Mechanistic insights into the Japanese encephalitis virus RNA dependent RNA polymerase protein inhibition by bioflavonoids from Azadirachta indica

Vivek Dhar Dwivedi,Ankita Singh,Mohammad Amjad Kamal,Arwa A Faizo,Esam Ibraheem Azhar,Sherif Aly El-Kafraway,Thamir A Alandijany,Leena Hussein Bajrai

doi:10.1038/s41598-021-96917-0

Abstract

Japanese encephalitis (JE) virus is a flavivirus causing encephalitis causing neurological damage. RNA-dependent-RNA-polymerase (RdRp) is responsible for genome replication making it excellent anti-viral target. In this study, the crystal structure of JE RdRp (jRdRp) and bioflavonoids reported in Azadirachta indica were retrieved from specific databases. Structure-based virtual screening was employed using MTiOpenScreen server and top four compounds selected with the most negative docking scores. Conformations were redocked using AutoDock Vina; these complexes showed mechanistic interactions with Arg474, Gly605, Asp668, and Trp800 residues in the active site of jRdRp, i.e., guanosine-5′-triphosphate. Furthermore, 100 ns classical molecular dynamics simulation and binding free energy calculation showed stability of docked bioflavonoids in the active jRdRp pocket and significant contribution of van-der-Waals interactions for docked complex stability during simulation. Therefore, this study predicted the anti-viral activity of Gedunin, Nimbolide, Ohchinin acetate, and Kulactone against jRdRp and can be considered for further antiviral drug development.

Highlights

Japanese encephalitis (JE), a serious vector-borne viral infection caused by the Japanese encephalitis virus (JEV), is responsible for causing Epidemic encephalitis B—an acute infectious disease of the central nervous system, in 24 countries of Southeast Asia and the Western Pacific[1,2,3]
A total of 43 bioflavonoids (Table S1) documented in Azadirachta indica were collected from the literature and used in virtual screening against the catalytic site in JE RdRp (jRdRp) protein
I.e., Gedunin, Nimbolide, Ohchinin acetate, and Kulactone, with higher docking scores were considered for further re-docking and intermolecular interaction analysis against native crystalized ligand, i.e., guanosine-5′-triphosphate (GTP) and Adenosine triphosphate (ATP) as reference molecules (Fig. 1)

Summary

Introduction

Japanese encephalitis (JE), a serious vector-borne viral infection caused by the Japanese encephalitis virus (JEV), is responsible for causing Epidemic encephalitis B—an acute infectious disease of the central nervous system, in 24 countries of Southeast Asia and the Western Pacific[1,2,3]. The seven NS proteins coordinate to form complex machinery regulating replication, cleavage of polyprotein, and fabrication of nascent viral p articles[13,14,15]. Among these NS protein, NS5 is the largest and the most conserved protein of the JEV which comprises an N-terminal S-adenosyl-l-methionine (SAM)-dependent methyltransferase (MTase) domain and a C-terminal RNA-dependent RNA polymerase (RdRp) r egion[12,16]. The RdRp in cooperation with other NS proteins and host cell proteins participates in the viral genome synthesis by forming a membrane-bound replication complex (RC)[17,18,19,20]. Following potential ligands were studied for binding stabilities and affinities using molecular simulations and free energy calculations, respectively to understand the detailed mechanistic mechanism and other characteristics involved in the RdRp inhibition of JEV

Methods

Results

Conclusion