| CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY |
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Accurate Evaluation on the Interactions of SARS-CoV-2 with Its Receptor ACE2 and Antibodies CR3022/CB6 |
| Hong-ming Ding1*, Yue-wen Yin1, Song-di Ni1, Yan-jing Sheng1, and Yu-qiang Ma2* |
1Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
2National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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| Cite this article: |
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Hong-ming Ding, Yue-wen Yin, Song-di Ni et al 2021 Chin. Phys. Lett. 38 018701 |
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Abstract The spread of the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a global health crisis. The binding affinity of SARS-CoV-2 (in particular the receptor binding domain, RBD) to its receptor angiotensin converting enzyme 2 (ACE2) and the antibodies is of great importance in understanding the infectivity of COVID-19 and evaluating the candidate therapeutic for COVID-19. We propose a new method based on molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) to accurately calculate the free energy of SARS-CoV-2 RBD binding to ACE2 and antibodies. The calculated binding free energy of SARS-CoV-2 RBD to ACE2 is $-13.3$ kcal/mol, and that of SARS-CoV RBD to ACE2 is $-11.4$ kcal/mol, which agree well with the experimental results of $-11.3$ kcal/mol and $-10.1$ kcal/mol, respectively. Moreover, we take two recently reported antibodies as examples, and calculate the free energy of antibodies binding to SARS-CoV-2 RBD, which is also consistent with the experimental findings. Further, within the framework of the modified MM/PBSA, we determine the key residues and the main driving forces for the SARS-CoV-2 RBD/CB6 interaction by the computational alanine scanning method. The present study offers a computationally efficient and numerically reliable method to evaluate the free energy of SARS-CoV-2 binding to other proteins, which may stimulate the development of the therapeutics against the COVID-19 disease in real applications.
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Received: 06 November 2020
Published: 18 December 2020
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| Fund: Supported by the National Natural Science Foundation of China (Grant Nos. 11874045 and 11774147). |
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