GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures

Abstract

The 826 G protein-coupled receptors (GPCRs) in the human proteome regulate key physiological processes, and thus have long been attractive as drug targets. With crystal structure determinations of more than 50 different human GPCRs during the last decade, an initial platform for structure-based rational design has been established for drugs that target GPCRs, which is currently being augmented with cryo-EM structures of higher-order GPCR complexes. Nuclear magnetic resonance (NMR) spectroscopy in solution is one of the key approaches for expanding this platform with dynamic features, which can be accessed at physiological temperature and with minimal modification of the wild-type GPCR covalent structures. Here, we review strategies for the use of advanced biochemistry and NMR techniques with GPCRs, survey projects where crystal or cryo-EM structures have been complemented with NMR investigations, and discuss the impact of this integrative approach on GPCR biology and drug discovery. More than 30% of all drugs approved by the US Food and Drug Administration target G protein-coupled receptors (GPCRs)1–3, and these drugs are utilized in a wide range of therapeutic areas, including inflammation and diseases of the central nervous system as well as the cardiovascular, respiratory and gastrointestinal systems2,4. Currently more than 300 agents are in clinical trials, of which around 60 target novel GPCRs for which no drug has as yet been approved2. The novel GPCR targets also include orphan GPCRs, for which endogenous ligands have not yet been discovered2. Overall, the drugs approved so far target only 27% of the human non-olfactory GPCRs2, indicating that much excitement still lies ahead. Identifying new GPCR drugs will need additional detailed knowledge of GPCR biology, especially knowledge from structural biology, given the complex structure–function relationships involved in GPCR signaling. Along this line, recent reviews on GPCRs have covered studies with antibodies5 and nanobodies6, allosteric modulation7–10 biased signaling11–15, methods in GPCR structural biology16–19, GPCR crystal structures20–27 and drug development2,4,28,29, with some reviews addressing specific GPCR families30,31. Complementing the substantial number of GPCR crystal structures that have become available in the past decade, as well as the recent demonstrations of the potential for cryo-EM to provide information on higher-order GPCR complexes32–36, dynamic studies of GPCRs are important for providing new insights into GPCR biology that can assist drug discovery. In this respect, nuclear magnetic resonance (NMR) spectroscopy in solution is a key tool for analysing function-related conformational equilibria in GPCRs as they relate to allosteric coupling, variable efficacies and biased signaling of GPCR ligands, which are of particular interest for their potential as drugs. Furthermore, NMR spectroscopy is also a useful tool for fragment-based lead discovery with GPCR targets. In this article, we first overview the structural biology of GPCRs ba...

Conformational plasticity of ligand-bound and ternary GPCR complexes studied by 19F NMR of the β1-adrenergic receptor

“…In addition to this static picture, NMR spectroscopy has demonstrated that these receptors are highly dynamic proteins, which populate multiple states that are in equilibrium with each other 12 . NMR has determined exchange kinetics and populations for some of these interconverting states 13,14 . Investigations of several class A receptors have revealed that their energy landscapes are unique with the differences relating to their individual signalling properties [15][16][17][18][19][20][21] .…”

High-affinity agonist binding to C5aR results from a cooperative two-site binding mechanism

“…Atomic-resolution structures are now available for more than 50 different GPCRs and over 250 of their complexes with different ligands (Shimada, Ueda et al , 2018). Crystal structures of C5aR in complex with NDT9513727, PMX53 and avacopan have recently been reported (Liu, Kim et al , 2018; Robertson, Rappas et al , 2018).…”

Conformational equilibrium defines the variable induction of the multidrug-binding transcriptional repressor QacR

“…As transcriptional regulations by preexisting conformational equilibria have been suggested to act in bacterial repressors as well as eukaryotic nuclear receptors (27,28), the conformational selection mechanisms would be shared widely among the ligand-inducible types of transcriptional regulators. The conformational equilibrium also allows various levels of responses in different biological systems such as G protein-coupled receptors (GPCRs), ion channels, kinases, and molecular chaperons (29)(30)(31)(32)(33)(34)(35)(36)(37)(38), which might be a fundamental mechanism shared by biological systems that require rapid responses to exert their functions.…”