Computational investigation of phytoalexins as potential antiviral RAP-1 and RAP-2 (Replication Associated Proteins) inhibitor for the management of cucumber mosaic virus (CMV): a molecular modeling, in silico docking and MM-GBSA study

Abstract

The Replication Associated Proteins (RAP-1 and RAP-2) encoded by CMV ORF 1a and ORF 2a are required for the different stages of the viral replication cycle; being multi-functional, they are good inhibitory targets for anti-CMV compounds. As a new perspective for sustainable crop improvement, we investigated the natural plant-based antimicrobial phytoalexins for their anti-CMV potential. Here, we modeled and predicted the functional domains of RAP-1 and RAP-2, docked with a ligand library comprising 128 phytoalexins reported with broad-spectrum activity, determined their binding energies (BEs), molecular interactions, and inhibition constant (Ki), and compared with the reference plant antiviral compounds ribavirin, ningnanmycin, and benzothiadiazole (BTH). Further, the change in Gibb’s free energy of binding (ΔG) and the per residue contribution of the selected top-scored ligand molecules was assessed by the prime MM-GBSA approach. Our results revealed RAP-1 as a discontinuous two-domain and RAP-2 as a multi-domain protein. The compounds glyceollidin (9.8 kcal/mol) and moracin D (7.8 kcal/mol) topped the list for RAP-1 and RAP-2 protein targets respectively and also, the lead molecules had energetically more favorable and comparative ΔG values than the top-scored plant antiviral agent ningnanmycin. The evaluation of in vitro toxicity and agrochemical-like properties showed the least toxicity of these anti-CMV compounds. Taken together, our results provide new insights in understanding the inhibitory effects of phytoalexins towards the RAP proteins and could be employed as new promising anti-CMV candidate compounds for their application in agriculture as biopesticides to combat the CMV disease incidence.

Communicated by Ramaswamy H. Sarma

The CMV replication cycle and the proposed effect of viral replication inhibitors. Upon entry, CMV un-coats the coat protein (CP), co-localizes in the endoplasmic reticulum for its replication, mRNA synthesis, and translation. The viral RNA particles are assembled with the CP in the cytoplasm and released. The proposed anti-CMV strategy of phytoalexins as potential inhibitors for targeting the two viral enzymes RAP-1 and RAP-2 may likely inhibit the key steps 3, 4, 5, and 6 essential for the successful completion of the CMV life cycle and minimize the viral spread.

Keywords:

• Anti-CMV
• biopesticides
• computational screening
• domain prediction
• glyceollidin
• MM-GBSA
• moracin D
• plant-based antivirals
• phytoalexins
• Replication Associated Proteins

Acknowledgements

We are thankful to the University of Agricultural Sciences, Bangalore, India to provide all the facilities to carry out this work. Roshni Mohan Kumar is thankful to Indian Council of Agricultural Research (ICAR), New Delhi for providing national doctoral fellowship, ICAR-SRF.

Disclosure statement

On behalf of all the authors, corresponding author states that there is no conflict of interest to declare.

Author contributions

Roshni Mohan Kumar designed the entire study, performed the in silico analysis and wrote the manuscript. Ramachandra Anantapur contributed in editing and organizing the manuscript. Anitha Peter edited and approved the final manuscript. Chaitra HV prepared the tables and revised the manuscript.

Ethics approval

This research does not involve any human participants or animal related and hence not applicable

Informed consent

Not applicable as the research did not involve any human participants/animals