In Silico Structural and Functional Characterization of the HMPV M2-1 Protein Reveals Its Potential as a Therapeutic Target

Saifullah Sarkar; Sanjay Das; Md. Hasan Ali

doi:10.71193/jmct.20250008

Authors

Saifullah Sarkar Department of Agriculture, Gopalganj Science and Technology University, Gopalganj-8100, Bangladesh Author https://orcid.org/0009-0009-5259-3809
Sanjay Das Department of Agriculture, Gopalganj Science and Technology University, Gopalganj-8100, Bangladesh Author
Md. Hasan Ali Department of Agriculture, Gopalganj Science and Technology University, Gopalganj-8100, Bangladesh Author https://orcid.org/0009-0004-7710-4286

DOI:

https://doi.org/10.71193/jmct.20250008

Keywords:

Human metapneumovirus (HMPV), Pneumovirus matrix protein 2 (M2), In silico, Homology modeling, Molecular docking

Abstract

Human metapneumovirus (HMPV) is a leading cause of acute respiratory infections in children, the elderly, and immunocompromised individuals, yet no licensed antivirals or vaccines exist. This study employed in-silico approaches to characterize the HMPV M2-1 protein, a key regulator of viral transcription, and to identify potential natural inhibitors. Physicochemical analysis revealed that M2-1 is a hydrophilic, thermally stable, and basic protein with properties favorable for RNA binding and transcriptional regulation. Conserved domain and motif analyses identified a transcription processivity factor and a zinc finger C3H1 motif, confirming its role in RNA stabilization. Gene Ontology and protein–protein interaction analyses positioned M2-1 as a multifunctional protein associated with viral replication, assembly, and host immune modulation. Homology modeling using SWISS-MODEL and I-TASSER generated high-quality 3D structures, with the SWISS-MODEL showing superior stereochemical quality and enabling accurate active site prediction. CASTpFold analysis revealed 22 potential binding pockets, with the largest active site measuring 279.006 Å³. Molecular docking using AutoDock Vina in PyRx with 58 garlic (Allium sativum) compounds identified IMPHY010911 as the most potent binder (-7.7 kcal/mol). These findings highlight M2-1 as a promising antiviral drug target and suggest garlic bulb-derived phytochemicals may serve as potential natural inhibitors against HMPV infection.

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