Designing Structure-specific and Switchable Allosteric Effectors for GPCRs Based on the Causality and Energetics of Inherent Signaling.

The pervasiveness and versatility of G protein-coupled receptors (GPCRs) in virtually all physiological processes is based on the receptors' capability to activate intracellular signal transduction pathways in response to diverse extracellular stimuli. While the importance of GPCRs makes them the largest group of drug targets (comprising about one-third of marketed medicines), more than half of GPCRs lack preclinical drug candidates because of high structural conservatism of their orthosteric sites. Recognizing that the mechanisms of GPCR function and regulation are chiefly allosteric in nature, we explore their allosteric control and the potential for developing allosteric drugs with high specificity. First, we obtained a picture of allosteric signaling in 280 non-olfactory GPCRs in human and explored archetypal structure-based patterns and sequence-determined variations of allosteric communication. We showed how the causality of allosteric effects due to ligand binding can be quantified, using the β₂-adrenergic receptor (ADRB2) and glucagon-like peptide 1 receptor (GLP1R) as case studies. Implementing our directed design protocol for developing allosteric drug candidates, switchable agonist-antagonist pairs were obtained for GPL1R. Moreover, we showed the predictive power of our approach for identification of latent allosteric sites and the capability for de novo design of agonistic and antagonistic effectors. We also performed efficacy-based design of ligands, demonstrating on the homologous GLP1R and GIPR that the strength of allosteric signaling induced by an effector can determine specificity to a target receptor. Our computational framework not only provides a foundation for addressing the problem of "difficult" GPCR targets with the allosteric approach, but also allows rational design of effectors with controllable mode switching and high specificity in general. The comprehensive data on allosteric signaling in classes A, B1, B2, C, F, and T GPCRs at single-residue resolution is available in the AlloMAPS database (https://allomaps.bii.a-star.edu.sg/browse/gpcraf).