Molecular principle of the cyclin-dependent kinase selectivity of 4-(thiazol-5-yl)-2-(phenylamino) pyrimidine-5-carbonitrile derivatives revealed by molecular modeling studies.

Due to the high sequence identity of the binding pockets of cyclin-dependent kinases (CDKs), designing highly selective inhibitors towards a specific CDK member remains a big challenge. 4-(thiazol-5-yl)-2-(phenylamino) pyrimidine derivatives are effective inhibitors of CDKs, among which the most promising inhibitor 12u demonstrates high binding affinity to CDK9 and attenuated binding affinity to other homologous kinases, such as CDK2. In this study, in order to rationalize the principle of the binding preference towards CDK9 over CDK2 and to explore crucial information that may aid the design of selective CDK9 inhibitors, MM/GBSA calculations based on conventional molecular dynamics (MD) simulations and enhanced sampling simulations (umbrella sampling and steered MD simulations) were carried out on two representative derivatives (12u and 4). The calculation results show that the binding specificity of 12u to CDK9 is primarily controlled by conformational change of the G-loop and variation of the van der Waals interactions. Furthermore, the enhanced sampling simulations revealed the different reaction coordinates and transient interactions of inhibitors 12u and 4 as they dissociate from the binding pockets of CDK9 and CDK2. The physical principles obtained from this study may facilitate the discovery and rational design of novel and specific inhibitors of CDK9.

[1]  N. Raje,et al.  Cyclin dependent kinases in cancer , 2012, Cancer biology & therapy.

[2]  C. Fegan,et al.  A novel Cdk9 inhibitor preferentially targets tumor cells and synergizes with fludarabine , 2013, Oncotarget.

[3]  Yongqi Huang,et al.  Do intrinsically disordered proteins possess high specificity in protein-protein interactions? , 2013, Chemistry.

[4]  Jing Zhang,et al.  Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance , 2010, Proceedings of the National Academy of Sciences.

[5]  X. Graña,et al.  Mechanisms controlling CDK9 activity. , 2006, Frontiers in bioscience : a journal and virtual library.

[6]  L. Nilsson,et al.  Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K , 2001 .

[7]  Dan Li,et al.  Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations , 2015, Scientific Reports.

[8]  P. Kollman,et al.  Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. , 2000, Journal of medicinal chemistry.

[9]  D. Case,et al.  Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. , 2003, Journal of molecular biology.

[10]  Tingjun Hou,et al.  Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations , 2011, J. Chem. Inf. Model..

[11]  Jaroslav Koca,et al.  CAVER: a new tool to explore routes from protein clefts, pockets and cavities , 2006, BMC Bioinformatics.

[12]  P. Kollman,et al.  A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .

[13]  S. Genheden,et al.  The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities , 2015, Expert opinion on drug discovery.

[14]  Jin-Ching Lee,et al.  The antiproliferative effect of C2-ceramide on lung cancer cells through apoptosis by inhibiting Akt and NFκB , 2014, Cancer Cell International.

[15]  Peter J Bond,et al.  Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity. , 2014, Journal of chemical theory and computation.

[16]  Ross C. Walker,et al.  An overview of the Amber biomolecular simulation package , 2013 .

[17]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[18]  Huimeng Sun,et al.  A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK. , 2012, Biochemical and biophysical research communications.

[19]  J. B. Wang,et al.  Transmission spectra of two-dimensional quantum structures , 2004, quant-ph/0408114.

[20]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[21]  Gerhard Hummer,et al.  Convergence and error estimation in free energy calculations using the weighted histogram analysis method , 2012, J. Comput. Chem..

[22]  L. Johnson,et al.  The structure of P‐TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation , 2008, The EMBO journal.

[23]  M. Buehler.  Mechanics of Protein Crystals: Atomistic Modeling of Elasticity and Fracture , 2006 .

[24]  Lin Li,et al.  Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase , 2012, J. Chem. Inf. Model..

[25]  Benoît Roux,et al.  Computational analysis of the binding specificity of Gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinases. , 2013, Journal of the American Chemical Society.

[26]  N. Pattabiraman,et al.  Selectivity and potency of cyclin-dependent kinase inhibitors , 2006, The AAPS Journal.

[27]  S. Baumli,et al.  Perspective of Cyclin-dependent kinase 9 (CDK9) as a Drug Target , 2012, Current pharmaceutical design.

[28]  Vivek S. Bharadwaj,et al.  Insights into the glycyl radical enzyme active site of benzylsuccinate synthase: a computational study. , 2013, Journal of the American Chemical Society.

[29]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[30]  T. Golub,et al.  Critical role of CDK2 for melanoma growth linked to its melanocyte-specific transcriptional regulation by MITF. , 2004, Cancer cell.

[31]  W. F. de Azevedo,et al.  Structural basis for inhibition of cyclin-dependent kinase 9 by flavopiridol. , 2002, Biochemical and biophysical research communications.

[32]  Marta Cascante,et al.  Targeting cell cycle regulation in cancer therapy. , 2013, Pharmacology & therapeutics.

[33]  E. Sausville.  Complexities in the development of cyclin-dependent kinase inhibitor drugs. , 2002, Trends in molecular medicine.

[34]  Charles L Brooks,et al.  Recent advances in implicit solvent-based methods for biomolecular simulations. , 2008, Current opinion in structural biology.

[35]  Tingjun Hou,et al.  Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches , 2013, J. Chem. Inf. Model..

[36]  Andrea Cavalli,et al.  Steered Molecular Dynamics Simulations for Studying Protein-Ligand Interaction in Cyclin-Dependent Kinase 5 , 2014, J. Chem. Inf. Model..

[37]  H. C. Andersen.  Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations , 1983 .

[38]  L. Gelbert,et al.  Cyclin dependent kinase (CDK) inhibitors as anticancer drugs. , 2015, Bioorganic & Medicinal Chemistry Letters.

[39]  Peter M Fischer,et al.  Cyclin-dependent kinase 9: a key transcriptional regulator and potential drug target in oncology, virology and cardiology. , 2008, Trends in pharmacological sciences.

[40]  George C Schatz,et al.  A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations. , 2013, Journal of the American Chemical Society.

[41]  M. Zurita,et al.  The basal transcription machinery as a target for cancer therapy , 2014, Cancer Cell International.

[42]  Alexander P Lyubartsev,et al.  An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. , 2012, Journal of chemical theory and computation.

[43]  Michael W. Parker,et al.  Targeting acute myeloid leukemia by dual inhibition of PI3K signaling and Cdk9-mediated Mcl-1 transcription. , 2013, Blood.

[44]  B. Kuhn,et al.  Validation and use of the MM-PBSA approach for drug discovery. , 2005, Journal of medicinal chemistry.

[45]  M. Noble,et al.  The CDK9 C-helix Exhibits Conformational Plasticity That May Explain the Selectivity of CAN508 , 2012, ACS chemical biology.

[46]  L. Johnson,et al.  Halogen bonds form the basis for selective P-TEFb inhibition by DRB. , 2010, Chemistry & biology.

[47]  G. Shapiro,et al.  Cyclin-dependent kinase pathways as targets for cancer treatment. , 2006, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[48]  Wei Cui,et al.  Unraveling the Allosteric Inhibition Mechanism of PTP1B by Free Energy Calculation Based on Umbrella Sampling , 2013, J. Chem. Inf. Model..

[49]  R. Swendsen,et al.  THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .

[50]  Jin Qin,et al.  Molecular Dynamics Simulation, Free Energy Calculation and Structure-Based 3D-QSAR Studies of B-RAF Kinase Inhibitors , 2011, J. Chem. Inf. Model..

[51]  Tingjun Hou,et al.  P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape , 2014, PLoS Comput. Biol..

[52]  L. Tsai,et al.  A family of human cdc2‐related protein kinases. , 1992, The EMBO journal.

[53]  W. C. Still,et al.  Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO) , 1999 .

[54]  M. Noble,et al.  Comparative Structural and Functional Studies of 4-(Thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile CDK9 Inhibitors Suggest the Basis for Isotype Selectivity , 2012, Journal of medicinal chemistry.

[55]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[56]  Jan H. Jensen,et al.  Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values. , 2011, Journal of chemical theory and computation.

[57]  S. Grant,et al.  Cyclin-dependent kinase inhibitor therapy for hematologic malignancies , 2013, Expert opinion on investigational drugs.

[58]  Weiwei Xue,et al.  Molecular mechanism of HIV‐1 integrase–vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective , 2012, J. Comput. Chem..

[59]  Holger Gohlke,et al.  MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. , 2012, Journal of chemical theory and computation.

[60]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[61]  Tingjun Hou,et al.  Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring. , 2014, Physical chemistry chemical physics : PCCP.

[62]  E. Bonmassar,et al.  The cyclin-dependent kinase inhibitor PHA-848125 suppresses the in vitro growth of human melanomas sensitive or resistant to temozolomide, and shows synergistic effects in combination with this triazene compound. , 2010, Pharmacological research.

[63]  M. Noble,et al.  Substituted 4-(Thiazol-5-yl)-2-(phenylamino)pyrimidines Are Highly Active CDK9 Inhibitors: Synthesis, X-ray Crystal Structures, Structure–Activity Relationship, and Anticancer Activities , 2013, Journal of Medicinal Chemistry.

[64]  B. Roux.  The calculation of the potential of mean force using computer simulations , 1995 .

[65]  Tingjun Hou,et al.  Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches , 2013, J. Chem. Inf. Model..

[66]  Pierre Dubus,et al.  Cdk2 is dispensable for cell cycle inhibition and tumor suppression mediated by p27(Kip1) and p21(Cip1). , 2005, Cancer cell.

[67]  Lisa S. Chen,et al.  Transcription Inhibition as a Therapeutic Target for Cancer , 2011, Cancers.

[68]  Lin-Li Li,et al.  Steered Molecular Dynamics Simulations Reveal the Likelier Dissociation Pathway of Imatinib from Its Targeting Kinases c-Kit and Abl , 2009, PloS one.