Genome-wide in silico discovery of conserved coat protein motifs in cotton leaf curl disease–associated Begomoviruses enabling peptide aptamer-mediated antiviral strategy

Cotton Leaf Curl Disease (CLCuD)-associated begomoviruses (CABs) cause significant cotton crop losses worldwide. The genetic diversity and rapid evolution of CABs have significantly undermined efficacy of conventional and biotechnological interventions targeting viral genome, highlighting an urgent need for alternative strategies. Thus, this study aimed to devise a novel resistance strategy by targeting coat protein (CP) through peptide aptamers, which could halt infection very early. Phylogenetic analysis of 1322 CP sequences of CABs showed three interspecies clustering, indicating high conservation. Motif analysis through MEME further enriched this understanding by identifying 5, 4, and 10 conserved motifs in phylogenetic groups I, II, and III, respectively. Since nuclear localization signal (NLS) region has been considered crucial in CP- importin α interactions, NLS mapper tool was used to reveal conserved bipartite NLS (3KR-16KvRRR) in all CP variants. To identify interaction between CPs and importin α, 3D structures of 51 CP variants and importin α were modelled, refined, and validated using Alphafold, Galaxyrefine, and Procheck, respectively. Interestingly, besides NLS, docking studies identified additional conserved CP sites interacting with importin α, which laid foundation for designing peptide aptamers. A library of peptide aptamers was constructed using an R script and selected using PeptideRanker, PepDraw, molecular dockings and simulations. Two peptides demonstrated favorable predicted interactions with multiple major CP binding sites. These results provide preliminary computational insights into peptide-based targeting of viral proteins; however, their antiviral potential remains speculative and requires experimental validation through binding and functional assays before their utility in controlling CABs can be established.