Identification of novel potential HIF-prolyl hydroxylase inhibitors by in silico screening

Molecular Diversity

Volumn 16, Issue 1, 2012, Pages 193-202

  Teli, Mahesh Kumar ^a   Rajanikant, G K ^a  

^a NATIONAL INSTITUTE OF TECHNOLOGY CALICUT   (India)

Author keywords

Docking; HIF prolyl hydroxylase inhibitor; Ischemia; Pharmacophore model; Virtual screening

Indexed keywords

ENZYME INHIBITOR; ESSENTIAL AMINO ACID; HYPOXIA INDUCIBLE FACTOR; HYPOXIA INDUCIBLE FACTOR PROCOLLAGEN PROLINE 2 OXOGLUTARATE 4 DIOXYGENASE INHIBITOR; PROCOLLAGEN PROLINE 2 OXOGLUTARATE 4 DIOXYGENASE; UNCLASSIFIED DRUG;

ARTICLE; COMPUTER MODEL; DRUG ABSORPTION; DRUG DISTRIBUTION; DRUG EXCRETION; DRUG METABOLISM; DRUG SCREENING; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; MOLECULAR DOCKING; PHARMACOPHORE; PRIORITY JOURNAL;

CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; DRUG EVALUATION, PRECLINICAL; ENZYME INHIBITORS; HUMANS; HYPOXIA-INDUCIBLE FACTOR 1; MODELS, MOLECULAR; PROCOLLAGEN-PROLINE DIOXYGENASE; REPRODUCIBILITY OF RESULTS;

EID: 84858705244     PISSN: 13811991     EISSN: 1573501X     Source Type: Journal    
DOI: 10.1007/s11030-011-9338-x     Document Type: Article

References (32)

1. Bergeron M, Gidday JM, Yu AY, Semenza GL, Ferriero DM et al (2000) Role of hypoxia-inducible factor-1 in hypoxia-induced ischemic tolerance in neonatal rat brain. Ann Neurol 48: 285-296. doi:10.1002/1531-8249(200009)48:3〈285:: AID-ANA2〉3.3.CO;2-#
2. Semenza GL (2003) Targeting HIF-1 for cancer therapy. Nat Rev Cancer 3: 721-732. doi:10.1038/nrc1187
3. Elvidge GP,Glenny L,Appelhoff RJ, Ratcliffe PJ, Ragoussis J et al (2006) Concordant regulation of gene expression by hypoxia and 2-oxoglutarate dependent dioxygenase inhibition; the role of HIF- 1α, HIF-2α and other pathways. J Biol Chem 281: 15215-15226. doi:10.1074/jbc.M511408200 (Pubitemid 43855111)
4. Wenger RH, Stiehl DP, CamenischG (2005) Integration of oxygen signaling at the consensus HRE. Sci Signal 306:re12. doi:10.1126/ stke.3062005re12
5. Gidday JM, Fitzgibbons JC, Shah AR, Park TS (1994) Neuroprotection from ischemic brain injury by hypoxic preconditioning in the neonatal rat. Neurosci Lett 168: 221-224. doi:10.1016/0304-3940(94)90455-3 (Pubitemid 24097362)
6. Miller BA, Perez RS, Shah AR, Gonzales ER, Park TS et al (2001) Cerebral protection by hypoxic preconditioning in amurine model of focal ischemia-reperfusion. Neuroreport 12: 1663-1669. doi:10.1097/00001756-200106130- 00030 (Pubitemid 32521483)
7. Harten SK, Ashcroft M, Maxwell PH (2010) Prolyl hydroxylase domain inhibitors: a route to HIF activation and neuroprotection. Antioxid Redox Signal 12: 459-480. doi:10.1089/ars.2009.2870
8. Tian YM, Yeoh KK, Lee MK, Eriksson T, Kessler BM et al (2011) Differential sensitivity of hypoxia inducible factor hydroxylation sites to hypoxia and hydroxylase inhibitors. J Biol Chem 286: 13041-13051. doi:10.1074/jbc.M110.211110
9. Murray JK, Balan C, Allgeier AM, Kasparian A, Viswanadhan V et al (2010) Dipeptidyl-quinolone derivatives inhibit hypoxia inducible factor-1α prolyl hydroxylases-1, -2, and -3 with altered selectivity. J Comb Chem 12: 676-686. doi:10.1021/cc100073a
10. Mecinović J, Loenarz C, Chowdhury R, Schofield CJ (2009) 2- Oxoglutarate analogue inhibitors of prolyl hydroxylase domain 2. Bioorg Med Chem Lett 19: 6192-6195. doi:10.1016/j.bmcl.2009.09.005
11. Siddiq A, Ayoub IA, Chavez JC, Aminova L, Shah S et al (2005) Hypoxia-inducible factor prolyl 4-hydroxylase inhibition. A target for neuroprotection in the central nervous system. J Biol Chem 280: 41732-41743. doi:10.1074/jbc.M504963200 (Pubitemid 41832236)
12. Semenza GL (2009) Regulation of vascularization by hypoxia-inducible factor 1. Ann N Y Acad Sci 1177: 2-8. doi:10.1111/j.1749-6632.2009.05032.x
13. Takeda K, Ichiki T, Narabayashi E, Inanaga K, Miyazaki R et al (2009) Inhibition of prolyl hydroxylase domain-containing protein suppressed lipopolysaccharide-induced TNF-α expression. Arterioscler Thromb Vasc Biol 29: 2132-2137. doi:10.1161/ATVBAHA.109.196071
14. Pala N, Dallocchio R, Dessì A, Brancale A, Carta F et al (2011) Virtual screening-driven identification of human carbonic anhydrase inhibitors incorporating an original, new pharmacophore. Bioorg Med Chem Lett 21: 2515-2520. doi:10.1016/j.bmcl.2011.02.059
15. Gupta AK, Bhunia SS, Balaramnavar VM, Saxena AK (2011) Pharmacophore modelling, molecular docking and virtual screening for EGFR (HER 1) tyrosine kinase inhibitors. SAR QSAR Environ Res 22: 239-263. doi:10.1080/1062936X.2010. 548830
16. Bagga V, Silakari O, Ghorela VS, Bahia MS, Rambabu G et al (2011) A three-dimensional pharmacophore modelling of ITK inhibitors and virtual screening for novel inhibitors. SAR QSAR Environ Res 22: 171-190. doi:10.1080/1062936X.2010.510480
17. Sala E, Guasch L, Iwaszkiewicz J, Mulero M, Salvadó MJ et al (2011) Identification of human IKK-2 inhibitors of natural origin (part I): modeling of the IKK-2 kinase domain, virtual screening and activity assays. PLoS One 6:e16903. doi:10.1371/journal.pone.0016903
18. John S, Thangapandian S, Sakkiah S, Lee KW (2011) Potent BACE-1 inhibitor design using pharmacophore modeling, in silico screening and molecular docking studies. BMCBioinformatics 12(suppl 1):S28. doi:10.1186/1471-2105-12-S1-S28
19. Lu SH,Wu JW, Liu HL, Zhao JH, Liu KT et al (2011) The discovery of potential acetylcholinesterase inhibitors: a combination of pharmacophore modeling, virtual screening, and molecular docking studies. J Biomed Sci 18:8. doi:10.1186/1423-0127-18-8
20. Noha SM, Atanasov AG, Schuster D, Markt P, Fakhrudin N et al (2011) Discovery of a novel IKK-β inhibitor by ligand-based virtual screening techniques. Bioorg Med Chem Lett 21: 577-583. doi:10.1016/j.bmcl.2010.10.051
21. Chen Z, Tian G, Wang Z, Jiang H, Shen J et al (2010) Multiple pharmacophore models combined with molecular docking: a reliable way for efficiently identifying novel PDE4 inhibitors with high structural diversity. J Chem Inf Model 50: 615-625. doi:10.1021/ci9004173
22. Peach ML, Nicklaus MC (2009) Combining docking with pharmacophore filtering for improved virtual screening. J Cheminform 1:6. doi:10.1186/1758- 2946-1-6
23. Maestro, version 9.1 (2010) Schrödinger, LLC, New York
24. LigPrep, version 2.4 (2010) Schrödinger, LLC, New York
25. Schrödinger Suite 2009 (2009) Protein Preparation Wizard; Epik version 2.0; Impact version 5.5; Prime version 2.1, Schrödinger, LLC, New York
26. Phase, version 3.2 (2010) Schrödinger, LLC, New York, NY
27. Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA (2006) PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des 20: 647-671. doi:10.1007/s10822-006-9087-6 (Pubitemid 46023928)
28. Warshakoon NC, Wu S, Boyer A, Kawamoto R, Sheville J, Bhatt RT, Renock S, Xu K, Pokross M, Zhou S, Walter R, Mekel M, Evdokimov AG, East S (2006) Design and synthesis of substituted pyridine derivatives as HIF-1alpha prolyl hydroxylase inhibitors. Bioorg Med Chem Lett 16: 5616-5620. doi:10.1016/j.bmcl. 2006.08.026 (Pubitemid 44415448)
29. QikProp, version 3.3 (2010) Schrödinger, LLC, New York, NY
30. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 46: 3-26. doi:10.1016/S0169-409X(00)00129-0
31. Schrödinger Suite 2010 (2010) Induced fit docking protocol; Glide version 5.6; Prime version 2.2, Schrödinger, LLC, New York
32. Glide, version 5.5 (2009) Schrödinger, LLC, New York, NY