A multiscale simulation protocol to probe ligand binding in monomeric and dimeric GPCRs

RWTH Publications (RWTH Aachen)

Abstract

G protein-coupled receptors (GPCRs) are arguably the most relevant family in drug discovery, serving as the targets for approximately 35% of all FDA-approved drugs. Despite this therapeutic success, achieving high subtype-specific selectivity remains a major challenge, prompting the exploration of novel avenues to develop more precise medicines. One promising direction is the consideration of receptor oligomerization, as accumulating evidence indicates these proteins dynamically assemble into functional dimers and higher- order oligomers, potentially reshaping their pharmacological profile. While dimerization is a well-characterized structural and functional requirement for Class B and Class C GPCRs, the prevalence and functional consequences of these interactions remain a subject of on- going debate for Class A GPCRs, the largest family. Increasing evidence suggests that many Class A receptors, including the Dopamine D2 Receptor (D2R), form such transient dimeric interactions. This thesis addresses the resulting molecular-level gap, focusing on the D2R, a key target for antipsychotic medications, to understand how its homodimerization modulates the binding thermodynamics and kinetics of the clinically relevant drug risperidone. A rigorous multi-scale computational approach was employed, combining all-atom molecular dynamics with enhanced sampling techniques (WT-MetaD for affinity and I- MetaD for kinetics) alongside Coarse-Grained (CG) simulations for extended, unbiased timescale exploration. This comprehensive analysis revealed that D2R dimerization fundamentally reshapes the receptor’s properties. Structural characterization showed that dimerization actively and consistently expands the orthosteric binding pocket, which allows risperidone to access a new, deeper binding pose stabilized by novel residue inter- actions. This structural change fundamentally alters the energetic landscape, resulting in a significantly increased thermodynamic affinity for the dimeric state compared to the monomer. Critically, kinetic analysis unveiled a profound functional binding asymmetry within the homodimer. One protomer forms an exceptionally stable complex, displaying a markedly prolonged residence time, indicative of a reinforced binding mode. In sharp contrast, the adjacent protomer displays an ultra-rapid dissociation rate, suggesting a high likelihood of fast unbinding. This kinetic divergence was mechanistically corroborated by unbiased CG simulations, which demonstrated that risperidone preferentially accesses and stably binds only to the reinforced protomer, failing to engage the structurally impaired second protomer. This suggests that inter-protomer interactions introduce structural or allosteric constraints that effectively hinder ligand engagement at one subunit. Collectively, the convergence of these multi-scale results establishes a coherent narrative: the transient homodimerization of D2R is able to modulate risperidone’s pharma-cological profile. These findings underscore the critical necessity of shifting the paradigm beyond traditional monomer-centric drug discovery, strongly recommending the integration of dimeric/oligomeric receptor models into next-generation structure-based drug de- sign strategies to facilitate the development of accurate, specific, and kinetically optimized GPCR-targeted therapeutics.

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