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Mechanistic Insights to the Binding of Antibody CR3022 Against RBD from SARS-CoV and HCoV-19/SARS-CoV-2: A Computational Study

Author(s):

Wei Yu, Xiaomin Wu, Jiayi Ren, Xiaochun Zhang, Yueming Wang, Chengming Li, Wenwen Xu, Jason Li, Gang Li, Weihong Zheng, Huaxin Liao and Xiaohui Yuan*   Pages 1 - 14 ( 14 )

Abstract:


Aims & Objective: Corona Virus Disease 2019 (COVID-19) caused by the human coronavirus 2019 (HCoV-19, also known as SARS-CoV-2) infection is currently in a global outbreak. COVID-19 has posed a huge threat to public health and economic stability worldwide. CR3022, a human monoclonal neutralizing antibody isolated from a Severe Acute Respiratory Syndrome (SARS) recovery patient, was confirmed to be able to bind the S protein of HCoV-19 with a certain degree of neutralizing activity. Crystal structural information indicated that CR3022 could bind to the epitope on the receptor binding domain (RBD) of HCoV-19, whose epitope consists of 28 amino acids, and 24 of them are conserved in SARS-CoV of SARS. However, the crystal structure is only a static conformation at a certain moment in time, and it cannot provide dynamic details of the interaction between antigen and antibody.

Methods: In this study, molecular dynamics (MD) simulation combined with MM/PBSA and CAS methods were performed to investigate the binding mechanism of binding of CR3022 against SARS-CoV-RBD and HCoV-19-RBD in order to determine their holographic dynamic information.

Results: It was found that the CR3022-SARS-CoV-RBD complex was more stable during 100ns MD run than that of the CR3022-HCoV19-RBD system. There were common conservative amino acids on the β2 sheet of RBD, including Tyr369, Phe377, Lys378, Tyr380, Gly381, Lys386, Leu390 and others. These conservative amino acids play significant roles in the binding process of CR3022 antibody against SARS-CoV-RBD and HCoV-19-RBD. It was also found that the binding mode of CR3022 to its native target SARS-CoV-RBD is more comprehensive and uniform. Moreover, the β2 sheet residue Thr385 and non-β2 sheet residues Arg408 and Asp428 of the CR3022- SARS-CoV-RBD system were found to be crucial for their binding affinities, thus forming a special conformational epitope. However, these key amino acids are not present in the CR3022-HCoV-19-RBD system. The binding mode of CR3022 and HCoV-19-RBD is similar to that of SARS-CoV-RBD, but the deficiency of crucial hydrogen-bonds and salt-bridges. Therefore, the binding of CR3022 and HCoV19-RBD only draws on the partial mode of the binding of CR3022 and SARS-CoV-RBD, so there is a loss of affinity.

Conclusion: Thus, in order to better fight the epidemic of COVID-19 with the CR3022 antibody, this antibody needs to further improve the neutralization efficiency of HCoV-19 through mutation of it’s CDR region.

Keywords:

Human Coronavirus 2019 (HCoV-19/SARS-CoV-2), Coronavirus Disease 2019 (COVID-19), Receptor Binding Domain (RBD), Molecular Dynamics (MD) Simulation, Molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA), Computational Alanine scanning (CAS).

Affiliation:

Institute of Biomedicine, Jinan University, Guangzhou, 510632, College of Life Science, Huaibei Normal University, Huaibei 235000, Anhui, Zhuhai College of Jilin University, Zhuhai, 519041, College of Life Science, Huaibei Normal University, Huaibei 235000, Anhui, Institute of Biomedicine, Jinan University, Guangzhou, 510632, Institute of Biomedicine, Jinan University, Guangzhou, 510632, Institute of Biomedicine, Jinan University, Guangzhou, 510632, Zhuhai Trinomab Biotechnology Co., Ltd. Zhuhai, 519040, Zhuhai Trinomab Biotechnology Co., Ltd. Zhuhai, 519040, Zhuhai Trinomab Biotechnology Co., Ltd. Zhuhai, 519040, Institute of Biomedicine, Jinan University, Guangzhou, 510632, Institute of Biomedicine, Jinan University, Guangzhou, 510632



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