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Mahmud S, Paul GK, Biswas S, Kazi T, Mahbub S, Mita MA, Afrose S, Islam A, Ahaduzzaman S, Hasan MR, Shimu MSS, Promi MM, Shehab MN, Rahman E, Sujon KM, Alom MW, Modak A, Zaman S, Uddin MS, Emran TB, Islam MS, Saleh MA. phytochemdb: a platform for virtual screening and computer-aided drug designing. Database (Oxford) 2022; 2022:6535291. [PMID: 35234849 PMCID: PMC9255273 DOI: 10.1093/database/baac002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/23/2021] [Accepted: 01/12/2022] [Indexed: 12/02/2022]
Abstract
The phytochemicals of medicinal plants are regarded as a rich source of diverse chemical spaces that have been used as supplements and alternative medicines in the millennium. Even in this era of combinatorial chemical drugs, phytomedicines account for a large share of the statistics of newly approved drugs. In the field of computational aided and rational drug design, there is an urgent need to develop and build a useful phytochemical database management system with a user-friendly interface that allows proper data storage, retrieval and management. We showed ‘phytochemdb’, a manually managed database that compiles 525 plants and their corresponding 8093 phytochemicals, aiming to incorporate the activities of phytochemicals from medicinal plants. The database collects molecular formula, three-dimensional/two-dimensional structure, canonical SMILES, molecular weight, no. of heavy atoms, no. of aromatic heavy atoms, fraction Csp3, no. of rotatable bonds, no. of H-bond acceptors, no. of H-bond donors, molar refractivity, topological polar surface area, gastrointestinal absorption, Blood–Brain Barrier (BBB) permeant, P-gp substrate, CYP1A2 inhibitor, CYP2C19 inhibitor, CYP2C9 inhibitor, CYP2D6 inhibitor, CYP3A4 inhibitor, Log Kp, Ghose, Veber, Egan, Muegge, bioavailability scores, pan-assay interference compounds, Brenk, Leadlikeness, synthetic accessibility, iLOGP and Lipinski rule of five with the number of violations for each compound. It provides open contribution functions for the researchers who screen phytochemicals in the laboratory and have released their data. ‘phytochemdb’ is a comprehensive database that gathers most of the information about medicinal plants in one platform, which is considered to be very beneficial to the work of researchers on medicinal plants. ‘phytochemdb’ is available for free at https://phytochemdb.com/.
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Affiliation(s)
- Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Suvro Biswas
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Taheruzzaman Kazi
- Department of Regenerative Dermatology, Graduate School of Medicine, Osaka University , Suita 565-0871, Japan
| | - Shafquat Mahbub
- Department of Computer Science and Engineering, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Ariful Islam
- Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Sheikh Ahaduzzaman
- Department of Computer Science and Engineering, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | | | - Maria Meha Promi
- Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Mobasshir Noor Shehab
- Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Ekhtiar Rahman
- Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Khaled Mahmud Sujon
- Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Md. Wasim Alom
- Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Anik Modak
- Department of Computer Science and Engineering, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Md. Salah Uddin
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh , Chittagong 4381, Bangladesh
| | - Md. Sayeedul Islam
- Department of Biological Sciences, Graduate School of Science, Osaka University , Machikaneyama-cho 1-1, Toyonaka, Osaka 560-0043, Japan
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi , Rajshahi 6205, Bangladesh
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Mahmud S, Uddin MAR, Zaman M, Sujon KM, Rahman ME, Shehab MN, Islam A, Alom MW, Amin A, Akash AS, Saleh MA. Molecular docking and dynamics study of natural compound for potential inhibition of main protease of SARS-CoV-2. J Biomol Struct Dyn 2020; 39:6281-6289. [PMID: 32705962 PMCID: PMC7441771 DOI: 10.1080/07391102.2020.1796808] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Newly emerged SARS-CoV-2 made recent pandemic situations across the globe is accountable for countless unwanted death and insufferable panic associated with co-morbidities among mass people. The scarcity of appropriate medical treatment and no effective vaccine or medicine against SARS-CoV-2 has turned the situation worst. Therefore, in this study, we made a deep literature review to enlist plant-derived natural compounds and considered their binding mechanism with the main protease of SARS-CoV-2 through combinatorial bioinformatics approaches. Among all, a total of 14 compounds were filtered where Carinol, Albanin, Myricetin were had better binding profile than the rest of the compounds with having binding energy of –8.476, –8.036, –8.439 kcal/mol, respectively. Furthermore, MM-GBSA calculations were also considered in this selection process to support docking studies. Besides, 100 ns molecular dynamics simulation endorsed the rigid nature, less conformational variation and binding stiffness. As this study, represents a perfect model for SARS-CoV-2 main protease inhibition through bioinformatics study, these potential drug candidates may assist the researchers to find a superior and effective solution against COVID-19 after future experiments. Communicated by Ramaswamy Sarma
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Affiliation(s)
- Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohammad Abu Raihan Uddin
- Department of Biochemistry and Biotechnology, University of Science and Technology (USTC), Chittagong, Bangladesh
| | - Meemtaheena Zaman
- Department of Biochemistry and Biotechnology, University of Science and Technology (USTC), Chittagong, Bangladesh
| | - Khaled Mahmud Sujon
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Ekhtiar Rahman
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Mobasshir Noor Shehab
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Ariful Islam
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Wasim Alom
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Al Amin
- Institute of Biological Science, University of Rajshahi, Rajshahi, Bangladesh
| | - Al Shahriar Akash
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong, Bangladesh
| | - Md Abu Saleh
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
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