State Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
School of Basic Medical Sciences, Hubei University of Science and Technology, Xianning 437100, China.
Molecules. 2023 Jun 7;28(12):4610. doi: 10.3390/molecules28124610.
The intricate complex system of the differentiation 47 (CD47) and the signal-regulatory protein alpha (SIRPα) cluster is a crucial target for cancer immunotherapy. Although the conformational state of the CD47-SIRPα complex has been revealed through crystallographic studies, further characterization is needed to fully understand the binding mechanism and to identify the hot spot residues involved. In this study, molecular dynamics (MD) simulations were carried out for the complexes of CD47 with two SIRPα variants (SIRPαv1, SIRPαv2) and the commercially available anti-CD47 monoclonal antibody (B6H12.2). The calculated binding free energy of CD47-B6H12.2 is lower than that of CD47-SIRPαv1 and CD47-SIRPαv2 in all the three simulations, indicating that CD47-B6H12.2 has a higher binding affinity than the other two complexes. Moreover, the dynamical cross-correlation matrix reveals that the CD47 protein shows more correlated motions when it binds to B6H12.2. Significant effects were observed in the energy and structural analyses of the residues (Glu35, Tyr37, Leu101, Thr102, Arg103) in the C strand and FG region of CD47 when it binds to the SIRPα variants. The critical residues (Leu30, Val33, Gln52, Lys53, Thr67, Arg69, Arg95, and Lys96) were identified in SIRPαv1 and SIRPαv2, which surround the distinctive groove regions formed by the B2C, C'D, DE, and FG loops. Moreover, the crucial groove structures of the SIRPα variants shape into obvious druggable sites. The C'D loops on the binding interfaces undergo notable dynamical changes throughout the simulation. For B6H12.2, the residues Tyr32, His92, Arg96, Tyr32, Thr52, Ser53, Ala101, and Gly102 in its initial half of the light and heavy chains exhibit obvious energetic and structural impacts upon binding with CD47. The elucidation of the binding mechanism of SIRPαv1, SIRPαv2, and B6H12.2 with CD47 could provide novel perspectives for the development of inhibitors targeting CD47-SIRPα.
CD47 和信号调节蛋白 alpha（SIRPα）簇的复杂分化系统是癌症免疫治疗的一个关键靶点。尽管通过晶体学研究已经揭示了 CD47-SIRPα 复合物的构象状态，但需要进一步的表征来完全理解结合机制并确定涉及的热点残基。在这项研究中，对 CD47 与两种 SIRPα 变体（SIRPαv1、SIRPαv2）和市售抗 CD47 单克隆抗体（B6H12.2）的复合物进行了分子动力学（MD）模拟。在所有三种模拟中，计算得到的 CD47-B6H12.2 结合自由能均低于 CD47-SIRPαv1 和 CD47-SIRPαv2，这表明 CD47-B6H12.2 具有更高的结合亲和力。此外，动态互相关矩阵表明，当 CD47 蛋白与 B6H12.2 结合时，它表现出更多的相关运动。当 CD47 与 SIRPα 变体结合时，在 CD47 蛋白的 C 链和 FG 区域的残基（Glu35、Tyr37、Leu101、Thr102、Arg103）的能量和结构分析中观察到显著的影响。在 SIRPαv1 和 SIRPαv2 中确定了关键残基（Leu30、Val33、Gln52、Lys53、Thr67、Arg69、Arg95 和 Lys96），这些残基环绕着由 B2C、C'D、DE 和 FG 环形成的独特凹槽区域。此外，SIRPα 变体的关键凹槽结构形成了明显的可成药位点。在整个模拟过程中，结合界面上的 C'D 环发生了显著的动力学变化。对于 B6H12.2，其轻链和重链前半部分的残基 Tyr32、His92、Arg96、Tyr32、Thr52、Ser53、Ala101 和 Gly102 在与 CD47 结合时表现出明显的能量和结构影响。阐明 SIRPαv1、SIRPαv2 和 B6H12.2 与 CD47 的结合机制，可以为开发针对 CD47-SIRPα 的抑制剂提供新的视角。
