Engineering SIRPα conformational plasticity to reveal a cryptic pocket suitable for structure-based drug design

Area of Science:

• Biochemistry
• Structural Biology
• Immunology

Background:

• The Signal Regulatory Protein alpha (SIRPα)-CD47 interaction is a crucial immune checkpoint exploited by tumors for immune evasion.
• Existing antibody therapies targeting this checkpoint face challenges due to the flat binding interface, limiting small-molecule inhibitor development.

Purpose of the Study:

• To identify novel druggable sites within SIRPα for small-molecule inhibitor development.
• To characterize the mechanism controlling access to a newly discovered cryptic pocket in SIRPα.

Main Methods:

• Structure-based fragment screening using X-ray crystallography.
• NMR spectroscopy, molecular dynamics simulations, and biophysical assays.
• Site-directed mutagenesis to engineer SIRPα variants.

Main Results:

• Discovery of a novel, druggable cryptic pocket (WYF pocket) in the SIRPα D1 domain.
• Identification of Gln52 as a gatekeeper residue controlling pocket accessibility via conformational equilibrium.
• Engineered SIRPα mutants demonstrated altered CD47 binding affinity and enhanced small-molecule fragment binding.

Conclusions:

• SIRPα possesses intrinsic conformational plasticity enabling the targeting of cryptic pockets.
• A 'flexibility-for-inhibition' strategy, trapping a non-binding conformation, is validated for developing allosteric inhibitors.
• This approach provides a roadmap for targeting SIRPα-CD47 and other challenging immune checkpoints.