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In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19.
Front Mol Biosci. 2021; 8:637122.FM

Abstract

COVID-19 is one of the members of the coronavirus family that can easily assail humans. As of now, 10 million people are infected and above two million people have died from COVID-19 globally. Over the past year, several researchers have made essential advances in discovering potential drugs. Up to now, no efficient drugs are available on the market. The present study aims to identify the potent phytocompounds from different medicinal plants (Zingiber officinale, Cuminum cyminum, Piper nigrum, Curcuma longa, and Allium sativum). In total, 227 phytocompounds were identified and screened against the proteins S-ACE2 and M pro through structure-based virtual screening approaches. Based on the binding affinity score, 30 active phytocompounds were selected. Amongst, the binding affinity for beta-sitosterol and beta-elemene against S-ACE2 showed -12.0 and -10.9 kcal/mol, respectively. Meanwhile, the binding affinity for beta-sitosterol and beta-chlorogenin against M pro was found to be -9.7 and -8.4 kcal/mol, respectively. Further, the selected compounds proceeded with molecular dynamics simulation, prime MM-GBSA analysis, and ADME/T property checks to understand the stability, interaction, conformational changes, binding free energy, and pharmaceutical relevant parameters. Moreover, the hotspot residues such as Lys31 and Lys353 for S-ACE2 and catalytic dyad His41 and Cys145 for M pro were actively involved in the inhibition of viral entry. From the in silico analyses, we anticipate that this work could be valuable to ongoing novel drug discovery with potential treatment for COVID-19.

Authors+Show Affiliations

Department of Bioinformatics, Alagappa University, Karaikudi, India.Department of Bioinformatics, Alagappa University, Karaikudi, India.Department of Bioinformatics, Alagappa University, Karaikudi, India.Department of Bioinformatics, Alagappa University, Karaikudi, India.Department of Bioinformatics, Alagappa University, Karaikudi, India.Kumaraguru College of Technology, Coimbatore, India.Department of Biotechnology, Alagappa University, Karaikudi, India.Department of Biotechnology, School of Life Science, Anyang Institute of Technology, Anyang, China.Department of Animal Health and Management, Science Campus, Alagappa University, Karaikudi, India.Sri Ramakrishna College of Arts and Science, Bharathiar University, Coimbatore, India.Faculty of Pharmacy, Philadelphia University-Jordan, Philadelphia University, Jordan.Faculty of Pharmacy, Philadelphia University-Jordan, Philadelphia University, Jordan.Department of Bioinformatics, Alagappa University, Karaikudi, India.Department of Industrial Chemistry, School of Chemical Sciences, Alagappa University, Karaikudi, India.Bioscience Research Foundation, Chennai, India.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

34291081

Citation

Sankar, Muthumanickam, et al. "In Silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19." Frontiers in Molecular Biosciences, vol. 8, 2021, p. 637122.
Sankar M, Ramachandran B, Pandi B, et al. In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19. Front Mol Biosci. 2021;8:637122.
Sankar, M., Ramachandran, B., Pandi, B., Mutharasappan, N., Ramasamy, V., Prabu, P. G., Shanmugaraj, G., Wang, Y., Muniyandai, B., Rathinasamy, S., Chandrasekaran, B., Bayan, M. F., Jeyaraman, J., Halliah, G. P., & Ebenezer, S. K. (2021). In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19. Frontiers in Molecular Biosciences, 8, 637122. https://doi.org/10.3389/fmolb.2021.637122
Sankar M, et al. In Silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19. Front Mol Biosci. 2021;8:637122. PubMed PMID: 34291081.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - In silico Screening of Natural Phytocompounds Towards Identification of Potential Lead Compounds to Treat COVID-19. AU - Sankar,Muthumanickam, AU - Ramachandran,Balajee, AU - Pandi,Boomi, AU - Mutharasappan,Nachiappan, AU - Ramasamy,Vidhyavathi, AU - Prabu,Poorani Gurumallesh, AU - Shanmugaraj,Gowrishankar, AU - Wang,Yao, AU - Muniyandai,Brintha, AU - Rathinasamy,Subaskumar, AU - Chandrasekaran,Balakumar, AU - Bayan,Mohammad F, AU - Jeyaraman,Jeyakanthan, AU - Halliah,Gurumallesh Prabu, AU - Ebenezer,Solomon King, Y1 - 2021/07/05/ PY - 2020/12/02/received PY - 2021/04/16/accepted PY - 2021/7/22/entrez PY - 2021/7/23/pubmed PY - 2021/7/23/medline KW - COVID-19 KW - S-ACE2 KW - main protease KW - molecular dynamics simulation KW - natural medicinal plants KW - structure-based virtual screening SP - 637122 EP - 637122 JF - Frontiers in molecular biosciences JO - Front Mol Biosci VL - 8 N2 - COVID-19 is one of the members of the coronavirus family that can easily assail humans. As of now, 10 million people are infected and above two million people have died from COVID-19 globally. Over the past year, several researchers have made essential advances in discovering potential drugs. Up to now, no efficient drugs are available on the market. The present study aims to identify the potent phytocompounds from different medicinal plants (Zingiber officinale, Cuminum cyminum, Piper nigrum, Curcuma longa, and Allium sativum). In total, 227 phytocompounds were identified and screened against the proteins S-ACE2 and M pro through structure-based virtual screening approaches. Based on the binding affinity score, 30 active phytocompounds were selected. Amongst, the binding affinity for beta-sitosterol and beta-elemene against S-ACE2 showed -12.0 and -10.9 kcal/mol, respectively. Meanwhile, the binding affinity for beta-sitosterol and beta-chlorogenin against M pro was found to be -9.7 and -8.4 kcal/mol, respectively. Further, the selected compounds proceeded with molecular dynamics simulation, prime MM-GBSA analysis, and ADME/T property checks to understand the stability, interaction, conformational changes, binding free energy, and pharmaceutical relevant parameters. Moreover, the hotspot residues such as Lys31 and Lys353 for S-ACE2 and catalytic dyad His41 and Cys145 for M pro were actively involved in the inhibition of viral entry. From the in silico analyses, we anticipate that this work could be valuable to ongoing novel drug discovery with potential treatment for COVID-19. SN - 2296-889X UR - https://www.unboundmedicine.com/medline/citation/34291081/In_silico_Screening_of_Natural_Phytocompounds_Towards_Identification_of_Potential_Lead_Compounds_to_Treat_COVID-19. L2 - https://doi.org/10.3389/fmolb.2021.637122 DB - PRIME DP - Unbound Medicine ER -
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