Identification and validation of novel non-nucleoside class of molecules inhibiting the dengue virus replication

Abstract

There is currently no drug available to treat mosquito-borne dengue. The C-terminal RNA-dependent RNA polymerase (RdRp) domain in the non-structural type 5 (NS5) protein of the dengue virus (DENV) is essential for viral RNA synthesis and replication, and therefore, it is an attractive target for the anti-dengue drug development. We report herein the discovery and validation of two novel non-nucleoside classes of small molecules as DENV RdRp inhibitors. Firstly, using the refined X-ray structure of the DENV NS5 RdRp domain (PDB-ID: 4V0R), we conducted docking, binding free-energy studies, and short-scale molecular dynamics simulation to investigate the binding sites of known small molecules that led to the optimized protein–ligand complex. Subsequently, protein structure-based screening of a commercial database (∼500,000 synthetic compounds), pre-filtered for the drug-likeness, led to the top-ranked 171 molecules, which was then subjected to structural diversity analysis and clustering. This process led to six structurally distinct and best-scored compounds that were procured from the commercial vendor, and then subjected to the in vitro testing in the MTT and dengue infection assays. It revealed two unique and structurally unique compounds, KKR-D-02 and KKR-D-03, exhibiting 84 and 81% reductions, respectively, in DENV copy number in repeated assays in comparison to the virus-infected cell controls. These active compounds represent novel scaffolds for further structure-based discovery of novel candidate molecules for the intervention of dengue.

Communicated by Ramaswamy H. Sarma

Keywords:

• Dengue
• DENV
• NS5
• RdRp
• virtual screening
• antiviral

Acknowledgments

The author KKR is thankful to the Science and Engineering Research Board (SERB), Department of Sciences and Technology, Government of India, New Delhi for providing the support in terms of funding. Authors are thankful to the NIPER Kolkata, Department of Pharmaceuticals, and the Ministry of Chemicals and Fertilizes for providing support to accomplish this research.

Authors’ Contributions

The manuscript is written through contributions of all authors. Kuldeep K. Roy and Soumi Sukla designed the study, while Deeti Jyothi and Udita Paul carried out the designed studies under the supervision of Kuldeep K. Roy and Soumi Sukla. All authors have given approval to the final version of the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

The Science and Engineering Research Board (SERB), Department of Sciences and Technology, Government of India, New Delhi, Funding reference number: SRG-2021-001734, and intramural funding from NIPER-Kolkata.