Analysis of phosphomotifs coupled to phosphoproteome and interactome unveils potential human kinase substrate proteins in SARS-CoV-2
Vineetha Shaji, Ahmad Rafi, Mukhtar Ahmed, Athira Perunelly Gopalakrishnan, Sowmya Soman, Amjesh Revikumar, Ganesh Prasad, Abhithaj Jayanandan, Rajesh Raju
Frontiers in Cellular and Infection Microbiology, doi:10.3389/fcimb.2025.1554760
Introduction: Viruses 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. Methods: Employing 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.
Results: The 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.
Ethics statement Ethical approval was not required for the study involving humans in accordance with the local legislation and institutional requirements. Written informed consent to participate in this study was not required from the participants or the participants' legal guardians/next of kin in accordance with the national legislation and the institutional requirements.
Author contributions
Conflict of interest The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Publisher's note All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
Supplementary material The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fcimb.2025.1554760/ full#supplementary-material
SUPPLEMENTARY FIGURE 1 Docking results of SRPK1 with experimentally validated phosphorylation sites on the N viral protein at T198 and S206.
SUPPLEMENTARY TABLE 1 List of predicted kinases, viral proteins, and their corresponding viral phosphosites.
SUPPLEMENTARY TABLE 2 The table highlights phosphosite-specific regulation (Upregulated or..
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doi:10.1038/nrd.2015.37DOI record:
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"abstract": "<jats:sec><jats:title>Introduction</jats:title><jats:p>Viruses 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.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Employing the protein kinase substrate sequence-preference motifs derived by Poll B G. <jats:italic>et. al</jats:italic>., 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.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The 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.</jats:p></jats:sec><jats:sec><jats:title>Discussion and Conclusions</jats:title><jats:p>This 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.</jats:p></jats:sec>",
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