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In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2.
Sci Rep. 2021 03 25; 11(1):6927.SR

Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a newly-discovered coronavirus and responsible for the spread of coronavirus disease 2019 (COVID-19). SARS-CoV-2 infected millions of people in the world and immediately became a pandemic in March 2020. SARS-CoV-2 belongs to the beta-coronavirus genus of the large family of Coronaviridae. It is now known that its surface spike glycoprotein binds to the angiotensin-converting enzyme-2 (ACE2), which is expressed on the lung epithelial cells, mediates the fusion of the cellular and viral membranes, and facilitates the entry of viral genome to the host cell. Therefore, blocking the virus-cell interaction could be a potential target for the prevention of viral infection. The binding of SARS-CoV-2 to ACE2 is a protein-protein interaction, and so, analyzing the structure of the spike glycoprotein of SARS-CoV-2 and its underlying mechanism to bind the host cell receptor would be useful for the management and treatment of COVID-19. In this study, we performed comparative in silico studies to deeply understand the structural and functional details of the interaction between the spike glycoprotein of SARS-CoV-2 and its cognate cellular receptor ACE2. According to our results, the affinity of the ACE2 receptor for SARS-CoV-2 was higher than SARS-CoV. According to the free energy decomposition of the spike glycoprotein-ACE2 complex, we found critical points in three areas which are responsible for the increased binding affinity of SARS-CoV-2 compared with SARS-CoV. These mutations occurred at the receptor-binding domain of the spike glycoprotein that play an essential role in the increasing the affinity of coronavirus to ACE2. For instance, mutations Pro462Ala and Leu472Phe resulted in the altered binding energy from - 2 kcal mol-1 in SARS-COV to - 6 kcal mol-1 in SARS-COV-2. The results demonstrated that some mutations in the receptor-binding motif could be considered as a hot-point for designing potential drugs to inhibit the interaction between the spike glycoprotein and ACE2.

Authors+Show Affiliations

Core Research Facilities (CRF), Isfahan University of Medical Science, Isfahan, Iran.Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran. m.ganjalikhany@sci.ui.ac.ir.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

33767306

Citation

Jafary, Farzaneh, et al. "In Silico Investigation of Critical Binding Pattern in SARS-CoV-2 Spike Protein With Angiotensin-converting Enzyme 2." Scientific Reports, vol. 11, no. 1, 2021, p. 6927.
Jafary F, Jafari S, Ganjalikhany MR. In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Sci Rep. 2021;11(1):6927.
Jafary, F., Jafari, S., & Ganjalikhany, M. R. (2021). In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Scientific Reports, 11(1), 6927. https://doi.org/10.1038/s41598-021-86380-2
Jafary F, Jafari S, Ganjalikhany MR. In Silico Investigation of Critical Binding Pattern in SARS-CoV-2 Spike Protein With Angiotensin-converting Enzyme 2. Sci Rep. 2021 03 25;11(1):6927. PubMed PMID: 33767306.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. AU - Jafary,Farzaneh, AU - Jafari,Sepideh, AU - Ganjalikhany,Mohamad Reza, Y1 - 2021/03/25/ PY - 2020/11/22/received PY - 2021/03/15/accepted PY - 2021/3/26/entrez PY - 2021/3/27/pubmed PY - 2021/4/15/medline SP - 6927 EP - 6927 JF - Scientific reports JO - Sci Rep VL - 11 IS - 1 N2 - Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a newly-discovered coronavirus and responsible for the spread of coronavirus disease 2019 (COVID-19). SARS-CoV-2 infected millions of people in the world and immediately became a pandemic in March 2020. SARS-CoV-2 belongs to the beta-coronavirus genus of the large family of Coronaviridae. It is now known that its surface spike glycoprotein binds to the angiotensin-converting enzyme-2 (ACE2), which is expressed on the lung epithelial cells, mediates the fusion of the cellular and viral membranes, and facilitates the entry of viral genome to the host cell. Therefore, blocking the virus-cell interaction could be a potential target for the prevention of viral infection. The binding of SARS-CoV-2 to ACE2 is a protein-protein interaction, and so, analyzing the structure of the spike glycoprotein of SARS-CoV-2 and its underlying mechanism to bind the host cell receptor would be useful for the management and treatment of COVID-19. In this study, we performed comparative in silico studies to deeply understand the structural and functional details of the interaction between the spike glycoprotein of SARS-CoV-2 and its cognate cellular receptor ACE2. According to our results, the affinity of the ACE2 receptor for SARS-CoV-2 was higher than SARS-CoV. According to the free energy decomposition of the spike glycoprotein-ACE2 complex, we found critical points in three areas which are responsible for the increased binding affinity of SARS-CoV-2 compared with SARS-CoV. These mutations occurred at the receptor-binding domain of the spike glycoprotein that play an essential role in the increasing the affinity of coronavirus to ACE2. For instance, mutations Pro462Ala and Leu472Phe resulted in the altered binding energy from - 2 kcal mol-1 in SARS-COV to - 6 kcal mol-1 in SARS-COV-2. The results demonstrated that some mutations in the receptor-binding motif could be considered as a hot-point for designing potential drugs to inhibit the interaction between the spike glycoprotein and ACE2. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/33767306/In_silico_investigation_of_critical_binding_pattern_in_SARS_CoV_2_spike_protein_with_angiotensin_converting_enzyme_2_ L2 - https://doi.org/10.1038/s41598-021-86380-2 DB - PRIME DP - Unbound Medicine ER -