Receptor binding domain of SARS‐CoV‐2 from Wuhan strain to Omicron B.1.1.529 attributes increased affinity to variable structures of human ACE2
Background: COVID-19 is an infectious disease declared as a global pandemic caused by SARS-CoV-2 virus. Genomic changes in the receptor binding domain (RBD) region of SARS‐CoV‐2 led to an increased, infectivity in humans through interaction with the angiotensin-converting enzyme2 (ACE2) receptor. Si...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-07-01
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| Series: | Journal of Infection and Public Health |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1876034122001502 |
| _version_ | 1811238379338072064 |
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| author | Shankargouda Patil Khalid J. Alzahrani Hamsa Jameel Banjer Ibrahim Faisal Halawani Hosam Alzahrani Malik A. Altayar Sarah Albogami Robert Fua Angeles Ali Abdel-Halim Abdel-Azim Hassan Shilpa Bhandi A. Thirumal Raj |
| author_facet | Shankargouda Patil Khalid J. Alzahrani Hamsa Jameel Banjer Ibrahim Faisal Halawani Hosam Alzahrani Malik A. Altayar Sarah Albogami Robert Fua Angeles Ali Abdel-Halim Abdel-Azim Hassan Shilpa Bhandi A. Thirumal Raj |
| author_sort | Shankargouda Patil |
| collection | DOAJ |
| description | Background: COVID-19 is an infectious disease declared as a global pandemic caused by SARS-CoV-2 virus. Genomic changes in the receptor binding domain (RBD) region of SARS‐CoV‐2 led to an increased, infectivity in humans through interaction with the angiotensin-converting enzyme2 (ACE2) receptor. Simultaneously, the genetic variants in ACE2 provide an opportunity for SARS‐CoV‐2 infection and severity. We demonstrate the binding efficiencies of RBDs of SARS‐CoV‐2 strain with ACE2 variants of the human host. Methodology: A Total of 615 SARS‐CoV‐2 genomes were retrieved from repository. Eighteen variations were identified contributing to structural changes in RBD that are distributed in 615 isolates. An analyses of 285 single nucleotide variances at the coding region of the ACE2 receptor showed 34 to be pathogenic. Homology models of 34 ACE2 and 18 RBD structures were constructed with 34 and 18 structural variants, respectively. Protein docking of 612 (34 *18) ACE2-RBD complexes showed variable affinities compared to wildtype Wuhan's and other SARS‐CoV‐2 RBDs, including Omicron B.1.1.529. Finally, molecular dynamic simulation was performed to determine the stability of the complexes. Results: Among 612, the top 3 complexes showing least binding energy were selected. The ACE2 with rs961360700 variant showed the least binding energy (−895.2 Kcal/mol) on binding with the RBD of Phe160Ser variant compared to Wuhan's RBD complex. Interestingly, the binding energy of RBD of Omicron B.1.1.529 with ACE2 (rs961360700) structure showed least binding energy of −1010 Kcal/mol. Additionally, molecular dynamics showed structure stability for all the analysed complexes with the RMSD (0.22–0.26 nm), RMSF (0.11–0.13 nm), and Rg (2.53–2.56 nm). Conclusion: In conclusion, our investigation highlights the clinical variants contributing to structural variants in ACE2 receptors that lead to efficient binding of SARS‐CoV‐2. Therefore, screening of these ACE2 polymorphisms will help detect COVID‐19 risk population so as to provide additional care and for safe management. |
| first_indexed | 2024-04-12T12:41:49Z |
| format | Article |
| id | doaj.art-996af4e1643f45ff8dd38f26f4c9fbd1 |
| institution | Directory Open Access Journal |
| issn | 1876-0341 |
| language | English |
| last_indexed | 2024-04-12T12:41:49Z |
| publishDate | 2022-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Infection and Public Health |
| spelling | doaj.art-996af4e1643f45ff8dd38f26f4c9fbd12022-12-22T03:32:46ZengElsevierJournal of Infection and Public Health1876-03412022-07-01157781787Receptor binding domain of SARS‐CoV‐2 from Wuhan strain to Omicron B.1.1.529 attributes increased affinity to variable structures of human ACE2Shankargouda Patil0Khalid J. Alzahrani1Hamsa Jameel Banjer2Ibrahim Faisal Halawani3Hosam Alzahrani4Malik A. Altayar5Sarah Albogami6Robert Fua Angeles7Ali Abdel-Halim Abdel-Azim Hassan8Shilpa Bhandi9A. Thirumal Raj10Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan 45412, Saudi Arabia; Centre of Molecular Medicine and Diagnostics (COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai - 600077, India; Corresponding author.Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi ArabiaDepartment of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi ArabiaDepartment of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi ArabiaDepartment of Physical Therapy, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi ArabiaDepartment of Medical Laboratory Technology, Faculty of Applied Medical Sciences,University of Tabuk, Tabuk 71491, Saudi ArabiaDepartment of Biotechnology, College of Science, Taif University, Taif 21944, Saudi ArabiaCollege of Nursing, Jazan University, Jazan 45412, Saudi ArabiaDepartment of Maxillofacial Surgery and Diagnostic Sciences, College of Dentistry, Jazan University, Jazan 45412, Saudi ArabiaDepartment of Restorative Dental Sciences, Division of Operative Dentistry, College of dentistry, Jazan University, Jazan 45412, Saudi Arabia; Department of Cariology. Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai - 600077, IndiaDepartment of Oral Pathology and Microbiology, Sri Venkateswara Dental College and Hospital, Chennai 600130, IndiaBackground: COVID-19 is an infectious disease declared as a global pandemic caused by SARS-CoV-2 virus. Genomic changes in the receptor binding domain (RBD) region of SARS‐CoV‐2 led to an increased, infectivity in humans through interaction with the angiotensin-converting enzyme2 (ACE2) receptor. Simultaneously, the genetic variants in ACE2 provide an opportunity for SARS‐CoV‐2 infection and severity. We demonstrate the binding efficiencies of RBDs of SARS‐CoV‐2 strain with ACE2 variants of the human host. Methodology: A Total of 615 SARS‐CoV‐2 genomes were retrieved from repository. Eighteen variations were identified contributing to structural changes in RBD that are distributed in 615 isolates. An analyses of 285 single nucleotide variances at the coding region of the ACE2 receptor showed 34 to be pathogenic. Homology models of 34 ACE2 and 18 RBD structures were constructed with 34 and 18 structural variants, respectively. Protein docking of 612 (34 *18) ACE2-RBD complexes showed variable affinities compared to wildtype Wuhan's and other SARS‐CoV‐2 RBDs, including Omicron B.1.1.529. Finally, molecular dynamic simulation was performed to determine the stability of the complexes. Results: Among 612, the top 3 complexes showing least binding energy were selected. The ACE2 with rs961360700 variant showed the least binding energy (−895.2 Kcal/mol) on binding with the RBD of Phe160Ser variant compared to Wuhan's RBD complex. Interestingly, the binding energy of RBD of Omicron B.1.1.529 with ACE2 (rs961360700) structure showed least binding energy of −1010 Kcal/mol. Additionally, molecular dynamics showed structure stability for all the analysed complexes with the RMSD (0.22–0.26 nm), RMSF (0.11–0.13 nm), and Rg (2.53–2.56 nm). Conclusion: In conclusion, our investigation highlights the clinical variants contributing to structural variants in ACE2 receptors that lead to efficient binding of SARS‐CoV‐2. Therefore, screening of these ACE2 polymorphisms will help detect COVID‐19 risk population so as to provide additional care and for safe management.http://www.sciencedirect.com/science/article/pii/S1876034122001502SARS‐CoV‐2Receptor binding domainAngiotensin-converting enzymeOmicronProtein dockingDynamic simulation |
| spellingShingle | Shankargouda Patil Khalid J. Alzahrani Hamsa Jameel Banjer Ibrahim Faisal Halawani Hosam Alzahrani Malik A. Altayar Sarah Albogami Robert Fua Angeles Ali Abdel-Halim Abdel-Azim Hassan Shilpa Bhandi A. Thirumal Raj Receptor binding domain of SARS‐CoV‐2 from Wuhan strain to Omicron B.1.1.529 attributes increased affinity to variable structures of human ACE2 Journal of Infection and Public Health SARS‐CoV‐2 Receptor binding domain Angiotensin-converting enzyme Omicron Protein docking Dynamic simulation |
| title | Receptor binding domain of SARS‐CoV‐2 from Wuhan strain to Omicron B.1.1.529 attributes increased affinity to variable structures of human ACE2 |
| title_full | Receptor binding domain of SARS‐CoV‐2 from Wuhan strain to Omicron B.1.1.529 attributes increased affinity to variable structures of human ACE2 |
| title_fullStr | Receptor binding domain of SARS‐CoV‐2 from Wuhan strain to Omicron B.1.1.529 attributes increased affinity to variable structures of human ACE2 |
| title_full_unstemmed | Receptor binding domain of SARS‐CoV‐2 from Wuhan strain to Omicron B.1.1.529 attributes increased affinity to variable structures of human ACE2 |
| title_short | Receptor binding domain of SARS‐CoV‐2 from Wuhan strain to Omicron B.1.1.529 attributes increased affinity to variable structures of human ACE2 |
| title_sort | receptor binding domain of sars cov 2 from wuhan strain to omicron b 1 1 529 attributes increased affinity to variable structures of human ace2 |
| topic | SARS‐CoV‐2 Receptor binding domain Angiotensin-converting enzyme Omicron Protein docking Dynamic simulation |
| url | http://www.sciencedirect.com/science/article/pii/S1876034122001502 |
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