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Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2.
Sci Rep. 2020 10 19; 10(1):17699.SR

Abstract

Angiotensin converting enzyme 2 (ACE2) (EC:3.4.17.23) is a transmembrane protein which is considered as a receptor for spike protein binding of novel coronavirus (SARS-CoV2). Since no specific medication is available to treat COVID-19, designing of new drug is important and essential. In this regard, in silico method plays an important role, as it is rapid and cost effective compared to the trial and error methods using experimental studies. Natural products are safe and easily available to treat coronavirus affected patients, in the present alarming situation. In this paper five phytochemicals, which belong to flavonoid and anthraquinone subclass, have been selected as small molecules in molecular docking study of spike protein of SARS-CoV2 with its human receptor ACE2 molecule. Their molecular binding sites on spike protein bound structure with its receptor have been analyzed. From this analysis, hesperidin, emodin and chrysin are selected as competent natural products from both Indian and Chinese medicinal plants, to treat COVID-19. Among them, the phytochemical hesperidin can bind with ACE2 protein and bound structure of ACE2 protein and spike protein of SARS-CoV2 noncompetitively. The binding sites of ACE2 protein for spike protein and hesperidin, are located in different parts of ACE2 protein. Ligand spike protein causes conformational change in three-dimensional structure of protein ACE2, which is confirmed by molecular docking and molecular dynamics studies. This compound modulates the binding energy of bound structure of ACE2 and spike protein. This result indicates that due to presence of hesperidin, the bound structure of ACE2 and spike protein fragment becomes unstable. As a result, this natural product can impart antiviral activity in SARS CoV2 infection. The antiviral activity of these five natural compounds are further experimentally validated with QSAR study.

Authors+Show Affiliations

Department of Biochemistry, Gurudas College, Calcutta, India.Computer Science and Engineering Department, Jadavpur University, Calcutta, India. anasua.sarkar@jadavpuruniversity.in.Computer Science and Engineering Department, Jadavpur University, Calcutta, India.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

33077836

Citation

Basu, Anamika, et al. "Molecular Docking Study of Potential Phytochemicals and Their Effects On the Complex of SARS-CoV2 Spike Protein and Human ACE2." Scientific Reports, vol. 10, no. 1, 2020, p. 17699.
Basu A, Sarkar A, Maulik U. Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2. Sci Rep. 2020;10(1):17699.
Basu, A., Sarkar, A., & Maulik, U. (2020). Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2. Scientific Reports, 10(1), 17699. https://doi.org/10.1038/s41598-020-74715-4
Basu A, Sarkar A, Maulik U. Molecular Docking Study of Potential Phytochemicals and Their Effects On the Complex of SARS-CoV2 Spike Protein and Human ACE2. Sci Rep. 2020 10 19;10(1):17699. PubMed PMID: 33077836.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2. AU - Basu,Anamika, AU - Sarkar,Anasua, AU - Maulik,Ujjwal, Y1 - 2020/10/19/ PY - 2020/04/22/received PY - 2020/10/06/accepted PY - 2020/10/20/entrez PY - 2020/10/21/pubmed PY - 2020/10/29/medline SP - 17699 EP - 17699 JF - Scientific reports JO - Sci Rep VL - 10 IS - 1 N2 - Angiotensin converting enzyme 2 (ACE2) (EC:3.4.17.23) is a transmembrane protein which is considered as a receptor for spike protein binding of novel coronavirus (SARS-CoV2). Since no specific medication is available to treat COVID-19, designing of new drug is important and essential. In this regard, in silico method plays an important role, as it is rapid and cost effective compared to the trial and error methods using experimental studies. Natural products are safe and easily available to treat coronavirus affected patients, in the present alarming situation. In this paper five phytochemicals, which belong to flavonoid and anthraquinone subclass, have been selected as small molecules in molecular docking study of spike protein of SARS-CoV2 with its human receptor ACE2 molecule. Their molecular binding sites on spike protein bound structure with its receptor have been analyzed. From this analysis, hesperidin, emodin and chrysin are selected as competent natural products from both Indian and Chinese medicinal plants, to treat COVID-19. Among them, the phytochemical hesperidin can bind with ACE2 protein and bound structure of ACE2 protein and spike protein of SARS-CoV2 noncompetitively. The binding sites of ACE2 protein for spike protein and hesperidin, are located in different parts of ACE2 protein. Ligand spike protein causes conformational change in three-dimensional structure of protein ACE2, which is confirmed by molecular docking and molecular dynamics studies. This compound modulates the binding energy of bound structure of ACE2 and spike protein. This result indicates that due to presence of hesperidin, the bound structure of ACE2 and spike protein fragment becomes unstable. As a result, this natural product can impart antiviral activity in SARS CoV2 infection. The antiviral activity of these five natural compounds are further experimentally validated with QSAR study. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/33077836/Molecular_docking_study_of_potential_phytochemicals_and_their_effects_on_the_complex_of_SARS_CoV2_spike_protein_and_human_ACE2_ L2 - https://doi.org/10.1038/s41598-020-74715-4 DB - PRIME DP - Unbound Medicine ER -