On the value of homology models for virtual screening: Discovering hCXCR3 antagonists by pharmacophore-based and structure-based approaches

Journal of Chemical Information and Modeling

Volumn 52, Issue 5, 2012, Pages 1356-1366

  Huang, Dane ^a   Gu, Qiong ^a   Ge, Hu ^a   Ye, Jiming ^b   Salam, Noeris K ^d   Hagler, Arnie ^c,d   Chen, Hongzhuan ^e   Xu, Jun ^a  

^a SUN YAT SEN UNIVERSITY   (China)

^b RMIT UNIVERSITY   (Australia)

^c UNIVERSITY OF MASSACHUSETTS   (United States)

^d Shifa Biomedical   (United States)

^e SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER VIRUSES; MOLECULAR DYNAMICS; PHARMACODYNAMICS;

ANTI-INFLAMMATORY AGENTS; CHEMOKINE RECEPTORS; FALSE NEGATIVE RATE; HOMOLOGY MODELING; MOLECULAR DYNAMICS SIMULATIONS; PHARMACOPHORE MODELING; THERAPEUTIC APPLICATION; VIRTUAL SCREENING;

COMPUTATIONAL CHEMISTRY;

CHEMOKINE RECEPTOR CXCR3; CXCR3 PROTEIN, HUMAN; LIGAND;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; COMPUTER SIMULATION; DRUG ANTAGONISM; DRUG DEVELOPMENT; DRUG SCREENING; HUMAN; IC 50; MOLECULAR DYNAMICS; QUANTITATIVE STRUCTURE ACTIVITY RELATION; QUANTUM THEORY;

BINDING SITES; COMPUTER SIMULATION; DRUG DISCOVERY; DRUG EVALUATION, PRECLINICAL; HUMANS; INHIBITORY CONCENTRATION 50; LIGANDS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; QUANTUM THEORY; RECEPTORS, CXCR3;

EID: 84861517739     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300067q     Document Type: Article

References (39)

1. Gerard, C.; Rollins, B. J. Chemokines and disease Nat. Immunol. 2001, 2, 108-115 (Pubitemid 33707927)
2. Charo, I. F.; Ransohoff, R. M. The many roles of chemokines and chemokine receptors in inflammation N. Engl. J. Med. 2006, 354, 610-621 (Pubitemid 43209108)
3. Zeremski, M.; Dimova, R.; Brown, Q.; Jacobson, I. M.; Markatou, M.; Talal, A. H. Peripheral CXCR3-associated chemokines as biomarkers of fibrosis in chronic hepatitis C virus infection J. Infect. Dis. 2009, 200, 1774-1780
4. Wareing, M. D.; Lyon, A. B.; Lu, B.; Gerard, C.; Sarawar, S. R. Chemokine expression during the development and resolution of a pulmonary leukocyte response to influenza A virus infection in mice J. Leukocyte Biol. 2004, 76, 886-895 (Pubitemid 39313726)
5. Clark-Lewis, I.; Mattioli, I.; Gong, J. H.; Loetscher, P. Structure-function relationship between the human chemokine receptor CXCR3 and its ligands J. Biol. Chem. 2003, 278, 289-295 (Pubitemid 36043575)
6. Vola, A.; Luster, A. D. Chemokines and their receptors: Drug targets in immunity and inflammation Annu. Rev. Pharmacol. Toxicol. 2008, 48, 171-197 (Pubitemid 351756361)
7. Huan, C.; Gui-Ying, Z. Advances in chemokine receptor CXCR3 research Pract. Prev. Med. 2010, 17, 1466-1468
8. Knight, R. L.; Allen, D. R.; Birch, H. L.; Chapman, G. A.; Galvin, F. C.; Jopling, L. A.; Lock, C. J.; Meissner, J. W.; Owen, D. A.; Raphy, G.; Watson, R. J.; Williams, S. C. Development of CXCR3 antagonists. Part 4: Discovery of 2-amino-(4-tropinyl)quinolines Bioorg. Med. Chem. Lett. 2008, 18, 629-633
9. Watson, R. J.; Allen, D. R.; Birch, H. L.; Chapman, G. A.; Galvin, F. C.; Jopling, L. A.; Knight, R. L.; Meier, D.; Oliver, K.; Meissner, J. W.; Owen, D. A.; Thomas, E. J.; Tremayne, N.; Williams, S. C. Development of CXCR3 antagonists. Part 3: Tropenyl and homotropenyl-piperidine urea derivatives Bioorg. Med. Chem. Lett. 2008, 18, 147-151
10. Watson, R. J.; Allen, D. R.; Birch, H. L.; Chapman, G. A.; Hannah, D. R.; Knight, R. L.; Meissner, J. W.; Owen, D. A.; Thomas, E. J. Development of CXCR3 antagonists. Part 2: Identification of 2-amino(4-piperidinyl)azoles as potent CXCR3 antagonists Bioorg. Med. Chem. Lett. 2007, 17, 6806-6810 (Pubitemid 350081103)
11. Shao, Y.; Anilkumar, G. N.; Carroll, C. D.; Dong, G.; Hall, J. W., 3rd; Hobbs, D. W.; Jiang, Y.; Jenh, C. H.; Kim, S. H.; Kozlowski, J. A.; McGuinness, B. F.; Rosenblum, S. B.; Schulman, I.; Shih, N. Y.; Shu, Y.; Wong, M. K.; Yu, W.; Zawacki, L. G.; Zeng, Q., II. SAR studies of pyridyl-piperazinyl-piperidine derivatives as CXCR3 chemokine antagonists Bioorg. Med. Chem. Lett. 2011, 21, 1527-1531
12. Du, X. H.; Gustin, D. J.; Chen, X. Q.; Duquette, J.; Mcgee, L. R.; Wang, Z. L.; Ebsworth, K.; Henne, K.; Lemon, B.; Ma, J.; Miao, S.; Sabalan, E.; Sullivan, T. J.; Tonn, G.; Collins, T. L.; Medina, J. C. Imidazo-pyrazine derivatives as potent CXCR3 antagonists Bioorg. Med. Chem. Lett. 2009, 19, 5200-5204
13. Wang, Y. H.; Busch-Petersen, J.; Wang, F.; Kiesow, T. J.; Graybill, T. L.; Jin, J.; Yang, Z.; Foley, J. J.; Hunsberger, G. E.; Schmidt, D. B.; Sarau, H. M.; Capper-Spudich, E. A.; Wu, Z. N.; Fisher, L. S.; McQueney, M. S.; Rivero, R. A.; Widdowson, K. L. Camphor sulfonamide derivatives as novel, potent and selective CXCR3 antagonists Bioorg. Med. Chem. Lett. 2009, 19, 114-118
14. Bongartz, J. P.; Buntinx, M.; Coesemans, E.; Hermans, B.; Lommen, G. V.; Wauwe, J. V. Synthesis and structure-activity relationship of benzetimide derivatives as human CXCR3 antagonists Bioorg. Med. Chem. Lett. 2008, 18, 5819-5823
15. Thoma, G.; Baenteli, R.; Lewis, I.; Wagner, T.; Oberer, L.; Blum, W.; Glickman, F.; Streiff, M. B.; Zerwes, H. G. Special ergolines are highly selective, potent antagonists of the chemokine receptor CXCR3: Discovery, characterization and preliminary SAR of a promising lead Bioorg. Med. Chem. Lett. 2009, 19, 6185-6188
16. Afantitis, A.; Melagraki, G.; Sarimveis, H.; Igglessi-Markopoulou, O.; Kollias, G. A novel QSAR model for predicting the inhibition of CXCR3 receptor by 4-N-aryl-[1,4] diazepane ureas Eur. J. Med. Chem. 2009, 44, 877-884
17. Afantitis, A.; Melagraki, G.; Sarimveis, H.; Koutentis, P. A.; Igglessi-Markopoulou, O.; Kollias, G. A combined LS-SVM & MLR QSAR workflow for predicting the inhibition of CXCR3 receptor by quinazolinone analogs Mol. Diversity 2010, 14, 225-235
18. Discovery Studio, version 2.1; Accelrys, Inc.: San Diego, CA, 2007.
19. Wu, B.; Chien, E. Y.; Mol, C. D.; Fenalti, G.; Liu, W.; Katritch, V.; Abagyan, R.; Brooun, A.; Wells, P.; Bi, F. C.; Hamel, D. J.; Kuhn, P.; Handel, T. M.; Cherezov, V.; Stevens, R. C. Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists Science 2010, 330, 1066-1071
20. Gao, J. M.; Xiang, R. L.; Jiang, L.; Li, W. H.; Feng, Q. P.; Guo, Z. J.; Sun, Q.; Zeng, Z. P.; Fang, F. D. Sulfated tyrosines 27 and 29 in the N-terminus of human CXCR3 participate in binding native IP-10 Acta Pharmacol. Sin. 2009, 30, 193-201
21. Bowers, K. J.; Chow, E.; Xu, H.; Dror, R. O.; Eastwood, M. P.; Gregersen, B. A.; Klepeis, J. L.; Kolossvary, I.; Moraes, M. A.; Sacerdoti, F. D.; Salmon, J. K.; Shan, Y.; Shaw, D. E. Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters. In Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, ACM: Tampa, FL, 2006.
22. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N [center-dot] log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
23. Krautler, V.; Van Gunsteren, W. F.; Hunenberger, P. H. A fast SHAKE: Algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations J. Comput. Chem. 2001, 22, 501-508 (Pubitemid 32291686)
24. Tuckerman, M.; Berne, B. J.; Martyna, G. J. Reversible multiple time scale molecular dynamics J. Chem. Phys. 1992, 97, 1990-2001
25. Du, X.; Chen, X.; Mihalic, J. T.; Deignan, J.; Duquette, J.; Li, A. R.; Lemon, B.; Ma, J.; Miao, S.; Ebsworth, K.; Sullivan, T. J.; Tonn, G.; Collins, T. L.; Medina, J. C. Design and optimization of imidazole derivatives as potent CXCR3 antagonists Bioorg. Med. Chem. Lett. 2008, 18, 608-613
26. Liu, J.; Fu, Z.; Li, A. R.; Johnson, M.; Zhu, L.; Marcus, A.; Danao, J.; Sullivan, T.; Tonn, G.; Collins, T.; Medina, J. Optimization of a series of quinazolinone-derived antagonists of CXCR3 Bioorg. Med. Chem. Lett. 2009, 19, 5114-5118
27. Crosignani, S.; Missotten, M.; Cleva, C.; Dondi, R.; Ratinaud, Y.; Humbert, Y.; Mandal, A. B.; Bombrun, A.; Power, C.; Chollet, A.; Proudfoot, A. Discovery of a novel series of CXCR3 antagonists Bioorg. Med. Chem. Lett. 2010, 20, 3614-3617
28. Johnson, M.; Li, A. R.; Liu, J.; Fu, Z.; Zhu, L.; Miao, S.; Wang, X.; Xu, Q.; Huang, A.; Marcus, A.; Xu, F.; Ebsworth, K.; Sablan, E.; Danao, J.; Kumer, J.; Dairaghi, D.; Lawrence, C.; Sullivan, T.; Tonn, G.; Schall, T.; Collins, T.; Medina, J. Discovery and optimization of a series of quinazolinone-derived antagonists of CXCR3 Bioorg. Med. Chem. Lett. 2007, 17, 3339-3343 (Pubitemid 46819037)
29. Cole, A. G.; Stroke, I. L.; Brescia, M. R.; Simhadri, S.; Zhang, J. J.; Hussain, Z.; Snider, M.; Haskell, C.; Ribeiro, S.; Appell, K. C.; Henderson, I.; Webb, M. L. Identification and initial evaluation of 4-N-aryl-[1,4]diazepane ureas as potent CXCR3 antagonists Bioorg. Med. Chem. Lett. 2006, 16, 200-203 (Pubitemid 41625670)
30. Li, A. R.; Johnson, M. G.; Liu, J.; Chen, X.; Du, X.; Mihalic, J. T.; Deignan, J.; Gustin, D. J.; Duquette, J.; Fu, Z.; Zhu, L.; Marcus, A. P.; Bergeron, P.; McGee, L. R.; Danao, J.; Lemon, B.; Carabeo, T.; Sullivan, T.; Ma, J.; Tang, L.; Tonn, G.; Collins, T. L.; Medina, J. C. Optimization of the heterocyclic core of the quinazolinone-derived CXCR3 antagonists Bioorg. Med. Chem. Lett. 2008, 18, 688-693
31. McGuinness, B. F.; Carroll, C. D.; Zawacki, L. G.; Dong, G.; Yang, C.; Hobbs, D. W.; Jacob-Samuel, B.; Hall, J. W., 3rd; Jenh, C. H.; Kozlowski, J. A.; Anilkumar, G. N.; Rosenblum, S. B. Novel CXCR3 antagonists with a piperazinyl-piperidine core Bioorg. Med. Chem. Lett. 2009, 19, 5205-5208
32. Glide, v5.7; Schrödinger, LLC: New York, 2011.
33. Manual of Molecular Operating Environment (MOE), version 2010; Chemical Computing Group, Inc.: Montreal, Quebec, Canada, 2010.
34. Zhao, W.; Gu, Q.; Wang, L.; Ge, H.; Li, J.; Xu, J. Three-dimensional pharmacophore modeling of liver-X receptor agonists J. Chem. Inf. Model. 2011, 51, 2147-2155
35. John, S.; Thangapandian, S.; Sakkiah, S.; Lee, K. W. Potent bace-1 inhibitor design using pharmacophore modeling, in silico screening and molecular docking studies BMC Bioinf. 2011, 12
36. Güner, O. F. Pharmacophore Perception, Development, and Use in Drug Design; International University Line: LaJolla, CA, 2000.
37. Luthy, R.; McLachlan, A. D.; Eisenberg, D. Secondary structure-based profiles: use of structure-conserving scoring tables in searching protein sequence databases for structural similarities Proteins 1991, 10, 229-239
38. Luthy, R.; Bowie, J. U.; Eisenberg, D. Assessment of protein models with three-dimensional profiles Nature 1992, 356, 83-85
39. Kyte, J.; Doolittle, R. F. A simple method for displaying the hydropathic character of a protein J. Mol. Biol. 1982, 157, 105-132