Current Topics in Medicinal Chemistry - Volume 15, Issue 24, 2015

With the apparition of concepts such as allosteric modulation and functional selectivity the field of G-protein coupled receptors drug discovery has regained its momentum. To better address this paradigm shift new screening technologies were developed. To identify novel GPCR ligands the screening method of choice was based upon functional assay for the last decade and is now being complemented by several innovative binding technologies. An overview of these assays, as well as an example of a fully integrated platform aiming at identifying novel allosteric modulator with the appropriate profile are presented in this review.

G protein-coupled receptors (GPCRs) constitute the largest group of human membrane proteins and have received significant attention in drug discovery for their important roles in physiological processes. Drug development for GPCRs has been remarkably successful and several of the most profitable pharmaceuticals on the market target members of this superfamily. Breakthroughs in structural biology for GPCRs have revealed how their binding sites recognize extracellular molecules at the atomic level. High-resolution crystal structures of GPCR-drug complexes capturing different receptor conformations are now available, which have provided insights into how ligands stabilize different functional states. Recently, the basis for subtype selectivity and novel allosteric binding sites has also been revealed by crystal structures. These accomplishments provide exciting opportunities to identify novel GPCR ligands using in silico structure-based methods such as molecular docking. Increased computational power now enables docking screens of large chemical libraries to identify molecules that complement GPCR binding sites, which may provide possibilities to identify ligands with tailored pharmacological properties. This review focuses on prospective docking screens against GPCRs and how this technique can be used to identify lead candidates with specific signaling or selectivity profiles. The current state of this field suggests that molecular docking, in combination with further understanding of GPCR signaling, will play an important role in future drug discovery.

Binding kinetics are the rates of association and dissociation of a drug-protein complex and are important molecular descriptors for the optimization of drug binding to G-protein coupled receptors (GPCRs). There are now many examples of binding kinetics in GPCR drug discovery. In this report, the first principles and examples of binding kinetics in GPCR drug discovery are reviewed. Addressed are the influence of binding kinetics on the translation of binding to the therapeutic window in the context of the equilibrium state of the system and molecular mechanisms of slow binding including induced fit, displacement of water, rebinding and heterovalency.

As the considerable technical challenges involved with generating crystal structures of G (guanine nucleotide- binding) protein-coupled receptors (GPCRs) are starting to be successfully addressed, opportunities to apply fragment-based drug discovery (FBDD) to this class of target are becoming a reality. GPCRs represent a large and important family of drug targets with considerable clinical and commercial interest. While their general seven transmembrane helix bundle structures are amenable to therapeutic intervention with small molecules, to date successful drugs have primarily been discovered using traditional competitive or function-based screening. With advances in biophysical screening techniques such as Surface Plasmon Resonance (SPR) and Target-Immobilised NMR Screening (TINS), being matched to developments in molecular dynamics simulations, virtual screening and stabilisation of biologically relevant conformations of GPCRs, structure-based approaches using fragment starting points are beginning to be applied to the discovery of new generations of small molecules.

Seven transmembrane domain receptors (7TMRs) constitute the largest family of transmembrane proteins in vertebrates and are the targets of more than 40% of currently marketed drugs. It is now accepted that these receptors are highly dynamic “microprocessors” that adopt a continuum of functionally distinct active conformations. The novel concept of biased agonism (or functional selectivity) posits that different ligands stabilize unique receptor conformations with each conformation imparting distinct signaling, and thus biological attributes, to a given receptor. The pharmacotherapeutic potential of biased agonism lies in possibility to develop molecules that selectively engage beneficial pathways while inhibiting or remaining inert towards those producing deleterious outcomes. Various strategies are now applied for the discovery of biased ligands. Many assays use second messenger levels (i.e., calcium, inositol trisphosphate, cAMP) as a quantitative readout of G-protein subtype-specific activity. However, due to complex cross-regulation between the various G-protein pathways, second messenger levels alone are not directly reflective of a ligand’s activity on a specific pathway. Consequently, direct measurements of receptor-proximal events (such as G-protein activation and β-arrestin coupling) are required for a more accurate quantification of ligand’s efficacy (or bias) towards different pathways. The discovery that various ligands of the same receptor can display different efficacies and potencies towards different receptor-downstream signaling pathways has not only revitalized the process of 7TMR drug discovery, but has significantly transformed the field of pharmacology as a whole. This review will showcase the current pharmacological toolbox available for the discovery and validation of biased ligands.

Nanobodies are therapeutic proteins derived from the variable domain (VHH) of naturally occurring heavy-chain antibodies. These VHH domains are the smallest functional fragments derived from a naturally occurring immunoglobulin. Nanobodies can be easily produced in prokaryotic or eukaryotic host organisms and their unique biophysical characteristics render these molecules ideal candidates for drug development. They are also emerging as an interesting new class of potential therapeutics for targets such as GPCRs, which have historically been challenging for small molecule drug discovery and even more difficult for biologics discovery. The ability to easily combine Nanobodies with different binding sites and different modes of action can be used to generate highly selective and highly potent drug candidates with very attractive pharmacological profiles. In addition, Nanobodies have been used as crystallization chaperones to enable or facilitate the structural determination of an active GPCR conformation.