High-throughput virtual screening of phloroglucinol derivatives against HIV-reverse transcriptase

Molecular Diversity

Volumn 17, Issue 1, 2013, Pages 97-110

  Belekar, Vilas ^a   Shah, Anup ^a   Garg, Prabha ^a  

^a NATIONAL INSTITUTE OF PHARMACEUTICAL EDUCATION AND RESEARCH NIPER   (India)

Author keywords

ADME toxicity prediction; HIV reverse transcriptase; Molecular docking; Off target search; Phloroglucinol derivatives; Virtual screening

Indexed keywords

1DX899; DELAVIRDINE; EFAVIRENZ; ETRAVIRINE; LERSIVIRINE; NEVIRAPINE; PHLOROGLUCINOL DERIVATIVE; RDEA 806; RILPIVIRINE; RNA DIRECTED DNA POLYMERASE; RNA DIRECTED DNA POLYMERASE INHIBITOR; UNCLASSIFIED DRUG;

ANTIVIRAL ACTIVITY; ARTICLE; BINDING AFFINITY; CHEMICAL INTERACTION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG ABSORPTION; DRUG DISTRIBUTION; DRUG EFFICACY; DRUG EXCRETION; DRUG METABOLISM; DRUG PENETRATION; DRUG SCREENING; GENOTOXICITY; HIGH THROUGHPUT SCREENING; HUMAN IMMUNODEFICIENCY VIRUS; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR DOCKING; NEPHROTOXICITY; PHYSICAL CHEMISTRY; PREDICTIVE VALUE; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION;

ANTI-HIV AGENTS; BINDING SITES; DRUG DESIGN; HIGH-THROUGHPUT SCREENING ASSAYS; HIV REVERSE TRANSCRIPTASE; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MOLECULAR DOCKING SIMULATION; PHLOROGLUCINOL; PROTEIN BINDING; REVERSE TRANSCRIPTASE INHIBITORS;

EID: 84873404601     PISSN: 13811991     EISSN: 1573501X     Source Type: Journal    
DOI: 10.1007/s11030-012-9417-7     Document Type: Article

References (54)

1. Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas A, Hufeisen SJ, Jensen HN, Kuijer BM (2009) Predicting new molecular targets for known drugs. Nature 462:175-181. doi: 10.1038/nature08506
2. Xie L, Xie L, Bourne PE (2011) Structure-based systems biology for analyzing off-target binding. Curr Opin Struct Biol 21:189-199. doi: 10.1016/j.sbi.2011.01.004
3. Butcher EC, Berg EL, Kunkel EJ (2004) Systems biology in drug discovery. Nat Biotechnol 22:1253-1259. doi: 10.1038/nbt1017
4. Yildirim MA, Goh KI, Cusick ME, Barabasi AL, Vidal M (2007) Drug target network. Nat Biotechnol 25:1119-1126. doi: 10.1038/nbt1338
5. Raman K, Chandra N (2008) Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance. BMC Microbiol 8:234. doi: 10.1186/1471-2180-8-234
6. Chang RL, Xie L, Xie L, Bourne PE, Palsson B (2010) Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comp Biol 6:e1000938. doi: 10.1371/journal.pcbi.1000938
7. Kinnings SL, Liu N, Buchmeier N, Tonge PJ, Xie L, Bourne PE (2009) Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis. PLoS Comp Biol 5:e1000423. doi: 10.1371/journal.pcbi.1000423
8. Tulp M, Bohlin L (2005) Rediscovery of known natural compounds: nuisance or goldmine? Bioorg Med Chem 13:5274-5282. doi: 10.1016/j.bmc.2005.05.067
9. Saklani A, Kutty SK (2008) Plant-derived compounds in clinical trials. Drug Discov Today 13:161-171. doi: 10.1016/j.drudis.2007.10.010
10. Butler MS (2008) Natural products to drugs: natural product-derived compounds in clinical trials. Nat Prod Rep 25:475-516. doi: 10.1039/B514294F
11. Vistoli G, Pedretti A, Testa B (2008) Assessing drug-likeness - what are we missing? Drug Discov Today 13:285-294. doi: 10.1016/j.drudis.2007.11.007
12. Ganesan A (2008) The impact of natural products upon modern drug discovery. Curr Opin Chem Biol 12:306-317. doi: 10.1016/j.cbpa.2008.03.016
13. Nishizawa M, Emura M, Kan Y, Yamada H, Ojima K, Hamanaka M (1992) Macrocarpals: HIV-RTase inhibitors of Eucalyptus globulus. Tetrahedron Lett 33:2983-2986. doi: 10.1016/S0040-4039(00)79578-5
14. Xu R, Snyder JK, Nakanishi K (1984) Robustadials A and B from Eucalyptus robusta. J Am Chem Soc 106:734-736. doi: 10.1021/ja00315a047
15. Bharate SB, Bhutani KK, Khan SI, Tekwani BL, Jacob MR, Khan IA, Singh IP (2006) Biomimetic synthesis, antimicrobial, antileishmanial and antimalarial activities of euglobals and their analogues. Bioorg Med Chem 14:1750-1760. doi: 10.1016/j.bmc.2005.10.027
16. Yamaki M, Miwa I, Ishiguro K, Takagi S (1994) Antimicrobial activity of naturally occurring and synthetic phloroglucinols against Staphylococcus aureus. Phytother Res 8:112-114. doi: 10.1002/ptr.2650080214
17. Mizobuchi S, Sato Y (1985) Antifungal activity of 2,4,6- trihydroxyacylophenone and related compound. Agric Biol Chem 49:719-724
18. Bharate SB, Khan SI, Yunus NAM, Chauthe SK, Jacob MR, Tekwani BL, Khan IA, Singh IP (2007) Antiprotozoal and antimicrobial activities of O-alkylated and formylated acylphloroglucinols. Bioorg Med Chem 15:87-96. doi: 10.1016/j.bmc.2006.10.006
19. Singh IP, Bharate SB (2006) Phloroglucinol compounds of natural origin. Nat Prod Rep 23:558-591. doi: 10.1039/B600518G
20. Nakane H, Arisawa M, Fujita A, Koshimura S, Ono K (1991) Inhibition of HIV-reverse transcriptase activity by some phloroglucinol derivatives. FEBS Lett 286:83-85. doi: 10.1016/0014-5793(91)80946-Z
21. Artan M, Li Y, Karadeniz F, Lee SH, Kim MM, Kim SK (2008) Anti-HIV-1 activity of phloroglucinol derivative, 6,6 ′ -bieckol, from Ecklonia cava. Bioorg Med Chem 16:7921-7926. doi: 10.1016/j.bmc.2008.07.078
22. Bokesch HR, Groweiss A, McKee TC, Boyd MR (1999) Laxifloranone, a new phloroglucinol derivative from Marila laxiflora. J Nat Prod 62:1197-1199. doi: 10.1021/np990136e
23. Appendino G, Ottino M, Marquez N, Bianchi F, Giana A, Ballero M, Sterner O, Fiebich BL, Munoz E (2007) Arzanol, an anti-inflammatory and anti-HIV-1 phloroglucinol alpha-Pyrone from Helichrysum italicum ssp. Microphyllum. J Nat Prod 70:608-612. doi: 10.1021/np060581r
24. Gupta P, Kumar R, Garg P, Singh IP (2010) Active site binding modes of dimeric phloroglucinols for HIV-1 reverse transcriptase, protease and integrase. Bioorg Med Chem Lett 20:4427-4431. doi: 10.1016/j.bmcl.2010.06.057
25. SYBYL, version 7.1 (2006) Tripos associates. St. Louis, MO, USA
26. Powell MJD (1977) Restart procedures for the conjugate gradient method. Math Program 12:241-254
27. Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges. Tetrahedron 36:3219-3228. doi: 10.1016/0040-4020(80)80168-2
28. Enslein K, Gombar VK, Blake BW (1994) International commission for protection against environmental mutagens and carcinogens. Use of SAR in computer-assisted prediction of carcinogenicity and mutagenicity of chemicals by the TOPKAT program. Mutat Res 305:47-61. doi: 10.1016/0027-5107(94)90125-2
29. Cariello NF, Wilson JD, Britt BH, Wedd DJ, Burlinson B, Gombar VK (2002) Comparison of the computer programs DEREK and TOPKAT to predict bacterial mutagenicity. Mutagenicity 17:321-329. doi: 10.1093/mutage/17.4.321
30. QikProp, version 3.4 (2011) Schrödinger, LLC, New York
31. Susnow RG, Dixon SL (2003) Use of robust classification techniques for the prediction of human cytochrome P450 2D6 inhibition. J Chem Inf Comput Sci 43:1308-1315. doi: 10.1021/ci030283p
32. ACD/LogP (2012) Advanced Chemistry Development, Inc., Toronto, ON, Canada
33. Schrödinger Suite (2011) Protein Preparation Wizard; Epik version 2.2, Schrödinger, LLC, New York
34. LigPrep, version 2.5 (2011) Schrödinger, LLC, New York
35. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK (2004) Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739-1749. doi: 10.1021/jm0306430
36. Verdonk M, Cole J, Hartshorn M, Murray C, Taylor R (2003) Improved protein-ligand docking using GOLD. Proteins 52:609-623. doi: 10.1002/prot.10465
37. Gombar VK, Enslein K, Reid DA (1996) Computer-assisted toxicity assessment: criteria for acceptance. Netw Sci. http://www.awod.com/netsci/ Issues/Feb96/feature2.html
38. Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA (1992) Crystal structure at 3.5 Å resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256:1783-1790. doi: 10.1126/science.1377403
39. Sarafianos SG et al (1999) Touching the heart of HIV-1 drug resistance: the fingers close down on the dNTP at the polymerase active site. Chem Biol 6:R137-R146. doi: 10.1016/S1074-5521(99)80071-4
40. Hsiou Y, Ding J, Das K, Clark AD Jr, Hughes SH, Arnold E (1996) Structure of unliganded HIV-1 reverse transcriptase at 2.7 Å resolution: implications of conformational changes for polymerization and inhibition mechanisms. Structure 4:853-860. doi: 10.1016/S0969-2126(96)00091-3
41. Fuller RW, Westergaard CK, Collins JW, Boyd MR (1999) Vismiaphenones D-G, new prenylated benzophenones from Vismia cayennensis. J Nat Prod 62:67-69. doi: 10.1021/np980152w
42. Yamakoshi Y, Murata M, Shimizu A, Homma S (1992) Isolation and characterization of macrocarpals B-G antibacterial compounds from Eucalyptus macrocarpa. Biosci Biotechnol Biochem 56:1570-1576
43. Arisawa M, Fujita A, Suzuki R, Hayashi T, Morita N, Kawano N, Koshimura S (1985) Studies on cytotoxic constituents in pericarps of Mallotus japonicus, Part I. J Nat Prod 48:455-459. doi: 10.1021/np50039a014
44. Arisawa M, Fujita A, Morita N (1990) Studies on cytotoxic constituents in pericarps of Mallotus japonicus, V. Three new phloroglucinol derivatives, butyrylmallotochromanol, isobutyrylmallotochromanol, and mallotojaponol. J Nat Prod 53:638-643. doi: 10.1021/np50069a016
45. Glombitza K-W, Gerstberger G (1985) Phlorotannins with dibenzodioxin structural elements from the brown alga Eisenia arborea. Phytochemistry 24:543-551. doi: 10.1016/S0031-9422(00)80764-5
46. Fukuyama Y, Kodama M, Miura I, Kinzyo Z, Mori H, Nakayama Y, Takahashi M (1989) Anti-plasmin inhibitor. V. Structures of novel dimeric eckols isolated from the brown alga Ecklonia kurome OKAMURA. Chem Pharm Bull 37:2438-2440
47. Kellenberger E, Rodrigo J, Muller P, Rognan D (2004) Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins 57:225-242. doi: 10.1002/prot.20149
48. McGann M (2011) FRED pose prediction and virtual screening accuracy. J Chem Inf Model 51:578-596. doi: 10.1021/ci100436p
49. Hansel R, Cybulski EM, Cubukcu B, Mericli AH, Bohlmann F, Zdero C (1980) Neue pyron-derivate aus Helichrysum-arten. Phytochemistry 19:639-644. doi: 10.1016/0031-9422(80)87030-0
50. Bohlmann F, Zdero C (1979) Neue phloroglucin-derivate aus Helichrysum natalitium und Helichrysum bellum. Phytochemistry 18:641-644. doi: 10.1016/S0031-9422(00)84276-4
51. Yamaki M, Kashihara M, Ishiguro K, Takagi S (1989) Antimicrobial principles of Xian he cao (Agrimonia pilosa). Planta Med 55:169-170. doi: 10.1055/s-2006-961915
52. Daikonya A, Katsuki S, Wu JB, Kitanaka S (2002) Anti-allergic agents from natural sources (4): anti-allergic activity of new phloroglucinol derivatives from Mallotus philippensis (Euphorbiaceae). Chem Pharm Bull 50:1566-1569. doi: 10.1248/cpb.50.1566
53. Arisawa M, Fujita A, Morita N, Koshimura S (1990) Cytotoxic and antitumor constituents in pericarps of Mallotus japonicus. Planta Med 56:377-379. doi: 10.1055/s-2006-960987
54. Ishiguro K, Yamaki M, Kashihara M, Takagi S (1987) Soroaspindin A, B, and C: additional antibiotic compounds from Hypericum japonicum. Planta Med 53:415-417. doi: 10.1055/s-2006-962760