Nucleic Acids Research, 2003, Vol. 31, No. 24 7117-7130
© 2003 Oxford University Press
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Molecular model of SARS coronavirus polymerase: implications for biochemical functions and drug design
1 Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China, 2 Department of Microbiology, University of Pennsylvania School of Medicine, 203A Johnson Pavilion, 36th Street and Hamilton Walk, Philadelphia, PA 19104-6076, USA and 3 Center for Advanced Biotechnology and Medicine (CABM) and Rutgers University Department of Chemistry and Chemical Biology, 679 Hoes Lane, Piscataway, NJ 08854-5638, USA
*To whom correspondence should be addressed. Tel: +86 21 54921619; Fax: +86 21 54921116; Email: jpding{at}sibs.ac.cn
Correspondence may also be addressed to Stefan G. Sarafianos. Tel: +1 732 2354482; Fax: +1 732 2355788; Email: stefan{at}cabm.rutgers.edu
The causative agent of severe acute respiratory syndrome (SARS) is a previously unidentified coronavirus, SARS-CoV. The RNA-dependent RNA polymerase (RdRp) of SARS-CoV plays a pivotal role in viral replication and is a potential target for anti-SARS therapy. There is a lack of structural or biochemical data on any coronavirus polymerase. To provide insights into the structure and function of SARS-CoV RdRp, we have located its conserved motifs that are shared by all RdRps, and built a three-dimensional model of the catalytic domain. The structural model permits us to discuss the potential functional roles of the conserved motifs and residues in replication and their potential interactions with inhibitors of related enzymes. We predict important structural attributes of potential anti-SARS-CoV RdRp nucleotide analog inhibitors: hydrogen-bonding capability for the 2' and 3' groups of the sugar ring and C3' endo sugar puckering, and the absence of a hydrophobic binding pocket for non-nucleoside analog inhibitors similar to those observed in hepatitis C virus RdRp and human immunodeficiency virus type 1 reverse transcriptase. We propose that the clinically observed resistance of SARS to ribavirin is probably due to perturbation of the conserved motif A that controls rNTP binding and fidelity of polymerization. Our results suggest that designing anti-SARS therapies can benefit from successful experiences in design of other antiviral drugs. This work should also provide guidance for future biochemical experiments.
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