Identification and characterization of domain-specific inhibitors of DENV NS3 and NS5 proteins by in silico screening methods

Abstract

The dengue virus (DENV) infects approximately 400 million people annually worldwide causing significant morbidity and mortality. Despite advances in understanding the virus life cycle and infectivity, no specific treatment for this disease exists due to the lack of therapeutic drugs. In addition, vaccines available currently are ineffective with severe side effects. Therefore, there is an urgent need for developing therapeutics suitable for effective management of DENV infection. In this study, we adopted a drug repurposing strategy to identify new therapeutic use of existing FDA approved drug molecules to target DENV2 non-structural proteins NS3 and NS5 using computational approaches. We used Drugbank database molecules for virtual screening and multiple docking analysis against a total of four domains, the NS3 protease and helicase domains and NS5 MTase and RdRp domains. Subsequently, MD simulations and MM-PBSA analysis were performed to validate the intrinsic atomic interactions and the binding affinities. Furthermore, the internal dynamics in all four protein domains, in presence of drug molecule binding were assessed using essential dynamics and free energy landscape analyses, which were further coupled with conformational dynamics-based clustering studies and cross-correlation analysis to map the regions that exhibit these structural variations. Our comprehensive analysis identified tolcapone, cefprozil, delavirdine and indinavir as potential inhibitors of NS5 MTase, NS5 RdRp, NS3 protease and NS3 helicase functions, respectively. These high-confidence candidate molecules will be useful for developing effective anti-DENV therapy to combat dengue infection.

Communicated by Ramaswamy H. Sarma

Keywords:

• DENV2
• non-structural protein
• MTase domain
• RdRp domain
• protease domain
• helicase domain
• drug repurposing
• virtual screening
• molecular docking
• molecular dynamics
• essential dynamics
• MM-pbsa

Disclosure statement

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

Additional information

Funding

This work was supported by the funds from the Department of IT, BT & ST, Government of Karnataka to IBAB. SG is supported by Ramalingaswami Re-entry Fellowship (No. BT/RLF/Re-entry/31/2016) from the Department of Biotechnology, Government of India. Department of Biotechnology, Ministry of Science and Technology, India;