Structure and Dynamics of SARS Coronavirus Proteinase: The Primary Key to the Designing and Screening for Anti-SARS Drugs

ScienceAsia

Volumn 29, Issue 2, 2003, Pages 181-188

  Lee, Vannajan Sanghiran ^a,b   Wittayanarakul, Kitiyaporn ^a   Remsungnen, Tawun ^a   Parasuk, Vudhichai ^a   Sompornpisut, Pornthep ^a   Chantratita, Wasun ^c   Sangma, Chak ^d   Vannarat, Sornthep ^e   Srichaikul, Piyawut ^e   Hannongbua, Supa ^d   Saparpakorn, Patchreenart ^d   Treesuwan, Witcha ^d   Aruksakulwong, Ornjira ^a   Pasomsub, Ekawat ^c   Promsri, Siriporn ^a   Chuakheaw, Daungmanee ^d   Hannongbua, Supot ^a  

^a CHULALONGKORN UNIVERSITY   (Thailand)

^b CHIANG MAI UNIVERSITY   (Thailand)

^c MAHIDOL UNIVERSITY   (Thailand)

^d KASETSART UNIVERSITY   (Thailand)

^e NATIONAL ELECTRONICS AND COMPUTER TECHNOLOGY CENTER   (Thailand)

Author keywords

Coronavirus; drug design; molecular dynamics; molecular structure; protease; proteinase; SARS

Indexed keywords

EID: 1242348379     PISSN: 15131874     EISSN: None     Source Type: Journal    
DOI: 10.2306/scienceasia1513-1874.2003.29.181     Document Type: Article

References (19)

1. Cumulative number of reported probable cases of SARS (http://www.who.int/csr/sars/en/).
2. WHO collaborative multi-center research project on Severe Acute Respiratory Syndrome (SARS) diagnosis (http://www.who.int/csr/sars/project/en/).
3. Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YS, Khattra J and Asano JK, et al (2003) The genome sequence of the SARS-associated coronavirus. Science 300, 1399-1404.
4. Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Penaranda S and Bankamp B, et al. (2003) Characterization of a novel coronavirus associated with Severe Acute Respiratory Syndrome. Science 300, 1394-9.
5. Fouchier RA, Kuiken T, Schutten M, Van Amerongen G, Van Doornum GJ, Van Den Hoogen BG, Peiris M, Lim W, Stohr K, Osterhaus AD (2003) Aetiology: Koch's postulates fulfilled for SARS virus. Nature 423, 240.
6. Holmes KV (2003) SARS-Associated Coronavirus. N Engl J Med 20, 1948.
7. Anand K, Ziebuhr J, Wadhwani P, Mesters JR, Hilgenfeld R. (2003) Coronavirus main proteinase (3CLpro) structure: Basis for design of anti-SARS drugs. Science 300, 1763-7.
8. Clarke T (2003) SARS' Achilles' heel revealed, Science update (http://www.nature.com/nsu/030505/030505-4.html)
9. Lee VS, Parasuk V, Sompornpisut P, Chantratita W, Sangma C, Vannarat S, Srichaikul P and Hannongbua S, et al. (2003) Three Dimensional structure of dimer of SARS proteinase: An appropriate model for design and screen for anti-SARS drugs, Submitted.
10. Combet C, Jambon M, Deléage G, Geourjon C (2002) Gen3D: Automatic comparative molecular modelling of protein. Bioinformatics 18, 213.
11. Berendsen HJC, Postma JMP, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Comp Phys 81, 3684.
12. Case DA, Pearlman DA, Caldwell JW, Cheatham III TE, Wang J, Ross WS, Simmerling C and Darden T, et al (2002) AMBER7, University of California, San Francisco.
13. Pearlman, DA, Case DA, Caldwell J W, Ross WS, Cheatham III TE, DeBolt S, Ferguson D, Seibel G, Kollman P, (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp Phys Commun 91, 1.
14. Goodsell, DS, Olson AJ, (1990) Automated docking of substrates to proteins by simulated annealing. Proteins 8, 195.
15. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function. J Comp Chem 19, 1639.
16. Morris GM, Goodsell DS, Huey R, Olson AJ, (1996) Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4. JCAMD 10, 293.
17. Laskowski RA, Mac Arthur MW, Moss DS, Thornton JM, (1993) Procheck-a program to check the stereochemical quality of protein structures. J Appl Cryst 26, 283-291.
18. National Cancer Institute (NCI) Database (http://cactus.nci.nih.gov/ncidb2/).
19. Brady Jr. GP, Stouten PFW, (2000) Fast prediction and visualization of protein binding pockets with PASS. JCAMD 14, 383. (http://www.delanet.com/~bradygp/pass/).