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Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism.
Biochem Biophys Res Commun. 2020 06 30; 527(3):702-708.BB

Abstract

The spread of COVID-19 caused by the SARS-CoV-2 outbreak has been growing since its first identification in December 2019. The publishing of the first SARS-CoV-2 genome made a valuable source of data to study the details about its phylogeny, evolution, and interaction with the host. Protein-protein binding assays have confirmed that Angiotensin-converting enzyme 2 (ACE2) is more likely to be the cell receptor through which the virus invades the host cell. In the present work, we provide an insight into the interaction of the viral spike Receptor Binding Domain (RBD) from different coronavirus isolates with host ACE2 protein. By calculating the binding energy score between RBD and ACE2, we highlighted the putative jump in the affinity from a progenitor form of SARS-CoV-2 to the current virus responsible for COVID-19 outbreak. Our result was consistent with previously reported phylogenetic analysis and corroborates the opinion that the interface segment of the spike protein RBD might be acquired by SARS-CoV-2 via a complex evolutionary process rather than a progressive accumulation of mutations. We also highlighted the relevance of Q493 and P499 amino acid residues of SARS-CoV-2 RBD for binding to human ACE2 and maintaining the stability of the interface. Moreover, we show from the structural analysis that it is unlikely for the interface residues to be the result of genetic engineering. Finally, we studied the impact of eight different variants located at the interaction surface of ACE2, on the complex formation with SARS-CoV-2 RBD. We found that none of them is likely to disrupt the interaction with the viral RBD of SARS-CoV-2.

Authors+Show Affiliations

Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. Electronic address: houcemoo@gmail.com.Laboratory of Veterinary Epidemiology and Microbiology LR16IPT03, Institut Pasteur of Tunis. University of Tunis El Manar, Tunis, Tunisia.Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia.Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia.Université de Tunis El Manar, Institut Pasteur de Tunis, LR11IPT08 Venins et Biomolécules Thérapeutiques, 1002, Tunis, Tunisia.Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32410735

Citation

Othman, Houcemeddine, et al. "Interaction of the Spike Protein RBD From SARS-CoV-2 With ACE2: Similarity With SARS-CoV, Hot-spot Analysis and Effect of the Receptor Polymorphism." Biochemical and Biophysical Research Communications, vol. 527, no. 3, 2020, pp. 702-708.
Othman H, Bouslama Z, Brandenburg JT, et al. Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism. Biochem Biophys Res Commun. 2020;527(3):702-708.
Othman, H., Bouslama, Z., Brandenburg, J. T., da Rocha, J., Hamdi, Y., Ghedira, K., Srairi-Abid, N., & Hazelhurst, S. (2020). Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism. Biochemical and Biophysical Research Communications, 527(3), 702-708. https://doi.org/10.1016/j.bbrc.2020.05.028
Othman H, et al. Interaction of the Spike Protein RBD From SARS-CoV-2 With ACE2: Similarity With SARS-CoV, Hot-spot Analysis and Effect of the Receptor Polymorphism. Biochem Biophys Res Commun. 2020 06 30;527(3):702-708. PubMed PMID: 32410735.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism. AU - Othman,Houcemeddine, AU - Bouslama,Zied, AU - Brandenburg,Jean-Tristan, AU - da Rocha,Jorge, AU - Hamdi,Yosr, AU - Ghedira,Kais, AU - Srairi-Abid,Najet, AU - Hazelhurst,Scott, Y1 - 2020/05/14/ PY - 2020/05/02/received PY - 2020/05/05/accepted PY - 2020/5/16/pubmed PY - 2020/6/9/medline PY - 2020/5/16/entrez KW - ACE2 KW - COVID-19 KW - Homology-based protein-protein docking KW - Variants KW - Viral spike receptor binding domain SP - 702 EP - 708 JF - Biochemical and biophysical research communications JO - Biochem Biophys Res Commun VL - 527 IS - 3 N2 - The spread of COVID-19 caused by the SARS-CoV-2 outbreak has been growing since its first identification in December 2019. The publishing of the first SARS-CoV-2 genome made a valuable source of data to study the details about its phylogeny, evolution, and interaction with the host. Protein-protein binding assays have confirmed that Angiotensin-converting enzyme 2 (ACE2) is more likely to be the cell receptor through which the virus invades the host cell. In the present work, we provide an insight into the interaction of the viral spike Receptor Binding Domain (RBD) from different coronavirus isolates with host ACE2 protein. By calculating the binding energy score between RBD and ACE2, we highlighted the putative jump in the affinity from a progenitor form of SARS-CoV-2 to the current virus responsible for COVID-19 outbreak. Our result was consistent with previously reported phylogenetic analysis and corroborates the opinion that the interface segment of the spike protein RBD might be acquired by SARS-CoV-2 via a complex evolutionary process rather than a progressive accumulation of mutations. We also highlighted the relevance of Q493 and P499 amino acid residues of SARS-CoV-2 RBD for binding to human ACE2 and maintaining the stability of the interface. Moreover, we show from the structural analysis that it is unlikely for the interface residues to be the result of genetic engineering. Finally, we studied the impact of eight different variants located at the interaction surface of ACE2, on the complex formation with SARS-CoV-2 RBD. We found that none of them is likely to disrupt the interaction with the viral RBD of SARS-CoV-2. SN - 1090-2104 UR - https://www.unboundmedicine.com/medline/citation/32410735/Interaction_of_the_spike_protein_RBD_from_SARS_CoV_2_with_ACE2:_Similarity_with_SARS_CoV_hot_spot_analysis_and_effect_of_the_receptor_polymorphism_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0006-291X(20)30936-0 DB - PRIME DP - Unbound Medicine ER -