Exploring the binding mechanism of the main proteinase in SARS-associated coronavirus and its implication to anti-SARS drug design

Bioorganic and Medicinal Chemistry

Volumn 12, Issue 9, 2004, Pages 2219-2223

  Zhang, Xue Wu ^a   Yap, Yee Leng ^a  

^a HKU PASTEUR RESEARCH CENTRE   (Hong Kong)

Author keywords

Binding; Inhibitor; Main proteinase; Noncanonical interactions; SARS CoV

Indexed keywords

ANTIVIRUS AGENT; PROTEINASE;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; DRUG DESIGN; ENZYME STRUCTURE; LIGAND BINDING; SARS CORONAVIRUS; SEVERE ACUTE RESPIRATORY SYNDROME;

AMINO ACID SEQUENCE; ANTIVIRAL AGENTS; CYSTEINE ENDOPEPTIDASES; DRUG DESIGN; ENDOPEPTIDASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; SEQUENCE HOMOLOGY, AMINO ACID; VIRAL PROTEINS;

CORONAVIRUS; DENGUE VIRUS; EQUIDAE; EQUINE ARTERITIS VIRUS; HEPATITIS A VIRUS; HEPATITIS C VIRUS; POLIOVIRUS; RHINOVIRUS;

EID: 1842737055     PISSN: 09680896     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmc.2004.02.015     Document Type: Article

References (19)

1. Bonanno, J. B., Fowler, R., Gupta, S., hendle, J., Lorimer, D., Romero, R., Sauder, M., Wei, C. L., Liu, E. T., Burley, S. K., Harris, T. X-ray crystal structure of the SARS coronavirus main protease. (in press) ( http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1Q2W )
2. Yang H., Yang M., Ding Y., Liu Y., Lou Z., Zhou Z., Sun L., Mo L., ye S., Pang H., Gao G., 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. 100:2003;13190-13195.
3. pro) structure: basis for design of anti-SARS drugs. Science. 300:2003;1763-1767.
4. Babu M.M. NCI: a server to identify non-canonical interactions in protein structures. Nucleic Acids Res. 31:2003;3345-3348.
5. Shindyalov I.N., Bourne P.E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11:1998;739-747.
6. Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res. 31:2003;3370-3374.
7. Chou K., Wei D., Zhong W. Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. Biochem. Biophys. Res. Commun. 308:2003;148-151.
8. Hirshberg M., Stockley R.W., Dodson G., Webb M.R. The crystal structure of human rac1, a member of the rho-family complexed with a GTP analogue. Nat. Struct. Biol. 4:1997;147-152.
9. Fabiola G.F., Krishnaswamy S., Nagarajan V., Pattabhi V. C-H. ⋯ O hydrogen bonds in beta sheets Acta Crystallogr., Sect. D. 53:1997;316-320.
10. Senes A., Ubarretxena-Belandia I., Engelman D.M. The C-H. ⋯ O hydrogen bond: a determinant of stability and specificity in transmembrane helix interactions Proc. Natl. Acad. Sci. U.S.A. 98:2001;9056-9061.
11. Babu M.M., Singh S., Balaram P. A C-H. ⋯ O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins J. Mol. Biol. 322:2002;871-880.
12. Kryger G., Silman I., Sussman J.L. Structure of acetylcholinesterase complexed with E2020: implications for the design of new anti-alzheimer drugs. Structure. 7:1999;297-307.
13. Barrette-Ng I.H., Ng K.K., Mark B.L., Van Aken D., Cherney M.M., Garen C., Kolodenko Y., Gorbalenya A.E., Snijder E.J., James M.N. Structure of arterivirus nsp4. The smallest chymotrypsin-like proteinase with an alpha/beta C-terminal extension and alternate conformations of the oxyanion hole. J. Biol. Chem. 277(42):2002;39960-39966.
14. Bergmann E.M., Cherney M.M., Mckendrick J., Frormann S., Luo C., Malcolm B.A., Vederas J.C., James M.N. Crystal structure of an inhibitor complex of the 3C proteinase from hepatitis A virus (HAV) and implications for the polyprotein processing in HAV. Virology. 265(1):1999;153-163.
15. Di Marco S., Rizzi M., Volpari C., Walsh M.A., Narjes F., Colarusso S., De Francesco R., Matassa V.G., Sollazzo M. Inhibition of the hepatitis C virus NS3/4A protease. The crystal structures of two protease-inhibitor complexes. J. Biol. Chem. 275(10):2000;7152-7157.
16. Mosimann S.C., Cherney M.M., Sia S., Plotch S., James M.N. Refined X-ray crystallographic structure of the poliovirus 3C gene product. J. Mol. Biol. 273(5):1997;1032-1047.
17. Murthy H.M., Judge K., DeLucas L., Padmanabhan R. Crystal structure of Dengue virus NS3 protease in complex with a Bowman-Birk inhibitor: implications for flaviviral polyprotein processing and drug design. J. Mol. Biol. 301(4):2000;759-767.
18. 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. 96(20):1999;11000-11007.
19. Cinatl J., Morgenstern B., Chandra P., Rabenau H., Doerr H.W. Treatment of SARS with human interferons. The Lancet. 362:2003;293-294.