Structure-Based Optimization Strategies for G Protein-Coupled Receptor (GPCR) Allosteric Modulators: A Case Study from Analyses of New Metabotropic Glutamate Receptor 5 (mGlu₅) X-ray Structures

Abstract

Two interesting new X-ray structures of negative allosteric modulator (NAM) ligands for the mGlu receptor, M-MPEP (3) and fenobam (4), are reported. The new structures show how the binding of the ligands induces different receptor water channel conformations to previously published structures. The structure of fenobam, where a urea replaces the acetylenic linker in M-MPEP and mavoglurant, reveals a binding mode where the ligand is rotated by 180° compared to a previously proposed docking model. The need for multiple ligand structures for accurate GPCR structure-based drug design is demonstrated by the different growing vectors identified for the head groups of M-MPEP and mavoglurant and by the unexpected water-mediated receptor interactions of a new chemotype represented by fenobam. The implications of the new structures for ligand design are discussed, with extensive analysis of the energetics of the water networks of both pseudoapo and bound structures providing a new design strategy for allosteric modulators.

Allosteric activation of metabotropic glutamate receptor 5

“…This highly conserved Trp residue was found to be part of the activation in several class A GPCRs (Trzaskowski et al, 2012), including rhodopsin (Ahuja & Smith, 2009). Nevertheless, its conformational change is not a universal toggle of GPCR activation (Rasmussen et al, 2011), and the conformation is ligand dependent in NAM complexes (Christopher et al, 2015(Christopher et al, , 2019Dor e et al, 2014) and both conformations are accessible in activated mGluR5 in complex with 3 (PAM). Y659 3.44c is close to the varying aromatic substituent (Me/ Cl/F; Scheme 1) of the complexes studied and its analogous 3.40 residue in class A GPCRs is part of the transmission switch (Trzaskowski et al, 2012).…”

“…The structural and functional importance of these interactions is underlined by several findings. The water molecule mediating the H-bond between Y659 3.44c and T781 6.46c is identified in all available X-ray structures of mGluR5-NAM complexes (Christopher et al, 2015(Christopher et al, , 2019Dor e et al, 2014) and the Hbond was also observed in MD simulations of the mGluR2 (P erez-Benito et al, 2017) and mGluR5 receptors in complex with NAMs (Llinas del Torrent, Casajuana-Martin, et al, 2019). Moreover, it was shown that mutations of Y659 3.44c and T781 6.46c in mGluR5 significantly impact the activity of allosteric ligands by either reducing (Gregory et al, 2014;Malherbe et al, 2006) or inverting (Turlington et al, 2013) their functional effect.…”

“…mGluR5 (Sengmany & Gregory, 2016) belongs to group I whose members are coupled to G q proteins and activate phospholipase C. The optimization of allosteric mGluR ligands is highly challenging owing to frequently observed steep structure-activity relationships (SAR) and the variation of functional response upon subtle structural changes of the allosteric ligands (molecular switch) (Lindsley et al, 2016). It has been demonstrated recently that steep SAR can be attributed to the flexibility of the allosteric pocket leading to induced binding and to the interaction of the allosteric ligand with the water network in the intrahelical chamber (Christopher et al, 2019).…”

“…Our MD simulations for the inactive receptor are based on the mavoglurant (NAM) complex for which X-ray structure is available, while the active receptor complex is modelled together with the G q protein and with a PAM having close structural similarity to mavoglurant. In analysing the results, we pay particular attention to analogy with class A GPCR activation and to the role of water within the allosteric pocket, as water was found to affect both activation in class A GPCRs (Angel, Chance, & Palczewski, 2009;Yuan, Filipek, Palczewski, & Vogel, 2014) and ligand binding in mGluR5 (Christopher et al, 2019).…”

Profiling the Structural Determinants of Aryl Benzamide Derivatives as Negative Allosteric Modulators of mGluR5 by In Silico Study

“…Therefore, two structural motifs, i.e., amide and urea functional groups, are proposed as the replacements of alkyne linkages in mGluR5 NAMs [18]. So far, altogether eight known mGluR5 NAMs have entered and/or are about to enter clinical trials, i.e., Mavoglurant [19][20][21], Basimglurant [8,21], MTEP [8], HTL14242 [20], Dipraglurant [21], Fenobam [21,22], Thiazole-2-carboxamides (6bc, 6bj) [18]. It is worth mentioning that, for a long time, the important structural information on mGluR5 NAMs was to combine mutation studies with homology modeling and/or a series of ligand analogs.…”