Multiple Ligand Simultaneous Docking: Orchestrated Dancing of Ligands in Binding Sites of Protein

Journal of Computational Chemistry

Volumn 31, Issue 10, 2010, Pages 2014-2022

  Li, Huameng ^a   Li, Chenglong ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

Fragment based drug design; Multiple ligand simultaneous docking; Optimization; Particle swarm; X ray crystallography

Indexed keywords

BINDING DYNAMICS; BINDING FREE ENERGY; BINDING MODES; CATALYTIC CYCLES; COFACTORS; DOCKING PROCESS; DRUG DESIGN; DYNAMIC COUPLINGS; E. COLI; ENZYMATIC MECHANISMS; LIGAND BINDING; LIGAND DOCKING; METAL-ION COORDINATION; MODEL SYSTEM; MOLECULAR BINDING; MOLECULAR SPECIES; MULTIPLE LIGAND SIMULTANEOUS DOCKING; MULTIPLE LIGANDS; NOISY X-RAYS; PARTICLE SWARM; POTENTIAL APPLICATIONS; PROTEIN-LIGAND INTERACTIONS; PURINE NUCLEOSIDE PHOSPHORYLASE; RECOGNITION PROCESS; RELATIVE BINDING; SYSTEMATIC TESTING; WATER MOLECULE;

BINDING SITES; BIOCHEMISTRY; DOCKING; DYNAMICS; ESCHERICHIA COLI; FREE ENERGY; LIGANDS; MACHINE DESIGN; METAL IONS; MINERALOGY; MOLECULAR BIOLOGY; MOLECULAR RECOGNITION; PARTICLE SWARM OPTIMIZATION (PSO); PHOSPHORYLATION; PROTEINS; SELF ASSEMBLY; SUBSTRATES; X RAY CRYSTALLOGRAPHY; X RAYS;

BINDING ENERGY;

4 [4 (4' CHLORO 2 BIPHENYLYLMETHYL) 1 PIPERAZINYL] N [4 [3 DIMETHYLAMINO 1 (PHENYLTHIOMETHYL)PROPYLAMINO] 3 NITROBENZENESULFONYL]BENZAMIDE; ABT-737; BIPHENYL DERIVATIVE; LIGAND; NITROPHENOL; PEPTIDE; PIPERAZINE DERIVATIVE; PROTEIN BCL X; PROTEIN TYROSINE PHOSPHATASE SHP 2; PURINE NUCLEOSIDE PHOSPHORYLASE; SULFONAMIDE;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENZYMOLOGY; ESCHERICHIA COLI; HUMAN; METABOLISM; PROTEIN BINDING; X RAY CRYSTALLOGRAPHY;

BCL-X PROTEIN; BINDING SITES; BIPHENYL COMPOUNDS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; HUMANS; LIGANDS; MODELS, MOLECULAR; NITROPHENOLS; PEPTIDES; PIPERAZINES; PROTEIN BINDING; PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 11; PURINE-NUCLEOSIDE PHOSPHORYLASE; SULFONAMIDES;

EID: 77953467124     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.10021/jcc.21486     Document Type: Article

References (21)

1. Everts, S. Chem Eng News 2008, 86, 15.
2. Hajduk, P.; Greer, J. Nat. Rev Drug Discov 2007, 6, 211.
3. Congreve, M.; Chessari, G.; Tisi, D.; Woodhead, A. J. J Med Chem 2008, 51, 3661.
4. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. J Comput Chem 1998, 19, 1639.
5. Huey, R.; Morris, G. M.; Olson, A. J.; Goodsell, D. S. J Comput Chem 2007, 28, 1145.
6. Kennedy, J.; Eberhart, R. In Proceedings of the IEEE International Conference on Neural Networks, Piscataway, NJ, 1995; pp. 1942-1948.
7. Shi, Y.; Eberhart, R. C. In Proceedings of the IEEE International Conference on Evolutionary Computation, Anchorage, AK, 1998; pp. 69-73.
8. Hart, W. E.; Kammeyer, T. E.; Belew, R. K. In Foundations of Genetic Algorithms III; Whitley, D.; Vose, M., Eds.; Morgan Kauffman: San Francisco, CA, 1994; pp. 299-313.
9. Solis, F J.; Wets, R. J.-B. Math Oper Res 1981, 6, 1.9.
10. Holland, J. H. Adaptation in Natural and Artificial Systems; University of Michigan Press: Ann Arbor, MI, 1975.
11. Kirkpatrick, S.; Gelatt. C. D., Jr.; Vecchi, M. P. Science 1983, 220, 671.
12. Korb, O.; Stiitzle, T.; Exner, T. E. In Ant Colony Optimization and Swarm Intelligence, 5th International Workshop, ANTS 2006, LNCS 4150, Brussels, Belgium, 2006.
13. Chen, H.-M.; Liu, B.-F.; Huang, H.-L.; Hwang, S.-F.; Ho, S.-Y. J Comput. Chem 2007, 28, 612.
14. Namasivayam, V.; Gunther, R. Chem Biol Drug Des 2007, 70, 475.
15. Janson, S.; Merkle, D.; Middendorf, M. Appl Soft Comput 2008, 8, 666.
16. Eberhart, R. C.; Shi, Y. In Proceedings of the 2000 IEEE Congress on Evolutionary Computation, San Diego, CA, 2000; pp. 84-88.
17. Clerc, M.; Kennedy, J. IEEE Trans Evol Comput 2002, 6, 58.
18. Kennedy, J. In Proceedings of the IEEE Swarm Intelligence Symposium (SIS2007), Honolulu, HI, 2007; pp. 162-169.
19. Sanner, M. F. J Mol Graphics Mod 1999, 17, 57.
20. Oltersdorf, T.; Elmore, S. W.; Shoemaker, A. R.; Armstrong, R. C.; Augeri, D. J.; Belli, B. A.; Bruncko, M.; Deckwerth, T. L.; Dinges, J.; Hajduk, P. J.; Joseph, M. K.; Kitada, S.; Korsmeyer, S. J.; Kunzer, A. R.; Letai, A.; Li, C.; Mitten, M. J.; Nettesheim, D. G.; Ng, S.; Nimmer, P. M.; O'Connor, J. M.; Oleksijew, A.; Petros, A. M.; Reed, J. C.; Shen, W.; Tahir, S. K.; Thompson, C. B.; Tomaselii, K. J.; Wang, B.; Wendt, M. D.; Zhang, H.; Fesik, S. W.; Rosenberg, S. H. Nature, 2005, 435, 7042.
21. Lee, E. F.; Czabotar, P. E.; Smith, B. J.; Deshayes, K.; Zobel, K.; Colman, P. M.; Fairlie, W. D. Cell Death Differ 2007, 14, 1711.