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Binding Mechanism of CD47 with SIRPα Variants and Its Antibody: Elucidated by Molecular Dynamics Simulations
Kaisheng Huang1, Yi Liu1, Shuixiu Wen1
1State Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
Abstract:
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 Tyr32LC, His92LC, Arg96LC, Tyr32HC, Thr52HC, Ser53HC, Ala101HC, and Gly102HC 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.
Insights
This study used molecular dynamics simulations to analyze the binding of CD47 to SIRPα variants and the B6H12.2 antibody. The B6H12.2 antibody shows higher binding affinity to CD47, identifying key residues for potential cancer immunotherapy drug development.
Area of Science:
- Biochemistry and Molecular Biology
- Immunology and Cancer Research
- Computational Biophysics
Background:
- The CD47-SIRPα pathway is a critical target in cancer immunotherapy.
- Understanding the binding mechanism and key residues of this complex is essential for developing targeted therapies.
- Previous crystallographic studies provided structural insights, but dynamic interactions require further investigation.
Purpose of the Study:
- To elucidate the binding mechanisms of CD47 with SIRPα variants (SIRPαv1, SIRPαv2) and the anti-CD47 antibody (B6H12.2) using molecular dynamics simulations.
- To identify critical 'hot spot' residues involved in the CD47-SIRPα and CD47-B6H12.2 interactions.
- To explore the druggability of identified binding sites within the SIRPα variants.
Main Methods:
- Molecular dynamics (MD) simulations were performed on complexes of CD47 with SIRPαv1, SIRPαv2, and the B6H12.2 antibody.
- Binding free energy calculations were used to quantify the affinity of these interactions.
- Dynamical cross-correlation matrix analysis, energy, and structural analyses were employed to identify key residues and conformational changes.
Main Results:
- The CD47-B6H12.2 complex exhibited a lower binding free energy, indicating higher binding affinity compared to CD47-SIRPαv1 and CD47-SIRPαv2.
- CD47 displayed more correlated motions when bound to B6H12.2.
- Specific residues in CD47 (e.g., Glu35, Tyr37) and SIRPα variants (e.g., Leu30, Val33) were identified as critical for binding, with SIRPα variants presenting druggable groove sites.
Conclusions:
- The B6H12.2 antibody demonstrates superior binding affinity to CD47 compared to SIRPα variants.
- Key residues and dynamic groove structures in SIRPα variants have been identified as potential targets for drug development.
- These findings provide valuable insights for designing novel inhibitors targeting the CD47-SIRPα interaction in cancer immunotherapy.
