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Publication

Development of a Selective CDK7 Covalent Inhibitor Reveals Predominant Cell-Cycle Phenotype.

Cell chemical biology | 2019

Cyclin-dependent kinase 7 (CDK7) regulates both cell cycle and transcription, but its precise role remains elusive. We previously described THZ1, a CDK7 inhibitor, which dramatically inhibits superenhancer-associated gene expression. However, potent CDK12/13 off-target activity obscured CDK7s contribution to this phenotype. Here, we describe the discovery of a highly selective covalent CDK7 inhibitor. YKL-5-124 causes arrest at the G1/S transition and inhibition of E2F-driven gene expression; these effects are rescued by a CDK7 mutant unable to covalently engage YKL-5-124, demonstrating on-target specificity. Unlike THZ1, treatment with YKL-5-124 resulted in no change to RNA polymerase II C-terminal domain phosphorylation; however, inhibition could be reconstituted by combining YKL-5-124 and THZ531, a selective CDK12/13 inhibitor, revealing potential redundancies in CDK control of gene transcription. These findings highlight the importance of CDK7/12/13 polypharmacology for anti-cancer activity of THZ1 and posit that selective inhibition of CDK7 may be useful for treatment of cancers marked by E2F misregulation.

Pubmed ID: 30905681 RIS Download

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Associated grants

Agency: NCI NIH HHS, United States
Id: R01 CA179483
Agency: NCI NIH HHS, United States
Id: R01 CA215452
Agency: NIGMS NIH HHS, United States
Id: T32 GM008307
Agency: NHLBI NIH HHS, United States
Id: U54 HL127365

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GraphPad Prism (tool)

RRID:SCR_002798

Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.

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Program DynaFit (tool)

RRID:SCR_008444

Program DynaFit Analysis of (bio)chemical kinetics and equilibria Welcome to the DynaFit home page. Purpose Symbolic Notation Bibliographic Reference Numerical Methods Minimum System Requirements Purpose The main purpose of the program DynaFit is to perform nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data. The experimental data can be either initial reaction velocities in dependence on the concentration of varied species (e.g., inhibitor concentration vs. velocity), or the reaction progress curves (e.g., time vs. absorbance). Symbolic Notation The main advantage in using the program DynaFit is in the ability to characterize the (bio)chemical reacting system in terms of symbolic, or stoichiometric, equations. For example, the ``slow, tight'''' inhibition of a dissociative dimeric enzyme is described by the following text: Monomer Monomer <==> Enzyme : k1 k2 Enzyme Inhibitor <==> Complex : k3 k4 Enzyme Substrate <==> ReactiveX : k5 k6 ReactiveX --> Product Enzyme : k7 k8 The names of chemical species (Monomer, Enzyme, etc.) are entirely arbitrary and can be freely chosen by the investigator. Bibliographic Reference If you publish any results obtained by using DYNAFIT, plase cite the following reference: Kuzmic, P. (1996) Anal. Biochem. 237, 260-273. Program DYNAFIT for the Analysis of Enzyme Kinetic Data: Application to HIV Proteinase ABSTRACT A computer program with the code name DYNAFIT was developed for fitting either the initial velocities, or the time-course of enzyme reactions, to an arbitrary molecular mechanism represented symbolically by a set of chemical equations. Seven numerical tests and five graphical tests are applied to judge the goodness of fit. Experimental data on the inhibition of the dissociative dimeric proteinase from HIV were used in four test examples. A set of initial velocities was analyzed to see if a tight-binding inhibitor could bind to the HIV proteinase monomer. Three different sets of progress curves were analyzed (i) to determine the kinetic properties of an irreversible inhibitor; (ii) to investigate the dissociation and denaturation mechanism for the protease dimer; and (iii) to investigate the inhibition mechanism for a transient inhibitor. See a MEDLINE abstract with related references concerning the kinetics of HIV-1 protease. Numerical Methods The nonlinear regression module uses the Levenberg-Marquardt algorithm [1]. The time-course of (bio)chemical reactions is computed by the numerical integration of simultaous first-order ordinary differential equations, using the Livermore Solver of ODe Systems (LSODE, [2]). The composition of complex mixtures at equilibrium (e.g., in the concentration jump experiment where a complex mixture is incubated prior to the addition of a reagent) is computed by solving simultaneous nonlinear algebraic equations, namely, the mass balance equations for the component species, by using the multidimensional Newton-Raphson method [3]. References G. A. F. Seber and C. J. Wild (1989) Nonlinear Regression, Wiley, New York, p. 624. A. C. Hindmarsh (1983) ODEPACK: a systematized collection of ODE solvers; in Scientific Computing, ed. R. S. Stepleman et al., North Holland, Amsterdam, pp. 55--64. E. Kreyszig (1993) Advanced Engineering Mathematics; 7th ed., John Wiley, New York, p. 929. Minimum System Requirements DynaFit for Windows Intel Pentium III or Celeron class 800 MHz or faster processor Microsoft Windows XP (SP1) or 2000 (SP2) 128 MB RAM 20 MB Hard Disk Space Ethernet Network Interface Card required for license activation(1) CD/DVD-ROM drive required for software installation(2) (1) The Network Interface Card is used to compute a unique Computer ID, tied to a particular DynaFit license. Essentially the Computer ID required for license activation is an encrypted Media Access Control (MAC address) associated with the given Network Card. (2) CD/DVD-ROM is not required if the software is being installed by using the downloadable installer file dynafit-install.zip. Sponsor. This work has been supported by the NIH, grant No. R43 AI52587-02 and the U.S. Department of Defense, U.S. Army Medical Research and Materials Command, Ft. Detrick, MD, administered by the Pacific Telehealth & Technology Hui, Honolulu, HI, contract No. V549P-6073.

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multiplierz (tool)

RRID:SCR_012058

An open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers'' proprietary data files via mzAPI.

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