Sarah Elizabeth Skerratt

Ion Channels as Therapeutic Targets: A Drug Discovery Perspective

Ion channels are membrane proteins expressed in almost all living cells. The sequencing of the human genome has identified more than 400 putative ion channels, but only a fraction of these have been cloned and functionally tested. The widespread tissue distribution of ion channels, coupled with the plethora of physiological consequences of their opening and closing, makes ion-channel-targeted drug discovery highly compelling. However, despite some important drugs in clinical use today, as a class, ion channels remain underexploited in drug discovery and many existing drugs are poorly selective with significant toxicities or suboptimal efficacy. This Perspective seeks to review the ion channel family, its structural and functional features, and the diseases that are known to be modulated by members of the family. In particular, we will explore the structure and properties of known ligands and consider the future prospects for drug discovery in this challenging but high potential area.

SAR mining and its application to the design of TRPA1 antagonists

Given the large amounts of screening data now available, empirical methods derived from matched-molecular pairs are being used as a means for suggesting bioisosteric replacements to the medicinal chemist. The pairwise analysis of compounds has been extended to the pairwise analysis of series to bring further context to these suggestions. A validation dataset derived from recent literature has been used to demonstrate that, given a series of active compounds, this approach would be expected to predict a more potent compound, if it exists, in around 46% of cases. The approach has been successfully applied to a series of TRPA1 antagonists.

Synthesis of NP25302.

An efficient synthesis of NP25302 is presented that relies on 5-endo-dig N-cyclization to establish the bicyclic core and Curtius rearrangement to install the N-acyl vinylogous urea functionality.

Identification of false positives in “HTS hits to lead”: The application of Bayesian models in HTS triage to rapidly deliver a series of selective TRPV4 antagonists

Herein, we describe the discovery and optimisation of a series of potent and selective TRPV4 antagonists. The application of a variety of computational techniques (including Bayesian modelling) at the HTS triage stage enabled the early deprioritisation of likely frequent hitters. The use of methods to positively prioritise compounds for follow-up screening allowed the rapid identification of a number of interesting TRPV4 antagonist series. The hit-to-lead efforts in one such series, the hydroxypiperidines, will be described.

Ion channel therapeutics for pain.

Pain is a complex disease which can progress into a debilitating condition. The effective treatment of pain remains a challenge as current therapies often lack the desired level of efficacy or tolerability. One therapeutic avenue, the modulation of ion channel signaling by small molecules, has shown the ability to treat pain. However, of the 215 ion channels that exist in the human genome, with 85 ion channels having a strong literature link to pain, only a small number of these channels have been successfully drugged for pain. The focus of future research will be to fully explore the possibilities surrounding these unexplored ion channels. Toward this end, a greater understanding of ion channel modulation will be the greatest tool we have in developing the next generation of drugs for the treatment of pain.

Evaluation and Characterization of Trk Kinase Inhibitors for the Treatment of Pain: Reliable Binding Affinity Predictions from Theory and Computation

Optimization of ligand binding affinity to the target protein of interest is a primary objective in small-molecule drug discovery. Until now, the prediction of binding affinities by computational methods has not been widely applied in the drug discovery process, mainly because of its lack of accuracy and reproducibility as well as the long turnaround times required to obtain results. Herein we report on a collaborative study that compares tropomyosin receptor kinase A (TrkA) binding affinity predictions using two recently formulated fast computational approaches, namely, Enhanced Sampling of Molecular dynamics with Approximation of Continuum Solvent (ESMACS) and Thermodynamic Integration with Enhanced Sampling (TIES), to experimentally derived TrkA binding affinities for a set of Pfizer pan-Trk compounds. ESMACS gives precise and reproducible results and is applicable to highly diverse sets of compounds. It also provides detailed chemical insight into the nature of ligand-protein binding. TIES can predict and thus optimize more subtle changes in binding affinities between compounds of similar structure. Individual binding affinities were calculated in a few hours, exhibiting good correlations with the experimental data of 0.79 and 0.88 from the ESMACS and TIES approaches, respectively. The speed, level of accuracy, and precision of the calculations are such that the affinity predictions can be used to rapidly explain the effects of compound modifications on TrkA binding affinity. The methods could therefore be used as tools to guide lead optimization efforts across multiple prospective structurally enabled programs in the drug discovery setting for a wide range of compounds and targets.

Optimisation of a pyrazole series of progesterone antagonists; Part 1.

The design and synthesis of a novel series of non-steroidal progesterone receptor antagonists is described. Ligand-lipophilicity efficiency (LLE) was used in the selection of a prototype agent for in vivo pharmacology studies.

The discovery of a potent series of carboxamide TRPA1 antagonists

A series of potent and selective carboxamide TRPA1 antagonists were identified by a high throughput screen. Structure–activity relationship studies around this series are described, resulting in a highly potent example of the series. Pharmacokinetic and skin flux data are presented for this compound. Efficacy was observed in a topical cinnamaldehyde flare study, providing a topical proof of pharmacology for this mechanism. These data suggest TRPA1 antagonism could be a viable mechanism to treat topical conditions such as atopic dermatitis.

Discovery of Compounds that Positively Modulate the High Affinity Choline Transporter

Cholinergic hypofunction is associated with decreased attention and cognitive deficits in the central nervous system in addition to compromised motor function. Consequently, stimulation of cholinergic neurotransmission is a rational therapeutic approach for the potential treatment of a variety of neurological conditions. High affinity choline uptake (HACU) into acetylcholine (ACh)-synthesizing neurons is critically mediated by the sodium- and pH-dependent high-affinity choline transporter (CHT, encoded by the SLC5A7 gene). This transporter is comparatively well-characterized but otherwise unexplored as a potential drug target. We therefore sought to identify small molecules that would enable testing of the hypothesis that positive modulation of CHT mediated transport would enhance activity-dependent cholinergic signaling. We utilized existing and novel screening techniques for their ability to reveal both positive and negative modulation of CHT using literature tools. A screening campaign was initiated with a bespoke compound library comprising both the Pfizer Chemogenomic Library (CGL) of 2,753 molecules designed specifically to help enable the elucidation of new mechanisms in phenotypic screens and 887 compounds from a virtual screening campaign to select molecules with field-based similarities to reported negative and positive allosteric modulators. We identified a number of previously unknown active and structurally distinct molecules that could be used as tools to further explore CHT biology or as a starting point for further medicinal chemistry.

Identification of a novel BODIPY minihepcidin tool for the high content analysis of ferroportin (SLC40A1) pharmacology

Iron is essential to life and is actively absorbed by enterocytes and secreted into plasma by the iron exporter ferroportin (SLC40A1). Dysregulation of iron homeostasis is a key component of many diseases such as hemochromatosis and beta-thalassemia. Ferroportin is the only known iron exporter protein, and as such is an important therapeutic target. To-date, modulators of ferroportin activity have shown promise in pre-clinical models, with recent screening assays enabling screening in a high throughput “loss of signal” format. Herein, we describe the design and synthesis of a novel BODIPY-labelled minihepcidin peptide to enable the high content analysis of ferroportin (SLC40A1) pharmacology, and the high throughput screening of compounds in a “gain of signal” assay format.