Virtual screening of novel noncovalent inhibitors for SARS-CoV 3C-like proteinase

Journal of Chemical Information and Modeling

Volumn 45, Issue 1, 2005, Pages 10-17

  Liu, Zhenming ^a,b   Huang, Changkang ^a   Fan, Keqiang ^a   Wei, Ping ^a   Chen, Hao ^a,b   Liu, Shiyong ^a,b   Pei, Jianfeng ^a,b   Shi, Lei ^a   Li, Bo ^a   Yang, Kun ^a,b   Liu, Ying ^a   Lai, Luhua ^a,b  

^a PEKING UNIVERSITY   (China)

^b PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SYSTEMS; ENZYME INHIBITION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; PULMONARY DISEASES; THREE DIMENSIONAL; VIRUSES;

DRUG DESIGN; NONCOVALENT INHIBITORS; PROTEINASE; VIRTUAL SCREENING;

ENZYMES;

3C LIKE PROTEASE, SARS CORONAVIRUS; 3C-LIKE PROTEASE, SARS CORONAVIRUS; CALMIDAZOLIUM; CYSTEINE PROTEINASE; IMIDAZOLE DERIVATIVE; PROTEINASE; PROTEINASE INHIBITOR; VIRUS PROTEIN;

ARTICLE; BINDING SITE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER AIDED DESIGN; COMPUTER SIMULATION; DRUG ANTAGONISM; DRUG DESIGN;

BINDING SITES; COMPUTER SIMULATION; COMPUTER-AIDED DESIGN; CYSTEINE ENDOPEPTIDASES; DRUG DESIGN; ENDOPEPTIDASES; IMIDAZOLES; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEASE INHIBITORS; VIRAL PROTEINS;

EID: 13844316622     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci049809b     Document Type: Article

References (40)

1. Lee, N.; Hui, D.; Wu, A.; Chan, P.; Cameron, P.; Joynt, G. M.; Ahuja, A.; Yung, M. Y.; Leung, C. B.; To, K. F.; Lui, S. F.; Szeto, C. C.; Chung, S.; Sung, J. J. A major outbreak of severe acute respiratory syndrome in Hong Kong. N. Engl. J. Med. 2003, 348, 1986.
2. Poutanen, S. M.; Low, D. E.; Henry, B.; Finkelstein, S.; Rose, D.; Green, K.; Tellier, R.; Draker, R.; Adachi, D.; Ayers, M.; Chan, A. K.; Skowronski, D. M.; Salit, I.; Simor, A. E.; Slutsky, A. S.; Doyle, P. W.; Krajden, M.; Petric, M.; Brunham, R. C.; McGeer, A. J. Identification of severe acute respiratory syndrome in Canada. N. Engl. J. Med. 2003, 348, 1995.
3. Holmes, K. V. SARS-associated Coronavirus. N. Engl. J. Med. 2003, 348, 1948.
4. Leng, Q.; Bentwich, Z. A novel Coronavirus and SARS. N. Engl. J. Med. 2003, 349, 709.
5. Rota, P. A.; Oberste, M. S.; Monroe, S. S.; Nix, W. A.; Campagnoli, R.; Icenogle, J. P.; Penaranda, S.; Bankamp, B.; Maher, K.; Chen, M. H.; Tong, S.; Tamin, A.; Lowe, L.; Frace, M.; DeRisi, J. L.; Chen, Q.; Wang, D.; Erdman, D. D.; Peret, T. C.; Burns, C.; Ksiazek, T. G.; Rollin, P. E.; Sanchez, A.; Liffick, S.; Holloway, B.; Limor, J.; McCaustland, K.; Olsen-Rasmussen, M.; Fouchier, R.; Gunther, S.; Osterhaus, A. D.; Drosten, C.; Pallansch, M. A.; Andersen, L. J.; Bellini, W. J. Characterization of a novel Coronavirus associated with severe acute respiratory syndrome. Science 2003, 300, 1394.
6. So, L. K.; Lau, A. C.; Yam, L. Y.; Cheung, T. M.; Poon, E.; Yung, R. W.; Yuen, K. Y. Development of a standard treatment protocol for severe acute respiratory syndrome. Lancet 2003, 361, 1615.
7. Guo, P. Q. [Clinical treatment of SARS by integrative Chinese and Western medicine]. Zhongguo Zhong. Xi. Yi. lie. He. Za Zhi. 2003, 23, 568.
8. Zhang, R.; Quo, Z.; Lu, J.; Meng, J.; Zhou, C.; Zhan, X.; Huang, B.; Yu, X.; Huang, M.; Pan, X.; Ling, W.; Chen, X.; Wan, Z.; Zheng, H.; Yan, X.; Wang, Y.; Ran, Y.; Liu, X.; Ma, J.; Wang, C.; Zhang, B. Inhibiting severe acute respiratory syndrome-associated Coronavirus by small interfering RNA. Chin Med. J. (Engl.) 2003, 116, 1262.
9. van Vonderen, M. G.; Bos, J. C.; Prins, J. M.; Wertheim-van Dillen, P.; Speelman, P. Ribavirin in the treatment of severe acute respiratory syndrome (SARS). Neth. J. Med. 2003, 61, 238.
10. Cinatl, J.; Morgenstern, B.; Bauer, G.; Chandra, P.; Rabenau, H.; Doerr, H. W. Treatment of SARS with human interferons. Lancet 2003, 362, 293.
11. Koren, G.; King, S.; Knowles, S.; Phillips, E. Ribavirin in the treatment of SARS: A new trick for an old drug? CMAJ 2003, 168, 1289.
12. Knowles, S. R.; Phillips, E. J.; Dresser, L.; Matukas, L. Common adverse events associated with the use of ribavirin for severe acute respiratory syndrome in Canada. Clin. Infect. Dis. 2003, 37, 1139
13. Jia, W.; Gao, W. Is traditional Chinese medicine useful in the treatment of SARS? Phytother. Res. 2003, 17, 840-841.
14. Fan, K.; Wei, P.; Feng, Q.; Chen, S.; Huang, C.; Ma, L.; Lai, B.; Pei, J.; Liu, Y.; Chen, J.; Lai, L. Biosynthesis, purification and substrate specificity of SARS Coronavirus 3C-like proteinase. J. Biol. Chem. 2004, 279, 1637.
15. Anand, K.; Ziebuhr, J.; Wadhwani, P.; Mesters, J. R.; Hilgenfeld, R. Coronavirus 3C-like proteinase (3C-likepro) structure: basis for design of anti-SARS drugs. Science 2003, 300, 1763.
16. Liu, S.; Pei, J.; Chen, H.; Zhu, X.; Liu, Z.; Ma, W.; He, F.; Lai, L. [Modeling of the SARS Coronavirus 3C-like proteinase and conformational flexibility of the active site]. Beijing Da. Xue. Xue. Bao. 2003, 35 Suppl, 62.
17. Xiong, B.; Gui, C. S.; Xu, X. Y.; Luo, C.; Chen, J.; Luo, H. B.; Chen, L. L.; Li, G. W.; Sun, T.; Yu, C. Y.; Yue, L. D.; Duan, W. H.; Shen, J. K.; Qin, L.; Shi, T. L.; Li, Y. X.; Chen, K. X.; Luo, X. M.; Shen, X.; Shen, J. H.; Jiang, H. L. A 3D model of SARS-CoV 3C-like proteinase and its inhibitors design by virtual screening. Acta Pharmacol. Sin. 2003, 24, 497.
18. Jenwitheesuk, E.; Samudrala, R. Identifying inhibitors of the SARS Coronavirus proteinase. Bioorg. Med. Chem. Lett. 2003, 13, 3989.
19. Chou, K. C.; Wei, D. Q.; Zhong, W. Z. Binding mechanism of Coronavirus 3C-like proteinase with ligands and its implication to drug design against SARS. Biochem. Biophys. Res. Commun. 2003, 308, 148.
20. Anand, K.; Palm, G. J.; Mesters, J. R.; Siddell, S. G.; Ziebuhr, J.; Hilgenfeld, R. Structure of Coronavirus 3C-like proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain. EMBO J. 2002, 21, 3213.
21. Yang, H.; Yang, M.; Ding, Y.; Liu, Y.; Lou, Z.; Zhou, Z.; Sun, L.; Mo, L.; Ye, S.; Pang, H.; Gao, G. F.; Anand, K.; Bartlam, M.; Hilgenfeld, R.; Rao, Z. The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13190.
22. Chernaia, M. M.; Malcolm, B. A.; Allaire, M.; James, M. N. Hepatitis A virus 3C proteinase: some properties, crystallization and preliminary crystallographic characterization. J. Mol. Biol. 1993, 234, 890.
23. Matthews, D. A.; Dragovich, P. S.; Webber, S. E.; Fuhrman, S. A.; Patick, A. K.; Zalman, L. S.; Hendrickson, T. F.; Love, R. A.; Prins, T. J.; Marakovits, J. T.; Zhou, R.; Tikhe, J.; Ford, C. E.; Meador, J. W.; Ferre, R. A.; Brown, E. L.; Binford, S. L.; Brothers, M. A.; DeLisle, D. M.; Worland, S. T. Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11000.
24. Allaire, M.; Chemaia, M. M.; Malcolm, B. A.; James, M. N. Picornaviral 3C cysteine proteinases have a fold similar to chymotrypsin-like serine proteinases. Nature 1994, 369, 72.
25. Chen, S. H.; Lamar, J.; Victor, F.; Snyder, N.; Johnson, R.; Heinz, B. A.; Wakulchik, M.; Wang, Q. M. Synthesis and evaluation of tripeptidyl alpha-ketoamides as human rhinovirus 3C protease inhibitors. Bioorg. Med. Chem. Lett. 2003, 13, 3531.
26. Lall, M. S.; Ramtohul, Y. K.; James, M. N.; Vederas, J. C. Serine and threonine beta-lactones: a new class of hepatitis A virus 3C cysteine proteinase inhibitors. J. Org. Chem. 2002, 67, 1536.
27. Zalman, L. S.; Brothers, M. A.; Dragovich, P. S.; Zhou, R.; Prins, T. J.; Worland, S. T.; Patick, A. K. Inhibition of human rhinovirusinduced cytokine production by AG7088, a human rhinovirus 3C protease inhibitor. Antimicrob. Agents Chemother. 2000, 44, 1236.
28. Kaiser, L.; Crump, C. E.; Hayden, F. G. In vitro activity of pleconaril and AG7088 against selected serotypes and clinical isolates of human rhinoviruses. Antiviral Res. 2000, 47, 215.
29. McKeage, M. J. Comparative adverse effect profiles of platinum drugs. Drug Saf. 1995, 13, 228.
30. Woessner, K. M. Crossreacting drugs and chemicals. Clin. Rev. Allergy Immunol. 2003, 24, 149.
31. Lyne, P. D. Structure-based virtual screening: an overview. Drug Discov. Today 2002, 7, 1047.
32. Mestres, J. Virtual screening: a real screening complement to high-throughput screening. Biochem. Soc. Trans. 2002, 30, 797.
33. Ewing, T. J.; Makino, S.; Skillman, A. G.; Kuntz, I. D. Dock 4.0: search strategies for automated molecular docking of flexible molecule databases. J. Comput.-Aided Mol. Des. 2001, 15, 411.
34. Wang, R. X.; Gao, Y.; Lai, L. H.; LigBuilder: A multi-purpose program for structure-base drug design. J. Mol. Model. 2000, 6, 498.
35. Wang, R. X.; Liu, L.; Lai, L. H., et al. SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex. J. Mol. Model. 1998, 4, 379.
36. Tao, P.; Lai, L. H. Protein ligand docking based on empirical method for binding affinity estimation. J. Comput.-Aided Mol. Des. 2001, 15, 429.
37. Wang, R.; Lai, L.; Wang, S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J. Comput.-Aided Mol. Des. 2002, 16, 11.
38. Huang, C. K.; Wei, P.; Fan, K. Q.; Liu, Y.; Lai, L. H. 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general base mechanism. Biochemistry 2004, 43, 4568.
39. Lee, V. S.; Wittayanarakul, K.; Remsungnen, T.; Parasuk, V.; Sompompisut, P., et al. Structure and Dynamics of SARS Coronavirus Proteinase: The Primary Key to the Designing and Screening for Anti-SARS Drugs. ScienceAsia 2003, 29, 181.
40. Toney, J. H.; Martin, S. N.; Weiss, S. R.; Sabadinine, A. K. A Potential Non-Peptide Anti-Severe Acute-Respiratory-Syndrome Agent Identified Using Structure-Aided Design. J. Med. Chem. 2004, 41, 1079.