Development of predictive pharmacophore model for in silico screening, and 3D QSAR CoMFA and CoMSIA studies for lead optimization, for designing of potent tumor necrosis factor alpha converting enzyme inhibitors

Journal of Computer-Aided Molecular Design

Volumn 24, Issue 2, 2010, Pages 143-156

  Murumkar, Prashant Revan ^a   Zambre, Vishal Prakash ^a   Yadav, Mange Ram ^a  

^a M S UNIVERSITY OF BARODA   (India)

Author keywords

3D QSAR; In silico screening; Pharmacophore model; TACE inhibitors

Indexed keywords

DATABASE SYSTEMS; DIAGNOSIS; ENZYMES; HYDROGEN BONDS; MACROPHAGES; MOLECULES; PHARMACODYNAMICS; TUMORS;

3D-QSAR; CHEMICAL FEATURES; CONVERTING ENZYME; ENZYME INHIBITORS; FEATURE-BASED; IN-SILICO SCREENING; LEAD OPTIMIZATION; PHARMACOPHORE MODELS; TACE INHIBITOR; TUMOR NECROSIS FACTOR-ALPHA;

LEAD COMPOUNDS;

LIGAND; TUMOR NECROSIS FACTOR ALPHA CONVERTING ENZYME INHIBITOR;

ARTICLE; CHEMICAL MODIFICATION; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; COMPUTER MODEL; CRYSTAL STRUCTURE; DATA BASE; DRUG ACTIVITY; DRUG DESIGN; DRUG STRUCTURE; HYDROGEN BOND; IC 50; PHARMACOPHORE; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; VALIDATION STUDY;

EID: 77950916156     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-010-9322-z     Document Type: Article

References (32)

1. RA Black CT Rauch CJ Kozlosky JJ Peschon JL Slack MF Wolfson BJ Castner KL Stocking P Reddy S Srinivasan N Nelson N Boiani KA Schooley M Gerhart R Davis JN Fitzner RS Johnson RJ Paxton CJ March DP Cerretti 1997 A metalloproteinase disintegrin that releases tumour-necrosis factor-α from cells Nature 385 729 733 10.1038/385729a0 10.1038/385729a0 1:CAS:528:DyaK2sXhsVGktLs%3D (Pubitemid 27098094)
2. P Vassalli 1992 The pathophysiology of tumor necrosis factors Ann Rev Immunol 10 411 452 10.1146/annurev.iy.10.040192.002211 10.1146/annurev.iy.10. 040192.002211 1:CAS:528:DyaK38XltV2ntLg%3D
3. RN Maini MJ Elliott FM Brennan M Feldmann 1995 Beneficial effects of tumour necrosis factor-alpha (TNF-alpha) blockade in rheumatoid arthritis (RA) Clin Exp Immunol 101 207 212 1:CAS:528:DyaK2MXosVGju7s%3D
4. MJ Elliott RN Maini M Feldmann A Long-Fox P Charles H Bijl JN Woody 1994 Repeated therapy with monoclonal antibody to tumour necrosis factor alpha (cA2) in patients with rheumatoid arthritis Lancet 344 1125 1127 10.1016/S0140- 6736(94)90632-7 1:STN:280:DyaK2M%2FitVWkuw%3D%3D (Pubitemid 24317633)
5. SL Dixon AM Smondyrev SN Rao 2006 PHASE: a novel approach to pharmacophore modeling and 3D database searching Chem Biol Drug Des 67 370 372 10.1111/j.1747-0285.2006.00384.x 10.1111/j.1747-0285.2006.00384.x 1:CAS:528:DC%2BD28XotVeqsbg%3D (Pubitemid 43910070)
6. O Mutasem LA Taha YB Dahabiyesh Z Hiba S Suhair 2008 Combining ligand-based pharmacophore modeling, quantitative structure-activity relationship analysis and in silico screening for the discovery of new potent hormone sensitive lipase inhibitors J Med Chem 51 6478 6494 10.1021/jm800718k 10.1021/jm800718k
7. K Maskos C Fernandez-Catalan R Huber GP Bourenkov H Bartunik GA Ellestad P Reddy MF Wolfson CT Rauch BJ Castner R Davis HR Clarke M Petersen JN Fitzner DP Cerretti CJ March RJ Paxton RA Black W Bode 1998 Crystal structure of the catalytic domain of human tumor necrosis factor-α-converting enzyme Proc Natl Acad Sci USA 95 3408 3412 10.1073/pnas.95.7.3408 1:CAS:528: DyaK1cXitlGqu7g%3D (Pubitemid 28173141)
8. RC Newton CP Decicco 1999 Therapeutic potential and strategies for inhibiting tumor necrosis factor-α J Med Chem 42 2295 2314 10.1021/jm980541n 10.1021/jm980541n 1:CAS:528:DyaK1MXktVOktb8%3D (Pubitemid 29305163)
9. Grootveld M, McDermott M (2003) BMS-561392 (Bristol-Myers Squibb). Curr Opin Investig Drugs 4:598-602. PMID: 12833656
10. GI Mustata A Brigo JM Briggs 2004 HIV-1 integrase pharmacophore model derived from diverse classes of inhibitors Bioorg Med Chem Lett 14 1447 1454 10.1016/j.bmcl.2004.01.027 10.1016/j.bmcl.2004.01.027 1:CAS:528: DC%2BD2cXhvV2it7s%3D (Pubitemid 38299427)
11. PR Murumkar R Giridhar MR Yadav 2008 3D-quantitative structure-activity relationship studies on benzothiadiazepine hydroxamates as inhibitors of tumor necrosis factor-α converting enzyme Chem Biol Drug Des 71 363 373 10.1111/j.1747-0285.2008.00639.x 10.1111/j.1747-0285.2008.00639.x 1:CAS:528:DC%2BD1cXkvFensr0%3D (Pubitemid 351347790)
12. PR Murumkar SD Dasgupta VP Zambre R Giridhar MR Yadav 2009 Development of predictive 3D-QSAR CoMFA and CoMSIA models for α-aminohydroxamic acid-derived tumor necrosis factor-α converting enzyme inhibitors Chem Biol Drug Des 73 97 107 10.1111/j.1747-0285.2008.00737.x 10.1111/j.1747-0285. 2008.00737.x 1:CAS:528:DC%2BD1MXptFCntw%3D%3D
13. PR Murumkar SD Dasgupta SR Chandani R Giridhar MR Yadav 2010 Novel TACE inhibitors in drug discovery: a review of patented compounds Expert Opin Ther Pat 20 31 57 10.1517/13543770903465157 10.1517/13543770903465157 1:CAS:528:DC%2BD1MXhs1SmsbvO
14. S Dasgupta PR Murumkar R Giridhar MR Yadav 2009 Current perspective of TACE inhibitors: a review Bioorg Med Chem 17 444 459 10.1016/j.bmc.2008.11.067 10.1016/j.bmc.2008.11.067 1:CAS:528:DC%2BD1MXhtFertLY%3D
15. S Dasgupta PR Murumkar R Giridhar MR Yadav 2009 Studies on novel 2-imidazolidinones and tetrahydropyrimidin-2(1H)-ones as potential TACE inhibitors: design, synthesis, molecular modeling, and preliminary biological evaluation Bioorg Med Chem 17 3604 3617 10.1016/j.bmc.2009.04.003 10.1016/j.bmc.2009.04.003 1:CAS:528:DC%2BD1MXlsVCksL4%3D
16. Yadav MR, Dasgupta S, Murumkar PR, Giridhar R (2010) In: Berhardt L (ed) Advances in medicine and biology, vol 3. Nova Science, New York (in press)
17. SL Dixon AM Smondyrev EH Knoll SN Rao DE Shaw RA Friesner 2006 PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1 methodology and preliminary results Computer-Aided Mol Des 20 647 667 10.1007/s10822-006-9087-6 10.1007/s10822-006-9087-6 1:CAS:528:DC%2BD28XhtlCksbvE (Pubitemid 46023928)
18. JJ Duan L Chen ZR Wasserman Z Lu RQ Liu MB Covington M Qian KD Hardman RL Magolda Christ DD Newton RR Wexler CP Decicco 2002 Discovery of γ-lactam hydroxamic acids as selective inhibitors of tumor necrosis factor-α converting enzyme: design, synthesis, and structure-activity relationships J Med Chem 45 4954 4957 10.1021/jm0255670 10.1021/jm0255670 1:CAS:528: DC%2BD38XnvV2lu70%3D (Pubitemid 35278690)
19. JJ Duan Z Lu C Xue X He JL Seng JJ Roderick ZR Wasserman R Liu MB Covington RL Magolda RC Newton JM Trzaskos CP Decicco 2003 Discovery of N-Hydroxy-2-(2-oxo-3-pyrrolidinyl)acetamides as potent and selective inhibitors of tumor necrosis factor-α converting enzyme (TACE) Bioorg Med Chem Lett 13 2035 2040 10.1016/S0960-894X(03)00313-5 10.1016/S0960-894X(03)00313-5 1:CAS:528:DC%2BD3sXktVGqtro%3D (Pubitemid 36638405)
20. C Xue X He J Roderick RL Corbett JJ Duan RQ Liu MB Covinton M Qian MD Ribadeneira K Vaddi DD Christ RC Newton JM Trzaskos RL Magolda RR Wexler CP Decicco 2003 Rational design, synthesis and structure-activity relationships of a cyclic succinate series of TNF-α converting enzyme inhibitors. Part 2: lead optimization Bioorg Med Chem Lett 13 4299 4304 10.1016/j.bmcl.2003.09.057 10.1016/j.bmcl.2003.09.057 1:CAS:528:DC%2BD3sXpt1yrt7Y%3D (Pubitemid 37490807)
21. JL Gilmore Bryan W King N Asakawa K Harrison A Tebben JE Sheppeck II RQ Liu M Covington JJW Duan 2007 Synthesis and structure-activity relationship of a novel, non-hydroxamate series of TNF-α converting enzyme inhibitors Bioorg Med Chem Lett 17 4678 4682 10.1016/j.bmcl.2007.05.100 10.1016/j.bmcl.2007.05.100 1:CAS:528:DC%2BD2sXotFSiuro%3D (Pubitemid 47058928)
22. JJW Duan Z Lu ZR Wasserman R Liu MB Convington CP Decicco 2005 Non-hydroxamate 5-phenylpyrimidine-2, 4, 6-trione derivatives as selective inhibitors of tumor necrosis factor-α converting enzyme Bioorg Med Chem Lett 15 2970 2973 10.1016/j.bmcl.2005.04.039 10.1016/j.bmcl.2005.04.039 1:CAS:528:DC%2BD2MXltFWgt7s%3D (Pubitemid 40755180)
23. JL Gilmore BW King C Harris T Maduskuie SE Mercer R Liu MB Convington M Qian MD Ribadeneria K Vaddi JM Trzaskos RC Newton CP Decicco JJW Duan 2006 Synthesis and structure-activity relationship of a novel, achiral series of TNF-α converting enzyme inhibitors Bioorg Med Chem Lett 16 2699 2704 10.1016/j.bmcl.2006.02.015 10.1016/j.bmcl.2006.02.015 1:CAS:528: DC%2BD28XjtFGitrs%3D
24. JE Sheppeck JL Gilmore A Yang ZR Wasserman CP Decicco JJW Duan 2007 A molecular modeling analysis of novel non-hydroxamate inhibitors of TACE Bioorg Med Chem Lett 17 1408 1412 10.1016/j.bmcl.2006.11.082 10.1016/j.bmcl.2006.11.082 1:CAS:528:DC%2BD2sXhvVyjt7Y%3D (Pubitemid 46240837)
25. JE Sheppeck JL Gilmore A Yang X Chen CB Xue J Roderick RQ Liu MB Covington CP Decicco JJW Duan 2007 Discovery of novel hydantoins as selective non-hydroxamate inhibitors of tumor necrosis factor-α converting enzyme (TACE) Bioorg Med Chem Lett 17 1413 1417 10.1016/j.bmcl.2006.11.089 10.1016/j.bmcl.2006.11.089 1:CAS:528:DC%2BD2sXhvVyjt7c%3D (Pubitemid 46240831)
26. GR Ott N Asakawa Z Lu RQ Liu MB Convington K Vaddi M Quin RC Newton D Christ JM Traskos CP Decicco JJW Duan 2008 α, β-Cyclic-β- benzamido hydroxamic acids: novel templates for the design, synthesis, and evaluation of selective inhibitors of TNF-α converting enzyme (TACE) Bioorg Med Chem Lett 18 694 699 10.1016/j.bmcl.2007.11.059 10.1016/j.bmcl.2007. 11.059 1:CAS:528:DC%2BD1cXosFWluw%3D%3D
27. GR Ott N Asakawa RQ Liu MB Convington K Vaddi RC Newton JM Traskos DD Christ L Galya T Cholz W Marshall JJW Duan 2008 α,β-Cyclic-β- benzamido hydroxamic acids: novel oxaspiro[4.4]nonane templates for the discovery of potent, selective, orally bioavailable inhibitors of tumor necrosis factor-α converting enzyme (TACE) Bioorg Med Chem Lett 18 1288 1292 10.1016/j.bmcl.2008.01.030 10.1016/j.bmcl.2008.01.030 1:CAS:528: DC%2BD1cXitlajt7g%3D (Pubitemid 351226547)
28. Z Lu GR Ott R Anad RQ Liu MB Convington K Vaddi M Qian RC Newton DD Christ JM Traskos JJW Duan 2008 Potent, selective, orally bioavailable inhibitors of tumor necrosis factor-α converting enzyme (TACE): discovery of indole, benzofuran, imidazopyridine and pyrazolopyridine P1 substituents Bioorg Med Chem Lett 18 1958 1962 10.1016/j.bmcl.2008.01.120 10.1016/j.bmcl.2008.01.120 1:CAS:528:DC%2BD1cXjtlyms7o%3D (Pubitemid 351380894)
29. GR Ott N Asakawa Z Lu R Anad RQ Liu MB Convington K Vaddi M Qian RC Newton DD Christ JM Traskos JJW Duan 2008 Potent, exceptionally selective, orally bioavailable inhibitors of TNF-α converting enzyme (TACE): novel 2-substituted-1H-benzo[d]imidazol-1-yl)methyl)benzamide P1 substituents Bioorg Med Chem Lett 18 1577 1582 10.1016/j.bmcl.2008.01.075 10.1016/j.bmcl.2008.01.075 1:CAS:528:DC%2BD1cXjt1Cksbo%3D (Pubitemid 351318259)
30. SYBYL 7.0 (1699) Tripos Inc., 1st Louis
31. http://www.expasy.org/blast
32. Entry A7Y1V1: http://www.expasy.org/uniport/A7Y1V1