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Updated: Sep 14, 2025
Identification of Kinase-substrate Pairs Using High Throughput Screening
Published on: August 29, 2015
Analysis of phosphomotifs coupled to phosphoproteome and interactome unveils potential human kinase substrate
Vineetha Shaji1,2, Ahmad Rafi1, Mukhtar Ahmed3
1Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, India.
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.
Discussion And Conclusions:
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.
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