 (5.31 g, 38.4 mmol, 1.5 eq.) in DMF (100 ml) was added benzyl bromide (6.57 g, 38.4 mmol, 1.5 eq.). Then, the mixture was stirred at r.t. for 4 hours. After completion, the reaction mixture was diluted with EtOAc (500 ml) and washed with brine (3 x 500 ml). The organic layer was dried over anhydrous Na2SC>4 and evaporated in vacuo. The product was then purified by flash chromatography (EtOAc / n-Hexane, 0%— >10%). Yield: 8.80 g (72%). 'H NMR (500 MHz, DMSO) 5 7.63 - 7.57 (m, 2H), 7.37 - 7.29 (m, 4H), 7.29 - 7.22 (m, 2H), 7.07 - 7.02 (m, 2H), 5.11 - 5.00 (m, 2H), 4.18 (ddd, J= 9.8, 8.0, 5.6 Hz, 1H), 2.94 (dd, J= 13.7, 5.6 Hz, 1H), 2.83 (dd, J= 13.7, 9.8 Hz, 1H), 1.30 (s, 9H). LC / MS m / z calculated [M+H]+482.08, found 482.18.
[0155] Benzyl (5)-2-((tert-butoxycarbonyl)amino)-3-(4- ((diethoxyphosphoryl)difluoromethyl)phenyl)propanoate (Intermediate 3)Intermediate 2 (10.00 g, 20.8 mmol, 1.0 eq.) was dissolved in anhydrous DMF (100 mL), then CuBr (5.97 g, 41.6 mmol, 2 equiv) and half of the supernatant solution of the Cd reagent 1 (ca. 1.7 equiv, prepared using the process known in the art, e.g., Synthesis 2011, 20, 255) was added in a dropwise manner. After 3 hours, further CuBr (2.98 g, 20.8 mmol, 1 equiv) and the other half of the Cd reagent solution were added. The reaction was allowed to stir at r.t. for 19 hours in total.The progress of the reaction was monitored by LC-MS. Upon completion, the reaction mixture was diluted with EtOAc (500 mL), filtered through Celite, and extracted with aq NH4Cl (2 x 500 mL) and brine (500 mL). The organic layer was dried over anhydrous Na2SO4and evaporated in vacuo. The product was then purified by flash chromatography (EtOAc / n-Hexane, 0%→10%). Yield 11.86 g (57%).1H NMR (500 MHz, DMSO) δ 7.45 (d, J = 7.9 Hz, 2H), 7.41 – 7.26 (m, 8H), 5.09 (s, 2H), 4.26 (ddd, J = 9.8, 8.1, 5.3 Hz, 1H), 4.16 – 3.99 (m, 4H), 3.09 (dd, J = 13.8, 5.4 Hz, 1H), 2.95 (dd, J = 13.8, 10.0 Hz, 1H), 1.29 (s, 9H), 1.19 (td, J = 7.1, 1.5 Hz, 6H). LC / MS m / z calculated [M+H]+542.21, found 542.28.
[0156] (S)-2-((tert-butoxycarbonyl)amino)-3-(4- ((diethoxyphosphoryl)difluoromethyl)phenyl)propanoic acid (Intermediate 4) To a solution of intermediate 3 (8.98 g, 16.6 mmol, 1.0 eq.) in EtOAc (50 mL) was added Pd / C (10 wt. % loading, 898.0 mg). The reaction mixture was evacuated and filled with H2for three times. The mixture was then stirred at r.t. for 12 hours. Upon completion, the reaction mixture was concentrated in vacuo. The product was then purified by flash chromatography (MeOH / DCM, 0%→5%). Yield 6.66 g (89%).1H NMR (500 MHz, DMSO) δ 7.45 (d, J = 8.0 Hz, 2H), 7.39 (d, J = 8.1 Hz, 2H), 7.12 (d, J = 8.5 Hz, 1H), 4.17 – 3.98 (m, 4H), 3.07 (dd, J = 13.8, 4.7 Hz, 2H), 2.91 – 2.83 (m, 1H), 1.29 (s, 9H), 1.19 (td, J = 7.0, 1.9 Hz, 6H). LC / MS m / z calculated [M+H]+452.16, found 452.23.
[0157] Synthesis of Intermediate 7Scheme 2
[0158] Benzyl N2-(((9H-fluoren-9-yl)methoxy)carbonyl)-N6-(tert-butoxycarbonyl)-L- lysinate (Intermediate 5) To a mixture of N2-(((9H-fluoren-9-yl)methoxy)carbonyl)-N6-(tert-butoxycarbonyl)-L-lysine (10.00 g, 21.34 mmol, 1.0 eq.) and K2CO3(4.42 g, 32.01 mmol, 1.5 eq.) in DMF (100 ml) was added Benzyl bromide (5.47 g, 32.01 mmol, 1.5 eq.). Then, the mixture was stirred at r.t. for 4 hours. After completion, the reaction mixture was diluted with EtOAc (500 ml) and washed with brine (3 x 500 ml). The organic layer was dried over anhydrous Na2SO4and evaporated in vacuo. The product was then purified by flash chromatography (EtOAc / n-Hexane, 0%→30%). Yield 9.06 g (76%).1H NMR (500 MHz, DMSO) δ 7.90 – 7.82 (m, 2H), 7.78 (d, J = 7.7 Hz, 1H), 7.69 (d, J = 7.5 Hz, 2H), 7.43 – 7.36 (m, 2H), 7.35 – 7.26 (m, 7H), 6.74 (t, J = 5.8 Hz, 1H), 5.10 (d, J = 1.3 Hz, 2H), 4.33 – 4.23 (m, 2H), 4.23 – 4.17 (m, 1H), 4.06 – 3.99 (m, 1H), 2.88 – 2.81 (m, 2H), 1.74 – 1.57 (m, 2H), 1.36 – 1.27 (m, 13H). LC / MS m / z calculated [M+H]+559.28, found 559.39.
[0159] Benzyl N2-(((9H-fluoren-9-yl)methoxy)carbonyl)-N6-(4-ethylbenzoyl)-L-lysinate (Intermediate 6) To a solution of Intermediate 5 (7.50 g, 13.42 mmol, 1.0 eq.) in DCM (80 mL), trifluoroacetic acid (20 mL) was added and stirred for 4 hours at r.t. Then, the excess reagent and solvent were evaporated under reduced pressure to give the deprotected amine, which was used in the next step without further purification. The deprotected amine, 4-ethyl benzoic acid (2.22 g, 14.76 mmol, 1.1 eq.), HOAt (2.19 g, 16.10 mmol, 1.2 eq.), and DIPEA (12.14g, 93.94 mmol, 7.0 eq.) were then dissolved in DMF (100 ml) and stirred at 0oC. To the stirred solution HATU (7.65 g 20.13 mmol, 1.5 eq.) was added slowly. After 15 minutes, the reaction mixture was diluted with EtOAc (800 ml) and washed with brine (3 x 500 ml). The organic layer was dried over anhydrous Na2SO4and evaporated in vacuo. The product was then purified by flash chromatography (EtOAc / n-Hexane, 0%→40%) to afford Intermediate 6.2 steps yield 6.39 g (81%). LC / MS m / z calculated [M+H]+591.28, found 591.27.
[0160] Benzyl N2-((S)-2-((tert-butoxycarbonyl)amino)-3-(4- ((diethoxyphosphoryl)difluoromethyl)phenyl) propanoyl)-N6-(4-ethylbenzoyl)-L-lysinate (Intermediate 7) To a solution of Intermediate 6 (6.39 g, 10.83 mmol, 1.0 eq.) in DCM (80 mL), diethyl amine (20 mL) was added and stirred for 4 hours at rt. Then, the excess reagent and solvent were evaporated under reduced pressure to give the crude deprotected amine, which was then purified by flash chromatography (MeOH / DCM, 0%→10%). The deprotected amine, intermediate 4 (5.38 g, 11.91 mmol, 1.1 eq.), HOAt (1.77 g, 12.98 mmol, 1.2 eq.), and DIPEA (5.59 g, 43.32 mmol, 4.0 eq.) were then dissolved in DMF (100 ml) and stirred at 0oC. To the stirred solution HATU (6.18 g,16.24 mmol, 1.5 eq.) was added slowly. After 15 minutes, the reaction mixture was diluted with EtOAc (800 ml) and washed with brine (3 x 500 ml). The organic layer was dried over anhydrous Na2SO4and evaporated in vacuo. The product was then purified by flash chromatography (EtOAc / n-Hexane, 10%→50%).2 steps yield 6.19 g (71%).1H NMR (500 MHz, DMSO) δ 8.39 – 8.32 (m, 2H), 7.77 – 7.71 (m, 2H), 7.48 – 7.37 (m, 4H), 7.37 – 7.27 (m, 5H), 7.27 – 7.21 (m, 2H), 6.92 (d, J = 8.9 Hz, 1H), 5.10 (s, 2H), 4.35 – 4.21 (m, 2H), 4.16 – 3.98 (m, 4H), 3.22 (q, J = 7.1 Hz, 2H), 3.16 (d, J = 5.3 Hz, 1H), 3.00 – 2.92 (m, 1H), 2.77 – 2.68 (m, 1H), 2.61 (q, J = 7.6 Hz, 2H), 1.83 – 1.74 (m, 1H), 1.73 – 1.64 (m, 1H), 1.57 – 1.45 (m, 2H), 1.42 – 1.31 (m, 2H), 1.25 (s, 9H), 1.23 – 1.10 (m, 11H). LC / MS m / z calculated [M+H]+802.36, found.802.42.
[0161] Synthesis of Intermediate 12Scheme 3
[0162] Methyl (2-(((1S,2R,5S)-2-isopropyl-5-methylcyclohexyl)oxy)acetyl)-L- phenylalaninate (Intermediate 8) Methyl L-phenylalaninate (5.00 g, 27.90 mmol, 1.0 eq.), (+)-menthoxyacetic acid (6.58 g, 30.69 mmol, 1.1 eq.), HOAt (4.56 g, 33.48 mmol, 1.2 eq.) and DIPEA (14.42, 111.60 mmol, 4.0 eq.) were then dissolved in DMF (100 ml) and stirred at 0oC. To the stirred solution HATU (15.91 g, 41.85 mmol, 1.5 eq.) was added slowly. After 15 minutes, the reaction mixture was diluted with EtOAc (600 ml) and washed with brine (3 x 500 ml). The organic layer was dried over anhydrous Na2SO4and evaporated in vacuo. The product was then purified by flash chromatography (EtOAc / n-Hexane, 10%→50%). Yield 7.91 g (76%).1H NMR (500 MHz, DMSO) δ 7.39 (d, J = 8.0 Hz, 1H), 7.28 – 7.13 (m, 5H), 4.51 (td, J = 8.0, 4.9 Hz, 1H), 3.93 (d, J = 15.0 Hz, 1H), 3.72(d, J = 15.0 Hz, 1H), 3.62 (s, 3H), 3.11 – 2.96 (m, 3H), 2.07 (ddq, J = 9.6, 6.9, 3.5 Hz, 1H), 2.01 (d, J = 11.0 Hz, 1H), 1.61 – 1.50 (m, 2H), 1.34 – 1.24 (m, 1H), 1.21 – 1.12 (m, 1H), 0.94 – 0.67 (m, 9H), 0.67 – 0.60 (m, 3H). LC / MS m / z calculated [M+H]+376.24, found 376.22.
[0163] (2-(((1S,2R,5S)-2-isopropyl-5-methylcyclohexyl)oxy)acetyl)-L-phenylalanine (Intermediate 9) To a solution of intermediate 8 (5.71 g, 15.20 mmol) in THF (50 ml), 0.5 M LiOH (aq.) was added. The mixture was stirred at r.t. for 4 hours. Then 50 ml 1.0 M HCl (aq.) was added to the reaction mixture. The mixture was extracted with EtOAc (3 x 250 ml) and washed with brine (2 x 250 ml). The organic layer was combined, dried over anhydrous Na2SO4, and evaporated in vacuo to give crude intermediate 9. This crude product was used in the following synthesis without further purification.
[0164] Synthesis of Intermediate 11 (TC-PTP ligand)Scheme 4
[0165] Benzyl N2-((S)-3-(4-((diethoxyphosphoryl)difluoromethyl)phenyl)-2-((S)-2-(2- (((1S,2R,5S)-2-isopropyl-5-methylcyclohexyl)oxy)acetamido)-3- phenylpropanamido)propanoyl)-N6-(4-ethylbenzoyl)-L-lysinate (Intermediate 10) To a solution of Intermediate 7 (5.36 g, 6.68 mmol, 1.0 eq.) in DCM (80 mL), trifluoroacetic acid (20 mL) was added and stirred for 6 hours at rt. The excess reagent and solvent were evaporatedunder reduced pressure to give the crude deprotected amine, which was used in the next step without further purification. The deprotected amine, intermediate 9 (2.66 g, 7.35 mmol, 1.1 eq.), HOAt (1.09 g, 8.02 mmol, 1.2 eq.) and DIPEA (6.04 g, 46.76 mmol, 7.0 eq.) were then dissolved in DMF (50 ml) and stirred at 0 °C. To the stirred solution HATU (3.81 g, 10.02 mmol, 1.5 eq.) was added slowly. After 15 minutes, the reaction mixture was diluted with EtOAc (300 ml) and washed with brine (3 x 300 ml). The organic layer was dried over anhydrous Na2SO4 and evaporated in vacuo. The product was then purified by flash chromatography (EtOAc / n-Hexane, 50%→100%).2 steps yield 4.19 g (60%).1H NMR (500 MHz, DMSO) δ 8.55 (d, J = 7.4 Hz, 1H), 8.40 – 8.32 (m, 2H), 7.74 (d, J = 8.3, 2H), 7.43 – 7.27 (m, 3H), 7.26 – 7.20 (m, 3H), 7.18– 7.05 (m, 5H), 5.12 (s, 2H), 4.64 (ddd, J = 9.9, 8.5, 4.1 Hz, 1H), 4.52 (td, J = 8.3, 4.4 Hz, 1H), 4.35 – 4.29 (m, 1H), 4.10 – 3.95 (m, 4H), 3.87 (d, J = 15.0 Hz, 1H), 3.61 (d, J = 15.0 Hz, 1H), 3.27 – 3.13 (m, 2H), 3.07 – 2.98 (m, 2H), 2.92 (dd, J = 13.8, 4.3 Hz, 1H), 2.2.84 – 2.76 (m, 2H), 2.61 (q, J = 7.6 Hz, 2H), 2.03 – 1.91 (m, 2H), 1.84 – 1.74 (m, 1H), 1.73 – 1.63 (m, 1H), 1.59 – 1.47 (m, 4H), 1.42 – 1.32 (m, 2H), 1.30 – 1.08 (m, 11H), 0.92 – 0.58 (m, 12H). LC / MS m / z calculated [M+H]+ 1045.52, found.1045.53.
[0166] N2-((S)-3-(4-(difluoro(phosphono)methyl)phenyl)-2-((S)-2-(2-(((1S,2R,5S)-2- isopropyl-5-methylcyclohexyl) oxy)acetamido)-3-phenylpropanamido)propanoyl)-N6-(4- ethylbenzoyl)-L-lysine (Intermediate 11) To a solution of intermediate 10 (2.42 g, 2.32 mmol, 1.0 eq.) in EtOAc (50 mL) was added PtO2(10 wt. % loading, 242.0 mg). The reaction mixture was evacuated and filled with H2for three times. The mixture was then stirred at r.t. for 12 hours. Upon completion, the reaction mixture was concentrated in vacuo to give crude deprotected carboxylic acid, which was directly used in the next step without further purification. The solution of the deprotected carboxylic acid in anhydrous DCM (25 ml) was cooled to 0 °C and stirred vigorously. Then trimethylsilyl iodide (3.25 g, 16.24 mmol, 7.0 eq.) was added to the solution dropwise. The reaction was kept at 0 °C and monitored with LCMS. Upon completion, the reaction mixture was added to a 50% MeCN / H2O mixture dropwise and stirred at r.t. for 30 minutes. Then the water and organic solvent was evaporated in vacuo to give crude intermediate 11, which was further purified by prep HPLC (50-90% gradient of MeOH in 0.1% TFA / H2O).2 steps yield 0.91 g (44%).1H NMR (500 MHz, DMSO) δ 8.39 – 8.31 (m, 3H), 7.93 (s, 1H), 7.74 (d, J = 8.2 Hz, 2H), 7.43 – 7.33 (m, 4H), 7.28 – 7.22 (m, 3H), 7.20 – 7.09 (m, 5H), 4.66 – 4.53 (m, 2H), 4.24 – 4.17 (m, 1H), 3.88 (d, J = 15.1 Hz, 1H), 3.62 (d, J = 15.0 Hz, 1H), 3.29 – 3.16 (m, 2H), 3.10 – 2.94 (m, 3H), 2.89 – 2.78 (m, 2H), 2.62 (q, J = 7.6 Hz, 2H), 2.04 – 1.92 (m, 2H), 1.81 – 1.72 (m, 1H), 1.68 – 1.59 (m, 1H), 1.58 – 1.47 (m, 4H), 1.42 – 1.33 (m, 2H), 1.31 – 1.20 (m, 1H), 1.19 – 1.09 (m, 4H), 0.92 – 0.65 (m, 9H),0.65 – 0.57 (m, 3H). LC / MS m / z calculated [M+H]+955.48, found.955.52. LC / MS m / z calculated [M-H]- 897.41, found 897.39.
[0167] Preparation of PROTAC linkers with E3 ligands Preparation of PROTAC linkers with pomalidomideScheme 5
[0168] General procedure to synthesize P1-P6 from A1-A6: To a solution of 0.5 mmol A1-A6 (A1-A6 was prepared using the process described in Bioorganic Chemistry 2018, 81, 373–381 and Bioorganic Chemistry 2022, 120, 105605) in DMF (5 ml) was added NaN3(1.0 mmol, 97.5 mg, 2 eq.), and the resulting mixture was stirred at 80 °C for 12h. Then the reaction was cooled, and 10 mL water was added. The mixture was extracted with EtOAc (3x 15 ml), and the combined organic phase was washed with water (20 ml) and brine (3 x 20 ml). The organic phase was dried with Na2SO4, filtered, and concentrated. The resulting yellow oil (N1-N6) was used in the next step without further purification. Triphenyl phosphine (1^mmol, 262.3 mg, 2 eq.) was added to a solution of azide N1- N6 (0.5^mmol) in 5^mL THF / 1^M HCl (4:1). The reaction mixture was allowed to stir for 4^h^at room temperature before it was concentrated to remove THF. Then the solution was extracted with EtOAc. The water layer was concentrated and purified with HPLC (20-60% gradient of MeOH in 0.1% TFA / H2O) to give the products P1-P6 as a light-yellow solid.
[0169] 5-amino-N-(2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)pentanamide (P1) 49% yield over 2 steps.1H NMR (500 MHz, DMSO) δ1H NMR (400^MHz, DMSO-d6) δ 11.15 (s, 1H), 9.74 (s, 1H), 8.42 (d, J^=^8.4^Hz, 1H), 7.91 – 7.78 (m, 3H), 7.63 (d, J^=^7.3^Hz, 1H), 5.13 (dd, J^=^12.7, 5.4^Hz, 1H), 2.94–2.71 (m, 3H), 2.66–2.45 (m, 4H), 2.10–2.01 (m, 1H), 1.68 – 1.50 (m, 4H). LC / MS m / z calculated [M+H]+373.15, found 373.21.
[0170] 6-amino-N-(2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)hexanamide (P2)45% yield over 2 steps.1H NMR (500 MHz, DMSO) δ 11.14 (s, 1H), 9.71 (s, 1H), 8.43 (d, J = 8.4 Hz, 1H), 7.90 – 7.75 (m, 3H), 7.60 (d, J = 7.4 Hz, 1H), 5.12 (dd, J = 12.9, 5.3 Hz, 1H), 2.94 – 2.71 (m, 3H), 2.64 – 2.44 (m, 4H), 2.10–2.00 (m, 1H), 1.66 – 1.51 (m, 4H), 1.40 – 1.31 (m, 2H). LC / MS m / z calculated [M+H]+387.17, found 387.16.
[0171] 7-amino-N-(2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)heptanamide (P3) 51% yield over 2 steps.1H NMR (500 MHz, DMSO) δ 11.14 (s, 1H), 9.71 (s, 1H), 8.43 (d, J = 8.4 Hz, 1H), 7.90 – 7.74 (m, 3H), 7.60 (d, J = 7.3 Hz, 1H), 5.12 (dd, J = 12.9, 5.2 Hz, 1H), 2.93 – 2.74 (m, 3H), 2.64–2.51 (m, 2H), 2.45 (t, J^=^7.3^Hz, 2H), 2.09–1.99 (m, 1H), 1.67 – 1.51 (m, 4H), 1.39 – 1.26 (m, 4H). LC / MS m / z calculated [M+H]+401.18, found 401.11.
[0172] 8-amino-N-(2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)octanamide (P4) 53% yield over 2 steps.1H NMR (500 MHz, DMSO) δ 11.14 (s, 1H), 9.71 (s, 1H), 8.43 (d, J = 8.4 Hz, 1H), 7.88 – 7.72 (m, 3H), 7.60 (d, J = 7.3 Hz, 1H), 5.12 (dd, J = 12.8, 5.4 Hz, 1H), 2.93 – 2.70 (m, 3H), 2.63–2.51 (m, 2H), 2.44 (t, J^=^7.3^Hz, 2H), 2.10–1.99 (m, 1H), 1.65 – 1.49 (m, 4H), 1.35 – 1.23 (m, 6H). LC / MS m / z calculated [M+H]+415.20, found 415.24.
[0173] 9-amino-N-(2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)nonanamide (P5) 60% yield over 2 steps.1H NMR (500 MHz, DMSO) δ 11.14 (s, 1H), 9.71 (s, 1H), 8.43 (d, J = 8.4 Hz, 1H), 7.82 (t, J^=^7.9^Hz, 1H), 7.60 (d, J = 7.4 Hz, 1H), 5.12 (dd, J = 12.8, 5.3 Hz, 1H), 2.93 – 2.69 (m, 3H), 2.62–2.50 (m, 2H), 2.43 (t, J^=^7.3^Hz, 2H), 2.09–1.99 (m, 1H), 1.63 – 1.49 (m, 4H), 1.34– 1.21 (m, 8H). LC / MS m / z calculated [M+H]+429.21, found 429.22.
[0174] 10-amino-N-(2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)decanamide (P6) 52% yield over 2 steps.1H NMR (500 MHz, DMSO) δ 11.14 (s, 1H), 9.70 (s, 1H), 8.43 (d, J = 8.4 Hz, 1H), 7.82 (t, J^=^7.9^Hz, 1H), 7.60 (d, J = 7.4 Hz, 1H), 5.12 (dd, J = 12.8, 5.2 Hz, 1H), 2.93 – 2.68 (m, 3H), 2.62–2.50 (m, 2H), 2.43 (t, J^=^7.3^Hz, 2H), 2.09–1.98 (m, 1H), 1.62 – 1.47 (m, 4H), 1.34– 1.22 (m, 10H). LC / MS m / z calculated [M+H]+443.23, found 443.28.
[0175] Preparation of PROTAC linkers with lenalidomide H351Scheme 6
[0176] General procedure to synthesize L1-L6 from lenalidomide: DIPEA (1.5 mmol, 261 μL, 3 eq.) was added to a solution of lenalidomide (0.5 mmol, 129.6 mg), carboxylic acids H1-H6 (0.5 mmol, 1 eq.), and HOAt (0.75 mmol, 102.1 mg, 1.5 eq.) in DMF, followed by the addition of HATU (0.75 mmol, 285.2 mg, 1.5 eq.), and the resulting mixture was stirred at room temperature for 1h. The reaction mixture was then directed subjected to reverse- phase flash chromatography to give the corresponding products (B1-B7). The Boc-protected linkers (B1-B7, 0.25 mmol) were dissolved in DCM (3 ml), and trifluoroacetic acid (0.3 ml) was added. The reaction was stirred for 12 hours at room temperature. The solvent and violates were evaporated, and the crude products were purified by HPLC (20-60% gradient of MeOH in 0.1% TFA / H2O) to give the corresponding amines (L1-L7).
[0177] 5-amino-N-(2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)pentanamide (L1) 61% yield over 2 steps.1H NMR (300 MHz, DMSO-d6) δ 11.02 (s, 1H), 9.76 (s, 1H), 7.91 - 7.60 (m, 4H), 7.54–7.46 (m, 2H), 5.14 (dd, J = 13.2, 5.0 Hz, 1H), 4.40 – 4.28 (m, 2H), 2.98–2.89 (m, 3H), 2.60 (d, J = 17.2 Hz, 1H), 2.40–2.31 (m, 3H), 2.02 (dd, J = 11.1, 5.9 Hz, 1H), 1.57 (dd, J = 14.6, 7.2 Hz, 2H), 1.46–1.40 (m, 2H). LC / MS m / z calculated [M+H]+359.17, found 359.22.
[0178] 6-amino-N-(2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)hexanamide (L2) 67% yield over 2 steps.1H NMR (300 MHz, DMSO-d6) δ 11.04 (s, 1H), 9.78 (s, 1H), 7.89–7.64 (m, 3H), 7.55–7.48 (m, 2H), 5.15 (dd, J = 13.2, 5.0 Hz, 1H), 4.42 – 4.29 (m, 2H), 2.96–2.88 (m, 3H), 2.60 (d, J = 16.3 Hz, 1H), 2.39–2.30 (m, 3H), 2.08–1.96 (m, 1H), 1.62–1.54 (m, 2H), 1.45– 1.37 (m, 2H), 1.35–1.28 (m, 2H). LC / MS m / z calculated [M+H]+373.19, found 373.21.
[0179] 7-amino-N-(2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)heptanamide (L3) 5270% yield over 2 steps.1H NMR (500 MHz, DMSO) δ 11.05 (s, 1H), 9.80 (s, 1H), 7.88–7.59 (m, 4H), 7.55–7.46 (m, 2H), 5.17 (dd, J = 13.2, 5.0 Hz, 1H), 4.43 – 4.30 (m, 2H), 3.02–2.86 (m, 3H), 2.64 (d, J = 16.3 Hz, 1H), 2.43–2.34 (m, 3H), 2.12–2.01 (m, 1H), 1.62–1.48 (m, 4H), 1.37–1.25 (m, 4H). LC / MS m / z calculated [M+H]+387.20, found 387.20.
[0180] 8-amino-N-(2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)octanamide (L4) 54% yield over 2 steps.1H NMR (500 MHz, DMSO) δ 11.03 (s, 1H), 9.79 (s, 1H), 7.88–7.60 (m, 4H), 7.55–7.44 (m, 2H), 5.15 (dd, J = 13.2, 5.0 Hz, 1H), 4.42 – 4.29 (m, 2H), 3.00–2.83 (m, 1H), 2.60 (d, J = 17.5 Hz, 1H), 2.41–2.30 (m, 3H), 2.13–1.94 (m, 1H), 1.64–1.48 (m, 4H), 1.35–1.24 (m, 6H). LC / MS m / z calculated [M+H]+401.22, found 401.18.
[0181] 9-amino-N-(2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)nonanamide (L5) 51% yield over 2 steps.1H NMR (500 MHz, DMSO) δ 11.02 (s, 1H), 9.81 (s, 1H), 7.87–7.60 (m, 3H), 7.51–7.43 (m, 2H), 5.15 (dd, J = 13.2, 5.0 Hz, 1H), 4.41 – 4.29 (m, 2H), 3.00–2.83 (m, 1H), 2.60 (d, J = 17.4 Hz, 1H), 2.41–2.30 (m, 3H), 2.12–1.93 (m, 1H), 1.63–1.47 (m, 4H), 1.33–1.24 (m, 8H). LC / MS m / z calculated [M+H]+415.23, found 415.20.
[0182] 3-(2-aminoethoxy)-N-(2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)propenamide (L6) 62% yield over 2 steps.1H NMR (500 MHz, DMSO) δ 11.01 (s, 1H), 9.92 (s, 1H), 7.86 – 7.76 (m, 3H), 7.55 – 7.45 (m, 2H), 5.14 (dd, J = 13.4, 5.1 Hz, 1H), 4.42 – 4.28 (m, 2H), 3.75 (t, J = 6.3 Hz, 2H), 3.59 (t, J = 5.3 Hz, 2H), 3.01 – 2.86 (m, 3H), 2.68 – 2.55 (m, 3H), 2.36 – 2.25 (m, 1H), 2.05 – 1.98 (m, 1H). LC / MS m / z calculated [M+H]+375.17, found 375.19.
[0183] N-(2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)-3-(piperazin-1-yl)propanamide (L7) 39% yield over 2 steps.1H NMR (500 MHz, DMSO) δ 11.01 (s, 1H), 10.16 (d, J = 18.9 Hz, 1H), 9.27 (brs, 1H), 7.85 – 7.79 (m, 1H), 7.55 – 7.45 (m, 2H), 5.15 (dd, J = 13.3, 5.2 Hz, 1H), 4.42 – 4.28 (m, 2H), 3.07 – 2.86 (m, 5H), 2.74 (t, J = 5.5 Hz, 2H), 2.68 – 2.49 (m, 7H), 2.35 – 2.23 (m, 1H), 2.08 – 1.98 (m, 1H). LC / MS m / z calculated [M+H]+400.20, found 400.22.
[0184] Preparation of TC-PTP PROTACs General method for synthesis of CRBN-based TC-PTP PROTACs 53Scheme 7 To a stirred solution of Intermediate 11 (29.9 mg, 0.05 mmol) and DIPEA (28 μL, 0.15 mmol) in DMF (2 mL) at ambient temperature was added the corresponding primary amine linkers (P1-P6 or L1-L7, 0.075 mmol) and HATU (28 mg, 0.075 mmol). The reaction mixture was stirred for 1 hour. The residue was purified by HPLC (40-85% gradient of MeOH in 0.1% TFA / H2O) to yield the corresponding product.
[0185] Example 1 ((4-((2S)-3-(((2S)-1-((5-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)-5- oxopentyl)amino)-6-(4-ethylbenzamido)-1-oxohexan-2-yl)amino)-2-((S)-2-(2-(((1S,2R,5S)- 2-isopropyl-5-methylcyclohexyl)oxy)acetamido)-3-phenylpropanamido)-3- oxopropyl)phenyl)difluoromethyl)phosphonic acid (compound 1)Compound 1 was prepared with P1 using the general method, yield 49%, yellow solid.1H NMR (500 MHz, DMSO) δ 11.12 (s, 1H), 9.71 (s, 1H), 8.45 – 8.26 (m, 3H), 8.13 (dd, J = 12.9, 7.8 Hz, 1 H), 7.83 (t, J^=^7.8^Hz, 1H), 7.76 – 7.60 (m, 3H), 7.54 – 7.29 (m, 4H), 7.29 – 7.04 (m, 7H), 5.13 (dd, J = 12.7, 5.4 Hz, 1H), 4.63 – 4.52 (m, 2H), 4.28 – 4.15 (m, 1H), 3.91 – 3.84 (m, 1H), 3.65 – 3.58 (m, 1H), 3.28 – 3.15 (m, 2H), 3.13 – 2.72 (m, 8H), 2.65 – 2.44 (m, 6H), 2.10 – 1.91 (m, 3H), 1.70 – 1.34 (m, 12H), 1.19 –1.05 (m, 5H), 0.88 – 0.65 (m, 9H), 0.64 – 0.56 (m, 3H). LC / MS m / z calculated [M+H]+1253.55, found 1253.52.
[0186] Example 2 54((4-((2S)-3-(((2S)-1-((6-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)-6- oxohexyl)amino)-6-(4-ethylbenzamido)-1-oxohexan-2-yl)amino)-2-((S)-2-(2-(((1S,2R,5S)-2- isopropyl-5-methylcyclohexyl)oxy)acetamido)-3-phenylpropanamido)-3- oxopropyl)phenyl)difluoromethyl)phosphonic acid (compound 2)Compound 2 was prepared with P2 using the general method, yield 59%, yellow solid.1H NMR (500 MHz, DMSO δ 11.10 (s, 1H), 9.69 (s, 1H), 8.47 – 8.26 (m, 3H), 8.13 (dd, J = 12.9, 7.8 Hz, 1 H), 7.83 (t, J^=^7.9^Hz, 1H), 7.76 – 7.67 (m, 2H), 7.60 (d, J = 7.4 Hz, 1H), 7.54 – 7.28 (m, 4H), 7.29 – 7.04 (m, 7H), 5.12 (dd, J = 12.9, 5.4 Hz, 1H), 4.63 – 4.52 (m, 2H), 4.28 – 4.15 (m, 1H), 3.91 – 3.84 (m, 1H), 3.65 – 3.58 (m, 1H), 3.28 – 3.16 (m, 2H), 3.15 – 2.73 (m, 8H), 2.65 – 2.45 (m, 6H), 2.10 – 1.91 (m, 3H), 1.69 – 1.31 (m, 14H), 1.29 –1.05 (m, 5H), 0.88 – 0.65 (m, 9H), 0.64 – 0.56 (m, 3H). LC / MS m / z calculated [M+H]+1267.57, found 1267.64.
[0187] Example 3 ((4-((2S)-3-(((2S)-1-((7-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)-7- oxoheptyl)amino)-6-(4-ethylbenzamido)-1-oxohexan-2-yl)amino)-2-((S)-2-(2-(((1S,2R,5S)- 2-isopropyl-5-methylcyclohexyl)oxy)acetamido)-3-phenylpropanamido)-3- oxopropyl)phenyl)difluoromethyl)phosphonic acid (compound 3)Compound 3 was prepared with P3 using the general method, yield 55%, yellow solid.1H NMR (500 MHz, DMSO δ 11.10 (s, 1H), 9.70 (s, 1H), 8.48 – 8.26 (m, 3H), 8.13 (dd, J = 12.8, 7.6 Hz, 1 H), 7.82 (t, J^=^7.8^Hz, 1H), 7.76 – 7.67 (m, 2H), 7.59 (d, J = 7.4 Hz, 1H), 7.54 – 7.28 (m, 4H), 557.29 – 7.04 (m, 7H), 5.12 (dd, J = 12.8, 5.4 Hz, 1H), 4.63 – 4.52 (m, 2H), 4.28 – 4.15 (m, 1H), 3.91 – 3.84 (m, 1H), 3.65 – 3.58 (m, 1H), 3.28 – 3.16 (m, 2H), 3.15 – 2.74 (m, 8H), 2.65 – 2.51 (m, 4H), 2.44 (t, J^=^7.2^Hz, 2H), 2.10 – 1.90 (m, 3H), 1.69 – 1.06 (m, 21H), 0.88 – 0.65 (m, 9H), 0.64 – 0.56 (m, 3H). LC / MS m / z calculated [M+H]+1281.58, found 1281.68.
[0188] Example 4 ((4-((2S)-3-(((2S)-1-((8-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)-8- oxooctyl)amino)-6-(4-ethylbenzamido)-1-oxohexan-2-yl)amino)-2-((S)-2-(2-(((1S,2R,5S)-2- isopropyl-5-methylcyclohexyl)oxy)acetamido)-3-phenylpropanamido)-3- oxopropyl)phenyl)difluoromethyl)phosphonic acid (compound 4)Compound 4 was prepared with P4 using the general method, yield 51%, yellow solid.1H NMR (500 MHz, DMSO δ 11.10 (s, 1H), 9.71 (s, 1H), 8.48 – 8.26 (m, 3H), 8.13 (dd, J = 12.8, 7.6 Hz, 1 H), 7.83 (t, J^=^7.9^Hz, 1H), 7.76 – 7.67 (m, 2H), 7.59 (d, J = 7.4 Hz, 1H), 7.54 – 7.28 (m, 4H), 7.29 – 7.04 (m, 7H), 5.12 (dd, J = 12.9, 5.3 Hz, 1H), 4.63 – 4.52 (m, 2H), 4.28 – 4.15 (m, 1H), 3.91 – 3.84 (m, 1H), 3.65 – 3.58 (m, 1H), 3.28 – 3.16 (m, 2H), 3.15 – 2.70 (m, 8H), 2.64 – 2.51 (m, 4H), 2.44 (t, J^=^7.3^Hz, 2H), 2.10 – 1.90 (m, 3H), 1.69 – 1.06 (m, 23H), 0.88 – 0.65 (m, 9H), 0.64 – 0.56 (m, 3H). LC / MS m / z calculated [M+H]+1295.60, found 1295.54.
[0189] Example 5 ((4-((2S)-3-(((2S)-1-((9-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)-9- oxononyl)amino)-6-(4-ethylbenzamido)-1-oxohexan-2-yl)amino)-2-((S)-2-(2-(((1S,2R,5S)-2- isopropyl-5-methylcyclohexyl)oxy)acetamido)-3-phenylpropanamido)-3- oxopropyl)phenyl)difluoromethyl)phosphonic acid (compound 5) 56Compound 5 was prepared with P5 using the general method, yield 48%, yellow solid.1H NMR (500 MHz, DMSO δ 11.10 (s, 1H), 9.71 (s, 1H), 8.48 – 8.26 (m, 3H), 8.13 (dd, J = 12.8, 7.6 Hz, 1 H), 7.83 (t, J^=^7.9^Hz, 1H), 7.76 – 7.67 (m, 2H), 7.59 (d, J = 7.4 Hz, 1H), 7.54 – 7.28 (m, 4H), 7.29 – 7.04 (m, 7H), 5.12 (dd, J = 12.9, 5.3 Hz, 1H), 4.63 – 4.52 (m, 2H), 4.28 – 4.15 (m, 1H), 3.91 – 3.84 (m, 1H), 3.65 – 3.58 (m, 1H), 3.28 – 3.16 (m, 2H), 3.15 – 2.70 (m, 8H), 2.62 – 2.51 (m, 4H), 2.43 (t, J^=^7.3^Hz, 2H), 2.10 – 1.90 (m, 3H), 1.69 – 1.06 (m, 25H), 0.88 – 0.65 (m, 9H), 0.64 – 0.56 (m, 3H). LC / MS m / z calculated [M+H]+1295.60, found 1295.54.
[0190] Example 6 ((4-((2S)-3-(((2S)-1-((10-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)-10- oxodecyl)amino)-6-(4-ethylbenzamido)-1-oxohexan-2-yl)amino)-2-((S)-2-(2-(((1S,2R,5S)-2- isopropyl-5-methylcyclohexyl)oxy)acetamido)-3-phenylpropanamido)-3- oxopropyl)phenyl)difluoromethyl)phosphonic acid (compound 6)Compound 6 was prepared with P6 using the general method, yield 48%, yellow solid.1H NMR (500 MHz, DMSO δ 11.10 (s, 1H), 9.71 (s, 1H), 8.48 – 8.26 (m, 3H), 8.13 (dd, J = 12.8, 7.6 Hz, 1 H), 7.83 (t, J^=^7.9^Hz, 1H), 7.76 – 7.67 (m, 2H), 7.59 (d, J = 7.4 Hz, 1H), 7.54 – 7.28 (m, 4H), 7.29 – 7.04 (m, 7H), 5.12 (dd, J = 12.9, 5.3 Hz, 1H), 4.63 – 4.52 (m, 2H), 4.28 – 4.15 (m, 1H), 3.91 – 3.84 (m, 1H), 3.65 – 3.58 (m, 1H), 3.28 – 3.16 (m, 2H), 3.15 – 2.68 (m, 8H), 2.62 – 2.50 (m, 4H), 2.43 (t, J^=^7.3^Hz, 2H), 2.10 – 1.90 (m, 3H), 1.69 – 1.06 (m, 25H), 0.88 – 0.65 (m, 9H), 0.64 – 0.56 (m, 3H). LC / MS m / z calculated [M+H]+1323.63, found 1323.71. 57
[0191] Example 7 ((4-((2S)-3-(((2S)-1-((5-((2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)amino)-5- oxopentyl)amino)-6-(4-ethylbenzamido)-1-oxohexan-2-yl)amino)-2-((S)-2-(2-(((1S,2R,5S)- 2-isopropyl-5-methylcyclohexyl)oxy)acetamido)-3-phenylpropanamido)-3- oxopropyl)phenyl)difluoromethyl)phosphonic acid (compound 7)Compound 7 was prepared with L1 using the general method, yield 46%, white solid.1H NMR (500 MHz, DMSO) δ1H NMR (500 MHz, DMSO) δ 10.99 (s, 1H), 9.84 (s, 1H), 8.38 – 8.26 (m, 2H), 8.17 – 8.08 (m, 1H), 8.00 – 7.86 (m, 1H), 7.82 (d, J = 8.0 Hz, 1H), 7.76 – 7.70 (m, 2H), 7.52 – 7.30 (m, 6H), 7.29 – 7.06 (m, 7H), 5.12 (dd, J = 13.3, 5.2 Hz, 1H), 4.64 – 4.56 (m, 2H), 4.40 – 4.28 (m, 2H), 4.28 – 4.15 (m, 1H), 3.92 – 3.84 (m, 1H), 3.68 (t, J = 6.4 Hz, 2H), 3.64 – 3.57 (m, 1H), 3.40 (td, J = 6.4, 3.2 Hz, 2H), 3.28 – 3.12 (m, 4H), 3.11 – 2.94 (m, 3H), 2.94 – 2.73 (m, 3H), 2.64 – 2.54 (m, 5H), 2.37 – 2.26 (m, 1H), 2.04 – 1.90 (m, 3H), 1.70 – 1.60 (m, 1H), 1.59 – 1.34 (m, 7H), 1.19 –1.07 (m, 5H), 0.89 – 0.68 (m, 9H), 0.64 – 0.58 (m, 3H). LC / MS m / z calculated [M+H]+1239.57, found 1239.60.
[0192] Example 8 ((4-((2S)-3-(((2S)-1-((6-((2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)amino)-6- oxohexyl)amino)-6-(4-ethylbenzamido)-1-oxohexan-2-yl)amino)-2-((S)-2-(2-(((1S,2R,5S)-2- isopropyl-5-methylcyclohexyl)oxy)acetamido)-3-phenylpropanamido)-3- oxopropyl)phenyl)difluoromethyl)phosphonic acid (compound 8) 58Compound 8 was prepared with L2 using the general method, yield 52%, white solid.1H NMR (500 MHz, DMSO) δ 11.01 (s, 1H), 9.74 (s, 1H), 8.38 – 8.26 (m, 2H), 8.13 (dd, J = 12.9, 7.8 Hz, 1 H), 7.80 (d, J = 8.0 Hz, 1H), 7.77 – 7.70 (m, 2H), 7.53 – 7.29 (m, 6H), 7.29 – 7.05 (m, 7H), 5.15 (dd, J = 13.4, 5.2 Hz, 1H), 4.63 – 4.52 (m, 2H), 4.42 – 4.29 (m, 2H), 4.28 – 4.15 (m, 1H), 3.91 – 3.84 (m, 1H), 3.65 – 3.58 (m, 1H), 3.28 – 3.16 (m, 2H), 3.07 – 2.73 (m, 8H), 2.66 – 2.55 (m, 3H), 2.40 – 2.30 (m, 3H), 2.07 – 1.91 (m, 3H), 1.69 – 1.28 (m, 14H), 1.28– 1.07 (m, 5H), 0.90 – 0.65 (m, 9H), 0.64 – 0.57 (m, 3H). LC / MS m / z calculated [M+H]+1253.59, found 1253.60. Example 9 ((4-((2S)-3-(((2S)-1-((7-((2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)amino)-7- oxoheptyl)amino)-6-(4-ethylbenzamido)-1-oxohexan-2-yl)amino)-2-((S)-2-(2-(((1S,2R,5S)- 2-isopropyl-5-methylcyclohexyl)oxy)acetamido)-3-phenylpropanamido)-3- oxopropyl)phenyl)difluoromethyl)phosphonic acid (compound 9)Compound 9 was prepared with L3 using the general method, yield 50%, white solid.1H NMR (500 MHz, DMSO) δ 11.03 (s, 1H), 9.79 (s, 1H), 8.38 – 8.26 (m, 2H), 8.13 (dd, J = 12.9, 7.8 Hz, 1 H), 7.80 (d, J = 8.0 Hz, 1H), 7.77 – 7.66 (m, 2H), 7.53 – 7.29 (m, 6H), 7.29 – 7.05 (m, 7H), 5.17 (dd, J = 13.2, 5.0 Hz, 1H), 4.63 – 4.52 (m, 2H), 4.42 – 4.30 (m, 2H), 4.28 – 4.15 (m, 1H), 3.91 – 3.84 (m, 1H), 3.65 – 3.58 (m, 1H), 3.28 – 3.15 (m, 4H), 3.06 – 2.73 (m, 8H), 2.70 – 2.56 (m, 3H), 592.42 – 2.33 (m, 3H), 2.12 – 1.91 (m, 3H), 1.681.07 (m, 21H), 0.90 – 0.65 (m, 9H), 0.64 – 0.57 (m, 3H). LC / MS m / z calculated [M+H]+1267.60, found 1267.60.
[0193] Example 10 ((4-((2S)-3-(((2S)-1-((8-((2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)amino)-8- oxooctyl)amino)-6-(4-ethylbenzamido)-1-oxohexan-2-yl)amino)-2-((S)-2-(2-(((1S,2R,5S)-2- isopropyl-5-methylcyclohexyl)oxy)acetamido)-3-phenylpropanamido)-3- oxopropyl)phenyl)difluoromethyl)phosphonic acid (compound 10)Compound 10 was prepared with L4 using the general method, yield 42%, white solid. 1H NMR (500 MHz, DMSO) δ 11.01 (s, 1H), 9.79 (s, 1H), 8.37 – 8.26 (m, 2H), 8.13 (dd, J = 12.9, 7.8 Hz, 1 H), 7.81 (d, J = 8.0 Hz, 1H), 7.76 – 7.70 (m, 2H), 7.55 – 7.29 (m, 6H), 7.29 – 7.04 (m, 7H), 5.16 (dd, J = 13.2, 5.0 Hz, 1H), 4.63 – 4.52 (m, 2H), 4.42 – 4.29 (m, 2H), 4.28 – 4.15 (m, 1H), 3.91 – 3.84 (m, 1H), 3.65 – 3.58 (m, 1H), 3.28 – 3.14 (m, 2H), 3.06 – 2.73 (m, 8H), 2.70 – 2.55 (m, 3H), 2.41 – 2.31 (m, 3H), 2.13 – 1.91 (m, 3H), 1.68 – 1.07 (m, 23H), 0.90 – 0.64 (m, 9H), 0.64 – 0.56 (m, 3H). LC / MS m / z calculated [M+H]+1281.62, found 1281.60.
[0194] Example 11 ((4-((2S)-3-(((2S)-1-((9-((2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)amino)-9- oxononyl)amino)-6-(4-ethylbenzamido)-1-oxohexan-2-yl)amino)-2-((S)-2-(2-(((1S,2R,5S)-2- isopropyl-5-methylcyclohexyl)oxy)acetamido)-3-phenylpropanamido)-3- oxopropyl)phenyl)difluoromethyl)phosphonic acid (compound 11) 60Compound 11 was prepared with L5 using the general method, yield 37%, white solid.1H NMR (500 MHz, DMSO) δ 11.00 (s, 1H), 9.79 (s, 1H), 8.37 – 8.26 (m, 2H), 8.13 (dd, J = 12.9, 7.8 Hz, 1 H), 7.80 (d, J = 8.0 Hz, 1H), 7.76 – 7.60 (m, 2H), 7.56 – 7.29 (m, 6H), 7.29 – 7.03 (m, 7H), 5.15 (dd, J = 13.2, 5.1 Hz, 1H), 4.63 – 4.52 (m, 2H), 4.41 – 4.28 (m, 2H), 4.28 – 4.15 (m, 1H), 3.91 – 3.84 (m, 1H), 3.65 – 3.58 (m, 1H), 3.28 – 3.14 (m, 4H), 3.05 – 2.73 (m, 8H), 2.70 – 2.55 (m, 3H), 2.41 – 2.31 (m, 3H), 2.13 – 1.91 (m, 3H), 1.68 – 1.07 (m, 25H), 0.90 – 0.64 (m, 9H), 0.64 – 0.55 (m, 3H). LC / MS m / z calculated [M+H]+1295.63, found 1295.70.
[0195] Example 12 ((4-((2S)-3-(((2S)-1-((2-(3-((2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)amino)-3- oxopropoxy)ethyl)amino)-6-(4-ethylbenzamido)-1-oxohexan-2-yl)amino)-2-((S)-2-(2- (((1S,2R,5S)-2-isopropyl-5-methylcyclohexyl)oxy)acetamido)-3-phenylpropanamido)-3- oxopropyl)phenyl)difluoromethyl)phosphonic acid (compound 12)Compound 12 was prepared with L6 using the general method, yield 49%, white solid.1H NMR (500 MHz, DMSO) δ 10.99 (s, 1H), 9.84 (s, 1H), 8.38 – 8.26 (m, 2H), 8.17 – 8.08 (m, 1H), 8.00 – 7.86 (m, 1H), 7.82 (d, J = 8.0 Hz, 1H), 7.76 – 7.70 (m, 2H), 7.52 – 7.30 (m, 6H), 7.29 – 7.06 (m, 7H), 5.12 (dd, J = 13.3, 5.2 Hz, 1H), 4.64 – 4.56 (m, 2H), 4.40 – 4.28 (m, 2H), 4.28 – 4.15 (m, 1H), 3.92 – 3.84 (m, 1H), 3.68 (t, J = 6.4 Hz, 2H), 3.64 – 3.57 (m, 1H), 3.40 (td, J = 6.4, 3.2 Hz, 2H), 3.28 – 3.12 (m, 4H), 3.11 – 2.95 (m, 3H), 2.94 – 2.73 (m, 3H), 2.64 – 2.54 (m, 5H), 612.37 – 2.26 (m, 1H), 2.04 – 1.90 (m, 3H), 1.70 – 1.60 (m, 1H), 1.59 – 1.34 (m, 7H), 1.29 –1.07 (m, 5H), 0.89 – 0.68 (m, 9H), 0.64 – 0.58 (m, 3H).13C NMR (126 MHz, DMSO) δ 173.34, 171.99, 171.54, 171.06, 170.99, 169.77, 169.49, 168.29, 166.49, 147.43, 140.43, 137.45 (d, J = 25.7 Hz), 134.12, 133.14, 132.61, 129.75, 129.58, 129.51, 129.12, 128.36, 128.00, 127.69, 126.75, 126.29, 125.67, 121.21, 119.55, 79.79, 79.66, 69.20, 67.73, 66.85, 54.30, 54.00, 53.17, 53.04, 52.00, 47.89, 47.82, 46.93, 38.96, 38.10, 37.94, 36.94, 34.44, 32.55, 31.68, 31.24, 29.40, 28.45, 25.59, 23.29, 23.16, 23.11, 22.60, 21.34, 16.46, 15.83. LC / MS m / z calculated [M+H]+1255.57, found 1255.60. HRMS m / z Calcd for C59H86Cl2N11O5S21255.5651; found 1255.5646.
[0196] Example 13 ((4-((2S)-3-(((2S)-1-(4-(3-((2-(2,6-dioxopiperidin-3-yl)-1-oxoisoindolin-4-yl)amino)-3- oxopropyl)piperazin-1-yl)-6-(4-ethylbenzamido)-1-oxohexan-2-yl)amino)-2-((S)-2-(2- (((1S,2R,5S)-2-isopropyl-5-methylcyclohexyl)oxy)acetamido)-3-phenylpropanamido)-3- oxopropyl)phenyl)difluoromethyl)phosphonic acid (compound 13)Compound 13 was prepared with L7 using the general method, yield 49%, white solid.1H NMR (500 MHz, DMSO) δ 10.98 (s, 1H), 9.28 (s, 1H), 8.38 – 8.26 (m, 2H), 8.17 – 8.08 (m, 1H), 8.00 – 7.86 (m, 1H), 7.85 – 7.79 (m, 1H),7.76 – 7.70 (m, 2H), 7.55 – 7.30 (m, 6H), 7.29 – 7.06 (m, 7H), 5.15 (dd, J = 13.3, 5.2 Hz, 1H), 4.64 – 4.56 (m, 2H), 4.43 – 4.28 (m, 2H), 4.28 – 4.15 (m, 1H), 3.92 – 3.84 (m, 1H), 3.64 – 3.57 (m, 1H), 3.50 – 3.12 (m, 8H), 3.11 – 2.73 (m, 8H), 2.64 – 2.53 (m, 7H), 2.37 – 2.26 (m, 1H), 2.04 – 1.90 (m, 3H), 1.77 – 1.60 (m, 1H), 1.59 – 1.33 (m, 7H), 1.28 –1.07 (m, 5H), 0.89 – 0.68 (m, 9H), 0.64 – 0.58 (m, 3H). LC / MS m / z calculated 1280.60, found 1280.60.
[0197] As used herein, the following terms and phrases shall have the meanings set forth below. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art. 62
[0198] The term "about" can allow for a degree of variability in a value or range, for example, within 10%, within 5%, or within 1% of a stated value or of a stated limit of a range.
[0199] The term "substantially" can allow for a degree of variability in a value or range, for example, within 90%, within 95%, or within 99% of a stated value or of a stated limit of a range.
[0200] The terms "a," "an," or "the" are used to include one or more than one unless the context clearly dictates otherwise. The term "or" is used to refer to a nonexclusive "or" unless otherwise indicated. In addition, the phraseology or terminology employed herein, and not otherwise defined, is for the purpose of description only and not of limitation. Any use of section headings is intended to aid the reading of the document and is not to be interpreted as limiting. Further, information that is relevant to a section heading may occur within or outside of that particular section. The terms "including" and "having" are defined as comprising (i.e., open language).
[0201] All patents, patent application publications, journal articles, textbooks, and other publications mentioned in the specification are indicative of the level of skill of those in the art to which the disclosure pertains. All such publications are incorporated herein by reference to the same extent as if each individual publication were specifically and individually indicated to be incorporated by reference.
[0202] It is recognized that various modifications are possible within the scope of the claimed invention. Thus, although the present invention has been specifically disclosed in the context of preferred embodiments and optional features, those skilled in the art may resort to modifications and variations of the concepts disclosed herein. Such modifications and variations are considered within the scope of the invention as claimed herein. 63
Claims
WE CLAIM 1. A compound of formula (I), or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof:wherein L is a linker selected from:wherein x is 1-15, w is 1-5, and each a and b is independently 0-3;a bond designated with "" is attached to E; and "*" represents the point of attachment of thelinker; and E is an E3 ligase ligand selected from E1and E2, wherein 64E1is represented by a structure:wherein X is CO or CH2; R1is fluoro, hydrogen, or deuterium; and a bond designated with "*" represents the point of attachment of linker L; and E2is represented by a structure:wherein R4is methyl, hydrogen, or deuterium; anda bond designated with" is attached to the linker.
2. The compound of claim 1, wherein E is E1.
3. The compound of claim 1, wherein the linker L is:wherein x is 1-15, w is 1-5, and each a and b is independently 0-3;a bond designated with "" is attached to E; and "*" represents the point of attachment of thelinker.
4. The compound of claim 1, 2 or 3, wherein the compound is: 65666768or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof.
5. A pharmaceutical composition comprising a compound of any one of claims 1-4, or a pharmaceutically acceptable salt, hydrate, tautomer, or stereoisomer thereof, and a pharmaceutically acceptable carrier, excipient, or diluent.
6. A method of inhibiting cancer in a patient, wherein the method comprises administering to the patient an effective amount of a compound of any one of claims 1-4, or a pharmaceutical composition of claim 5, whereupon cancer in the patient is inhibited.
7. The method of claim 6, wherein the cancer is colon cancer, lung adenocarcinoma, squamous cell carcinoma, or melanoma.
8. The method of claim 6 or 7, wherein the compound is administered orally.
9. A method of degrading T-cell protein tyrosine phosphatase (TC-PTP) proteins in a patient, wherein the method comprises administering to the patient an effective amount of a compound of any one of claims 1-4 or a pharmaceutical composition of claim5, whereupon TC-PTP in the patient is degraded.
10. The method of claim 9, wherein the patient has cancer.
11. The method of claim 9, wherein the patient has type II diabetes.
12. The method of claim 9, wherein the patient is obese. 69
Citation Information
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