New Pipelines for Novel Allosteric GPCR Modulators

Abstract

Hormonal, neurotransmitter, visual, and olfactory signaling is largely regulated by a versatile class of membrane receptors, referred to as G-protein coupled receptors (GPCRs). Humans possess at least 800 distinct GPCRs, and, not surprisingly, 40% of current pharmaceuticals are meant to directly target GPCRs (1). However, the pharmacology of GPCRs has never been easy to understand, and phenomena such as constitutive activity, biased agonism, partial and full agonism, and allostery speak to the complexity and versatility of these receptors. The paper by Bhattacharya and Vaidehi (2), in this issue of Biophysical Journal, addresses some of these complexities by examining the mechanisms of activation through analysis of molecular dynamics (MD) trajectories. Activation of GPCRs cannot currently be observed by all-atom MD. However, it is possible to monitor MD trajectories of GPCRs for tens of microseconds. This was accomplished earlier by the D.E. Shaw group (3,4), which identified an inactive, activation intermediate, and active state, starting from either the inactive or active crystal structures of the adrenergic receptor, β2AR. Bhattacharya and Vaidehi (2) make use of MD trajectories associated with these states and analyze torsional angle correlations in the spirit of earlier work on soluble proteins by Pandini et al. (5). Beginning with the extracellular terminal residues, distinct allosteric pathways can be identified from an analysis of torsional angle correlations in the above MD trajectories. Remarkably, these pathways prove to be grossly different in the inactive, activation intermediate, and active states. By considering overlap and common hubs through which information is propagated, these pathways can be further grouped or clustered into pipelines. Binding of an agonist results in residues in the vicinity of the orthosteric binding site serving as initiators of allosteric communication, where there is observed to be an increased correlation between these residues, the extracellular loops, and both intracellular and extracellular transmembrane domains (Fig. 1). In the intermediate state, the top half of the receptor becomes effectively decoupled from the G protein binding domain, and the G protein interface of the receptor becomes more dynamic. The active state acquires new pipelines, some of which are thought to reinforce specific interactions between the G protein and receptor. Figure 1 Changes in allosteric communication upon agonist binding. Dominant allosteric pathways in the inactive state are illustrated by the red arrows. The binding of agonist results in a distinct shift in allosteric pathways, as illustrated by ... The above approach can be corroborated by examining the effects of two kinds of mutations on pipelines (i.e., those mutations that increase agonist binding and activation and those that suppress activation). Invariably, the majority of activating mutations tend to lie along allosteric pipelines in the inactive state, whereas inactivating mutations are associated with allosteric pipelines in the active state. Although this analysis helps us to understand activation mechanisms and the role of allosteric clusters, it also suggests a strategy for the design of allosteric pharmacophores with novel activity, which is an important area of study in GPCR pharmacology (6,7). The orthosteric binding site is known to be highly conserved among very functionally diverse class A GPCRs. Therefore, an allosteric ligand that perturbs a hub residue outside the orthosteric pocket might specifically modify/regulate the activity of a given receptor. The authors point to pockets along allosteric pipelines, which might be ideal for allosteric drug design. In any case, this computational approach seems fruitful in terms of knitting together structural and dynamical information on GPCRs and understanding their function.