G protein-coupled receptors: structure- and function-based drug discovery

Abstract

As one of the most successful therapeutic target families, G protein-coupled receptors (GPCRs) have experienced a transformation from random ligand screening to knowledge-driven drug design. We are eye-witnessing tremendous progresses made recently in the understanding of their structure-function relationships that facilitated drug development at an unprecedented pace. This article intends to provide a comprehensive overview of this important field to a broader readership that shares some common interests in drug discovery.

Fig. 1

Phylogenetic tree of GPCRs as drug targets. Node represents GPCR named according to its gene name. Receptors with approved drugs on the market are highlighted by color. GPCRs are organized according to GPCR database. Approved drug list was derived from previous publications,^, complemented by additional search of newly approved entities at Drugs@FDA (accessdata.fda.gov) until June 2020. See Table S2 for details

Fig. 2

Analysis on agents targeting GPCRs. Distribution of molecule type (left) and action mode (right). Positive, PAM; Negative, NAM

Fig. 3

SAR studies that led to the discovery of the dual orexin receptor antagonist lemborexant

Fig. 4

SAR studies that resulted in the discovery of CGRP antagonists

Fig. 5

Structural features and common activation mechanism of class A GPCRs. a Ligand-binding pockets. Agonist, antagonist, and allosteric ligand are indicated as sticks in yellow, green, and salmon, respectively. Ligands are shown from the following structures (PDB code): 2RH1, 3PWH, 3VW7, 4IAR, 4MQT, 4PHU, 4RWS, 4XEE, 4XNV, 4Z35, and 4ZJ8. b–f The common activation pathway of class A GPCRs as exampled by the structures of inactive (gray, PDB code 3NYA) and active β₂AR (green, PDB code 3SN6). The conformational changes of conserved “micro-switches”, including CWxP (b), PIF (c), Na⁺ pocket (d), NPxxY (e), and DRY (f), are highlighted. Side chains of residues in “micro-switches” are shown as sticks. Red arrows indicate the shift and swing directions of elements in the active β₂AR structure relative to the inactive one

Fig. 6

Structural features and common activation mechanism of class B GPCRs. a, b Structural features of the peptide-binding pocket. The shift of peptide C-terminus (a) and ECD (b) is indicated as red arrows. The peptides urocortin 1 (UCN1) bound to CRF1R (light blue, PDB code: 6PB0), UCN1 bound to CRF2R (salmon, PDB code: 6PB1), PACAP38 (red, PDB code: 6P9Y), long-acting PTH (LA-PTH, green, PDB code: 6NBF), GLP-1 (cyan, PDB code: 5VAI), sCT (yellow, PDB code: 6NIY), and CGRP (magenta, PDB code: 6PB1) are shown as cartoons. Binding poses of the antagonist (green) and allosteric ligand (salmon) are shown as sticks (c, PDB codes: 4K5Y, 5EE7, 4Z9G, 5VEW, and 5VEX). d, e The common activation mechanism of class B GPCRs as exampled by the structures of inactive GCGR (gray, PDB code 3NYA) and active VIP1R (green, PDB code 6VN7). Side chains of residues in three conserved polar network are shown in stick presentation. The conserved P^6.47bxxG^6.50b motifs in TM6 are shown as single red spheres

Fig. 7

Structural features and activation mechanism of class C GPCRs. The structures of mGlu5 in resting state (a, PDB code: 6N52) and active state (b, PDB code: 6N51), as well as GABA_BR in inactive (c, PDB code: 7C7S) and active states (d, PDB code: 7C7Q) are displayed, respectively. Agonists L-quisqualate (b, magenta) and antagonist CGP54626 (c, cyan) of mGlu5 as well as agonist baclofen (d, magenta) and allosteric modulator (+)-BHFF (d, yellow) of GABA_BR are shown as spheres. Cholesterols (c, yellow) and phospholipids (c, d, salmon) are indicated as sticks. Binding of allosteric ligands to TMD of class C GPCR is indicated as salmon sticks (e, PDB codes: 4OR2, 4OO9, 5CGC, and 6FFH)

Fig. 8

Structural feature of class F GPCRs. a Superposition of SMO crystal structures bound to agonists (yellow sticks) and antagonists (green sticks). The following structures are shown (PDB codes): 4JKV, 4N4W, 4O9R, 4QIM, and 5V56. CRD and LD (linker domain) are highlighted; b A comparison of structures of full-length SMO in the active state (PDB codes: 5L7D and 6O3C). Cholesterols are indicated. SAG21K, the agonist of SMO, is shown as yellow spheres. c The cryo-EM structure of SMO TMD in complex with G_i heterotrimer (PDB code: 6OT0). The agonist 24(S),25-epoxycholesterol is shown as magenta sticks. d Crystal structures of the Wnt3-FZD8 CRD complex. e Crystal structures of the Norrin-FZD4 CRD complex. f A comparison of the apo TMD structures of FZD4 (PDB code: 6BD4, yellow) and FZD5 (PDB code: 6WW2, green)

Fig. 9

Schematic diagram of allosteric sites at the lipidic surface identified by complex structures. The binding sites are manually labeled on the crystal structure of β₂AR (PDB code: 6OBA). Solid line, allosteric site at front side; dashed line, allosteric site at back side. UP, upper part aka close to the extracellular end; LOW, lower part aka close to the cytoplasmic end; numbers, main interacting transmembrane helices

Fig. 10

Binding sites of allosteric modulators in GPCRs reported after October 2018, in comparison with related ligands. a NAM ORG27569 in CB1 (PDB code: 6KQI) in comparison with cholesterol (PDB code: 5XRA); b NAM AS408 (PDB code: 6OBA) and PAM Cmpd-6FA (PDB code: 6N48) in β₂AR, in comparison with NDT9513727 in C5AR1 (PDB code: 6C1Q) and PAM AP8 (PDB code: 5TZY); c NAM maraviroc in CCR5 (PDB code: 4MBS) in comparison with chemokine analog antagonist [5P7]CCL5 (PDB code: 5UIW) and HIV envelope glycoprotein gp120 (PDB code: 6MEO); d PAM TT-OAD2 in GLP-1R (PDB code: 6ORV) in comparison with GLP-1 (PDB code: 5VAI)

Fig. 11

Developing affinity MS approaches for GPCR ligand screening. a Experimental workflow of membrane-based affinity MS. b Membrane-based affinity MS screening of 4333 compounds split into 9 cocktails against GLP-1R. Initial hits are indicated by red dots, while gray dots represent negatives. c Binding of one new ligand to 5-HT_2C (upper) and four new ligands to GLP-1R (lower) were validated by a radioligand-binding assay. d Experimental workflow of affinity MS-based screening of natural herb extracts. e Initial hits from screening fractionated herbal extracts toward 5-HT_2C. Aporphines are annotated with larger pink dots. BI binding index. f Structural validation of 1857 by MSMS analysis. g 1857 displayed selective agonism at 5-HT_2C. Source: adapted from Qin et al. and Zhang et al.