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ProtLID, a residue-based pharmacophore approach to identify cognate protein ligands in the Immunoglobulin Superfamily #MMPMID27889206
Yap EH; Fiser A
Structure 2016[Dec]; 24 (12): 2217-26 PMID27889206show ga
Members of extracellular Immunoglobulin Superfamily (IgSFs) play a key role in immune regulation through the control of the co-stimulatory pathway, and have emerged as potent drug targets in cancers, infectious diseases, and autoimmunity. Despite the difficult experimental access to this class of proteins, single structures of ectodomains of IgSF proteins are solved with regularity. However, the most biologically critical challenge for this class of proteins is the identification of their cognate ligands that communicate intercellular signals. We describe a conceptually novel method, Protein Ligand Interface Design (ProtLID), for the problem of identifying cognate ligands from a sub-proteome for a given target receptor protein. ProtLID designs an optimal protein interface for a given receptor by running extensive molecular dynamics simulations of single residue probes. The type and location of residue preferences establish a residue-based pharmacophore, which is subsequently used to find potential matches among candidate ligands within a sub-proteome.