1. Two RNA Tunnel Inhibitors Bind in Highly Conserved Sites in Dengue Virus NS5 Polymerase: Structural and Functional Studies.
- Author
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Arora, Rishi, Chong Wai Liew, Soh, Tingjin Sherryl, Otoo, Dorcas Adobea, Cheah Chen Seh, Yue, Kimberley, Nilar, Shahul, Gang Wang, Fumiaki Yokokawa, Noble, Christian G., Yen Liang Chen, Pei-Yong Shi, Lescar, Julien, Smith, Thomas M., Benson, Timothy E., and Siew Pheng Lim
- Subjects
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DENGUE viruses , *RNA replicase , *MESSENGER RNA , *RNA polymerases , *CATALYTIC RNA , *RNA , *DNA replication - Abstract
Dengue virus (DENV) NS5 RNA-dependent RNA polymerase (RdRp), an important drug target, synthesizes viral RNA and is essential for viral replication. While a number of allosteric inhibitors have been reported for hepatitis C virus RdRp, few have been described for DENV RdRp. Following a diverse compound screening campaign and a rigorous hit-to-lead flowchart combining biochemical and biophysical approaches, two DENV RdRp nonnucleoside inhibitors were identified and characterized. These inhibitors show low- to high-micromolar inhibition in DENV RNA polymerization and cell-based assays. X-ray crystallography reveals that they bind in the enzyme RNA template tunnel. One compound (NITD-434) induced an allosteric pocket at the junction of the fingers and palm subdomains by displacing residue V603 in motif B. Binding of another compound (NITD-640) ordered the fingers loop preceding the F motif, close to the RNA template entrance. Most of the amino acid residues that interacted with these compounds are highly conserved in flaviviruses. Both sites are important for polymerase de novo initiation and elongation activities and essential for viral replication. This work provides evidence that the RNA tunnel in DENV RdRp offers interesting target sites for inhibition. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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