Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: Participation in the SAMPL4 protein-ligand binding challenge

Journal of Computer-Aided Molecular Design

Volumn 28, Issue 4, 2014, Pages 429-441

  Perryman, Alexander L ^a,c   Santiago, Daniel N ^a   Forli, Stefano ^a   Santos Martins, Diogo ^a,b   Olson, Arthur J ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF PORTO   (Portugal)

^c RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

Author keywords

AutoDock Vina; Computational drug design; Computational pipeline; Docking challenge; HIV integrase; Ligand docking; Virtual screening

Indexed keywords

BINDING SITES; DIGITAL LIBRARIES; ENGINES; FORECASTING; FREE ENERGY; LIBRARIES; LIGANDS; PROTEINS; SEARCH ENGINES;

AUTODOCK VINAS; COMPUTATIONAL DRUG DESIGN; COMPUTATIONAL PIPELINE; DOCKING CHALLENGE; DRUG DESIGN; HIV INTEGRASE; INTEGRASE; LIGAND DOCKING; PHARMACOPHORES; VIRTUAL SCREENING;

BINDING ENERGY;

INTEGRASE; INTEGRASE INHIBITOR; VIRUS ENZYME; LIGAND;

ALLOSTERISM; ARTICLE; BINDING AFFINITY; BINDING SITE; COMPUTER PROGRAM; CONFORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DRUG PROTEIN BINDING; DRUG SCREENING; ENZYME ACTIVE SITE; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR RECOGNITION; NONHUMAN; PHARMACOPHORE; PRIORITY JOURNAL; PROTEIN DATA BANK; CHEMISTRY; COMPUTER AIDED DESIGN; DRUG DESIGN; ENZYMOLOGY; HIV INFECTIONS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; METABOLISM; VIROLOGY;

ALLOSTERIC SITE; BINDING SITES; COMPUTER-AIDED DESIGN; DRUG DESIGN; HIV; HIV INFECTIONS; HIV INTEGRASE; HIV INTEGRASE INHIBITORS; HUMANS; LIGANDS; MOLECULAR DOCKING SIMULATION;

EID: 84902833181     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-014-9709-3     Document Type: Article

References (39)

1. Mobley DL, Liu S, Lim NM, Wymer KL, Perryman AL, Forli S, Deng N, Su J, Branson K, Olson AJ (2014) J Comput Aided Mol Des. doi:10.1007/s10822-014-9723-5
2. Tiefenbrunn T, Forli S, Happer M, Gonzalez A, Tsai Y, Soltis M, Elder JH, Olson AJ, Stout CD (2013) Chem Biol Drug Des 83(2):141
3. Tiefenbrunn T, Forli S, Baksh MM, Chang MW, Happer M, Lin YC, Perryman AL, Rhee JK, Torbett BE, Olson AJ, Elder JH, Finn MG, Stout CD (2013) ACS Chem Biol 8(6):1223
4. Lin YC, Perryman AL, Olson AJ, Torbett BE, Elder JH, Stout CD (2011) Acta Crystallogr D Biol Crystallogr 67(Pt 6):540
5. Perryman AL, Zhang Q, Soutter HH, Rosenfeld R, McRee DE, Olson AJ, Elder JE, Stout CD (2010) Chem Biol Drug Des 75(3):257
6. Vajragupta O, Boonchoong P, Morris GM, Olson AJ (2005) Bioorg Med Chem Lett 15(14):3364
7. Perryman AL, Forli S, Morris GM, Burt C, Cheng Y, Palmer MJ, Whitby K, McCammon JA, Phillips C, Olson AJ (2010) J Mol Biol 397(2):600
8. Gallicchio E, Deng N, He P, Perryman AL, Santiago DN, Forli S, Olson AJ, Levy R (2014) J Comput Aided Mol Des 28(1)
9. Greenwald J, Le V, Butler SL, Bushman FD, Choe S (1999) Biochemistry 38(28):8892
10. Perryman AL, Forli S, Morris GM, Burt C, Cheng Y, Palmer MJ, Whitby K, McCammon JA, Phillips C, Olson AJ (2010) J Mol Biol 397(2):600
11. Dewdney TG, Wang Y, Kovari IA, Reiter SJ, Kovari LC (2013) J Struct Biol 184(2):245
12. Kessl JJ, Jena N, Koh Y, Taskent-Sezgin H, Slaughter A, Feng L, de Silva S, Wu L, Le Grice SFJ, Engelman A, Fuchs JR, Kvaratskhelia M (2012) J Biol Chem 287(20):16801
13. Tsiang M, Jones GS, Niedziela-Majka A, Kan E, Lansdon EB, Huang W, Hung M, Samuel D, Novikov N, Xu Y, Mitchell M, Guo H, Babaoglu K, Liu X, Geleziunas R, Sakowicz R (2012) J Biol Chem 287(25):21189
14. Christ F, Shaw S, Demeulemeester J, Desimmie BA, Marchand A, Butler S, Smets W, Chaltin P, Westby M, Debyser Z, Pickford C (2012) Antimicrob Agents Chemother 56(8):4365
15. Jurado KA, Wang H, Slaughter A, Feng L, Kessl JJ, Koh Y, Wang W, Ballandras-Colas A, Patel PA, Fuchs JR, Kvaratskhelia M, Engelman A (2013) Proc Natl Acad Sci 110(21):8690
16. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28(1):235
17. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C (2002) Acta Crystallogr D 58(6 Part 1):899
18. Chen VB, Arendall WB III, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) Acta Crystallogr D 66(1):12
19. Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, Snoeyink J, Richardson JS, Richardson DC (2007) Nucleic Acids Res 35(suppl 2):W375
20. Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR (2012) J Cheminform 4(1):17
21. Gasteiger J, Marsili M (1980) Tetrahedron 36(22):3219
22. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) J Comput Chem 30(16):2785
23. Forli S. Raccoon (2010) Molecular Graphics Laboratory, The Scripps Research Institute, La Jolla. http://autodock.scripps.edu/resources/raccoon. Accessed 2013
24. Trott O, Olson AJ (2010) J Comput Chem 31(2):455
25. Peat TS, Rhodes DI, Vandegraaff N, Le G, Smith JA, Clark LJ, Jones ED, Coates JAV, Thienthong N, Newman J, Dolezal O, Mulder R, Ryan JH, Savage GP, Francis CL, Deadman JJ (2012) PLoS One 7(7):e40147
26. Rhodes DI, Peat TS, Vandegraaff N, Jeevarajah D, Le G, Jones ED, Smith JA, Coates JA, Winfield LJ, Thienthong N, Newman J, Lucent D, Ryan JH, Savage GP, Francis CL, Deadman JJ (2011) Antivir Chem Chemother 21(4):155
27. Wielens J, Headey SJ, Deadman JJ, Rhodes DI, Le GT, Parker MW, Chalmers DK, Scanlon MJ (2011) Chem Med Chem 6(2):258
28. Wielens J, Headey SJ, Rhodes DI, Mulder RJ, Dolezal O, Deadman JJ, Newman J, Chalmers DK, Parker MW, Peat TS, Scanlon MJ (2013) J Biomol Screen 18(2):147
29. Greenwood JR, Calkins D, Sullivan AP, Shelley JC (2010) J Comput Aided Mol Des 24(6-7):591
30. LigPrep. 2.6. (2013) Schrödinger LLC, New York
31. Gallicchio E, Lapelosa M, Levy RM (2010) J Chem Theory Comput 6(9):2961
32. Güner OF (1999) Pharmacophore perception, development, and use in drug design. International University Line, La Jolla, CA
33. Langer T, Hoffman RD (2006) Pharmacophores and pharmacophore searches. Wiley-VCH, Weinheim, Germany
34. Zhu T, Cao S, Su P-C, Patel R, Shah D, Chokshi HB, Szukala R, Johnson ME, Hevener KE (2013) J Med Chem 56(17):6560
35. Sanner MF (1999) J Mol Graph Model 17(1):57
36. Lin J-H, Perryman AL, Schames JR, McCammon JA (2002) J Am Chem Soc 124(20):5632
37. Amaro RE, Baron R, McCammon JA (2008) J Comput Aided Mol Des 22(9):693
38. Nichols SE, Baron R, Ivetac A, McCammon JA (2011) J Chem Inf Model 51(6):1439
39. Lin JH, Perryman AL, Schames JR, McCammon JA (2003) Biopolymers 68(1):47