Selection of in silico drug screening results for G-protein-coupled receptors by using universal active probes

Journal of Chemical Information and Modeling

Volumn 51, Issue 9, 2011, Pages 2398-2407

  Wada, Mitsuhito ^a,b   Kanamori, Eiji ^a,c   Nakamura, Haruki ^d   Fukunishi, Yoshifumi ^e  

^a Japan Biological Informatics Consortium   (Japan)

^b FUJITSU LABORATORIES LTD   (Japan)

^c Hitachi Solutions   (Japan)

^d OSAKA UNIVERSITY   (Japan)

^e NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; MODEL STRUCTURES; MOLECULAR DYNAMICS; PROBES;

ADENOSINE RECEPTOR; ADRENERGIC RECEPTORS; G PROTEIN COUPLED RECEPTORS; IN-SILICO SCREENING; MOLECULAR DYNAMICS SIMULATIONS; PERIODIC BOUNDARY CONDITIONS; POSITIVE CORRELATIONS; THREE DIMENSIONAL (3D) STRUCTURES;

PROTEINS;

G PROTEIN COUPLED RECEPTOR;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG EFFECT; DRUG SCREENING; HUMAN; MOLECULAR PROBE;

DRUG EVALUATION, PRECLINICAL; HUMANS; MODELS, MOLECULAR; MOLECULAR PROBES; RECEPTORS, G-PROTEIN-COUPLED;

EID: 80053300057     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200236x     Document Type: Article

References (35)

1. McGovern, S. L.; Shoichet, B. K. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes J. Med. Chem. 2003, 46, 2895-2907 (Pubitemid 36775915)
2. Oshiro, C.; Bradley, E. K.; Eksterowicz, J.; Evensen, E.; Lamb, M. L.; Lanctot, K.; Putta, S.; Stanton, R.; Grootenhuis, D. J. Performance of 3D-database molecular docking studies into homology models J. Med. Chem. 2004, 47, 764-767 (Pubitemid 38129734)
3. DeWesse-Scott, C.; Moult, J. Molecular modeling of protein function regions Proteins 2004, 55, 942-961 (Pubitemid 38702952)
4. Diller, D. J.; Li, R. Kinases, homology models, and high throughput docking J. Med. Chem. 2003, 46, 4638-4647 (Pubitemid 37271613)
5. Bissantz, C.; Bernard, P.; Hibert, M.; Rognan, D. Protein-based virtual screening of chemical databases. II. Are homology models of G-Protein Coupled Receptors suitable targets? Proteins 2003, 50, 5-25 (Pubitemid 36090604)
6. Omagari, K.; Mitomo, D.; Kubota, S.; Nakamura, H.; Fukunishi, Y. A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening Adv. Appl. Bioinf. Chem. 2008, 1, 19-28
7. Lerner, M. G.; Bowman, A. L.; Carlson, H. A. Incorporating dynamics in E. coli dihydrofolate reductase enhances structure-based drug discovery J. Chem. Inf. Model. 2007, 47, 2358-2365 (Pubitemid 350275100)
8. Warren, G. L.; Webster Andrews, C.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A Critical Assessment of Docking Programs and Scoring Functions J. Med. Chem. 2006, 49, 5912-5931 (Pubitemid 44484938)
9. Rueda, M.; Bottegoni, G.; Abagyan, R. Recipes for the selection of experimental protein conformations for virtual screening J. Chem. Inf. Model. 2010, 50, 186-193
10. Barakat, K.; Mane, J.; Friesen, D.; Tuszynski, J. Ensemble-based virtual screening reveals dual-inhibitors for the p53-MDM2/MDMX interactions J. Mol. Graphics Modell. 2010, 28, 555-568
11. Craig, I. R.; Essex, J.; Spiegel, K. Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichment J. Chem. Inf. Model. 2010, 50, 511-524
12. Fukunishi, Y.; Ono, K.; Orita, M.; Nakamura, H. Selection of in silico drug screening result by using universal active probes (UAPs) J. Chem. Inf. Model. 2010, 50, 1233-1240
13. Standley, D. M.; Toh, H.; Nakamura, H. ASH structure alignment package: sensitivity and selectivity in domain classification BMC Bioinformatics 2007, 8, 116
14. Katoh, K.; Misawa, K.; Kuma, K.; Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Res. 2002, 30, 3059-3066 (Pubitemid 34851225)
15. Sali, A.; Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 1993, 234, 779-815 (Pubitemid 24007801)
16. Marti-Renom, M. A.; Stuart, A.; Fiser, A.; Sánchez, R.; Melo, F.; Sali, A. Comparative protein structure modeling of genes and genomes Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 291-325 (Pubitemid 30599596)
17. Case, D. A.; Darden, T. A.; Cheatham, T. E., III.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Wang, B.; Pearlman, D. A.; Crowley, M.; Brozell, S.; Tsui, V.; Gohlke, H.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Schafmeister, C.; Caldwell, J. W.; Ross, W. S.; Kollman, P. A. AMBER 8; University of California: San Francisco, CA, 2004.
18. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating lipid water J. Chem. Phys. 1983, 79, 926-935
19. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath J. Chem. Phys. 1984, 81, 3684-3690
20. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
21. 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. 1997, 23, 327-341
22. Fukunishi, Y.; Mikami, Y.; Nakamura, H. The filling potential method: A method for estimating the free energy surface for protein-ligand docking J. Phys. Chem. B. 2003, 107, 13201-13210
23. Fukunishi, Y.; Sugihara, Y.; Mikami, Y.; Sakai, K.; Kusudo, H.; Nakamura, H. Advanced in silico drug screeing to achieve high hit ratio-development of 3D-compound database Synthesiology 2009, 2, 60-68
24. Gasteiger, J.; Marsili, M. Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges Tetrahedron 1980, 36, 3219-3228
25. Gasteiger, J.; Marsili, M. A new model for calculating atomic charges in molecules Tetrahedron Lett. 1978, 3181-3184
26. Wang, J.; 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
27. Fukunishi, Y.; Mikami, Y.; Nakamura, H. Similarities among receptor pockets and among compounds: Analysis and application to in silico ligand screening J. Mol. Graphics Modell. 2005, 24, 34-45 (Pubitemid 41318116)
28. Fukunishi, Y.; Mikami, Y.; Kubota, S.; Nakamura, H. Multiple target screening method for robust and accurate in silico ligand screening J. Mol. Graphics Modell. 2005, 25, 61-70 (Pubitemid 44376445)
29. Fukunishi, Y.; Kubota, S.; Nakamura, H. Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening J. Chem. Inf. Model. 2006, 46, 2071-2084 (Pubitemid 44625978)
30. Nissink, J. W. M.; Murray, C.; Hartshorn, M.; Verdonk, M. L.; Cole, J. C.; Taylor, R. A new test set for validating predictions of protein-ligand interaction Proteins 2002, 49, 457-471 (Pubitemid 35388132)
31. Fukunishi, Y.; Mashimo, T.; Orita, M.; Ohno, K.; Nakamura, H. In silico fragment screening by replica generation (FSRG) method for fragment-based drug design J. Chem. Inf. Model. 2009, 49, 925-933
32. Fukunishi, Y.; Nakamura, H. Improvement of protein-compound docking scores by using amino-acid sequence similarities of proteins J. Chem. Inf. Model. 2008, 48, 148-156 (Pubitemid 351271060)
33. Kontoyianni, M.; Sokol, G. S.; McClellan, L. M. Evaluation of library ranking efficacy in virtual screening J. Comput. Chem. 2005, 26, 11-22 (Pubitemid 40021619)
34. Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking sets for molecular docking J. Med. Chem. 2006, 49, 6789-6801 (Pubitemid 44749746)
35. Fukunishi, Y.; Nakamura, H. A new method for in silico drug screening and similarity search using molecular-dynamics maximum-volume overlap (MD-MVO) method J. Mol. Graphics Modell. 2009, 27, 628-636