ORIGINAL RESEARCH article
Front. Bioinform.
Sec. Protein Bioinformatics
Volume 5 - 2025 | doi: 10.3389/fbinf.2025.1678189
Uncovering human kinase substrates in the Nipah proteome
Provisionally accepted
Vineetha Shaji1,2Akash Anil1Ayisha A Jabbar1Althaf Mahin1,2Ahmad Rafi1Sowmya Soman1Amjesh Revikumar1
Dr.Ganesh Prasad3*Dr. Sneha M. Pinto4
Yashwanth Subbannayya5Abhithaj Jayanandan1*
rajesh raju1,3*- 1Centre for Integrative Omics Data Science, Yenepoya Mangalore, India
- 2Centre for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore 575018, India, Mangalore, India
- 3Yenepoya (Deemed to be University), Mangaluru, India
- 4School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK, Guildford GU2 7XH, United Kingdom
- 5Surrey Institute for People-Centred AI, University of Surrey, Guildford, Surrey, GU2 7XH, UK., Surrey, GU2 7XH, UK., United Kingdom
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This study explores the critical role of kinase–substrate interactions in viral pathogenesis, focusing on phosphorylation events that regulate Nipah virus (NiV) protein function and host signaling pathways during infection. We employed a robust kinase–substrate phosphomotif pattern-based approach combined with NiV–human protein–protein interaction data, redundancy assessment, and conservation analysis to identify 51 human kinases that could potentially phosphorylate 1,180 sites across nine NiV proteins. Among these, EEF2K, HASPIN, MAPK9, MAST2, and SYK emerged as key kinases, predicted to phosphorylate multiple conserved phosphosites with potential functional significance. To validate these findings, we performed in silico docking, which revealed strong binding affinities and structural specificity between predicted kinases and their viral substrates. This study presents a comprehensive framework for investigating virus–host interactions and post-translational modifications in NiV proteins, offering insights into therapeutic opportunities targeting kinase-mediated pathways, and providing a transferable approach applicable to other emerging pathogens for uncovering host–viral kinase–substrate interactions. We believe these findings will be of significant interest to the readership of Frontiers in Immunology, particularly those focused on viral immunology, host–pathogen interactions, and antiviral strategies.
Keywords: Nipah Virus, Phosphorylation, Protein-protein docking, Molecular dynamics simulation (MD), kinase-substrate phosphomotif search
Received: 04 Aug 2025; Accepted: 14 Oct 2025.
Copyright: © 2025 Shaji, Anil, Jabbar, Mahin, Rafi, Soman, Revikumar, Prasad, Pinto, Subbannayya, Jayanandan and raju. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Dr.Ganesh Prasad, ganesh@yenepoya.edu.in
Abhithaj Jayanandan, abhithaj.j.ciods@yenepoya.edu.in
rajesh raju, rajeshraju@yenepoya.edu.in
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