Development of a theoretical model for the inhibition of nsP3 of Chikungunya virus using pyranooxazoles

Abstract

Chikungunya virus (CHIKV) causes Chikungunya fever (CHIKF) and till date no effective medicine for its cure is available in market. Different research groups find various possible interactions between small molecules and non-structural proteins, viz. nsP3, one of the most important viral elements in CHIKV. In this work, authors have studied the interactions of nsP3 of CHIKV with pyranooxazoles. Initially, a one-pot three-component reaction was designed using oxazolidine-2,4-dione, benzaldehyde and cyanoethylacetate to get a proposed biological active molecule, i.e. based on pyranooxazoles. The mechanism for the synthesis of the product based on pyranooxazole was studied through density functional theory (DFT) using Gaussian. Then, a library of the obtained pyranooxazole was created through computational tools by varying the substituents. Further, virtual screening of the designed library of pyranooxazoles (200 compounds) against nsP3 of CHIKV was performed. Herein, CMPD 104 showed strongest binding affinity toward the targeted nsP3 of CHIKV, based on the least binding energy obtained from docking. Based on docking results, the pharmacological, toxicity, biological score and Lipinski’s filters were studied. Further, DFT studies of top five compounds were done using Gaussian. Molecular dynamics (MD) simulation of nsP3 of CHIKV with and without 104 was performed using AMBER18 utilizing ff14SB force field in three steps (minimization, equilibration and production). This work is emphasized to designing of one-pot three-component synthesis and to develop a theoretical model to inhibit the nsP3 of CHIKV.

Communicated by Ramaswamy H. Sarma

KEYWORDS::

• Chikungunya virus
• nsP3
• one-pot reaction
• docking
• MD simulation
• MM-GBSA and DFT

View correction statement:

Correction

Correction

Acknowledgments

D. Kumar thanks Prof. B. Jayaram, Incharge, SCFBio, Indian Institute of Technology, Delhi, India for accessing the facilities and training at SCFBio. D. Kumar also thanks the Department of Chemistry, University of Delhi, Delhi, India for the facilities to carry out research work. P. Singh dedicates his contribution in this article to his guide, Late Dr. N. N. Ghosh.

Disclosure statement

No potential conflict of interest was reported by the authors.