Mapping the Druggable Allosteric Space of G‐Protein Coupled Receptors: a Fragment‐Based Molecular Dynamics Approach

Anthony Ivetac,J Andrew Mccammon

doi:10.1111/j.1747-0285.2010.01012.x

Abstract

To address the problem of specificity in G-protein coupled receptor (GPCR) drug discovery, there has been tremendous recent interest in allosteric drugs that bind at sites topographically distinct from the orthosteric site. Unfortunately, structure-based drug design of allosteric GPCR ligands has been frustrated by the paucity of structural data for allosteric binding sites, making a strong case for predictive computational methods. In this work, we map the surfaces of the β1 (β1AR) and β2 (β2AR) adrenergic receptor structures to detect a series of five potentially druggable allosteric sites. We employ the FTMAP algorithm to identify ‘hot spots’ with affinity for a variety of organic probe molecules corresponding to drug fragments. Our work is distinguished by an ensemble-based approach, whereby we map diverse receptor conformations taken from molecular dynamics (MD) simulations totaling approximately 0.5 μs. Our results reveal distinct pockets formed at both solvent-exposed and lipid-exposed cavities, which we interpret in light of experimental data and which may constitute novel targets for GPCR drug discovery. This mapping data can now serve to drive a combination of fragment-based and virtual screening approaches for the discovery of small molecules that bind at these sites and which may offer highly selective therapies.

Highlights

To address the problem of specificity in G-protein coupled receptor (GPCR) drug discovery, there has been tremendous recent interest in allosteric drugs that bind at sites topographically distinct from the orthosteric site
It is apparent that the structures of some copies are still evolving from the experimental structure, which may be attributed to the simulation of the ligand-free state, the inherent structural plasticity of GPCRs and timescale limitations
The allosteric modulation of GPCR activity is the focus of a growing branch of drug discovery, searching for novel therapeutic agents to control the numerous pathologies they play a role in

Summary

Introduction

Our results reveal distinct pockets formed at both solvent-exposed and lipid-exposed cavities, which we interpret in light of experimental data and which may constitute novel targets for GPCR drug discovery This mapping data can serve to drive a combination of fragment-based and virtual screening approaches for the discovery of small molecules that bind at these sites and which may offer highly selective therapies. G-protein coupled receptor structural biology has recently enjoyed a boom [13], with high-resolution crystallographic structures available for the avian b1 adrenergic receptor (b1AR) [14], human b2 adrenergic receptor (b2AR) [15,16,17] and human adenosine A2A receptor [18], as well as the proposed active conformation of bovine opsin in complex with a G-protein fragment [19] These structures have yielded great insights into the structure–function relationship between ligand binding and G-protein activation, whereby ligands are thought to stabilize ⁄ induce a variety of conformational rearrangements, which are characteristic of different states and can have diverse downstream effects [20,21,22]. New structure-based virtual screening efforts have emerged, in a traditionally ligand-based field, reporting the successful discovery of several new active compounds [24,25]

Methods

Results

Conclusion