Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach
During the second phase of SARS-CoV-2, an unknown fungal infection, identified as black fungus, was transmitted to numerous people among the hospitalized COVID-19 patients and increased the death rate. The black fungus is associated with the Mycolicibacterium smegmatis, Mucor lusitanicus, and Rhizom...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-04-01
|
| Series: | Frontiers in Pharmacology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fphar.2023.1140494/full |
| _version_ | 1797844246096510976 |
|---|---|
| author | Shopnil Akash Arafat Hossain Nobendu Mukerjee Nobendu Mukerjee Md. Moklesur Rahman Sarker Md. Moklesur Rahman Sarker Mohammad Firoz Khan Md. Jamal Hossain Mohammad A. Rashid Ajoy Kumer Arabinda Ghosh Darwin A. León-Figueroa Joshuan J. Barboza Bijaya Kumar Padhi Ranjit Sah Ranjit Sah Ranjit Sah |
| author_facet | Shopnil Akash Arafat Hossain Nobendu Mukerjee Nobendu Mukerjee Md. Moklesur Rahman Sarker Md. Moklesur Rahman Sarker Mohammad Firoz Khan Md. Jamal Hossain Mohammad A. Rashid Ajoy Kumer Arabinda Ghosh Darwin A. León-Figueroa Joshuan J. Barboza Bijaya Kumar Padhi Ranjit Sah Ranjit Sah Ranjit Sah |
| author_sort | Shopnil Akash |
| collection | DOAJ |
| description | During the second phase of SARS-CoV-2, an unknown fungal infection, identified as black fungus, was transmitted to numerous people among the hospitalized COVID-19 patients and increased the death rate. The black fungus is associated with the Mycolicibacterium smegmatis, Mucor lusitanicus, and Rhizomucor miehei microorganisms. At the same time, other pathogenic diseases, such as the Monkeypox virus and Marburg virus, impacted global health. Policymakers are concerned about these pathogens due to their severe pathogenic capabilities and rapid spread. However, no standard therapies are available to manage and treat those conditions. Since the coptisine has significant antimicrobial, antiviral, and antifungal properties; therefore, the current investigation has been designed by modifying coptisine to identify an effective drug molecule against Black fungus, Monkeypox, and Marburg virus. After designing the derivatives of coptisine, they have been optimized to get a stable molecular structure. These ligands were then subjected to molecular docking study against two vital proteins obtained from black fungal pathogens: Rhizomucor miehei (PDB ID: 4WTP) and Mycolicibacterium smegmatis (PDB ID 7D6X), and proteins found in Monkeypox virus (PDB ID: 4QWO) and Marburg virus (PDB ID 4OR8). Following molecular docking, other computational investigations, such as ADMET, QSAR, drug-likeness, quantum calculation and molecular dynamics, were also performed to determine their potentiality as antifungal and antiviral inhibitors. The docking score reported that they have strong affinities against Black fungus, Monkeypox virus, and Marburg virus. Then, the molecular dynamic simulation was conducted to determine their stability and durability in the physiological system with water at 100 ns, which documented that the mentioned drugs were stable over the simulated time. Thus, our in silico investigation provides a preliminary report that coptisine derivatives are safe and potentially effective against Black fungus, Monkeypox virus, and Marburg virus. Hence, coptisine derivatives may be a prospective candidate for developing drugs against Black fungus, Monkeypox and Marburg viruses. |
| first_indexed | 2024-04-09T17:19:11Z |
| format | Article |
| id | doaj.art-38e500350e754968ab04f32eac11b889 |
| institution | Directory Open Access Journal |
| issn | 1663-9812 |
| language | English |
| last_indexed | 2024-04-09T17:19:11Z |
| publishDate | 2023-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Pharmacology |
| spelling | doaj.art-38e500350e754968ab04f32eac11b8892023-04-19T05:18:19ZengFrontiers Media S.A.Frontiers in Pharmacology1663-98122023-04-011410.3389/fphar.2023.11404941140494Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approachShopnil Akash0Arafat Hossain1Nobendu Mukerjee2Nobendu Mukerjee3Md. Moklesur Rahman Sarker4Md. Moklesur Rahman Sarker5Mohammad Firoz Khan6Md. Jamal Hossain7Mohammad A. Rashid8Ajoy Kumer9Arabinda Ghosh10Darwin A. León-Figueroa11Joshuan J. Barboza12Bijaya Kumar Padhi13Ranjit Sah14Ranjit Sah15Ranjit Sah16Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, BangladeshDepartment of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, BangladeshDepartment of Microbiology, West Bengal State University, Kolkata, West Bengal, IndiaDepartment of Health Sciences, Novel Global Community Educational Foundation, Hebersham, NSW, AustraliaHealth Med. Science Research Network, Dhaka, BangladeshDepartment of Pharmacy, State University of Bangladesh, Dhaka, BangladeshDepartment of Pharmacy, State University of Bangladesh, Dhaka, BangladeshDepartment of Pharmacy, State University of Bangladesh, Dhaka, BangladeshDepartment of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka, BangladeshLaboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, BangladeshMicrobiology Division, Department of Botany, Gauhati University, Guwahati, Assam, India0Facultad de Medicina Humana, Universidad de San Martín de Porres, Chiclayo, Peru1Escuela de Medicina, Universidad Cesar Vallejo, Trujillo, Peru2Department of Community Medicine, School of Public Health, Postgraduate Institute of Medical Education and Research, Chandigarh, India3Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal4Dr. D.Y Patil Medical College, Hospital and Research Centre, Pune, Maharashtra, India5Green City Hospital, Tokha, NepalDuring the second phase of SARS-CoV-2, an unknown fungal infection, identified as black fungus, was transmitted to numerous people among the hospitalized COVID-19 patients and increased the death rate. The black fungus is associated with the Mycolicibacterium smegmatis, Mucor lusitanicus, and Rhizomucor miehei microorganisms. At the same time, other pathogenic diseases, such as the Monkeypox virus and Marburg virus, impacted global health. Policymakers are concerned about these pathogens due to their severe pathogenic capabilities and rapid spread. However, no standard therapies are available to manage and treat those conditions. Since the coptisine has significant antimicrobial, antiviral, and antifungal properties; therefore, the current investigation has been designed by modifying coptisine to identify an effective drug molecule against Black fungus, Monkeypox, and Marburg virus. After designing the derivatives of coptisine, they have been optimized to get a stable molecular structure. These ligands were then subjected to molecular docking study against two vital proteins obtained from black fungal pathogens: Rhizomucor miehei (PDB ID: 4WTP) and Mycolicibacterium smegmatis (PDB ID 7D6X), and proteins found in Monkeypox virus (PDB ID: 4QWO) and Marburg virus (PDB ID 4OR8). Following molecular docking, other computational investigations, such as ADMET, QSAR, drug-likeness, quantum calculation and molecular dynamics, were also performed to determine their potentiality as antifungal and antiviral inhibitors. The docking score reported that they have strong affinities against Black fungus, Monkeypox virus, and Marburg virus. Then, the molecular dynamic simulation was conducted to determine their stability and durability in the physiological system with water at 100 ns, which documented that the mentioned drugs were stable over the simulated time. Thus, our in silico investigation provides a preliminary report that coptisine derivatives are safe and potentially effective against Black fungus, Monkeypox virus, and Marburg virus. Hence, coptisine derivatives may be a prospective candidate for developing drugs against Black fungus, Monkeypox and Marburg viruses.https://www.frontiersin.org/articles/10.3389/fphar.2023.1140494/fullBlack FungusMonkeypoxMarburg virusmolecular dockingadmetQSAR |
| spellingShingle | Shopnil Akash Arafat Hossain Nobendu Mukerjee Nobendu Mukerjee Md. Moklesur Rahman Sarker Md. Moklesur Rahman Sarker Mohammad Firoz Khan Md. Jamal Hossain Mohammad A. Rashid Ajoy Kumer Arabinda Ghosh Darwin A. León-Figueroa Joshuan J. Barboza Bijaya Kumar Padhi Ranjit Sah Ranjit Sah Ranjit Sah Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach Frontiers in Pharmacology Black Fungus Monkeypox Marburg virus molecular docking admet QSAR |
| title | Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach |
| title_full | Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach |
| title_fullStr | Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach |
| title_full_unstemmed | Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach |
| title_short | Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach |
| title_sort | modified coptisine derivatives as an inhibitor against pathogenic rhizomucor miehei mycolicibacterium smegmatis black fungus monkeypox and marburg virus by molecular docking and molecular dynamics simulation based drug design approach |
| topic | Black Fungus Monkeypox Marburg virus molecular docking admet QSAR |
| url | https://www.frontiersin.org/articles/10.3389/fphar.2023.1140494/full |
| work_keys_str_mv | AT shopnilakash modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT arafathossain modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT nobendumukerjee modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT nobendumukerjee modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT mdmoklesurrahmansarker modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT mdmoklesurrahmansarker modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT mohammadfirozkhan modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT mdjamalhossain modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT mohammadarashid modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT ajoykumer modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT arabindaghosh modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT darwinaleonfigueroa modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT joshuanjbarboza modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT bijayakumarpadhi modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT ranjitsah modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT ranjitsah modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach AT ranjitsah modifiedcoptisinederivativesasaninhibitoragainstpathogenicrhizomucormieheimycolicibacteriumsmegmatisblackfungusmonkeypoxandmarburgvirusbymoleculardockingandmoleculardynamicssimulationbaseddrugdesignapproach |