Drug Design for G‐Protein‐Coupled Receptors by a Ligand‐Based NMR Method

Abstract

More than 50 % of all drug targets are membrane proteins. [1] Recent progress in membrane protein crystallography has made a few of these targets amenable to established structurebased design methods.[2] However, crystallization of a membrane protein target remains a challenge, and medicinal chemists must rely on ligand-based design approaches for the targets that do not crystallize. These approaches can benefit from the knowledge of the bioactive conformation of the ligand conformation and the relative orientation of different chemotypes in the receptor binding site (cross-chemotype alignments). The generation of hypotheses for the bioactive conformation and cross-chemotype alignments depend on the availability of sufficient data on ligand structure-activity relationships (SARs). Herein, we demonstrate that these insights can be derived in the absence of protein-ligand crystal structures by straightforward ligand-based approaches relying on NMR spectroscopy. We show that a qualitative and fast analysis of INPHARMA NMR data [3,4] can be used within the timelines of the drug-discovery process without extended modeling and detailed data interpretation. We performed this study using intact biological membranes rather than reconstituted proteins [5,6] to eliminate solubilization-related artefacts, to expand the applicability to receptors that do not tolerate solubilization, and to significantly enhance the speed of the method. Here we demonstrate that a straightforward ligand-based NMR approach can be used to establish a nonradioactive binding assay for a Gprotein-coupled receptor (GPCR) and to give access to the relative orientation of multiple chemotypes supporting ligand-based drug design.

The Pharmacology of TUG-891, a Potent and Selective Agonist of the Free Fatty Acid Receptor 4 (FFA4/GPR120), Demonstrates Both Potential Opportunity and Possible Challenges to Therapeutic Agonism

“…Considering this, there is clearly a need to develop assays that can directly measure the affinity of ligands at FFA4. Although such assays have been challenging for receptors with very lipophilic ligands, several approaches have now been reported to directly measure ligand affinity at FFA1 (Hara et al, 2009b;Bartoschek et al, 2010;Negoro et al, 2012) and may be equally suitable for studies with FFA4.…”

Progress in Structure Based Drug Design for G Protein-Coupled Receptors

“…In another more recent example, a ligand-based NMR method has been successfully applied to GPR40 to identify hits, and this method has the potential for use in FBDD. 174 In the authors’ own research, we have used StaRs to several GPCRs in both families A and B as reagents for fragment based screening using high-concentration screens, surface plasmon resonance (Biacore), and target-immobilized NMR (TINS NMR) based screening. 175 SPR screening of an A 2A -StaR and TINS NMR screening of a β 1 AR StaR both identified hits that could be validated by showing activity in orthogonal assays.…”

Overview of Probing Protein‐Ligand Interactions Using NMR

“…Nevertheless, a qualitative analysis of IN-PHARMA data can also provide valuable structural information for structure-based drug design, as well as in the FBDD process (Bartoschek et al, 2010;Krimm, 2012).…”