Molecular Determinants for the Binding of the Highly Infectious SARS-CoV-2 Omicron (BA.1) Variant to the Human ACE2 Receptor
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continually undergoes mutation, leading to variants with altered pathogenicity and transmissibility. The Omicron variant (B.1.1.529), first identified in South Africa in 2021, has become the dominant strai...
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2025-02-01
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| author | Majed S. Aljohani Pawan Bhatta Xiche Hu |
| author_facet | Majed S. Aljohani Pawan Bhatta Xiche Hu |
| author_sort | Majed S. Aljohani |
| collection | DOAJ |
| description | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continually undergoes mutation, leading to variants with altered pathogenicity and transmissibility. The Omicron variant (B.1.1.529), first identified in South Africa in 2021, has become the dominant strain worldwide. It harbors approximately 50 mutations compared to the original strain, with 15 located in the receptor-binding domain (RBD) of the spike protein that facilitates viral entry via binding to the human angiotensin-converting enzyme 2 (ACE2) receptor. How do these mutated residues modulate the intermolecular interactions and binding affinity between the RBD and ACE2? This is a question of great theoretical importance and practical implication. In this study, we employed quantum chemical calculations at the B2PLYP-D3/def2-TZVP level of theory to investigate the molecular determinants governing Omicron’s ACE2 interaction. Comparative analysis of the Omicron and wild-type RBD–ACE2 interfaces revealed that mutations including S477N, Q493R, Q498R, and N501Y enhance binding through the formation of bifurcated hydrogen bonds, π–π stacking, and cation–π interactions. These favorable interactions counterbalance such destabilizing mutations as K417N, G446S, G496S, and Y505H, which disrupt salt bridges and hydrogen bonds. Additionally, allosteric effects improve the contributions of non-mutated residues (notably A475, Y453, and F486) via structural realignment and novel hydrogen bonding with ACE2 residues such as S19, leading to an overall increase in the electrostatic and π-system interaction energy. In conclusion, our findings provide a mechanistic basis for Omicron’s increased infectivity and offer valuable insights for the development of targeted antiviral therapies. Moreover, from a methodological perspective, we directly calculated mutation-induced binding energy changes at the residue level using advanced quantum chemical methods rather than relying on the indirect decomposition schemes typical of molecular dynamics-based free energy analyses. The strong correlation between calculated energy differences and experimental deep mutational scanning (DMS) data underscores the robustness of the theoretical framework in predicting the effects of RBD mutations on ACE2 binding affinity. This demonstrates the potential of quantum chemical methods as predictive tools for studying mutation-induced changes in protein–protein interactions and guiding rational therapeutic design. |
| format | Article |
| id | doaj-art-25d5ea0dd91f4ab7ba0295ff46f03de9 |
| institution | OA Journals |
| issn | 2673-7167 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | MDPI AG |
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| series | Physchem |
| spelling | doaj-art-25d5ea0dd91f4ab7ba0295ff46f03de92025-08-20T01:48:53ZengMDPI AGPhyschem2673-71672025-02-0151810.3390/physchem5010008Molecular Determinants for the Binding of the Highly Infectious SARS-CoV-2 Omicron (BA.1) Variant to the Human ACE2 ReceptorMajed S. Aljohani0Pawan Bhatta1Xiche Hu2Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USADepartment of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USADepartment of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USASevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, continually undergoes mutation, leading to variants with altered pathogenicity and transmissibility. The Omicron variant (B.1.1.529), first identified in South Africa in 2021, has become the dominant strain worldwide. It harbors approximately 50 mutations compared to the original strain, with 15 located in the receptor-binding domain (RBD) of the spike protein that facilitates viral entry via binding to the human angiotensin-converting enzyme 2 (ACE2) receptor. How do these mutated residues modulate the intermolecular interactions and binding affinity between the RBD and ACE2? This is a question of great theoretical importance and practical implication. In this study, we employed quantum chemical calculations at the B2PLYP-D3/def2-TZVP level of theory to investigate the molecular determinants governing Omicron’s ACE2 interaction. Comparative analysis of the Omicron and wild-type RBD–ACE2 interfaces revealed that mutations including S477N, Q493R, Q498R, and N501Y enhance binding through the formation of bifurcated hydrogen bonds, π–π stacking, and cation–π interactions. These favorable interactions counterbalance such destabilizing mutations as K417N, G446S, G496S, and Y505H, which disrupt salt bridges and hydrogen bonds. Additionally, allosteric effects improve the contributions of non-mutated residues (notably A475, Y453, and F486) via structural realignment and novel hydrogen bonding with ACE2 residues such as S19, leading to an overall increase in the electrostatic and π-system interaction energy. In conclusion, our findings provide a mechanistic basis for Omicron’s increased infectivity and offer valuable insights for the development of targeted antiviral therapies. Moreover, from a methodological perspective, we directly calculated mutation-induced binding energy changes at the residue level using advanced quantum chemical methods rather than relying on the indirect decomposition schemes typical of molecular dynamics-based free energy analyses. The strong correlation between calculated energy differences and experimental deep mutational scanning (DMS) data underscores the robustness of the theoretical framework in predicting the effects of RBD mutations on ACE2 binding affinity. This demonstrates the potential of quantum chemical methods as predictive tools for studying mutation-induced changes in protein–protein interactions and guiding rational therapeutic design.https://www.mdpi.com/2673-7167/5/1/8severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)Omicron variant (BA.1)angiotensin-converting enzyme 2 (ACE2)receptor-binding domain (RBD)molecular recognitionnon-bonded interactions |
| spellingShingle | Majed S. Aljohani Pawan Bhatta Xiche Hu Molecular Determinants for the Binding of the Highly Infectious SARS-CoV-2 Omicron (BA.1) Variant to the Human ACE2 Receptor Physchem severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (BA.1) angiotensin-converting enzyme 2 (ACE2) receptor-binding domain (RBD) molecular recognition non-bonded interactions |
| title | Molecular Determinants for the Binding of the Highly Infectious SARS-CoV-2 Omicron (BA.1) Variant to the Human ACE2 Receptor |
| title_full | Molecular Determinants for the Binding of the Highly Infectious SARS-CoV-2 Omicron (BA.1) Variant to the Human ACE2 Receptor |
| title_fullStr | Molecular Determinants for the Binding of the Highly Infectious SARS-CoV-2 Omicron (BA.1) Variant to the Human ACE2 Receptor |
| title_full_unstemmed | Molecular Determinants for the Binding of the Highly Infectious SARS-CoV-2 Omicron (BA.1) Variant to the Human ACE2 Receptor |
| title_short | Molecular Determinants for the Binding of the Highly Infectious SARS-CoV-2 Omicron (BA.1) Variant to the Human ACE2 Receptor |
| title_sort | molecular determinants for the binding of the highly infectious sars cov 2 omicron ba 1 variant to the human ace2 receptor |
| topic | severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (BA.1) angiotensin-converting enzyme 2 (ACE2) receptor-binding domain (RBD) molecular recognition non-bonded interactions |
| url | https://www.mdpi.com/2673-7167/5/1/8 |
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