From Receptors to Ligands: Fragment-assisted Drug Design for GPCRs Applied to the Discovery of H3 and H4 Receptor Antagonists

Alexander Heifetz Michael P Mazanetz

doi:10.4172/2161-0444.1000158

Abstract

G-Protein Coupled Receptors (GPCRs) have enormous physiological and biomedical importance, being the primary target of a large number of modern drugs. The availability of structural information of the binding site of the targeted GPCR plays a key role in rationalization, efficiency and cost-effectiveness of the drug discovery process. However, obtaining structural information on GPCRs using X-ray crystallography or NMR requires a large investment of time and is technically very challenging. This situation significantly limits the ability of these methods to have an impact in drug discovery for GPCR targets in the short term and hence there is an urgent need for other effective and cost-efficient alternatives. We present here a practical approach that integrates GPCR modelling with fragment based screening to provide structural insights on the H3 and H4 histamine receptor binding sites. This approach creates a cost-efficient new avenue for structure-based drug design (SBDD) against GPCR targets. We report here a success of using this protocol for the discovery of selective and dual H3 and H4 antagonists. Our fragment screen yielded 44 H3, 21 H4 selective and 20 dual fragment hits. These fragments were used to construct high- quality H3 and H4 models followed by binding site exploration and structure based virtual screening (VS). Overall, 172 compounds were purchased for testing based on the virtual screening results. Of the 74 compounds predicted to have dual activity, 33 had activity against one or other of the two receptors (44%), of which 17 had activity against both. Of the 19 compounds predicted to be H3 selective, 13 were active against H3 (68%) and 10 of these also had selectivity over H4. Of the 79 compounds predicted to be H4 selective, 36 were active against H4 (45%) and 2 of these also had selectivity over H3

Highlights

G-Protein Coupled Receptors (GPCRs) have enormous physiological and biomedical importance, being the primary target of a large number of modern drugs
We present here a practical approach that integrates GPCR modelling with fragment based screening to provide structural insights on the Histamine 3 Receptor (H3) and Histamine 4 (H4) histamine receptor binding sites
A collection of five compound plates representing 1,708 fragments from Evotec’s fragment library, were screened at 2 and 20 μM in the functional calcium flux assays on the H3 and H4 receptors to identify antagonists

Summary

Introduction

G-Protein Coupled Receptors (GPCRs) have enormous physiological and biomedical importance, being the primary target of a large number of modern drugs. X-ray crystallography and NMR, the major experimental sources of structural information, are very slow processes for membrane proteins, and are not currently feasible for every GPCR or GPCR-ligand complex This situation significantly limits the ability of these methods to impact the drug discovery process for GPCR targets in “real-time” and there is an urgent need for other practical and cost-efficient alternatives [1]. While the majority of historical fragment screens have been focused towards biochemical targets, only few examples, to date, have been published in which this method has been used to identify ligands for GPCRs [4] This is due to the current infeasibility of regularly crystallizing the GPCR-fragment complexes that are required for further fragment expansion. These publications encouraged us to try this approach in the discovery of GPCR antagonists

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Conclusion