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