Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI)

Journal of Computational Chemistry

Volumn 36, Issue 25, 2015, Pages 1859-1873

  Su, Pin Chih ^a   Tsai, Cheng Chieh ^a   Mehboob, Shahila ^a   Hevener, Kirk E ^a,b   Johnson, Michael E ^a  

^a Chicago College of Pharmacy   (United States)

^b UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

Author keywords

enoyl acyl reductase (FabI) implicit solvent models; molecular dynamics; quantum mechanics molecular mechanics; radii sets

Indexed keywords

ENTROPY; FORECASTING; LIGANDS; MOLECULAR DYNAMICS; MOLECULAR MODELING; QUANTUM THEORY; SCAFFOLDS; SOLVENTS;

ACCURATE PREDICTION; BINDING AFFINITIES; EXPERIMENTAL VALUES; FRANCISELLA TULARENSIS; IMPLICIT SOLVENT MODEL; PHYSIO-CHEMICAL PROPERTIES; QUANTUM MECHANICS/MOLECULAR MECHANICS; RADII SETS;

BINDING ENERGY;

BENZIMIDAZOLE; BENZIMIDAZOLE DERIVATIVE; ENOYL ACYL CARRIER PROTEIN REDUCTASE (NADH); ENZYME INHIBITOR; LIGAND; PROTEIN BINDING;

ANTAGONISTS AND INHIBITORS; CHEMISTRY; COMPARATIVE STUDY; DRUG DESIGN; ENTROPY; ENZYMOLOGY; FRANCISELLA TULARENSIS; HUMAN; METABOLISM; MICROBIOLOGY; MOLECULAR DYNAMICS; TULAREMIA;

BENZIMIDAZOLES; DRUG DESIGN; ENOYL-(ACYL-CARRIER-PROTEIN) REDUCTASE (NADH); ENTROPY; ENZYME INHIBITORS; FRANCISELLA TULARENSIS; HUMANS; LIGANDS; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; TULAREMIA;

EID: 84940447634     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.24011     Document Type: Article

References (52)

1. M. D. Christian, Crit. Care Clin. 2013, 29, 717.
2. World Health Organization, Geneva, Switzerland, 2007.
3. K. E. Hevener, S. Mehboob, P. C. Su, K. Truong, T. Boci, J. Deng, M. Ghassemi, J. L. Cook, M. E. Johnson, J. Med. Chem. 2012, 55, 268.
4. S. Mehboob, K. E. Hevener, K. Truong, T. Boci, B. D. Santarsiero, M. E. Johnson, J. Med. Chem. 2012, 55, 5933.
5. H. Lu, K. England, C. am Ende, J. J. Truglio, S. Luckner, B. G. Reddy, N. L. Marlenee, S. E. Knudson, D. L. Knudson, R. A. Bowen, C. Kisker, R. A. Slayden, P. J. Tonge, ACS Chem. Biol. 2009, 4, 221.
6. S. Mehboob, J. Song, K. E. Hevener, P.-C. Su, T. Boci, L. Brubaker, L. Truong, T. Mistry, J. Deng, J. L. Cook, B. D. Santarsiero, A. K. Ghosh, M. E. Johnson, Bioorg. Med. Chem. Lett. 2015, 25, 1292.
7. Y. Y. Zhang, Y. Liu, S. Mehboob, J. H. Song, T. Boci, M. E. Johnson, A. K. Ghosh, H. Jeong, Xenobiotica 2013, 44, 404.
8. C. R. Guimaraes, M. Cardozo, J. Chem. Inf. Model 2008, 48, 958.
9. N. Homeyer, H. Gohlke, J. Comput. Chem. 2013, 34, 965.
10. T. Zhu, H. Lee, H. Lei, C. Jones, K. Patel, M. E. Johnson, K. E. Hevener, J. Chem. Inf. Model 2013, 53, 560.
11. G. Rastelli, A. Del Rio, G. Degliesposti, M. Sgobba, J. Comput. Chem. 2010, 31, 797.
12. D. A. Pearlman, J. Med. Chem. 2005, 48, 7796.
13. T. Steinbrecher, D. A. Case, A. Labahn, J. Med. Chem. 2006, 49, 1837.
14. J. Wang, P. Morin, W. Wang, P. A. Kollman, J. Am. Chem. Soc. 2001, 123, 5221.
15. S. Genheden, I. Nilsson, U. Ryde, J. Chem. Inf. Model. 2011, 51, 947.
16. S. Genheden, U. Ryde, J. Chem. Theory Comput. 2011, 7, 3768.
17. R. E. Amaro, X. Cheng, I. Ivanov, D. Xu, J. A. McCammon, J. Am. Chem. Soc. 2009, 131, 4702.
18. D. P. Oehme, R. T. Brownlee, D. J. Wilson, J. Comput. Chem. 2012, 33, 2566.
19. T. Hou, J. Wang, Y. Li, W. Wang, J. Chem. Inf. Model. 2011, 51, 69.
20. S. Genheden, J. Comput. Aided Mol. Des. 2011, 25, 1085.
21. T. Hou, J. Wang, Y. Li, W. Wang, J. Chem. Inf. Model. 2011, 51, 69.
22. M. Nina, D. Beglov, B. Roux, J. Phys. Chem. B 1997, 101, 5239.
23. G. D. Hawkins, C. J. Cramer, D. G. Truhlar, J. Phys. Chem. 1996, 100, 19824.
24. A. Onufriev, D. Bashford, D. A. Case, J. Phys. Chem. B 2000, 104, 3712.
25. A. Onufriev, D. Bashford, D. A. Case, Proteins 2004, 55, 383.
26. J. Mongan, C. Simmerling, J. A. McCammon, D. A. Case, A. Onufriev, J. Chem. Theory Comput. 2006, 3, 156.
27. H. Nguyen, D. R. Roe, C. Simmerling, J. Chem. Theory Comput. 2013, 9, 2020.
28. D. R. Roe, A. Okur, L. Wickstrom, V. Hornak, C. Simmerling, J. Phys. Chem. B 2007, 111, 1846.
29. C. Tan, Y.-H. Tan, R. Luo, J. Phys. Chem. B 2007, 111, 12263.
30. S. Genheden, U. Ryde, J. Comput. Chem. 2010, 31, 837.
31. G. D. M. Seabra, R. C. Walker, M. Elstner, D. A. Case, A. E. Roitberg, J. Phys. Chem. A 2007, 111, 5655.
32. K. Park, A. W. Götz, R. C. Walker, F. Paesani, J. Chem. Theory Comput. 2012, 8, 2868.
33. A. E. Cho, V. Guallar, B. J. Berne, R. Friesner, J. Comput. Chem. 2005, 26, 915.
34. A. W. Götz, M. A. Clark, R. C. Walker, J. Comput. Chem. 2014, 35, 95.
35. R. C. Walker, M. F. Crowley, D. A. Case, J. Comput. Chem. 2008, 29, 1019.
36. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr,., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, N. J. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, Ö. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian, Inc., Wallingford CT, 2009.
37. C. I. Bayly, P. Cieplak, W. Cornell, P. A. Kollman, J. Phys. Chem. 1993, 97, 10269.
38. F. Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, N. Grivel, D. Lelong, W. Rosanski, P. Cieplak, Phys. Chem. Chem. Phys. 2010, 12, 7821.
39. E. Vanquelef, S. Simon, G. Marquant, E. Garcia, G. Klimerak, J. C. Delepine, P. Cieplak, F. Y. Dupradeau, Nucleic Acids Res. 2011, 39, W511.
40. J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, D. A. Case, J. Comput. Chem. 2004, 25, 1157.
41. D. A. Case, T. A. Darden, T. E. Cheatham, III, C. L. Simmerling, J. Wang, R. E. Duke, R. Luo, R. C. Walker, W. Zhang, K. M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A. W. Goetz, I. Kolossváry, K. F. Wong, F. Paesani, J. Vanicek, R. M. Wolf, J. Liu, X. Wu, S. R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D. R. Roe, D. H. Mathews, M. G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, P.A. Kollman, University of California, San Francisco, 2012.
42. B. R. Miller, T. D. McGee, J. M. Swails, N. Homeyer, H. Gohlke, A. E. Roitberg, J. Chem. Theory Comput. 2012, 8, 3314.
43. D. Sitkoff, K. A. Sharp, B. Honig, J. Phys. Chem. 1994, 98, 1978.
44. D. A. Pearlman, D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham Iii, S. DeBolt, D. Ferguson, G. Seibel, P. Kollman, Comput. Phys. Commun. 1995, 91, 1.
45. H. Nguyen, D. R. Roe, C. Simmerling, J. Chem. Theory Comput. 2013, 9, 2020.
46. J. J. P. Stewart, J. Comput. Chem. 1989, 10, 209.
47. J. J. P. Stewart, J. Comput. Chem. 1989, 10, 221.
48. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, J. J. P. Stewart, J. Am. Chem. Soc. 1985, 107, 3902.
49. J. P. Stewart, J. Mol. Model. 2007, 13, 1173.
50. M. W. Jurema, G. C. Shields, J. Comput. Chem. 1993, 14, 89.
51. J. P. Stewart, J. Mol. Model 2009, 15, 765.
52. E. Pellegrini, M. J. Field, J. Phys. Chem. A 2002, 106, 1316.