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Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target.
J Biomol Struct Dyn. 2020 May 02 [Online ahead of print]JB

Abstract

The 2019-novel coronavirus (nCoV) has caused a global health crisis by causing coronavirus disease-19 (COVID-19) pandemic in the human population. The unavailability of specific vaccines and anti-viral drug for nCoV, science demands sincere efforts in the field of drug design and discovery for COVID-19. The novel coronavirus main protease (SARS-CoV-2 Mpro) play a crucial role during the disease propagation, and hence SARS-CoV-2 Mpro represents as a drug target for the drug discovery. Herein, we have applied bioinformatics approach for screening of chemical compounds from Indian spices as potent inhibitors of SARS-CoV-2 main protease (PDBID: 6Y84). The structure files of Indian spices chemical compounds were taken from PubChem database or Zinc database and screened by molecular docking, by using AutoDock-4.2, MGLTools-1.5.6, Raccoon virtual screening tools. Top 04 hits based on their highest binding affinity were analyzed. Carnosol exhibited highest binding affinity -8.2 Kcal/mol and strong and stable interactions with the amino acid residues present on the active site of SARS-CoV-2 Mpro. Arjunglucoside-I (-7.88 Kcal/mol) and Rosmanol (-7.99 Kcal/mol) also showed a strong and stable binding affinity with favourable ADME properties. These compounds on MD simulations for 50ns shows strong hydrogen-bonding interactions with the protein active site and remains stable inside the active site. Our virtual screening results suggest that these small chemical molecules can be used as potential inhibitors against SARS-CoV-2 Mpro and may have an anti-viral effect on nCoV. However, further validation and investigation of these inhibitors against SARS-CoV-2 main protease are needed to claim their candidacy for clinical trials.

Authors+Show Affiliations

School of Biochemical Engineering, Indian Institute of Technology BHU, Varanasi, UP - 221005, India.School of Biochemical Engineering, Indian Institute of Technology BHU, Varanasi, UP - 221005, India.Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu - 630003, India.Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu - 630003, India.School of Biochemical Engineering, Indian Institute of Technology BHU, Varanasi, UP - 221005, India.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32362243

Citation

Umesh, , et al. "Identification of New anti-nCoV Drug Chemical Compounds From Indian Spices Exploiting SARS-CoV-2 Main Protease as Target." Journal of Biomolecular Structure & Dynamics, 2020, pp. 1-9.
Umesh , Kundu D, Selvaraj C, et al. Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target. J Biomol Struct Dyn. 2020.
Umesh, ., Kundu, D., Selvaraj, C., Singh, S. K., & Dubey, V. K. (2020). Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target. Journal of Biomolecular Structure & Dynamics, 1-9. https://doi.org/10.1080/07391102.2020.1763202
Umesh , et al. Identification of New anti-nCoV Drug Chemical Compounds From Indian Spices Exploiting SARS-CoV-2 Main Protease as Target. J Biomol Struct Dyn. 2020 May 2;1-9. PubMed PMID: 32362243.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target. AU - Umesh,, AU - Kundu,Debanjan, AU - Selvaraj,Chandrabose, AU - Singh,Sanjeev Kumar, AU - Dubey,Vikash Kumar, Y1 - 2020/05/02/ PY - 2020/5/5/entrez PY - 2020/5/5/pubmed PY - 2020/5/5/medline KW - ADME KW - bioinformatics KW - corona virus disease-2019 (COVID-19 KW - molecular docking KW - novel coronavirus (nCoV) KW - novel coronavirus main protease (SARS-CoV-2 Mpro) SP - 1 EP - 9 JF - Journal of biomolecular structure & dynamics JO - J. Biomol. Struct. Dyn. N2 - The 2019-novel coronavirus (nCoV) has caused a global health crisis by causing coronavirus disease-19 (COVID-19) pandemic in the human population. The unavailability of specific vaccines and anti-viral drug for nCoV, science demands sincere efforts in the field of drug design and discovery for COVID-19. The novel coronavirus main protease (SARS-CoV-2 Mpro) play a crucial role during the disease propagation, and hence SARS-CoV-2 Mpro represents as a drug target for the drug discovery. Herein, we have applied bioinformatics approach for screening of chemical compounds from Indian spices as potent inhibitors of SARS-CoV-2 main protease (PDBID: 6Y84). The structure files of Indian spices chemical compounds were taken from PubChem database or Zinc database and screened by molecular docking, by using AutoDock-4.2, MGLTools-1.5.6, Raccoon virtual screening tools. Top 04 hits based on their highest binding affinity were analyzed. Carnosol exhibited highest binding affinity -8.2 Kcal/mol and strong and stable interactions with the amino acid residues present on the active site of SARS-CoV-2 Mpro. Arjunglucoside-I (-7.88 Kcal/mol) and Rosmanol (-7.99 Kcal/mol) also showed a strong and stable binding affinity with favourable ADME properties. These compounds on MD simulations for 50ns shows strong hydrogen-bonding interactions with the protein active site and remains stable inside the active site. Our virtual screening results suggest that these small chemical molecules can be used as potential inhibitors against SARS-CoV-2 Mpro and may have an anti-viral effect on nCoV. However, further validation and investigation of these inhibitors against SARS-CoV-2 main protease are needed to claim their candidacy for clinical trials. SN - 1538-0254 UR - https://www.unboundmedicine.com/medline/citation/32362243/Identification_of_new_anti_nCoV_drug_chemical_compounds_from_Indian_spices_exploiting_SARS_CoV_2_main_protease_as_target_ L2 - http://www.tandfonline.com/doi/full/10.1080/07391102.2020.1763202 DB - PRIME DP - Unbound Medicine ER -
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