AUTHOR=Shaji Vineetha , Rafi Ahmad , Ahmed Mukhtar , Gopalakrishnan Athira Perunelly , Soman Sowmya , Revikumar Amjesh , Prasad Ganesh , Jayanandan Abhithaj , Raju Rajesh 

TITLE=Analysis of phosphomotifs coupled to phosphoproteome and interactome unveils potential human kinase substrate proteins in SARS-CoV-2

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=Volume 15 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2025.1554760

DOI=10.3389/fcimb.2025.1554760

ISSN=2235-2988

ABSTRACT=IntroductionViruses exploit host kinases to phosphorylate their proteins, enabling viral replication and interference with host-cell functions. Understanding phosphorylation in SARS-CoV-2 proteins necessitates identifying viral phosphoproteins, their phosphosites, and the host kinase–viral protein interactions critical for evading host antiviral responses.MethodsEmploying the protein kinase substrate sequence-preference motifs derived by Poll B G. et. al., 2024, we performed kinase-substrate phosphomotif pattern analysis on the SARS-CoV-2 proteome. We identified major host kinases by analyzing SARS-CoV-2 perturbed phosphoproteomes from various studies and cell systems. These kinases were subjected to interactome analysis and literature-based validation for the impact of kinase inhibitors on infection. Further, conservation of viral phosphosites across SARS CoV-2 variants were also assessed.ResultsThe human kinome–substrate phosphomotif analysis predicted 49 kinases capable of phosphorylating 639 phosphosites across 33 SARS-CoV-2 proteins. From these, 24 kinases were also perturbed in SARS-CoV-2-infected phosphoproteomes. Literature review identified seven kinases, including MAP2K1, whose inhibition may reduce viral replication. MAP2K1 was found to target key viral phosphosites, including N protein (S206, T198) and ORF9b (S50), conserved across SARS-CoV-2 variants. Docking analysis showed MAP2K1 forms stronger, closer interactions with N protein compared to SRPK1, highlighting MAP2K1 as a potential host kinase for therapeutic targeting in SARS-CoV-2 infection.Discussion and ConclusionsThis study presents a framework for predicting human kinases of specific SARS-CoV-2 protein phosphosites by integrating kinase specificity, virus–host interactions, and post-translational modifications. MAP2K1 was identified as a key host kinase, showing stronger interactions than SRPK1, and is proposed as an antiviral drug target for repurposing in SARS-CoV-2 infections.