De-Novo Protein Design Strategies for Targeting Rotavirus Proteins: Evolutionary Conservation and Therapeutic Implications

Rotavirus (RV) is a leading cause of pediatric gastroenteritis, with existing vaccines showing reduced efficacy due to strain diversity and limited immunogenicity. This study aimed to design de novo proteins targeting highly conserved RV proteins to develop potential therapeutic inhibitors.

Protein sequences from nine RV strains were retrieved from UniProtKB and aligned using T-Coffee to identify conserved regions. Structural modeling was performed with OmegaFold and SWISS-MODEL, and domain analysis was carried out via InterPro. Protein–protein docking with ClusPro and HDOCK identified interactions between viral proteins (VP4, VP7, RNA-dependent RNA polymerase) and host proteins (integrins and VP2). De novo proteins were computationally designed using residue-frequency constraints and screened for stability (DeepStabP), toxicity (CSM-Toxin), and docking affinity to RV targets.

VP4, VP7, and RNA polymerase were the most conserved proteins across RV strains (77–85%). Domain-specific interactions with integrins and VP2 were identified. Designed proteins exhibited high binding affinities, notably with VP4 membrane interaction domains, VP7 domain 1, and RNA polymerase C-terminal regions. Over 96% of the designed sequences were predicted to be non-toxic, and most showed favorable thermal stability. Docking revealed conserved interaction sites across strains, suggesting broad-spectrum inhibitory potential.

These findings demonstrate that de-novo-designed proteins can selectively target conserved rotavirus domains, potentially overcoming strain variability and vaccine limitations. While computational results support structural stability and non-toxicity, experimental validation is essential. Limitations include reliance on in-silico predictions and the absence of in-vivo confirmation.

This study highlights designing de novo proteins as a promising approach for developing novel antivirals against rotavirus, warranting further experimental and clinical investigations.