An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review
The first infection case of new coronavirus was reported at the end of 2019 and after then, the cases are reported in all nations across the world in a very short period. Further, the regular news of mutations in the virus has made life restricted with appropriate behavior. To date, a new strain (Om...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-11-01
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| Series: | Journal of Infection and Public Health |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1876034122002702 |
| _version_ | 1811235480839127040 |
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| author | Madhur Babu Singh Ritika Sharma Durgesh Kumar Pankaj Khanna Mansi Leena Khanna Vinod Kumar Kamlesh Kumari Akanksha Gupta Preeti Chaudhary Neha Kaushik Eun Ha Choi Nagendra Kumar Kaushik Prashant Singh |
| author_facet | Madhur Babu Singh Ritika Sharma Durgesh Kumar Pankaj Khanna Mansi Leena Khanna Vinod Kumar Kamlesh Kumari Akanksha Gupta Preeti Chaudhary Neha Kaushik Eun Ha Choi Nagendra Kumar Kaushik Prashant Singh |
| author_sort | Madhur Babu Singh |
| collection | DOAJ |
| description | The first infection case of new coronavirus was reported at the end of 2019 and after then, the cases are reported in all nations across the world in a very short period. Further, the regular news of mutations in the virus has made life restricted with appropriate behavior. To date, a new strain (Omicron and its new subvariant Omicron XE) has brought fear amongst us due to a higher trajectory of increase in the number of cases. The researchers thus started giving attention to this viral infection and discovering drug-like candidates to cure the infections. Finding a drug for any viral infection is not an easy task and takes plenty of time. Therefore, computational chemistry/bioinformatics is followed to get promising molecules against viral infection. Molecular dynamics (MD) simulations are being explored to get drug candidates in a short period. The molecules are screened via molecular docking, which provides preliminary information which can be further verified by molecular dynamics (MD) simulations. To understand the change in structure, MD simulations generated several trajectories such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonding, and radius of gyration for the main protease (Mpro) of the new coronavirus (nCoV) in the presence of small molecules. Additionally, change in free energy for the formation of complex of Mpro of nCoV with the small molecule can be determined by applying molecular mechanics with generalized born and surface area solvation (MM-GBSA). Thus, the promising molecules can be further explored for clinical trials to combat coronavirus disease-19 (COVID-19). |
| first_indexed | 2024-04-12T11:52:34Z |
| format | Article |
| id | doaj.art-693c073ff1e440cb9d6333d676e84593 |
| institution | Directory Open Access Journal |
| issn | 1876-0341 |
| language | English |
| last_indexed | 2024-04-12T11:52:34Z |
| publishDate | 2022-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Infection and Public Health |
| spelling | doaj.art-693c073ff1e440cb9d6333d676e845932022-12-22T03:34:08ZengElsevierJournal of Infection and Public Health1876-03412022-11-01151113261349An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic reviewMadhur Babu Singh0Ritika Sharma1Durgesh Kumar2Pankaj Khanna3 Mansi4Leena Khanna5Vinod Kumar6Kamlesh Kumari7Akanksha Gupta8Preeti Chaudhary9Neha Kaushik10Eun Ha Choi11Nagendra Kumar Kaushik12Prashant Singh13Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, IndiaDepartment of Biochemistry, University of Delhi, New Delhi, IndiaDepartment of Chemistry, Maitreyi College, University of Delhi, Delhi, IndiaDepartment of Chemistry, Acharya Narendra Dev College, University of Delhi, New Delhi, IndiaUniversity School of Basic and Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, IndiaUniversity School of Basic and Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, IndiaSpecial Centre for Nanoscience (SCNS), Jawaharlal Nehru University, New Delhi, IndiaDepartment of Zoology, University of Delhi, New Delhi, IndiaDepartment of Chemistry, Sri Venkateswara College, University of Delhi, New Delhi, IndiaDepartment of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, IndiaDepartment of Biotechnology, College of Engineering, The University of Suwon, Hwaseong-si 18323, Republic of Korea; Corresponding authors.Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of KoreaPlasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea; Corresponding authors.Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India; Corresponding authors.The first infection case of new coronavirus was reported at the end of 2019 and after then, the cases are reported in all nations across the world in a very short period. Further, the regular news of mutations in the virus has made life restricted with appropriate behavior. To date, a new strain (Omicron and its new subvariant Omicron XE) has brought fear amongst us due to a higher trajectory of increase in the number of cases. The researchers thus started giving attention to this viral infection and discovering drug-like candidates to cure the infections. Finding a drug for any viral infection is not an easy task and takes plenty of time. Therefore, computational chemistry/bioinformatics is followed to get promising molecules against viral infection. Molecular dynamics (MD) simulations are being explored to get drug candidates in a short period. The molecules are screened via molecular docking, which provides preliminary information which can be further verified by molecular dynamics (MD) simulations. To understand the change in structure, MD simulations generated several trajectories such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonding, and radius of gyration for the main protease (Mpro) of the new coronavirus (nCoV) in the presence of small molecules. Additionally, change in free energy for the formation of complex of Mpro of nCoV with the small molecule can be determined by applying molecular mechanics with generalized born and surface area solvation (MM-GBSA). Thus, the promising molecules can be further explored for clinical trials to combat coronavirus disease-19 (COVID-19).http://www.sciencedirect.com/science/article/pii/S1876034122002702SARS-CoV-2Promising drug like candidateMpro of nCoVMolecular dynamics simulations |
| spellingShingle | Madhur Babu Singh Ritika Sharma Durgesh Kumar Pankaj Khanna Mansi Leena Khanna Vinod Kumar Kamlesh Kumari Akanksha Gupta Preeti Chaudhary Neha Kaushik Eun Ha Choi Nagendra Kumar Kaushik Prashant Singh An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review Journal of Infection and Public Health SARS-CoV-2 Promising drug like candidate Mpro of nCoV Molecular dynamics simulations |
| title | An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review |
| title_full | An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review |
| title_fullStr | An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review |
| title_full_unstemmed | An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review |
| title_short | An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review |
| title_sort | understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the mpro of ncov to combat the covid 19 a systematic review |
| topic | SARS-CoV-2 Promising drug like candidate Mpro of nCoV Molecular dynamics simulations |
| url | http://www.sciencedirect.com/science/article/pii/S1876034122002702 |
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