Computational studies on searching potential phytochemicals against DNA polymerase activity of the monkeypox virus

Objectives: The outbreak of monkeypox virus (MPXV) is an emerging epidemic of medical concern with 65353 confirmed cases of infection and a fatality of 115 worldwide. Since May 2022, MPXV has been rapidly disseminating across the globe through various modes of transmission, including direct contact, respiratory droplets, and consensual sex. Because of the limited medical countermeasures available to treat MPXV, the present study aimed to identify potential phytochemicals (limonoids, triterpenoids, and polyphenols) as antagonists to target the DNA polymerase protein of MPXV with the ultimate goal to inhibit the viral DNA replication mechanism and immune-mediated responses. Methods: The protein-DNA and protein-ligand molecular docking were performed with the help of computational programs AutoDock Vina, iGEMDOCK and HDOCK server. The BIOVIA Discovery studio and ChimeraX were used to evaluate the protein-ligand interactions. The GROMACS 2021 was used for the molecular dynamics simulations. The ADME and toxicity properties were computed by using online servers SwissADME and pKCSM. Results: Molecular docking of 609 phytochemicals and molecular dynamics simulations of lead phytochemicals glycyrrhizinic acid and apigenin-7-O-glucuronide generated useful data that supported the ability of phytochemicals to obstruct the DNA polymerase activity of the monkeypox virus. Conclusions: The computational results supported that appropriate phytochemicals can be used to formulate an adjuvant therapy for the monkeypox virus. (c) 2023 Center for Food and Biomolecules, National Taiwan University. Production and hosting by Elsevier Taiwan LLC. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/ licenses/by-nc-nd/4.0/).

Automated summary

This study aimed to identify phytochemicals as antagonists to target the DNA polymerase protein of monkeypox virus. Molecular docking and molecular dynamics simulations were performed to evaluate the interactions between protein and ligand. The results supported the potential use of phytochemicals as an adjuvant therapy for monkeypox virus.