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Methods of treating cancer in biomarker-identified patients with non-covalent inhibitors of cyclin-dependent kinase 7 (CDK7)

Pending Publication Date: 2021-12-30
SYROS PHARMACEUTICALIS INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

The present invention is about a new method for identifying cancer patients who are likely to respond well to treatment with a non-covalent CDK7 inhibitor. The method involves analyzing biomarkers in a biological sample from the patient to determine if they are present and in what amount. The biomarkers can include gene expression, mutations, chromosomal translocations, epigenetic modifications, and protein levels. The method can also involve analyzing the state of certain proteins or their interactions with other molecules. The invention also includes methods for treating patients with the CDK7 inhibitor alone or in combination with other therapeutic agents. The technical effect of the invention is to provide a more effective way of identifying and treating cancer patients with CDK7 inhibitors.

Problems solved by technology

However, it is challenging to develop molecular diagnostics and few are commercially available.

Method used

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  • Methods of treating cancer in biomarker-identified patients with non-covalent inhibitors of cyclin-dependent kinase 7 (CDK7)
  • Methods of treating cancer in biomarker-identified patients with non-covalent inhibitors of cyclin-dependent kinase 7 (CDK7)
  • Methods of treating cancer in biomarker-identified patients with non-covalent inhibitors of cyclin-dependent kinase 7 (CDK7)

Examples

Experimental program
Comparison scheme
Effect test

example 1

of Benzyl (2R, 5R)-5-amino-2-methyl-piperidine-1-carboxylate and benzyl (2S, 5S)-5-amino-2-methyl-piperidine-1-carboxylate

Step 1: Benzyl 5-(tert-butoxycarbonylamino)-2-methyl-piperidine-1-carboxylate

[0103]

[0104]To a solution containing commercially available racemic trans tert-butyl N-(6-methyl-3-piperidyl)carbamate (5 g, 23.33 mmol, 1 eq,) and NaHCO3 (13.72 g, 163.32 mmol, 7 eq) in tetrahydrofuran (THF; 50 mL) and H2O (50 mL), we added CbzCl (5.97 g, 35.00 mmol, 4.98 mL, 1.5 eq) dropwise at 0° C. The mixture was stirred at 15° C. for 2 hours then poured into water (50 mL) and extracted with ethyl acetate (EtOAc; 50 mL×3). The combined organic layer was washed with brine (50 mL×3), dried over Na2SO4, and filtered. The filtrate was concentrated under reduced pressure, and the residue was purified by medium pressure liquid chromatography (MPLC; SiO2, PE:EtOAc=5:1 to 1:1) to give the title compound as a yellow solid (9.7 g, 18.04 mmol, 77.32% yield, 64.8% purity).

Step 2: Benzyl (2R, 5R...

example 2

of 7-dimethylphosphoryl-3-[2-[[(3S, 6S)-6-methyl-3-piper-idyl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1H-indole-6-carbonitrile (Compound 100)

Step 1: Benzyl (2S, 5S)-5-[[4-(7-chloro-6-cyano-1H-indol-3-yl)-5-(trifluoromethyl) pyrimidin-2-yl] amino]-2-methyl-piperidine-1-carboxylate

[0107]

[0108]We stirred a mixture of 7-chloro-3-[2-chloro-5-(trifluoromethyl)pyrimidin-4-yl]-1H-indole-6-carbonitrile (0.81 g, 2.27 mmol, 1 eq), benzyl (2S,5S)-5-amino-2-methyl-piperidine-1-carboxylate (732.20 mg, 2.95 mmol, 1.3 eq) and N,N-diisopropylethylamine (DIEA or DIPEA; 879.41 mg, 6.80 mmol, 1.19 mL, 3 eq) in N-methyl-2-pyrrolidone (NMP; 8 mL) at 140° C. for 1 hour. The reaction mixture was diluted with H2O (100 mL) and extracted with EtOAc (50 mL×2). The combined organic layers were washed with brine (100 mL×2), dried over Na2SO4, filtered, and concentrated under reduced pressure to give a residue that was purified by column chromatography (SiO2, petroleum ether / ethyl acetate=10:1 to 4:1) to afford...

example 3

of (S)-6,6-dimethylpiperidin-3-amine

[0114]

[0115]We dissolved (S)-tert-butyl (6-oxopiperidin-3-yl)carbamate (1.00 g, 4.67 mmol) (Tetrahedron Letters, 36:8205, 1995) in THF (47 mL) and cooled the solution to −10° C. Zirconium (IV) chloride (2.61 g, 11.22 mmol) was added, and the mixture was stirred for 30 minutes at this temperature. A methylmagnesium bromide solution (3M in ether, 20.25 mL, 60.75 mmol) was added, and the reaction mixture was allowed to slowly warm up to room temperature, at which it was stirred overnight. The solution was quenched with 30% aqueous NaOH, diluted with EtOAc, filtered, and then extracted 3 times with EtOAc. The organics were combined, dried over sodium sulfate, filtered, and concentrated in vacuo to provide the crude product as a yellow oil that was used without purification. The oil was dissolved in dichloromethane (DCM; 47 mL) and trifluoroacetic acid (TFA; 3.58 mL, 46.73 mmol) was added. We stirred the reaction mixture at room temperature for 16 hour...

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Abstract

The present invention relates to methods of identifying patients suffering from various types of cancer who are more likely to respond to treatment with a CDK7 inhibitor conforming to structural Formula (I), (Ia), a species thereof, or a specified form thereof (as described herein), either when administered or used alone or in combination with a second therapeutic agent (e.g., another anti-cancer therapy). Patients are identified based on one or more features (e.g., gene copy number or expression level) of certain biomarkers (e.g., RB1 or another member of the E2F pathway). In addition, the present invention relates to methods of treating an identified patient with a compound conforming to structural Formula (I), (Ia), a species thereof, or a specified form thereof, either alone or in combination with a second therapeutic agent. In another aspect, the present invention features kits including instructions for treating a patient identified as described herein.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application claims the benefit of the filing date of U.S. provisional application No. 62 / 754,398, filed Nov. 1, 2018; U.S. provisional application No. 62 / 877,189, filed Jul. 22, 2019; U.S. provisional application No. 62 / 915,983, filed Oct. 16, 2019, and U.S. provisional application No. 62 / 927,469, filed Oct. 29, 2019. The content of each of these prior applications is hereby incorporated by reference herein in its entirety.BACKGROUND OF THE INVENTION[0002]The long evolution of healthcare has reached a point in time where the promise of biomarker analysis is beginning to be realized. When physicians can stratify patients, even those who share many similar physiological traits and exhibit common symptoms of a given disease, into more specific groups, they can better tailor treatment and optimize the outcome for each patient. However, it is challenging to develop molecular diagnostics and few are commercially available.SUMMARY OF THE IN...

Claims

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Application Information

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IPC IPC(8): A61K31/675A61P35/00
CPCA61K31/675A61P35/00A61K31/519C07F9/65583A61K31/506A61K31/7068A61K31/555A61K31/4439A61K9/0019A61K31/565A61K45/06A61K2300/00A61K9/0053A61K9/20A61K9/48A61K47/26A61K47/36A61K47/38C07B2200/05
Inventor HODGSON, JOHN GRAEMEJOHANNESSEN, LIV HELENA
Owner SYROS PHARMACEUTICALIS INC