Characterization of the ligand receptor encounter complex and its potential for in silico kinetics-based drug development

Journal of Chemical Theory and Computation

Volumn 8, Issue 1, 2012, Pages 314-321

  Elsawy, Karim M ^a   Twarock, Reidun ^a   Lane, David P ^b   Verma, Chandra S ^c   Caves, Leo S D ^a  

^a UNIVERSITY OF YORK   (United Kingdom)

^b AGENCY FOR SCIENCE   (Singapore)

^c BIOINFORMATICS INSTITUTE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84855680584     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct200560w     Document Type: Article

References (56)

1. Copeland, R. A.; Pompliano, D. L.; Meek, T. D. Drug-target residence time and its implications for lead optimization Nat. Rev. Drug Discovery 2006, 5 (9) 730-739 (Pubitemid 44323700)
2. Kenakin, T. Quantifying Biological Activity in Chemical Terms: A Pharmacology Primer to Describe Drug Effect ACS Chem. Biol. 2009, 4 (4) 249-260
3. Tummino, P. J.; Copeland, R. A. Residence time of receptor-ligand complexes and its effect on biological function Biochemistry 2008, 47 (20) 5481-92 (Pubitemid 351711169)
4. Copeland, R. A. The dynamics of drug-target interactions: drug-target residence time and its impact on efficacy and safety Expert Opin. Drug Discovery 2010, 5 (4) 305-310
5. Andersson, K.; Hämäläinen, M. D. Replacing affinity with binding kinetics in QSAR studies resolves otherwise confounded effects J. Chemom. 2006, 20 (8-10) 370-375
6. Maschera, B.; Darby, G.; Palå, G.; Wright, L. L.; Tisdale, M.; Myers, R.; Blair, E. D.; Furfine, E. S. Human Immunodeficiency Virus. Mutations in the viral protease that confer resistance to saquinavir increase the dissociation rate constant of the protease-saquinavir complex J. Biol. Chem. 1996, 271 (52) 33231-33235 (Pubitemid 27010130)
7. Shuman, C. F.; Markgren, P. O.; Hamalainen, M.; Danielson, U. H. Elucidation of HIV-1 protease resistance by characterization of interaction kinetics between inhibitors and enzyme variants Antiviral Res. 2003, 58 (3) 235-42 (Pubitemid 36589014)
8. Yun, C.-H.; Mengwasser, K. E.; Toms, A. V.; Woo, M. S.; Greulich, H.; Wong, K.-K.; Meyerson, M.; Eck, M. J. The T790M mutation in EGFR kinase causes drug resistance by increasing the affinity for ATP Proc. Natl. Acad. Sci. U.S.A. 2008, 105 (6) 2070-2075 (Pubitemid 351439466)
9. Petty, T. J.; Emamzadah, S.; Costantino, L.; Petkova, I.; Stavridi, E. S.; Saven, J. G.; Vauthey, E.; Halazonetis, T. D. An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity EMBO J. 2011, 30 (11) 2167-2176
10. Swinney, D. C. Applications of Binding Kinetics to Drug Discovery: Translation of Binding Mechanisms to Clinically Differentiated Therapeutic Responses Pharm. Med. 2008, 22 (1) 23-34
11. Swinney, D. C. The role of binding kinetics in therapeutically useful drug action Curr. Opin. Drug Discovery Dev. 2009, 12 (1) 31-9
12. Zhang, R.; Monsma, F. The importance of drug-target residence time Curr. Opin. Drug Discovery Dev. 2009, 12 (4) 488-96
13. Lu, H.; Tonge, P. J. Drug-target residence time: critical information for lead optimization Curr. Opin. Chem. Biol. 2010, 14 (4) 467-74
14. Gabdoulline, R. R.; Wade, R. C. On the protein-protein diffusional encounter complex J. Mol. Recognit. 1999, 12 (4) 226-34 (Pubitemid 29375354)
15. Tzafriri, A. R.; Levin, A. D.; Edelman, E. R. Diffusion-limited binding explains binary dose response for local arterial and tumour drug delivery Cell Proliferation 2009, 42 (3) 348-363
16. Raman, C. S.; Jemmerson, R.; Nall, B. T.; Allen, M. J. Diffusion-limited rates for monoclonal antibody binding to cytochrome c Biochemistry 1992, 31 (42) 10370-10379
17. McGahay, V. Inertial effects and diffusion J. Non-Cryst. Solids 2004, 349, 234-241
18. Zoete, V.; Grosdidier, A.; Michielin, O. Docking, virtual high throughput screening and in silico fragment-based drug design J. Cell. Mol. Med. 2009, 13 (2) 238-248
19. Gilson, M. K.; Zhou, H. X. Calculation of protein-ligand binding affinities Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 21-42 (Pubitemid 46998108)
20. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. The statistical-thermodynamic basis for computation of binding affinities: a critical review Biophys. J. 1997, 72 (3) 1047-1069 (Pubitemid 27113632)
21. Durrant, J. D.; McCammon, J. A., Computer-aided drug-discovery techniques that account for receptor flexibility. Curr. Opin. Pharmacol. 10, (6), 770-774.
22. Colizzi, F.; Perozzo, R.; Scapozza, L.; Recanatini, M.; Cavalli, A. Single-Molecule Pulling Simulations Can Discern Active from Inactive Enzyme Inhibitors J. Am. Chem. Soc. 2010, 132 (21) 7361-7371
23. Shan, Y.; Kim, E. T.; Eastwood, M. P.; Dror, R. O.; Seeliger, M. A.; Shaw, D. E. How Does a Drug Molecule Find Its Target Binding Site? J. Am. Chem. Soc. 2011, 133 (24) 9181-9183
24. Buch, I.; Giorgino, T.; De Fabritiis, G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations Proc. Natl. Acad. Sci. U.S.A. 2011, 10.1073/pnas.1103547108
25. Jorgensen, W. L. Efficient Drug Lead Discovery and Optimization Acc. Chem. Res. 2009, 42 (6) 724-733
26. Gabdoulline, R. R.; Wade, R. C. Simulation of the diffusional association of barnase and barstar Biophys. J. 1997, 72 (5) 1917-1929 (Pubitemid 27184422)
27. Gabdoulline, R. R.; Wade, R. C. Brownian dynamics simulation of protein-protein diffusional encounter Methods 1998, 14 (3) 329-41
28. Donald, L. E.; McCammon, J. A. Brownian dynamics with hydrodynamic interactions J. Chem. Phys. 1978, 69 (4) 1352-1360
29. García de la Torre, J.; Huertas, M. L.; Carrasco, B. Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure Biophys. J. 2000, 78 (2) 719-730 (Pubitemid 30211830)
30. Dastidar, S. G.; Lane, D. P.; Verma, C. S. Modulation of p53 binding to MDM2: computational studies reveal important roles of Tyr100 BMC Bioinf. 2009, 10 (Suppl 15) S6
31. Im, W.; Beglov, D.; Roux, B. Continuum Solvation Model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation Comput. Phys. Commun. 1998, 111 (1-3) 59-75 (Pubitemid 128400465)
32. Coalson, R.; Beck, T. L. Numerical Methods for Solving Poisson and Poisson-Boltzmann Type Equations. In Encyclopedia of Computational Chemistry; von Rague Schleyer, P., Ed.; John-Wiley: New York, 1998; Vol. 3, pp 2086-2100.
33. Baker, N. A.; Sept, D.; Joseph, S.; Holst, M. J.; McCammon, J. A. Electrostatics of nanosystems: Application to microtubules and the ribosome Proc. Natl. Acad. Sci. U.S.A. 2001, 98 (18) 10037-10041 (Pubitemid 32802969)
34. Dolinsky, T. J.; Czodrowski, P.; Li, H.; Nielsen, J. E.; Jensen, J. H.; Klebe, G.; Baker, N. A. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations Nucleic Acids Res. 2007, 35 (suppl 2) W522-W525
35. Czodrowski, P.; Dramburg, I.; Sotriffer, C. A.; Klebe, G. Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes Proteins: Struct., Funct., Bioinf. 2006, 65 (2) 424-437 (Pubitemid 44454114)
36. Gabdoulline, R. R.; Wade, R. C. Protein-protein association: investigation of factors influencing association rates by Brownian dynamics simulations J. Mol. Biol. 2001, 306 (5) 1139-1155 (Pubitemid 33030010)
37. Gabdoulline, R. R.; Wade, R. C. Effective Charges for Macromolecules in Solvent J. Phys. Chem. 1996, 100 (9) 3868-3878 (Pubitemid 126788408)
38. Elcock, A. H.; Gabdoulline, R. R.; Wade, R. C.; McCammon, J. A. Computer simulation of protein-protein association kinetics: acetylcholinesterase- fasciculin J. Mol. Biol. 1999, 291 (1) 149-162 (Pubitemid 29391411)
39. Hummer, G. Molecular binding: Under water's influence Nat. Chem. 2010, 2 (11) 906-7
40. Setny, P.; Baron, R.; McCammon, J. A. How Can Hydrophobic Association Be Enthalpy Driven? J. Chem. Theory Comput. 2010, 6 (9) 2866-2871
41. Seco, J.; Luque, F. J.; Barril, X. Binding site detection and druggability index from first principles J. Med. Chem. 2009, 52 (8) 2363-71
42. Brooks, C. L.; Onuchic, J. N.; Wales, D. J. Taking a Walk on a Landscape Science 2001, 293 (5530) 612-613
43. Huang, D.; Caflisch, A., The free energy landscape of small molecule unbinding. PLoS Comput. Biol. 2011, 7 (2), e1002002.
44. Conn, P. J.; Christopoulos, A.; Lindsley, C. W. Allosteric modulators of GPCRs: a novel approach for the treatment of CNS disorders Nat. Rev. Drug Discovery 2009, 8 (1) 41-54
45. Neckers, L.; Ivy, S. P. Heat shock protein 90 Curr. Opin. Oncol. 2003, 15 (6) 419-24 (Pubitemid 38147036)
46. Sharp, S. Y.; Prodromou, C.; Boxall, K.; Powers, M. V.; Holmes, J. L.; Box, G.; Matthews, T. P.; Cheung, K.-M. J.; Kalusa, A.; James, K.; Hayes, A.; Hardcastle, A.; Dymock, B.; Brough, P. A.; Barril, X.; Cansfield, J. E.; Wright, L.; Surgenor, A.; Foloppe, N.; Hubbard, R. E.; Aherne, W.; Pearl, L.; Jones, K.; McDonald, E.; Raynaud, F.; Eccles, S.; Drysdale, M.; Workman, P. Inhibition of the heat shock protein 90 molecular chaperone in vitro and in vivo by novel, synthetic, potent resorcinylic pyrazole/isoxazole amide analogues. Mol. Cancer Ther. 2007, 6 (4), 1198-1211. (Pubitemid 46711983)
47. Coe, D.; Armer, R.; Ratcliffe, A. Medicines research: current trends and case histories. Highlights of the Society for Medicines Research Symposium Drugs Future 2009, 34 (3) 247-254
48. Moll, U. M.; Petrenko, O. The MDM2-p53 Interaction Mol. Cancer Res. 2003, 1 (14) 1001-1008 (Pubitemid 38044975)
49. Brown, C. J.; Cheok, C. F.; Verma, C. S.; Lane, D. P. Reactivation of p53: from peptides to small molecules Trends Pharmacol. Sci. 2010, 32 (1) 53-62
50. Lane, D. P.; Hupp, T. R. Drug discovery and p53 Drug Discovery Today 2003, 8 (8) 347-355 (Pubitemid 36398162)
51. Murray, J. K.; Gellman, S. H. Targeting protein-protein interactions: lessons from p53/MDM2 Biopolymers 2007, 88 (5) 657-86 (Pubitemid 47556148)
52. Joseph, T. L.; Madhumalar, A.; Brown, C. J.; Lane, D. P.; Verma, C. Differential binding of p53 and nutlin to MDM2 and MDMX: Computational studies Cell Cycle 2010, 9 (6) 1167-81
53. Walensky, L. D.; Kung, A. L.; Escher, I.; Malia, T. J.; Barbuto, S.; Wright, R. D.; Wagner, G.; Verdine, G. L.; Korsmeyer, S. J. Activation of Apoptosis in Vivo by a Hydrocarbon-Stapled BH3 Helix Science 2004, 305, 1466-1470 (Pubitemid 39167667)
54. Guo, Z.; Mohanty, U.; Noehre, J.; Sawyer, T. K.; Sherman, W.; Krilov, G. Probing the α-Helical Structural Stability of Stapled p53 Peptides: Molecular Dynamics Simulations and Analysis Chem. Biol. Drug Des. 2010, 75 (4) 348-359
55. Joseph, T. L.; Lane, D.; Verma, C. S. Stapled peptides in the p53 pathway: Computer simulations reveal novel interactions of the staples with the target protein Cell Cycle 2010, 9 (22) 4560-4568
56. Okazaki, K.-i.; Takada, S. Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms Proc. Natl. Acad. Sci. U.S.A. 2008, 105 (32) 11182-11187