Application of docking and QM/MM-GBSA rescoring to screen for novel Myt1 kinase inhibitors

Journal of Chemical Information and Modeling

Volumn 54, Issue 3, 2014, Pages 881-893

  Wichapong, Kanin ^a   Rohe, Alexander ^a   Platzer, Charlott ^a   Slynko, Inna ^a   Erdmann, Frank ^a   Schmidt, Matthias ^a   Sippl, Wolfgang ^a  

^a MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME INHIBITION; FREE ENERGY;

BINDING AFFINITIES; BINDING FREE ENERGY; INACTIVE COMPOUNDS; KINASE INHIBITORS; MICROMOLAR LEVEL; NON-TRIVIAL TASKS; STRUCTURE BASED DRUG DESIGNS; VIRTUAL SCREENING;

BINDING ENERGY;

1,3 BENZODIOXOLE DERIVATIVE; 6 (2,6 DICHLOROPHENYL) 2 (4 FLUORO 3 METHYLANILINO) 8 METHYL 8H PYRIDO[2,3 D]PYRIMIDIN 7 ONE; 8-(2,6-DICHLOROPHENYL)-10-METHYL-3-((4-MORPHOLIN-4-YLPHENYL)AMINO)-2,4,10-TRIAZABICYCLO(4.4.0)DECA-1,3,5,7-TETRAEN-9-ONE; HETEROCYCLIC COMPOUND; LIGAND; MEMBRANE PROTEIN; MORPHOLINE DERIVATIVE; PKMYT1 PROTEIN, HUMAN; PROTEIN BINDING; PROTEIN KINASE INHIBITOR; PROTEIN SERINE THREONINE KINASE; PROTEIN TYROSINE KINASE; PYRIDONE DERIVATIVE; PYRIMIDINE DERIVATIVE; QUINAZOLINE DERIVATIVE; SARACATINIB;

ANTAGONISTS AND INHIBITORS; CHEMISTRY; DRUG DESIGN; HUMAN; METABOLISM; MOLECULAR DOCKING;

AZA COMPOUNDS; BENZODIOXOLES; DRUG DESIGN; HUMANS; LIGANDS; MEMBRANE PROTEINS; MOLECULAR DOCKING SIMULATION; MORPHOLINES; PROTEIN BINDING; PROTEIN KINASE INHIBITORS; PROTEIN-SERINE-THREONINE KINASES; PROTEIN-TYROSINE KINASES; PYRIDONES; PYRIMIDINES; QUINAZOLINES;

EID: 84896961990     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci4007326     Document Type: Article

References (34)

1. Rapp, C.; Kalyanaraman, C.; Schiffmiller, A.; Schoenbrun, E. L.; Jacobson, M. P. A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions: Relative Binding Affinities in Congeneric Series J. Chem. Inf. Model. 2011, 51, 2082-2089
2. Lindstrom, A.; Edvinsson, L.; Johansson, A.; Andersson, C. D.; Andersson, I. E.; Raubacher, F.; Linusson, A. Postprocessing of Docked Protein-Ligand Complexes Using Implicit Solvation Models J. Chem. Inf. Model. 2011, 51, 267-282
3. Wichapong, K.; Lindner, M.; Pianwanit, S.; Kokpol, S.; Sippl, W. Receptor-based 3D-QSAR studies of checkpoint Wee1 kinase inhibitors Eur. J. Med. Chem. 2009, 44, 1383-1395
4. Wichapong, K.; Lawson, M.; Pianwanit, S.; Kokpol, S.; Sippl, W. Postprocessing of Protein-Ligand Docking Poses Using Linear Response MM-PB/SA: Application to Wee1 Kinase Inhibitors J. Chem. Inf. Model. 2010, 50, 1574-1588
5. Mueller, P. R.; Coleman, T. R.; Kumagai, A.; Dunphy, W. G. Myt1-a Membrane-Associated Inhibitory Kinase That Phosphorylates Cdc2 on Both Threonine-14 and Tyrosine-15 Science 1995, 270, 86-90
6. Suganuma, M.; Kawabe, T.; Hori, H.; Funabiki, T.; Okamoto, T. Sensitization of cancer cells to DNA damage-induced cell death by specific cell cycle G2 checkpoint abrogation Cancer Res. 1999, 59, 5887-91
7. Levine, A. J. p53, the cellular gatekeeper for growth and division Cell 1997, 88, 323-331
8. Rohe, A.; Gollner, C.; Wichapong, K.; Erdmann, F.; Al-Mazaideh, G. M.; Sippl, W.; Schmidt, M. Evaluation of potential Myt1 kinase inhibitors by TR-FRET based binding assay Eur. J. Med. Chem. 2013, 61, 41-48
9. Davis, M. I.; Hunt, J. P.; Herrgard, S.; Ciceri, P.; Wodicka, L. M.; Pallares, G.; Hocker, M.; Treiber, D. K.; Zarrinkar, P. P. Comprehensive analysis of kinase inhibitor selectivity Nat. Biotechnol. 2011, 29, 1046-1051
10. Rastelli, G.; Del Rio, A.; Degliesposti, G.; Sgobba, M. Fast and Accurate Predictions of Binding Free Energies Using MM-PBSA and MM-GBSA J. Comput. Chem. 2010, 31, 797-810
11. Hou, T.; Wang, J.; Li, Y.; Wang, W. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations J. Chem. Inf. Model. 2011, 51, 69-82
12. Kuhn, B.; Gerber, P.; Schulz-Gasch, T.; Stahl, M. Validation and use of the MM-PBSA approach for drug discovery J. Med. Chem. 2005, 48, 4040-4048
13. Hou, T.; Wang, J.; Li, Y.; Wang, W. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking J. Comput. Chem. 2011, 32, 866-877
14. Weis, A.; Katebzadeh, K.; Soderhjelm, P.; Nilsson, I.; Ryde, U. Ligand affinities predicted with the MM/PBSA method: Dependence on the simulation method and the force field J. Med. Chem. 2006, 49, 6596-6606
15. Molecular Operating Environment (MOE); 2011.10, Chemical Computing Group, Inc.: Montreal, Canada. 2011.
16. Jones, G.; Willett, P.; Glen, R. C. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation J. Mol. Biol. 1995, 245, 43-53
17. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking J. Mol. Biol. 1997, 267, 727-748
18. Kolb, P.; Huang, D.; Dey, F.; Caflisch, A. Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model J. Med. Chem. 2008, 51, 1179-1188
19. Lyne, P. D.; Lamb, M. L.; Saeh, J. C. Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring J. Med. Chem. 2006, 49, 4805-4808
20. Case, D. A.; Darden, T. A.; Cheatham, I. T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; KolossvaÌry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. AMBER 11; University of California, San Francisco, 2010.
21. Wang, J. M.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field J. Comput. Chem. 2004, 25, 1157-1174
22. Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation J. Comput. Chem. 2002, 23, 1623-1641
23. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics J. Am. Chem. Soc. 1990, 112, 6127-6129
24. Srinivasan, J.; Trevathan, M. W.; Beroza, P.; Case, D. A. Application of a pairwise generalized Born model to proteins and nucleic acids: inclusion of salt effects Theor. Chem. Acc. 1999, 101, 426-434
25. Luo, R.; David, L.; Gilson, M. K. Accelerated Poisson-Boltzmann calculations for static and dynamic systems J. Comput. Chem. 2002, 23, 1244-1253
26. Hayik, S. A.; Dunbrack, R., Jr.; Merz, K. M., Jr. A Mixed QM/MM Scoring Function to Predict Protein-Ligand Binding Affinity J. Chem. Theory Comput. 2010, 6, 3079-3091
27. Raha, K.; Merz, K. M., Jr. A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding J. Am. Chem. Soc. 2004, 126, 1020-1021
28. Thompson, D. C.; Humblet, C.; Joseph-McCarthy, D. Investigation of MM-PBSA rescoring of docking poses J. Chem. Inf. Model. 2008, 48, 1081-1091
29. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926-935
30. Pastor, R. W.; Brooks, B. R.; Szabo, A. An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms Mol. Phys. 1988, 65, 1409-1419
31. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 1977, 23, 327-341
32. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
33. Rohe, A.; Erdmann, F.; Bassler, C.; Wichapong, K.; Sippl, W.; Schmidt, M. In vitro and in silico studies on substrate recognition and acceptance of human PKMYT1, a Cdk1 inhibitory kinase Bioorg. Med. Chem. Lett. 2012, 22, 1219-1223
34. Rohe, A.; Henze, C.; Erdmann, F.; Sippl, W.; Schmidt, M. A Fluorescence Anisotropy-Based Myt1 Kinase Binding Assay Assay Drug Dev. Technol. 2013, 10.1089/adt.2013.534