Binding Mechanism of CD47 with SIRP Variants and Its Antibody: Elucidated by Molecular Dynamics Simulations

The intricate complex system of the differentiation 47 (CD47) and the signal-regulatory protein alpha (SIRPa) cluster is a crucial target for cancer immunotherapy. Although the conformational state of the CD47-SIRPa 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 SIRPa variants (SIRPav1, SIRPav2) 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-SIRPav1 and CD47-SIRPav2 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 SIRPa variants. The critical residues (Leu30, Val33, Gln52, Lys53, Thr67, Arg69, Arg95, and Lys96) were identified in SIRPav1 and SIRPav2, which surround the distinctive groove regions formed by the B2C, C'D, DE, and FG loops. Moreover, the crucial groove structures of the SIRPa 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(LC), His92(LC), Arg96(LC), Tyr32(HC), Thr52(HC), Ser53(HC), Ala101(HC), and Gly102(HC) 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 SIRPav1, SIRPav2, and B6H12.2 with CD47 could provide novel perspectives for the development of inhibitors targeting CD47-SIRPa.