Detection of the peptidyl epitope for vaccine development against MPV

Indrani Sarkar; Gargi Sen; Mohammd Ajmal Ali; Saeedah Musaed Almutairi; Joongku Lee; Arnab Sen

doi:10.1016/j.jksus.2022.102458

Detection of the peptidyl epitope for vaccine development against MPV

J King Saud Univ Sci. 2023 Jan;35(1):102458. doi: 10.1016/j.jksus.2022.102458. Epub 2022 Nov 24.

Authors

Indrani Sarkar¹, Gargi Sen¹, Mohammd Ajmal Ali², Saeedah Musaed Almutairi², Joongku Lee³, Arnab Sen^{1

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Affiliations

¹ Bioinformtics Facility, University of North Bengal, Raja Rammonahpur, Siliguri 734013, India.
² Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia.
³ Department of Environment and Forest Resources, Chungnam National University, Daejeon, Republic of Korea.
⁴ Department of Botany, University of North Bengal, Raja Rammonahpur, Siliguri 734013, India.
⁵ Biswa Bangla Genome Center, University of North Bengal, Raja Rammonahpur, Siliguri 734013, India.

Abstract

Background: Monkeypox Virus (MPV) is the cause of zoonotic disease characterized by skin-eruption with pus cell formation and lymphadenopathy. This virus belongs to the Orthopoxvirus genus with DNA as its genetic material. Previously, this infection was reported from Africa and occasionally from USA and UK. However, recently there is a sudden surge of infection in non-epidemic countries and a new strain of MPVhas been discovered. Therefore it is important to revisit the phylogeny of MPV with the addition of new strains. Recently WHO also stressed the need of developing vaccines for new strains. In this scenario we have two objectives for this study -first, to reveal the exact phylogenetic position of the 2022 strain and second, to identify specific peptides which may be used for vaccine development in the future.

Methods: The phylogenetic analysis was done with the help of Bayesian phylogeny. The dN/dS calculation was performed based on DNA polymerase genes of selected MPV strains. The peptidyl-epitope was searched in MPV2022/2 SLO strain with the help of several algorithms implemented in Allergen FP v.1.0, NetMHCII 2.3, MHCpred and Toxin Pred. The structure prediction of the proteins and peptides was performed through Hpepdock. The quality of the structures was validated through the Ramachandran plot. The molecular dynamics and simulation were performed through Gromacs software. The interaction between peptide and protein was assessed through Ligplot software.

Results: The phylogenetic analysis revealed that the considered 2022 MPVstrains were close to the USA strains. The evolutionary analysis showed the volatile nature of the genome. Moreover, 9-mer peptide sequence was identified as an epitope for vaccine development.

Conclusions: The emergence of more virulent strains in near future may not be ruled out. Immunocompromised patients are more susceptible to this virus hence sub-unit vaccine is a better choice than a recombinant or attenuated vaccine against monkeypox. We have identified a small stretch of specific peptide which may be used for developing a subunit vaccine against this virus.

Keywords: Epitopes; Evolution; Molecular docking and dynamics; Monkeypox virus; Phylogenomics.