Computational analysis of target genes in monkeypox virus infection and potential therapeutic precursors

ABSTRACT

Background

Monkeypox is an orthopoxvirus that is responsible for zoonotic infections in humans. The virus has recently spread rapidly and the WHO has listed it as an international public health emergency of concern.

Research design and methods

Here, we used network analysis and gene enrichment protocols and analyzed datasets of MPXV infection that induced host cell gene expression list and subsequently mapped them against two herbal target gene lists which highlighted considerable coherence in pharmacological attributes with COVID-19. Molecular docking and simulation were performed for the screened compounds.

Results

Our results identified β-carotene and kaempferol possessing tremendous ability against the MPXV PLD protein. Both compounds were subjected to each of 100 ns molecular dynamics simulation and were found native to the PLD pocket. MM-PB (GB) SA analyses indicated −25.4, −40.1 kcal/mol and −17.2, −26.4kcal/mol of ΔG_bind to the active pocket of PLD. Our data suggest the adaptive nature of the MPXV PLD active pocket toward hydrophobic inhibitors.

Conclusion

These results will be of high importance for the viral researchers to be tested in wet lab settings in designing potential inhibitors.

KEYWORDS:

• Monkeypox
• COVID-19
• AlphaFold2
• network analysis
• PLD
• molecular dynamics simulation

Declaration of financial/other relationships

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

Reviewer disclosures

Peer reviewers on this manuscript have no relevant financial or other relationships to disclose.

Data availability statement

Analyzed data can be found from supplementary data or by request.

Acknowledgments

The authors acknowledge the efforts of Amr Amin, Biology Department, UAE University, UAE, and Ansal Diasova, Department of Biology, School of Sciences and Humanities, Nazarbayev University, for their valuable suggestions and kind assistance during the preparation of this manuscript.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/14787210.2023.2259614

Additional information

Funding

There is no specific funding for the paper, but the corresponding author received funding during the project; Nazarbayev University Faculty-Development Competitive Research Grants Program, with reference ID 32729571, ID 15798117 [Funder Project References: 11022021FD2920 and 110119FD4531] to Yingqiu Xie; AUA-UAEU grant [12R118] to Amr Amin and Yingqiu Xie. The funder had no function in research design, data collection/analysis, preparation of the manuscript, or decision to publish.