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Journal of Computer-Aided Molecular Design

Volumn 22, Issue 5, 2008, Pages 287-297

Docking and multivariate methods to explore HIV-1 drug-resistance: A comparative analysis

(3) Almerico, Anna Maria a Tutone, Marco a Lauria, Antonino a

a UNIVERSITY OF PALERMO (Italy)

Author keywords

HIV 1; Molecular docking; Multivariate analysis; Mutation; NNRTIs; PIs; Resistance

Indexed keywords

DRUG THERAPY; ENZYME INHIBITION; MOLECULAR MODELING;

COMPARATIVE ANALYZES; DOCKING METHODS; DRUG-RESISTANCE; HIV-1; MOLECULAR DOCKING; MULTI VARIATE ANALYSIS; MUTATION; NNRTI; PI; RESISTANCE;

MULTIVARIANT ANALYSIS;

EFAVIRENZ; NEVIRAPINE; PROTEINASE INHIBITOR; RNA DIRECTED DNA POLYMERASE INHIBITOR; VIRUS ENZYME; ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT; LIGAND; P16 PROTEASE, HUMAN IMMUNODEFICIENCY VIRUS 1; PROTEINASE; REVERSE TRANSCRIPTASE, HUMAN IMMUNODEFICIENCY VIRUS 1; RNA DIRECTED DNA POLYMERASE;

ANTIVIRAL RESISTANCE; ANTIVIRAL SUSCEPTIBILITY; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG STRUCTURE; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR DOCKING; MULTIVARIATE ANALYSIS; NONHUMAN; PRIORITY JOURNAL; VIRUS MUTANT; VIRUS STRAIN; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER AIDED DESIGN; DRUG DESIGN; DRUG EFFECT; ENZYMOLOGY; GENETICS; HUMAN; METABOLISM; MUTATION;

ANTI-HIV AGENTS; BINDING SITES; COMPUTER-AIDED DESIGN; DRUG DESIGN; DRUG RESISTANCE, VIRAL; HIV PROTEASE; HIV PROTEASE INHIBITORS; HIV REVERSE TRANSCRIPTASE; HIV-1; HUMANS; LIGANDS; MODELS, MOLECULAR; MULTIVARIATE ANALYSIS; MUTATION; REVERSE TRANSCRIPTASE INHIBITORS;

EID: 47249083852 PISSN: 0920654X EISSN: 15734951 Source Type: Journal
DOI: 10.1007/s10822-008-9186-7 Document Type: Article

Times cited : (22)

References (27)

1
- 0037055027
- 10.1001/jama.288.2.169 1:CAS:528:DC%2BD38XltFGru7o%3D
- S Hammer F Vaida K Bennett M Holohan L Sheiner J Eron L Wheat R Mitsuyasu R Gulick F Valentine J Aberg M Rogers C Karol A Saah R Lewis L Bessen C Brosgart V DeGruttola J Mellors 2002 J Am Med Assoc 288 169 10.1001/jama.288.2. 169 1:CAS:528:DC%2BD38XltFGru7o%3D
- (2002) J Am Med Assoc , vol.288 , pp. 169
- Hammer, S.¹ Vaida, F.² Bennett, K.³ Holohan, M.⁴ Sheiner, L.⁵ Eron, J.⁶ Wheat, L.⁷ Mitsuyasu, R.⁸ Gulick, R.⁹ Valentine, F.¹⁰ Aberg, J.¹¹ Rogers, M.¹² Karol, C.¹³ Saah, A.¹⁴ Lewis, R.¹⁵ Bessen, L.¹⁶ Brosgart, C.¹⁷ Degruttola, V.¹⁸ Mellors, J.¹⁹

2
- 0034051154
- 10.1001/jama.283.10.1329 1:STN:280:DC%2BD3c7nslaitA%3D%3D
- J Gallant 2000 J Am Med Assoc 283 1329 10.1001/jama.283.10.1329 1:STN:280:DC%2BD3c7nslaitA%3D%3D
- (2000) J Am Med Assoc , vol.283 , pp. 1329
- Gallant, J.¹

3
- 0034685037
- 10.1001/jama.283.3.381 1:STN:280:DC%2BD3c7ht1ehug%3D%3D
- C Carpenter D Cooper M Fischl J Gatell B Gazzard S Hammer M Hirsch D Jacobsen D Katzenstein J Montaner D Richman M Saag M Schechter R Schooley M Thompson S Vella P Yeni P Volberding 2000 J Am Med Assoc 283 381 10.1001/jama.283.3.381 1:STN:280:DC%2BD3c7ht1ehug%3D%3D
- (2000) J Am Med Assoc , vol.283 , pp. 381
- Carpenter, C.¹ Cooper, D.² Fischl, M.³ Gatell, J.⁴ Gazzard, B.⁵ Hammer, S.⁶ Hirsch, M.⁷ Jacobsen, D.⁸ Katzenstein, D.⁹ Montaner, J.¹⁰ Richman, D.¹¹ Saag, M.¹² Schechter, M.¹³ Schooley, R.¹⁴ Thompson, M.¹⁵ Vella, S.¹⁶ Yeni, P.¹⁷ Volberding, P.¹⁸

4
- 0034605535
- 10.1001/jama.284.13.1649
- M Hirsch D Richman 2000 J Am Med Assoc 284 1649 10.1001/jama.284.13.1649
- (2000) J Am Med Assoc , vol.284 , pp. 1649
- Hirsch, M.¹ Richman, D.²

5
- 0033763897
- A genotypic analysis of patients receiving Zidovudine with either Lamivudine, Didanosine or Zalcitabine dual therapy using the LiPA point mutation assay to detect genotypic variation at codons 41, 69, 70, 74, 184 and 215
- DOI 10.1016/S1386-6532(00)00087-1, PII S1386653200000871
- S Rusconi S La Seta Catamancio F Sheridan D Parker 2000 J Clin Virol 19 135 10.1016/S1386-6532(00)00087-1 1:CAS:528:DC%2BD3cXot1ygt7Y%3D (Pubitemid 30827212)
- (2000) Journal of Clinical Virology , vol.19 , Issue.3 , pp. 135-142
- Rusconi, S.¹ La Seta Catamancio, S.² Sheridan, F.³ Parker, D.⁴

6
- 0027481325
- 1:STN:280:ByyB3cvgtFE%3D
- M Holodniy D Katzenstein M Winters J Montoya R Shafer M Kozal M Ragni T Merigan 1993 J Acquir Immune Defic Syndr 6 366 1:STN:280:ByyB3cvgtFE%3D
- (1993) J Acquir Immune Defic Syndr , vol.6 , pp. 366
- Holodniy, M.¹ Katzenstein, D.² Winters, M.³ Montoya, J.⁴ Shafer, R.⁵ Kozal, M.⁶ Ragni, M.⁷ Merigan, T.⁸

7
- 0033037358
- 1:CAS:528:DyaK1MXktFGms7k%3D
- R Schuurman L Demeter P Reichelderfer J Tijnagel T de Groot C Boucher 1999 J Clin Microbiol 37 2291 1:CAS:528:DyaK1MXktFGms7k%3D
- (1999) J Clin Microbiol , vol.37 , pp. 2291
- Schuurman, R.¹ Demeter, L.² Reichelderfer, P.³ Tijnagel, J.⁴ De Groot, T.⁵ Boucher, C.⁶

8
- 0032552167
- Correlation of response to treatment and HIV genotypic changes during Phase III trials with saquinavir and reverse transcriptase inhibitor combination therapy
- DOI 10.1097/00002030-199812000-00008
- E Race S Gilbert J Sheldon J Rose A Moffatt G Sitbon S Dissanayeke N Cammack I Duncan 1998 AIDS 12 1465 10.1097/00002030-199812000-00008 1:CAS:528:DyaK1cXlvVCntrw%3D (Pubitemid 28369646)
- (1998) AIDS , vol.12 , Issue.12 , pp. 1465-1474
- Race, E.¹ Gilbert, S.M.² Sheldon, J.G.³ Rose, J.S.L.⁴ Moffatt, A.R.⁵ Sitbon, G.⁶ Dissanayeke, S.R.⁷ Cammack, N.⁸ Duncan, I.B.⁹

9
- 0036222716
- Genotypic testing for human immunodeficiency virus type 1 drug resistance
- DOI 10.1128/CMR.15.2.247-277.2002
- R Shafer 2002 Clin Microbiol Rev 15 247 10.1128/CMR.15.2.247-277.2002 1:CAS:528:DC%2BD38XjslGrurY%3D (Pubitemid 34303765)
- (2002) Clinical Microbiology Reviews , vol.15 , Issue.2 , pp. 247-277
- Shafer, R.W.¹

10
- 0034083833
- R Schinazi B Larder J Mellors 2000 Int Antiv News 8 65
- (2000) Int Antiv News , vol.8 , pp. 65
- Schinazi, R.¹ Larder, B.² Mellors, J.³

11
- 0033920318
- A randomized study of antiretroviral management based on plasma genotypic antiretroviral resistance testing in patients failing therapy
- DOI 10.1097/00002030-200006160-00001
- J Baxter D Mayers D Wentworth J Neaton M Hoover M Winters S Mannheimer M Thompson D Abrams B Brizz 2000 AIDS 14 F83 10.1097/00002030-200006160-00001 1:CAS:528:DC%2BD3cXltFWnu70%3D (Pubitemid 30420686)
- (2000) AIDS , vol.14 , Issue.9
- Baxter, J.D.¹ Mayers, D.L.² Wentworth, D.N.³ Neaton, J.D.⁴ Hoover, M.L.⁵ Winters, M.A.⁶ Mannheimer, S.B.⁷ Thompson, M.A.⁸ Abrams, D.I.⁹ Brizz, B.J.¹⁰ Ioannidis, J.P.A.¹¹ Merigan, T.C.¹² Pettinelli, C.¹³ Canady, K.¹⁴ Johnston-Dow, L.¹⁵ Perille, E.¹⁶ Bohn, H.¹⁷ Martinez, A.¹⁸ Munk, R.¹⁹ Day, T.²⁰ more..

12
- 0029063951
- 10.1021/jm00002a012 1:CAS:528:DyaK2MXivFOqtLo%3D
- M Holloway J Wai T Halgren P Fitzgerald J Vacca B Dorsey R Levin W Thompson L Chen S deSolms 1995 J Med Chem 38 305 10.1021/jm00002a012 1:CAS:528:DyaK2MXivFOqtLo%3D
- (1995) J Med Chem , vol.38 , pp. 305
- Holloway, M.¹ Wai, J.² Halgren, T.³ Fitzgerald, P.⁴ Vacca, J.⁵ Dorsey, B.⁶ Levin, R.⁷ Thompson, W.⁸ Chen, L.⁹ Desolms, S.¹⁰

13
- 0037075124
- Computational studies on tetrahydropyrimidine-2-one HIV-1 protease inhibitors: Improving three-dimensional quantitative structure-activity relationship comparative molecular field analysis models by inclusion of calculated inhibitor- and receptor-based properties
- DOI 10.1021/jm010417v
- A Nair P Jayatilleke X Wang S Miertus W Welsh 2002 J Med Chem 45 973 10.1021/jm010417v 1:CAS:528:DC%2BD38Xkt12jtg%3D%3D (Pubitemid 34173949)
- (2002) Journal of Medicinal Chemistry , vol.45 , Issue.4 , pp. 973-983
- Nair, A.C.¹ Jayatilleke, P.² Wang, X.³ Miertus, S.⁴ Welsh, W.J.⁵

14
- 0032510317
- Comparative binding energy analysis of HIV-1 protease inhibitors: Incorporation of solvent effects and validation as a powerful tool in receptor-based drug design
- DOI 10.1021/jm970535b
- C Perez M Pastor A Ortiz F Gago 1998 J Med Chem 41 836 10.1021/jm970535b 1:CAS:528:DyaK1cXhtF2mu70%3D (Pubitemid 28146240)
- (1998) Journal of Medicinal Chemistry , vol.41 , Issue.6 , pp. 836-852
- Perez, C.¹ Pastor, M.² Ortiz, A.R.³ Gago, F.⁴

15
- 0041341885
- Structure-based phenotyping predicts HIV-1 protease inhibitor resistance
- DOI 10.1110/ps.0301103
- M Shenderovich R Kagan P Heseltine K Ramnarayan 2003 Protein Sci 12 1706 10.1110/ps.0301103 1:CAS:528:DC%2BD3sXlvFSjurw%3D (Pubitemid 36910051)
- (2003) Protein Science , vol.12 , Issue.8 , pp. 1706-1718
- Shenderovich, M.D.¹ Kagan, R.M.² Heseltine, P.N.R.³ Ramnarayan, K.⁴

16
- 16244403666
- 1:CAS:528:DC%2BD2MXis1Kmurs%3D
- E Jenwitheesuk R Samudrala 2005 Antivir Ther 10 157 1:CAS:528: DC%2BD2MXis1Kmurs%3D
- (2005) Antivir Ther , vol.10 , pp. 157
- Jenwitheesuk, E.¹ Samudrala, R.²

17
- 1042300010
- 10.1002/qsar.200330834
- AM Almerico A Lauria M Tutone P Diana P Barraja A Montalbano G Cirrincione G Dattolo 2003 QSAR Comb Sci 22 984 10.1002/qsar.200330834
- (2003) QSAR Comb Sci , vol.22 , pp. 984
- Almerico, A.M.¹ Lauria, A.² Tutone, M.³ Diana, P.⁴ Barraja, P.⁵ Montalbano, A.⁶ Cirrincione, G.⁷ Dattolo, G.⁸

18
- 33244496701
- A multivariate analysis of HIV-1 protease inhibitors and resistance induced by mutation
- DOI 10.1021/ci050139z
- AM Almerico M Tutone A Lauria P Diana P Barraja A Montalbano G Cirrincione G Dattolo 2006 J Chem Inf Model 46 168 10.1021/ci050139z 1:CAS:528:DC%2BD2MXht1SgtrrF (Pubitemid 43282112)
- (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.1 , pp. 168-179
- Almerico, A.M.¹ Tutone, M.² Lauria, A.³ Diana, P.⁴ Barraja, P.⁵ Montalbano, A.⁶ Cirrincione, G.⁷ Dattolo, G.⁸

19
- 72849123497
- http://www.niaid.nih.gov/daids/dtpdb

20
- 72849147498
- http://www.rcsb.org/pdb

21
- 72849117288
- Oxford Molecular Limited
- All of the calculations were run on a Silicon Graphics Indigo II workstation using the software TSAR 3.2 (Tools for Structure Activity Relationships), VAMP 6.0, and ASP 3.2 (Automated Similarity Packages) (Oxford Molecular-Accelrys). Molecular descriptors were derived according to the method and assumptions reported in the TSAR 3.2 Reference Guide, Oxford Molecular Limited (1998)
- (1998) All of the Calculations Were Run on A Silicon Graphics Indigo II Workstation Using the Software TSAR 3.2 (Tools for Structure Activity Relationships), VAMP 6.0, and ASP 3.2 (Automated Similarity Packages) (Oxford Molecular-Accelrys). Molecular Descriptors Were Derived According to the Method and Assumptions Reported in the TSAR 3.2 Reference Guide

22
- 60849115022
- Accelrys Inc
- Ligandfit User Manual, Accelrys Inc (2003)
- (2003) Ligandfit User Manual

23
- 0037212102
- LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites
- DOI 10.1016/S1093-3263(02)00164-X, PII S109332630200164X
- C Venkatachalam X Jiang T Oldfield M Waldman 2003 J Mol Graph Model 21 289 10.1016/S1093-3263(02)00164-X 1:CAS:528:DC%2BD38XptlWmuro%3D (Pubitemid 35441326)
- (2003) Journal of Molecular Graphics and Modelling , vol.21 , Issue.4 , pp. 289-307
- Venkatachalam, C.M.¹ Jiang, X.² Oldfield, T.³ Waldman, M.⁴

24
- 0032112137
- 10.1023/A:1007999920146
- H Böhm 1998 J Comput Aided Mol Des 12 309 10.1023/A:1007999920146
- (1998) J Comput Aided Mol des , vol.12 , pp. 309
- Böhm, H.¹

25
- 0033670301
- 10.1023/A:1008158231558 1:CAS:528:DC%2BD3MXjtlSn
- G Verkhivker D Bouzida D Gehlhaar P Rejto S Arthurs A Colson S Freer V Larson B Luty T Marrone P Rose 2000. J Comput Aided Mol Des 14 731 10.1023/A:1008158231558 1:CAS:528:DC%2BD3MXjtlSn
- (2000) J Comput Aided Mol des , vol.14 , pp. 731
- Verkhivker, G.¹ Bouzida, D.² Gehlhaar, D.³ Rejto, P.⁴ Arthurs, S.⁵ Colson, A.⁶ Freer, S.⁷ Larson, V.⁸ Luty, B.⁹ Marrone, T.¹⁰ Rose, P.¹¹

26
- 0029294584
- 10.1016/1074-5521(95)90050-0 1:CAS:528:DyaK2MXmvVClsbg%3D
- D Gehlhaar G Verkhivker P Rejto C Sherman D Fogel L Fogel S Freer 1995 Chem Biol 2 317 10.1016/1074-5521(95)90050-0 1:CAS:528:DyaK2MXmvVClsbg%3D
- (1995) Chem Biol , vol.2 , pp. 317
- Gehlhaar, D.¹ Verkhivker, G.² Rejto, P.³ Sherman, C.⁴ Fogel, D.⁵ Fogel, L.⁶ Freer, S.⁷

27
- 0033545622
- A general and fast scoring function for protein-ligand interactions: A simplified potential approach
- DOI 10.1021/jm980536j
- I Muegge Y Martin 1999 J Med Chem 42 791 10.1021/jm980536j 1:CAS:528:DyaK1MXht1aksrk%3D (Pubitemid 29136170)
- (1999) Journal of Medicinal Chemistry , vol.42 , Issue.5 , pp. 791-804
- Muegge, I.¹ Martin, Y.C.²

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