A hybrid structure/pharmacophore-based virtual screening approach to design potential leads: A computer-aided design of South African HIV-1 subtype C protease inhibitors

Drug Development Research

Volumn 74, Issue 5, 2013, Pages 283-295

  Soliman, Mahmoud E S ^a  

^a UNIVERSITY OF KWAZULU NATAL   (South Africa)

Author keywords

computer aided drug design; docking; HIV 1 protease inhibitors; pharmacophore based and structure based virtual screening

Indexed keywords

ENZYME VARIANT; HUMAN IMMUNODEFICIENCY VIRUS PROTEINASE INHIBITOR; LIGAND;

ARTICLE; BIOFILTER; CHEMICAL STRUCTURE; COMPUTER AIDED DESIGN; DRUG BINDING SITE; DRUG SCREENING; HYBRID; PHARMACOPHORE;

EID: 84880320396     PISSN: 02724391     EISSN: 10982299     Source Type: Journal    
DOI: 10.1002/ddr.21078     Document Type: Article

References (51)

1. Ahmed SM, Kruger HG, Govender T, Maguire GE, Sayed Y, Ibrahim MA, Naicker P, Soliman ME,. 2013. Comparison of the molecular dynamics and calculated binding free energies for nine FDA-approved HIV-1 PR drugs against subtype B and C-SA HIV PR. Chem Biol Drug Des 81: 208-218.
2. Alperin I, Ma B, Wolfson H, Nussinov R,. 2002. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins Struct Funct Bioinf 47: 409-443. (Pubitemid 34614722)
3. Bajorath J,. 2002. Integration of virtual and high-throughput screening. Nat Rev Drug Discov 1: 882-894. (Pubitemid 37361583)
4. Barreiro G, Guimaraes CRW, Tubert-Brohman I, Lyons TM, Tirado-Rives J, Jorgensen WL,. 2007. Search for non-nucleoside inhibitors of HIV-1 reverse transcriptase using chemical similarity, molecular docking, and MM-GB/SA scoring. J Chem Inf Model 47: 2416-2428. (Pubitemid 350275106)
5. Bissantz C, Schalon C, Guba W, Stahl M,. 2005. Focused library design in GPCR projects on the example of 5-HT(2c) agonists: comparison of structure-based virtual screening with ligand-based search methods. Proteins Struct Funct Bioinf 61: 938-952. (Pubitemid 41753164)
6. Cheng T, Li Q, Zhou Z, Wang Y, Bryant S,. 2012. Structure-based virtual screening for drug discovery: a problem-centric review. AAPS J 14: 133-141.
7. Cornelissen M, van den Burg R, Zorgdrager F, Lukashov V, Goudsmit J,. 1997. pol gene diversity of five human immunodeficiency virus type 1 subtypes: evidence for naturally occurring mutations that contribute to drug resistance, limited recombination patterns, and common ancestry for subtypes B and D. J Virol 71: 6348-6358. (Pubitemid 27355288)
8. Das K, Aramini JM, Ma LC, Krug RM, Arnold E,. 2010. Structures of influenza A proteins and insights into antiviral drug targets. Nat Struct Mol Biol 17: 530-538.
9. Eckert H, Bajorath J,. 2007. Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches. Drug Discov Today 12: 225-233.
10. Halgren TA,. 1999. MMFFVI. MMFF94s option for energy minimization studies. J Comput Chem 20: 720-729. (Pubitemid 129652635)
11. Hawkins PCD, Skillman AG, Warren GL, Ellingson BA, Stahl MT,. 2010. Conformer generation with OMEGA: algorithm and validation using high quality structures from the protein databank and Cambridge structural database. J Chem Inf Model 50: 572-584.
12. Heikamp K, Bajorath J,. 2013. The future of virtual compound screening. Chem Biol Drug Des 81: 33-40.
13. Honarparvar B, Makatini MM, Pawar SA, Petzold K, Soliman ME, Arvidsson PI, Sayed Y, Govender T, Maguire GE, Kruger HG,. 2012. Pentacycloundecane-diol- based HIV-1 protease inhibitors: biological screening, 2D NMR, and molecular simulation studies. ChemMedChem 7: 1009-1019.
14. Hornak V, Okur A, Rizzo RC, Simmerling C,. 2006. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proc Natl Acad Sci U S A 103: 915-920. (Pubitemid 43212196)
15. Huey R, Morris GM, Olson AJ, Goodsell DS,. 2007. A semiempirical free energy force field with charge-based desolvation. J Comput Chem 28: 1145-1152. (Pubitemid 46506716)
16. Jain AN,. 2004. Virtual screening in lead discovery and optimization. Curr Opin Drug Discov Devel 7: 396-403.
17. Karpoormath R, Sayed Y, Govender P, Govender T, Kruger HG, Soliman ME, Maguire GE,. 2012. Pentacycloundecane derived hydroxy acid peptides: a new class of irreversible non-scissile ether bridged type isoster as potential HIV-1 wild type C-SA protease inhibitors. Bioorg Chem 40: 19-29.
18. Kitchen DB, Decornez H, Furr JR, Bajorath J,. 2004. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3: 935-949. (Pubitemid 39529931)
19. Klebe G,. 2006. Virtual ligand screening: strategies, perspectives and limitations. Drug Discov Today 11: 580-594.
20. Koes DR, Camacho CJ,. 2012. ZINCPharmer: pharmacophore search of the ZINC database. Nucleic Acids Res 40 (W1): W409-W414.
21. Lipinski C,. 2000. Drug-like properties and the causes of poor solubility and poor permeability. J Pharmacol Toxicol 44: 235-249. (Pubitemid 32239479)
22. Makatini M, Petzold K, Sriharsha NS, Ndlovu N, Soliman MES, Honarparvar B, Parboosing R, Naidoo A, Arvidsson PI, Sayed Y, et al. 2011a. Synthesis and structural studies of pentacycloundecane-based HIV-1 PR inhibitors: a hybrid 2D-NMR and docking/QM/MM/MD approach. Eur J Med Chem 46: 3976-3985.
23. Makatini M, Petzold K, Sriharsha S, Soliman MES, Honarparvar B, Arvidson PI, Sayed Y, Govender P, Maguire GEM, Kruger H, et al. 2011b. Pentacycloundecane-based inhibitors of wild-type C-South African HIV protease. Bioorg Med Chem Lett 15: 2274-2277.
24. Makatini MM, Petzold K, Alves CN, Arvidsson PI, Honarparvar B, Govender P, Govender T, Kruger HG, Sayed Y, Lameira Silva J, et al. 2013. Synthesis, 2D-NMR and molecular modelling studies of pentacycloundecane lactam-peptides and peptoids as potential HIV-1 wild type C-SA protease inhibitors. J Enzyme Inhib Med Chem 28: 78-88.
25. Miller M, Schneider J, Sathyanarayana BK, Toth MV, Marshall GR, Clawson L, Selk L, Kent SBH, Wlodawer A,. 1989. Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3-a resolution. Science 246: 1149-1152. (Pubitemid 20012771)
26. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ,. 1998. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19: 1639-1662. (Pubitemid 128590223)
27. Mosebi S, Morris L, Dirr HW, Sayed Y,. 2008. Active-site mutations in the South African human immunodeficiency virus type 1 subtype C protease have a significant impact on clinical inhibitor binding: kinetic and thermodynamic study. J Virol 82: 11476-11479.
28. Naicker P, Achilonu I, Fanucchi S, Fernandes M, Ibrahim M, Dirr H, Soliman M, Sayed Y,. 2012. Structural insights into the South African HIV-1 subtype C protease. J Biomol Struct Dyn in press; http://www.ncbi.nlm.nih.gov/ pubmed/23140382 (ahead of print).
29. Navia MA, Fitzgerald PM, McKeever BM, Leu CT, Heimbach JC, Herber WK, Sigal IS, Darke PL, Springer JP,. 1989. Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1. Nature 337: 615-620. (Pubitemid 19054290)
30. Perez-Pineiro R, Burgos A, Jones DC, Andrew LC, Rodriguez H, Suarez M, Fairlamb AH, Wishart DS,. 2009. Development of a novel virtual screening cascade protocol to identify potential trypanothione reductase inhibitors. J Med Chem 52: 1670-1680.
31. Pieniazek D, Rayfield M, Hu DJ, Nkengasong J, Wiktor SZ, Downing R, Biryahwaho B, Mastro T, Tanuri A, Soriano V, et al. 2000. Protease sequences from HIV-1 group M subtypes A-H reveal distinct amino acid mutation patterns associated with protease resistance in protease inhibitor-naive individuals worldwide. HIV Variant Working Group. AIDS 14: 1489-1495.
32. Prabu-Jeyabalan M, Nalivaika E, Schiffer CA,. 2002. Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes. Structure 10: 369-381. (Pubitemid 34230624)
33. Sanner MF,. 1999. Python: a programming language for software integration and development. J Mol Graph Model 17: 57-61. (Pubitemid 30029318)
34. Shoichet BK,. 2004. Virtual screening of chemical libraries. Nature 432: 862-865. (Pubitemid 40037142)
35. Sirci F, Goracci L, Rodríguez D, Muijlwijk-Koezen J, Gutiérrez-de-Terán H, Mannhold R,. 2012. Ligand-, structure- and pharmacophore-based molecular fingerprints: a case study on adenosine A1, A2A, A2B, and A3 receptor antagonists. J Comput Aided Mol Des 26: 1247-1266.
36. Stahura FL, Bajorath J,. 2005. New methodologies for ligand- based virtual screening. Curr Pharm Des 11: 1189-1202. (Pubitemid 40403377)
37. Stefano F,. Fox/AutoDock VS: an automated tool for preparing AutoDock virtual screenings. http://www.autodock.scripps.edu/resources/fox Accessed 13 June 2012.
38. Stefano F,. Raccoon/AutoDock VS: an automated tool for preparing AutoDock virtual screenings. http://www.autodock.scripps.edu/resources/raccoon Accessed 13 June 2012.
39. Swain AL, Miller MM, Green J, Rich DH, Schneider J, Kent SB, Wlodawer A,. 1990. X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor. Proc Natl Acad Sci U S A 87: 8805-8809. (Pubitemid 120007597)
40. Tan L, Geppert H, Sisay MT, Gütschow M, Bajorath J,. 2008. Integrating structure- and ligand-based virtual screening: comparison of individual, parallel, and fused molecular docking and similarity search calculations on multiple targets. ChemMedChem 3: 1566-1571.
41. Thomsen R, Christensen M,. 2006. MolDock: a new technique for high-accuracy molecular docking. J Med Chem 1: 3315-3321. (Pubitemid 43830529)
42. Tikhonova IG, Sum CS, Neumann S, Engel S, Raaka BM, Costanzi S, Gershengorn MC,. 2008. Discovery of novel agonists and antagonists of the free fatty acid receptor 1 (FFAR1) using virtual screening. J Med Chem 51: 625-633. (Pubitemid 351252290)
43. UNAIDS. Available from: http://www.unaids.org/globalreport/Global-report. htm. Date accessed, June 2012.
44. Vainio MJ, Puranen JS, Johnson MS,. 2009. ShaEP: molecular overlay based on shape and electrostatic potential. J Chem Inf Model 49: 492-502.
45. Velazquez-Campoy A, Vega S, Freire E,. 2002. Amplification of the effects of drug resistance mutations by background polymorphisms in HIV-1 protease from African subtypes. Biochemistry 41: 8613-8619. (Pubitemid 34743300)
46. Vidal D, Thormann M, Pons M,. 2006. A novel search engine for virtual screening of very large databases. J Chem Inf Model 46: 836-843.
47. Vogt M, Bajorath J,. 2009. Data mining approaches for compound selection and iterative screening. In:, Balakin KV, editor. Pharmaceutical data mining: approaches and applications for drug discovery. Hoboken, NJ: John Wiley & Sons, p 115-143.
48. Wallace AC, Laskowski RA, Thornton JM,. 1995. Ligplot-A program to generate schematic diagrams of protein ligand interactions. Protein Engineering 8 (2): 127-134.
49. Wei D, Zhang R, Du Q, Gao W, Li Y, Gao H, Wang S, Zhang X, Li A, Sirois S, et al. 2006. Anti-SARS drug screening by molecular docking. Amino Acids 31: 73-80. (Pubitemid 44086400)
50. Willett P,. 2006. Similarity-based virtual screening using 2D fingerprints. Drug Discov Today 11: 1046-1053. (Pubitemid 44792477)
51. Wlodawer A, Miller M, Jaskolski M, Sathyanarayana BK, Baldwin E, Weber IT, Selk LM, Clawson L, Schneider J, Kent SB,. 1989. Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. Science 245: 616-621. (Pubitemid 19213338)