Computational investigation of the Nucleoprotein/Phosphoprotein interaction of the human Metapneumovirus: exploring mimetic peptides as potential antiviral agents

Ricardo de Paiva Caetano¹, João Victor Piloto¹, Evelyn R. D. de Araujo¹, Wan Suk Augusto Mazucato¹, Marcelo Andres Fossey¹, Fátima Pereira de Souza¹, Icaro Putinhon Caruso¹

¹Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), São Paulo State University, São José do Rio Preto, SP, Brazil, (email: [email protected])

The human Metapneumovirus (hMPV) is one of the most common causes of respiratory diseases, such as bronchiolitis and pneumonia, in children and the elderly. Currently, there are no vaccines or specific therapies against infections caused by this virus. The hMPV N nucleoprotein stands out for its role in protecting the viral RNA by forming the nucleocapsid (NC) and for its involvement in the replication and transcription process promoted by the viral polymerase complex. Recognition of the NC by the viral polymerase is mediated by the interaction of the last six residues (Ile298-Met294) of the C-terminus of the P phosphoprotein with a binding pocket in the N-terminal domain of the N protein (N-NTD). This N/P interaction hotspot in the hMPV N-NTD can be exploited as a druggable binding site, as has already been done for the N-NTD of a virus of the same subfamily Pneumovirinae, the human Respiratory Syncytial Virus (hRSV). The present work aimed to rationalize the design of mimetics for the Ile289-Met294 peptide, which binds to the N-NTD of hMPV, using molecular dynamics (MD) simulations and binding free energy calculations (MM-GBSA). The proposed modifications (Q291S, Q291N, I293D, I293E, and I293T) for the Ile289-Met294 peptide (298-YIQLIM-294) to generate its mimetics were based on naturally observed substitutions in the C-terminal region of the P protein of avian Metapneumovirus (aMPV) by comparing conserved and non-conserved residues from sequence alignment. Computational simulations allowed the evaluation of the conformational stability of the N-NTD/peptide complexes and the identification of Ile298-Met294 mimetics with higher affinity for the interaction site. The results provide insights for the development of peptide inhibitors that can interfere with the N/P interaction, contributing to new antiviral approaches against hMPV.

This work was supported by FAPESP (2022/13050-5, 2023/01632-2) and CNPq (317157/2023-0, 445484/2024-5).