Computational investigation of potential natural compounds as inhibitors of monkeypox virus cysteine proteinase
IntroductionMonkeypox is a serious viral illness that is rarely seen but is spread from person to person and from animals to humans. Cysteine proteinase, an essential enzyme involved in the replication of the monkeypox virus (MPXV), is one of many possible therapeutic targets for MPXV. The primary f...
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Frontiers Media S.A.
2025-07-01
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| Series: | Frontiers in Bioinformatics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2025.1637207/full |
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| author | Riya Nalwa Anis Ahmad Chaudhary Mandeep Chouhan Prashant Kumar Tiwari Saurabh Gupta Hassan Ahmed Rudayni Vivek Dhar Dwivedi Vivek Dhar Dwivedi Sanjay Kumar Sanjay Kumar Sanjay Kumar |
| author_facet | Riya Nalwa Anis Ahmad Chaudhary Mandeep Chouhan Prashant Kumar Tiwari Saurabh Gupta Hassan Ahmed Rudayni Vivek Dhar Dwivedi Vivek Dhar Dwivedi Sanjay Kumar Sanjay Kumar Sanjay Kumar |
| author_sort | Riya Nalwa |
| collection | DOAJ |
| description | IntroductionMonkeypox is a serious viral illness that is rarely seen but is spread from person to person and from animals to humans. Cysteine proteinase, an essential enzyme involved in the replication of the monkeypox virus (MPXV), is one of many possible therapeutic targets for MPXV. The primary function of this enzyme is to cleave the precursor polyprotein into the distinct proteins required for viral assembly. The aim was to develop potential drugs that can inhibit the proteinase and stop the spread of the MPXV.MethodsVirtual screening, molecular docking, molecular dynamics simulation, and free binding energy calculations were used to explore the potential of 569 phytochemicals from a variety of plants that could inhibit the proteinase of the MPXV.ResultsThe four compounds (Unii-CQ2F5O6yiy, lithospermic acid, kaempferol, and rhamnocitrin) with the best docking scores displayed docking score values ranging from −9.5 to −7.4 kcal/mol and were used for further analysis. Out of these, Unii-CQ2F5O6yiy exhibited a docking score of −9.5 kcal/mol, indicating the highest binding to the proteinase. Unii-CQ2F5O6yiy had the most stable and consistent root mean square deviation (RMSD) of <3 Å.DiscussionWe identified the top four phytochemicals that exhibited better docking scores than the reference compound. The RMSDs of proteins in all the phytochemical complexes exhibited acceptable deviation except for lithospermic acid, whereas atoms of Unii-CQ2F5O6yiy and kaempferol in their docked complexes displayed less fluctuation than the reference compound (<5.4 Å).ConclusionUnii-CQ2F5O6yiy could be used as a potential antiviral agent for the management of monkeypox virus. However, further experimental validation under in vitro and in vivo conditions is required to confirm its antiviral activity against MPXV. |
| format | Article |
| id | doaj-art-e7b64b96d3b247bfab3b31ec9dfc1944 |
| institution | Matheson Library |
| issn | 2673-7647 |
| language | English |
| publishDate | 2025-07-01 |
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| series | Frontiers in Bioinformatics |
| spelling | doaj-art-e7b64b96d3b247bfab3b31ec9dfc19442025-07-28T05:30:36ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472025-07-01510.3389/fbinf.2025.16372071637207Computational investigation of potential natural compounds as inhibitors of monkeypox virus cysteine proteinaseRiya Nalwa0Anis Ahmad Chaudhary1Mandeep Chouhan2Prashant Kumar Tiwari3Saurabh Gupta4Hassan Ahmed Rudayni5Vivek Dhar Dwivedi6Vivek Dhar Dwivedi7Sanjay Kumar8Sanjay Kumar9Sanjay Kumar10Biological and Bio-computational Lab, Department of Life Science, Sharda School of Bio-Science and Technology, Sharda University, Greater Noida, Uttar Pradesh, IndiaDepartment of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi ArabiaBiological and Bio-computational Lab, Department of Life Science, Sharda School of Bio-Science and Technology, Sharda University, Greater Noida, Uttar Pradesh, IndiaBiological and Bio-computational Lab, Department of Life Science, Sharda School of Bio-Science and Technology, Sharda University, Greater Noida, Uttar Pradesh, IndiaDepartment of Biotechnology, GLA University, Mathura, Uttar Pradesh, IndiaDepartment of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi ArabiaCenter for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IndiaBioinformatics Research Division, Quanta Calculus, Greater Noida, IndiaBiological and Bio-computational Lab, Department of Life Science, Sharda School of Bio-Science and Technology, Sharda University, Greater Noida, Uttar Pradesh, IndiaDST-Facility, Sharda University, Greater Noida, Uttar Pradesh, IndiaCentre of Excellence in Artificial Intelligence in Medicine, Imaging and Forensic, Sharda University, Greater Noida, IndiaIntroductionMonkeypox is a serious viral illness that is rarely seen but is spread from person to person and from animals to humans. Cysteine proteinase, an essential enzyme involved in the replication of the monkeypox virus (MPXV), is one of many possible therapeutic targets for MPXV. The primary function of this enzyme is to cleave the precursor polyprotein into the distinct proteins required for viral assembly. The aim was to develop potential drugs that can inhibit the proteinase and stop the spread of the MPXV.MethodsVirtual screening, molecular docking, molecular dynamics simulation, and free binding energy calculations were used to explore the potential of 569 phytochemicals from a variety of plants that could inhibit the proteinase of the MPXV.ResultsThe four compounds (Unii-CQ2F5O6yiy, lithospermic acid, kaempferol, and rhamnocitrin) with the best docking scores displayed docking score values ranging from −9.5 to −7.4 kcal/mol and were used for further analysis. Out of these, Unii-CQ2F5O6yiy exhibited a docking score of −9.5 kcal/mol, indicating the highest binding to the proteinase. Unii-CQ2F5O6yiy had the most stable and consistent root mean square deviation (RMSD) of <3 Å.DiscussionWe identified the top four phytochemicals that exhibited better docking scores than the reference compound. The RMSDs of proteins in all the phytochemical complexes exhibited acceptable deviation except for lithospermic acid, whereas atoms of Unii-CQ2F5O6yiy and kaempferol in their docked complexes displayed less fluctuation than the reference compound (<5.4 Å).ConclusionUnii-CQ2F5O6yiy could be used as a potential antiviral agent for the management of monkeypox virus. However, further experimental validation under in vitro and in vivo conditions is required to confirm its antiviral activity against MPXV.https://www.frontiersin.org/articles/10.3389/fbinf.2025.1637207/fullMonkeypox viruscysteine proteinasestructure-based virtual screeningphytochemicalsmolecular dynamics simulation |
| spellingShingle | Riya Nalwa Anis Ahmad Chaudhary Mandeep Chouhan Prashant Kumar Tiwari Saurabh Gupta Hassan Ahmed Rudayni Vivek Dhar Dwivedi Vivek Dhar Dwivedi Sanjay Kumar Sanjay Kumar Sanjay Kumar Computational investigation of potential natural compounds as inhibitors of monkeypox virus cysteine proteinase Frontiers in Bioinformatics Monkeypox virus cysteine proteinase structure-based virtual screening phytochemicals molecular dynamics simulation |
| title | Computational investigation of potential natural compounds as inhibitors of monkeypox virus cysteine proteinase |
| title_full | Computational investigation of potential natural compounds as inhibitors of monkeypox virus cysteine proteinase |
| title_fullStr | Computational investigation of potential natural compounds as inhibitors of monkeypox virus cysteine proteinase |
| title_full_unstemmed | Computational investigation of potential natural compounds as inhibitors of monkeypox virus cysteine proteinase |
| title_short | Computational investigation of potential natural compounds as inhibitors of monkeypox virus cysteine proteinase |
| title_sort | computational investigation of potential natural compounds as inhibitors of monkeypox virus cysteine proteinase |
| topic | Monkeypox virus cysteine proteinase structure-based virtual screening phytochemicals molecular dynamics simulation |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2025.1637207/full |
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