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增强 CR3022 与 RBD 结合的亲和力;使用分子动力学模拟方法进行定点突变。

Affinity enhancement of CR3022 binding to RBD; site directed mutagenesis using molecular dynamics simulation approaches.

机构信息

Health Products Safety Research Center, Qazvin University of Medical Sciences, Qazvin, Iran.

Cellular and Molecular Research Center, Research Institute for Prevention of Non-Communicable Diseases, Qazvin University of Medical Sciences, Qazvin, Iran.

出版信息

J Biomol Struct Dyn. 2023 Jan;41(1):81-90. doi: 10.1080/07391102.2021.2004230. Epub 2021 Nov 19.


DOI:10.1080/07391102.2021.2004230
PMID:34796779
Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a disease which caused by a novel beta coronavirus. Structural and non-structural proteins are expressed by the virus gene fragments. The RBD of the S1 protein of the virus has the ability to interact with potent antibodies including CR3022, which was characterized to target the S protein of the virus which can efficiently neutralize the SARS-CoV and . In current study, we aimed to design CR3022 based antibody with high affinity compared with wild-type CR3022 using MD simulation method. Two variants were designed based on the amino acid binding conformation and the free binding energy of the critical amino acids which involved in CR3022-RBD interactions were evaluated. In this study three complexes were evaluated; CR3022-RBD, V1-RBD and V2-RBD using molecular dynamics simulations carried out for 100 ns in each case. Then, all the complexes were simulated for 100 ns. In the next step, to calculate the free binding affinity of the wild CR3022 and mutant antibody (V1 and V2) with RBD, the PMF method was performed. The RMSD profile demonstrated that all three complexes were equilibrated after 85 ns. Furthermore, the free binding energy results indicated that the V2-RBD complex has the higher binding affinity than V1-RBD and CR3022-RBD complexes. It should be noted that in above variants, the electrostatic energy and the number of H-bonds between the antibody and RBD increased. Thus, it is suggested that both designed antibodies could be considered as appropriate candidates for covid-19 disease treatment.Communicated by Ramaswamy H. Sarma.

摘要

严重急性呼吸系统综合征冠状病毒 2 (SARS-CoV-2) 是一种由新型β冠状病毒引起的疾病。病毒基因片段表达结构蛋白和非结构蛋白。病毒 S1 蛋白的 RBD 具有与包括 CR3022 在内的强效抗体相互作用的能力,CR3022 被鉴定为靶向病毒 S 蛋白,能够有效中和 SARS-CoV-2。在目前的研究中,我们旨在使用 MD 模拟方法设计与野生型 CR3022 相比具有高亲和力的基于 CR3022 的抗体。基于氨基酸结合构象和涉及 CR3022-RBD 相互作用的关键氨基酸的自由结合能设计了两种变体,并对其进行了评估。在这项研究中,使用分子动力学模拟方法对三个复合物进行了评估;CR3022-RBD、V1-RBD 和 V2-RBD,每个复合物的模拟时间均为 100ns。然后,对所有复合物进行了 100ns 的模拟。下一步,为了计算野生型 CR3022 和突变抗体 (V1 和 V2) 与 RBD 的自由结合亲和力,采用 PMF 方法。RMSD 图谱表明,所有三个复合物在 85ns 后达到平衡。此外,自由结合能结果表明,V2-RBD 复合物比 V1-RBD 和 CR3022-RBD 复合物具有更高的结合亲和力。需要注意的是,在上述变体中,抗体与 RBD 之间的静电能和氢键数量增加。因此,建议将这两种设计的抗体都可以考虑作为治疗 COVID-19 疾病的合适候选药物。

相似文献

[1]
Affinity enhancement of CR3022 binding to RBD; site directed mutagenesis using molecular dynamics simulation approaches.

J Biomol Struct Dyn. 2023-1

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

Comb Chem High Throughput Screen. 2021

[3]
Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental Approaches.

Viruses. 2022-1-19

[4]
Exploring the role of framework mutations in enabling breadth of a cross-reactive antibody (CR3022) against the SARS-CoV-2 RBD and its variants of concern.

J Biomol Struct Dyn. 2023-4

[5]
Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study.

J Biomol Struct Dyn. 2021-11

[6]
Electrostatic Interactions Explain the Higher Binding Affinity of the CR3022 Antibody for SARS-CoV-2 than the 4A8 Antibody.

J Phys Chem B. 2021-7-15

[7]
Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants.

Colloids Surf B Biointerfaces. 2023-1

[8]
Rapid production of SARS-CoV-2 receptor binding domain (RBD) and spike specific monoclonal antibody CR3022 in Nicotiana benthamiana.

Sci Rep. 2020-10-19

[9]
A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody.

PLoS Pathog. 2020-12

[10]
structural inhibition of ACE-2 binding site of SARS-CoV-2 and SARS-CoV-2 omicron spike protein by lectin antiviral dyad system to treat COVID-19.

Drug Dev Ind Pharm. 2022-10

引用本文的文献

[1]
Biophysics of SARS-CoV-2 spike protein's receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights.

Biophys Rev. 2025-3-8

[2]
Computational redesign of Beta-27 Fab with substantially better predicted binding affinity to the SARS-CoV-2 Omicron variant than human ACE2 receptor.

Sci Rep. 2023-9-19

[3]
Insights on the interaction of SARS-CoV-2 variant B.1.617.2 with antibody CR3022 and analysis of antibody resistance.

J Genet Eng Biotechnol. 2023-3-20

[4]
High-Affinity Antibodies Designing of SARS-CoV-2 Based on Molecular Dynamics Simulations.

Int J Mol Sci. 2022-12-28

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