9tf5
Structure of human wild-type signal regulatory protein alpha V2 variant (SIRPaV2) with zinc
Structural highlights
FunctionSHPS1_HUMAN Immunoglobulin-like cell surface receptor for CD47. Acts as docking protein and induces translocation of PTPN6, PTPN11 and other binding partners from the cytosol to the plasma membrane. Supports adhesion of cerebellar neurons, neurite outgrowth and glial cell attachment. May play a key role in intracellular signaling during synaptogenesis and in synaptic function (By similarity). Involved in the negative regulation of receptor tyrosine kinase-coupled cellular responses induced by cell adhesion, growth factors or insulin. Mediates negative regulation of phagocytosis, mast cell activation and dendritic cell activation. CD47 binding prevents maturation of immature dendritic cells and inhibits cytokine production by mature dendritic cells.[1] [2] Publication Abstract from PubMedThe protein-protein interaction between Signal Regulatory Protein alpha (SIRPalpha) and CD47 is a critical immune checkpoint that enables tumor immune escape, making it a key target for cancer immunotherapy. While antibody-based therapies exist, the development of small-molecule inhibitors has been hindered by the flat, featureless binding interface. Here, we report the discovery of a novel, druggable cryptic pocket within the SIRPalpha D1 domain (the WYF pocket), revealed through a structure-based fragment screening campaign using x-ray crystallography. This pocket, defined by residues Trp38, Tyr50, and Phe74, is only accessible in a conformation that is incompatible with CD47 binding, making it a candidate for structure-based drug design and immune checkpoint inhibitor development. Through a combination of NMR spectroscopy, molecular dynamics simulations, and biophysical assays, we demonstrate that access to this cryptic site is dynamically controlled by a single "gatekeeper" residue, Gln52. The rotameric state of Gln52 dictates a conformational equilibrium between a "closed," state and a ligand-accessible "open" state. We validated this mechanism by engineering SIRPalpha mutants to bias this equilibrium. A Q52F mutation locked the pocket in a closed state, abolishing both CD47 and fragment binding, while Q52A and Q52R mutations biased the protein toward an open state. These "open-biased" mutants not only exhibited decreased affinity for CD47 but also significantly improved binding to small-molecule fragments that inhibit the SIRPalpha-CD47 interaction. This work reveals the intrinsic conformational plasticity of SIRPalpha and establishes a validated structure-based roadmap for a new class of allosteric inhibitors. This 'flexibility-for-inhibition' strategy functions by trapping a non-binding conformation and represents a broadly applicable framework for targeting this and other challenging immune checkpoints. Engineering SIRPalpha conformational plasticity to reveal a cryptic pocket suitable for structure-based drug design.,Storder M, Barelier S, Cordier F, Yacoub T, Ilari L, Barral K, Mahmoodi S, Saez-Ayala M, Combes S, Betzi S, Derviaux C, Ulliana A, Torres F, Rubin J, Roche P, Morelli X, Garcin ED, Miller TW bioRxiv [Preprint]. 2025 Dec 23:2025.12.10.693509. doi: , 10.64898/2025.12.10.693509. PMID:41497624[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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