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Akash S, Hossain A, Mukerjee N, Sarker MMR, Khan MF, Hossain MJ, Rashid MA, Kumer A, Ghosh A, León-Figueroa DA, Barboza JJ, Padhi BK, Sah R. 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. Front Pharmacol 2023; 14:1140494. [PMID: 37153804 PMCID: PMC10154673 DOI: 10.3389/fphar.2023.1140494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/29/2023] [Indexed: 05/10/2023] Open
Abstract
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.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Arafat Hossain
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Kolkata, West Bengal, India
- Department of Health Sciences, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Md. Moklesur Rahman Sarker
- Health Med. Science Research Network, Dhaka, Bangladesh
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| | | | - Md. Jamal Hossain
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| | - Mohammad A. Rashid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Ajoy Kumer
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, Bangladesh
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, Assam, India
| | | | - Joshuan J. Barboza
- Escuela de Medicina, Universidad Cesar Vallejo, Trujillo, Peru
- *Correspondence: Joshuan J. Barboza, ; Ranjit Sah,
| | - Bijaya Kumar Padhi
- Department of Community Medicine, School of Public Health, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ranjit Sah
- Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
- Dr. D.Y Patil Medical College, Hospital and Research Centre, Pune, Maharashtra, India
- Green City Hospital, Tokha, Nepal
- *Correspondence: Joshuan J. Barboza, ; Ranjit Sah,
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Jain S, Rana M, Sultana R, Mehandi R, Rahisuddin. Schiff Base Metal Complexes as Antimicrobial and Anticancer Agents. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2117210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Shruti Jain
- Department of Chemistry, Jamia Millia Islamia, New Delhi, India
| | - Manish Rana
- Department of Chemistry, Jamia Millia Islamia, New Delhi, India
| | - Razia Sultana
- Department of Chemistry, Jamia Millia Islamia, New Delhi, India
| | - Rabiya Mehandi
- Department of Chemistry, Jamia Millia Islamia, New Delhi, India
| | - Rahisuddin
- Department of Chemistry, Jamia Millia Islamia, New Delhi, India
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Synthesis of Two Novel Copper (II) Complexes as Potential Inhibitors of HIV-1 Protease Enzyme: Experimental and Theoretical Investigations. CRYSTALS 2022. [DOI: 10.3390/cryst12081066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In this study, we report the synthesis of two new copper complexes: [Cu(C11H7O2)(SCN)(C10H8N2)], denoted as (C-1), and [Cu(C11H7O2) (C12H8N2) Cl]·H2O, denoted as (C-2). They are based on 2,2′-bipyridine or 1,10-phenanthroline and 2-hydroxy-1-naphtaldehyde ligands. The obtained complexes were characterized by FT-IR, UV-visible spectroscopy, and single-crystal X-ray diffraction analysis. Molecular docking was employed to predict the binding mode involved in the interaction between the two synthetic copper (II) complexes and HIV-1 protease enzyme. The X-ray structural analysis revealed that the crystal structures of both complexes are mainly stabilized by several intra- and intermolecular hydrogen bonds. The fingerprint plots associated with the Hirshfeld surfaces of both complexes clearly show that H···H interactions provide the largest contributions. According to the docking results, the synthesized complexes exhibit promising features which enable them to be bound to the HIV-protease enzyme.
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Synthesis, structural elucidation, in vitro antibacterial activity, DFT calculations, and molecular docking aspects of mixed-ligand complexes of a novel oxime and phenylalanine. Bioorg Chem 2022; 121:105685. [DOI: 10.1016/j.bioorg.2022.105685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/03/2022] [Accepted: 02/12/2022] [Indexed: 11/17/2022]
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Ragole VD, Wankhede DS, Gayakwad SV. Biologically active mixed ligand complexes of Co(II), Ni(II), Cu(II) and Zn(II) as potential antimalarial, antidibetic and anticancer agents. INORG NANO-MET CHEM 2022. [DOI: 10.1080/24701556.2022.2043377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Vikas D. Ragole
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, Maharashtra, India
| | - Dnyaneshwar S. Wankhede
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, Maharashtra, India
| | - Sonaji V. Gayakwad
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, Maharashtra, India
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Mohapatra RK, Perekhoda L, Azam M, Suleiman M, Sarangi AK, Semenets A, Pintilie L, Al-Resayes SI. Computational investigations of three main drugs and their comparison with synthesized compounds as potent inhibitors of SARS-CoV-2 main protease (M pro): DFT, QSAR, molecular docking, and in silico toxicity analysis. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2021; 33:101315. [PMID: 33390681 PMCID: PMC7765764 DOI: 10.1016/j.jksus.2020.101315] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 05/28/2023]
Abstract
In this study, we examined five previously synthesized compounds and checked their binding affinity towards the SARS-CoV-2 main protease (Mpro) by molecular docking study, and compared the data with three FDA approved drugs, i.e., Remdesivir, Ivermectine and Hydroxychlorochine. In addition, we have investigated the docking study against the main protease of SARS-CoV-2 (Mpro) by using Autodock 4.2 software package. The results suggested that the investigated compounds have property to bind the active position of the protein as reported in approved drugs. Hence, further experimental studies are required. The formation of intermolecular interactions, negative values of scoring functions, free binding energy and the calculated binding constants confirmed that the studied compounds have significant affinity for the specified biotarget. These studied compounds were passed the drug-likeness criteria as suggested by calculating ADME data by SwissADME server. Moreover, the ADMET properties suggested that the investigated compounds to be orally active compounds in human. Furthermore, density functional computations (DFT) were executed by applying GAUSSIAN 09 suit program. In addition, Quantitative Structure-Activity Relationship (QSAR) was studied by applying HyperChem Professional 8.0.3 program.
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Affiliation(s)
- Ranjan K Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar, Odisha 758002, India
| | - Lina Perekhoda
- Department of Medicinal Chemistry, National University of Pharmacy, Pushkinska Str. 53, Kharkiv 61002, Ukraine
| | - Mohammad Azam
- Department of Chemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Marharyta Suleiman
- Department of Medicinal Chemistry, National University of Pharmacy, Pushkinska Str. 53, Kharkiv 61002, Ukraine
| | - Ashish K Sarangi
- Department of Chemistry, School of Applied Sciences, Centurion University of Technology and Management, Odisha, India
| | - Anton Semenets
- Department of Medicinal Chemistry, National University of Pharmacy, Pushkinska Str. 53, Kharkiv 61002, Ukraine
| | - Lucia Pintilie
- Department of Synthesis of Bioactive Substances and Pharmaceutical Technologies, National Institute for Chemical & Pharmaceutical Research and Development, Bucharest, Romania
| | - Saud I Al-Resayes
- Department of Chemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
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