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Kumar D, Sharma P, Mahajan A, Dhawan R, Dua K. Pharmaceutical interest of in-silico approaches. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2018-0157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The virtual environment within the computer using software performed on the computer is known as in-silico studies. These drugs designing software play a vital task in discovering new drugs in the field of pharmaceuticals. These designing programs and software are employed in gene sequencing, molecular modeling, and in assessing the three-dimensional structure of the molecule, which can further be used in drug designing and development. Drug development and discovery is not only a powerful, extensive, and an interdisciplinary system but also a very complex and time-consuming method. This book chapter mainly focused on different types of in-silico approaches along with their pharmaceutical applications in numerous diseases.
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Affiliation(s)
- Dinesh Kumar
- Sri Sai College of Pharmacy , Manawala , Amritsar 143001 , Punjab , India
| | - Pooja Sharma
- Department of Pharmaceutical Sciences and Drug Research , Punjabi University , Patiala 147002 , Punjab , India
- Khalsa College of Pharmacy , Amritsar 143001 , Punjab , India
| | - Ayush Mahajan
- Sri Sai College of Pharmacy , Manawala , Amritsar 143001 , Punjab , India
| | - Ravi Dhawan
- Khalsa College of Pharmacy , Amritsar 143001 , Punjab , India
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney , Ultimo 2007 , NSW , Australia
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney , Ultimo 2007 , New South Wales , Australia
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Rafi MO, Bhattacharje G, Al-Khafaji K, Taskin-Tok T, Alfasane MA, Das AK, Parvez MAK, Rahman MS. Combination of QSAR, molecular docking, molecular dynamic simulation and MM-PBSA: analogues of lopinavir and favipiravir as potential drug candidates against COVID-19. J Biomol Struct Dyn 2020; 40:3711-3730. [PMID: 33251975 PMCID: PMC7754938 DOI: 10.1080/07391102.2020.1850355] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pandemic COVID-19 infections have spread throughout the world. There is no effective treatment against this disease. Viral RNA-dependent RNA polymerase (RdRp) catalyzes the replication of RNA from RNA and the main protease (Mpro) has a role in the processing of polyproteins that are translated from the RNA of SARS-CoV-2, and thus these two enzymes are strong candidates for targeting by anti-viral drugs. Small molecules such as lopinavir and favipiravir significantly inhibit the activity of Mpro and RdRp in vitro. Studies have shown that structurally modified lopinavir, favipiravir, and other similar compounds can inhibit COVID-19 main protease (Mpro) and RNA-dependent RNA polymerase (RdRp). In this study, lopinavir and its structurally similar compounds were chosen to bind the main protease, and favipiravir was chosen to target RNA-dependent RNA polymerase. Molecular docking and the quantitative structure-activity relationships (QSAR) study revealed that the selected candidates have favorable binding affinity but less druggable properties. To improve the druggability, four structural analogues of lopinavir and one structural analogue of favipiravir was designed by structural modification. Molecular interaction analyses have displayed that lopinavir and favipiravir analogues interact with the active site residues of Mpro and RdRp, respectively. Absorption, distribution, metabolism, excretion and toxicity (ADMET) properties, medicinal chemistry profile, and physicochemical features were shown that all structurally modified analogues are less toxic and contain high druggable properties than the selected candidates. Subsequently, 50 ns molecular dynamics simulation of the top four docked complexes demonstrated that CID44271905, a lopinavir analogue, forms the most stable complex with the Mpro. Further MMPBSA analyses using the MD trajectories also confirmed the higher binding affinity of CID44271905 towards Mpro. In summary, this study demonstrates a new way to identify leads for novel anti-viral drugs against COVID-19. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Gourab Bhattacharje
- Department of Biotechnology, Indian Institute of Technology-Kharagpur, Kharagpur, India
| | - Khattab Al-Khafaji
- Department of Chemistry, Faculty of Arts and Sciences, Gaziantep University, Gaziantep, Turkey
| | - Tugba Taskin-Tok
- Department of Chemistry, Faculty of Arts and Sciences, Gaziantep University, Gaziantep, Turkey.,Department of Bioinformatics and Computational Biology, Institute of Health Sciences, Gaziantep University, Gaziantep, Turkey
| | | | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology-Kharagpur, Kharagpur, India
| | - Md Anowar Khasru Parvez
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh.,Treasurer Office, Pabna University of Science and Technology, Pabna, Bangladesh
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
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Gupta R, Kumar P, Narasimhan B. Synthesis, antimicrobial evaluation and QSAR studies of monochloroacetic acid derivatives. ARAB J CHEM 2017. [DOI: 10.1016/j.arabjc.2012.12.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Kumar M, Narasimhan B, Kumar P, Ramasamy K, Mani V, Mishra RK, Majeed ABA. 4-(1-Aryl-5-chloro-2-oxo-1,2-dihydro-indol-3-ylideneamino)-N-substituted benzene sulfonamides: Synthesis, antimicrobial, anticancer evaluation and QSAR studies. ARAB J CHEM 2014. [DOI: 10.1016/j.arabjc.2013.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Sharma SK, Kumar P, Narasimhan B, Ramasamy K, Mani V, Mishra RK, Majeed ABA. Synthesis, antimicrobial, anticancer evaluation and QSAR studies of 6-methyl-4-[1-(2-substituted-phenylamino-acetyl)-1H-indol-3-yl]-2-oxo/thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid ethyl esters. Eur J Med Chem 2012; 48:16-25. [DOI: 10.1016/j.ejmech.2011.11.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 11/11/2011] [Accepted: 11/15/2011] [Indexed: 10/15/2022]
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Narang R, Narasimhan B, Sharma S. (Naphthalen-1-yloxy)-acetic acid benzylidene/(1-phenyl-ethylidene)-hydrazide derivatives: synthesis, antimicrobial evaluation, and QSAR studies. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9776-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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