Discovery of a small molecule inhibitor targeting dengue virus NS5 RNA-dependent RNA polymerase.

Abstract

Dengue is a mosquito-borne viral infection that has spread globally in recent years. Around half of the world's population, especially in the tropics and subtropics, is at risk of infection. Every year, 50-100 million clinical cases are reported, and more than 500,000 patients develop the symptoms of severe dengue infection: dengue haemorrhagic fever and dengue shock syndrome, which threaten life in Asia and Latin America. No antiviral drug for dengue is available. The dengue virus (DENV) non-structural protein 5 (NS5), which possesses the RNA-dependent RNA polymerase (RdRp) activity and is responsible for viral replication and transcription, is an attractive target for anti-dengue drug development. In the present study, 16,240 small-molecule compounds in a fragment library were screened for their capabilities to inhibit the DENV type 2 (DENV2) RdRp activities in vitro. Based on in cellulo antiviral and cytotoxity assays, we selected the compound RK-0404678 with the EC50 value of 6.0 μM for DENV2. Crystallographic analyses revealed two unique binding sites for RK-0404678 within the RdRp, which are conserved in flavivirus NS5 proteins. No resistant viruses emerged after nine rounds of serial passage of DENV2 in the presence of RK-0404678, suggesting the high genetic barrier of this compound to the emergence of a resistant virus. Collectively, RK-0404678 and its binding sites provide a new framework for antiviral drug development.

• Authors: Hideaki Shimizu, Akatsuki Saito, Junko Mikuni, Emi E Nakayama, Hiroo Koyama, Teruki Honma, Mikako Shirouzu, Shun-Ichi Sekine, Tatsuo Shioda
• Journal: PLoS neglected tropical diseases (PLoS Negl Trop Dis) Vol. 13 Issue 11 Pg. e0007894 (11 2019) ISSN: 1935-2735 [Electronic] United States
• PMID: 31738758 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)

Chemical References

• Antiviral Agents
• NS5 protein, dengue virus
• Viral Nonstructural Proteins
• RNA-Dependent RNA Polymerase

Topics

• Antiviral Agents (isolation & purification, pharmacology)
• Binding Sites
• Crystallography, X-Ray
• Dengue Virus (drug effects)
• Drug Evaluation, Preclinical
• Microbial Sensitivity Tests
• Protein Binding
• RNA-Dependent RNA Polymerase (antagonists & inhibitors, chemistry, metabolism)
• Viral Nonstructural Proteins (antagonists & inhibitors, chemistry, metabolism)