Probing Antibody Binding Sites on G Protein-Coupled Receptors Using Genetically Encoded Photo-Activatable Cross-Linkers

Allosteric modulators of G-protein-coupled receptors interact with binding sites that are topographically distinct from the orthosteric site recognized by the receptor's endogenous agonist. Allosteric ligands offer a number of advantages over orthosteric drugs, including the potential for greater receptor subtype selectivity and a more ‘physiological’ regulation of receptor activity. However, the manifestations of allosterism at G-protein-coupled receptors are quite varied, and significant challenges remain for the optimization of screening methods to ensure the routine detection and validation of allosteric ligands.

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Structural characterization and binding sites of G-protein-coupled receptors

Drug Discovery Today ◽

10.1016/s1359-6446(96)10042-8 ◽

1996 ◽

Vol 1 (12) ◽

pp. 502-513 ◽

Cited By ~ 51

Author(s):

Annette G. Beck-Sickinger

Keyword(s):

G Protein ◽

Structural Characterization ◽

Binding Sites ◽

G Protein Coupled Receptors ◽

G Protein Coupled

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Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservation

10.1101/461681 ◽

2018 ◽

Cited By ~ 1

Author(s):

Ashley R. Vidad ◽

Stephen Macaspac ◽

Ho-Leung Ng

Keyword(s):

Ligand Binding ◽

G Protein ◽

Binding Sites ◽

G Protein Coupled Receptors ◽

Sequence Conservation ◽

Surface Geometry ◽

A2a Adenosine Receptors ◽

Ligand Binding Sites ◽

G Protein Coupled ◽

Homology Models

AbstractG-protein coupled receptors (GPCRs) are the largest protein family of drug targets. Detailed mechanisms of binding are unknown for many important GPCR-ligand pairs due to the difficulties of GPCR recombinant expression, biochemistry, and crystallography. We describe our new method, ConDock, for predicting ligand binding sites in GPCRs using combined information from surface conservation and docking starting from crystal structures or homology models. We demonstrate the effectiveness of ConDock on well-characterized GPCRs such as the β2 adrenergic and A2A adenosine receptors. We also demonstrate that ConDock successfully predicts ligand binding sites from high-quality homology models. Finally, we apply ConDock to predict ligand binding sites on a structurally uncharacterized GPCR, GPER. GPER is the G-protein coupled estrogen receptor, with four known ligands: estradiol, G1, G15, and tamoxifen. ConDock predicts that all four ligands bind to the same location on GPER, centered on L119, H307, and N310; this site is deeper in the receptor cleft than predicted by previous studies. We compare the sites predicted by ConDock and traditional methods that utilize information from surface geometry, surface conservation, and ligand chemical interactions. Incorporating sequence conservation information in ConDock overcomes errors introduced from physics-based scoring functions and homology modeling.

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