Structure-Guided Design of Highly Selective and Potent Covalent Inhibitors of ERK1/2

The RAS/RAF/MEK/ERK signaling pathway has been targeted with a number of small molecule inhibitors in oncology clinical development across multiple disease indications. Importantly, cell lines with acquired resistance to B-RAF and MEK inhibitors have been shown to maintain sensitivity to ERK1/2 inhibition by small molecule inhibitors. There are a number of selective, noncovalent ERK1/2 inhibitors reported along with the promiscuous hypothemycin (and related analogues) that act via a covalent mechanism of action. This article reports the identification of multiple series of highly selective covalent ERK1/2 inhibitors informed by structure-based drug design (SBDD). As a starting point for these covalent inhibitors, reported ERK1/2 inhibitors and a chemical series identified via high-throughput screening were exploited. These approaches resulted in the identification of selective covalent tool compounds for potential in vitro and in vivo studies to assess the risks and or benefits of targeting this pathway through such a mechanism of action.

A Screening Assay Cascade to Identify and Characterize Novel Selective Estrogen Receptor Downregulators (SERDs)

Here, we describe an approach to identify novel selective estrogen receptor downregulator (SERD) compounds with improved properties such as oral bioavailability and the potential of increased efficacy compared to currently marketed drug treatments. Previously, methodologies such as Western blotting and transient cell reporter assays have been used to identify and characterize SERD compounds, but such approaches can be limited due to low throughput and sensitivity, respectively. We have used an endogenous cell-imaging strategy that has both the throughput and sensitivity to support a large-scale hit-to-lead program to identify novel compounds. A screening cascade with a suite of assays has been developed to characterize compounds that modulate estrogen receptor α (ERα)-mediated signaling or downregulate ERα levels in cells. Initially, from a focused high-throughput screening, novel ERα binders were identified that could be modified chemically into ERα downregulators. Following this, cellular assays helped determine the mechanism of action of compounds to distinguish between on-target and off-target compounds and differentiate SERDs, selective estrogen receptor modulator (SERM) compounds, and agonist ERα ligands. Data are shown to exemplify the characterization of ERα-mediated signaling inhibitors using a selection of literature compounds and illustrate how this cascade has been used to drive the chemical design of novel SERD compounds.

Framework of outcome measures recommended for use in the evaluation of childhood obesity treatment interventions: the CoOR framework

INTRODUCTION

Consensus is lacking in determining appropriate outcome measures for assessment of childhood obesity treatments. Inconsistency in the use and reporting of such measures impedes comparisons between treatments and limits consideration of effectiveness. This study aimed to produce a framework of recommended outcome measures: the Childhood obesity treatment evaluation Outcomes Review (CoOR) framework.

METHODS

A systematic review including two searches was conducted to identify (1) existing trial outcome measures and (2) manuscripts describing development/evaluation of outcome measures. Outcomes included anthropometry, diet, eating behaviours, physical activity, sedentary time/behaviour, fitness, physiology, environment, psychological well-being and health-related quality of life. Eligible measures were appraised by the internal team using a system developed from international guidelines, followed by appraisal from national external expert collaborators.

RESULTS

A total of 25,486 papers were identified through both searches. Eligible search 1 trial papers cited 417 additional papers linked to outcome measures, of which 56 were eligible. A further 297 outcome development/evaluation papers met eligibility criteria from search 2. Combined, these described 191 outcome measures. After internal and external appraisal, 52 measures across 10 outcomes were recommended for inclusion in the CoOR framework.

CONCLUSION

Application of the CoOR framework will ensure greater consistency in choosing robust outcome measures that are appropriate to population characteristics.

Demonstration of an 8-dimensional modulation format with reduced inter-channel nonlinearities in a polarization multiplexed coherent system

We demonstrate a polarization-managed 8-dimensional modulation format that is time domain coded to reduce inter-channel nonlinearity. Simulation results show a 2.3 dB improvement in maximum net system margin (NSM) relative to polarization multiplexed (PM)-BPSK, and a 1.0 dB improvement relative to time interleaved return-to-zero (RZ)-PM-BPSK, for five WDM channels propagating over 1600 km ELEAF with 90% inline optical dispersion compensation. In contrast to the other modulations considered, the new 8-dimensional format has negligible sensitivity to the polarization states of the neighboring WDM channels. High-density WDM (HD-WDM) measurements on a 5000 km dispersion-managed link show a 1.0 dB improvement in net system margin relative to PM-BPSK.

Potent, selective small molecule inhibitors of type III phosphatidylinositol-4-kinase α- but not β-inhibit the phosphatidylinositol signaling cascade and cancer cell proliferation

Two series of inhibitors of type III phosphatidylinositol-4-kinase were identified by high throughput screening and optimised to derive probe compounds that independently and selectively inhibit the α- and the β-isoforms with no significant activity towards related kinases in the pathway. In a cellular environment, inhibition of the α- but not the β-subtype led to a reduction in phosphatidylinositol-4-phosphate and phosphatidylinositol-4,5-bisphosphate concentration, causing inhibition of inositol-1-phosphate formation and inhibition of proliferation in a panel of cancer cell lines.

Deep brain stimulation in ireland for Parkinson's disease and essential tremor

Deep brain stimulation (DBS) is highly effective neurosurgery for idiopathic Parkinson's disease (IPD), essential tremor (ET) and primary dystonia. DBS involves stereotactic surgical implantation of a battery-operated stimulator into deep brain nuclei. Irish patients are referred abroad for DBS and have to travel repeatedly for pre and post-operative care resulting in stress, anxiety and hardship. Safe pre and post-operative care of these complex, ageing patients is compromised by the absence of a DBS service in Ireland. Moreover, both DBS surgery and the subsequent post-operative care abroad incurs substantial cost to the state. The Dublin Neurological Institute at the Mater Misericordiae University Hospital (DNI) is a non-profit institute for the care of patients with neurological diseases. The DNI developed, in collaboration with the Mater Private Hospital (MPH) and the Walton Centre, Liverpool, a DBS programme in 2008/2009. We performed DBS at the Mater Campus on three carefully selected patients from a cohort of movement disorder patients attending the DNI and continue to provide pre-operative assessment and post operative care for patients following DBS in Ireland and abroad.

A rare event sampling method for diffusion Monte Carlo using smart darting

We identify a set of multidimensional potential energy surfaces sufficiently complex to cause both the classical parallel tempering and the guided or unguided diffusion Monte Carlo methods to converge too inefficiently for practical applications. The mathematical model is constructed as a linear combination of decoupled Double Wells [(DDW)(n)]. We show that the set (DDW)(n) provides a serious test for new methods aimed at addressing rare event sampling in stochastic simulations. Unlike the typical numerical tests used in these cases, the thermodynamics and the quantum dynamics for (DDW)(n) can be solved deterministically. We use the potential energy set (DDW)(n) to explore and identify methods that can enhance the diffusion Monte Carlo algorithm. We demonstrate that the smart darting method succeeds at reducing quasiergodicity for n ≫ 100 using just 1 × 10(6) moves in classical simulations (DDW)(n). Finally, we prove that smart darting, when incorporated into the regular or the guided diffusion Monte Carlo algorithm, drastically improves its convergence. The new method promises to significantly extend the range of systems computationally tractable by the diffusion Monte Carlo algorithm.

Cellular Assay Optimization

This report describes the implementation of an automated work cell with commercially available hardware and software, capable of handling up to 15 separate reagents for performing 96-well or 384-well assays but with a small footprint and only a single liquid dispenser and two plate washers. Extremely flexible software was used to enable this simple work cell to perform processes that would traditionally require a much larger, more expensive automation platform. With the development of the C-Myc assays for the targets DYRK, BMX, PERK, and FAK, the authors describe a software solution to multibatch assays to run simultaneously, reducing reagent dead volume and increasing the efficiency of running multiple assays such that the time to generate data across multiple targets was significantly shortened. Although a larger automated system with multiple robotic arms and extensive equipment would also be able to process multiple assays simultaneously, the work cell we have described represents an inexpensive and flexible, easily upgradable option suitable for a wider range of labs.

Cellular Assay Optimization

This study investigated the use of large-scale transiently transfected cryopreserved cells for medium-throughput cellular screening. The data generated indicated that preprepared transiently transfected cryobanks can be used for cell-based assays and in fact can greatly enhance the consistency of data generated by cellular screens. In addition to this, a generic enzyme-linked immunosorbent assay method was designed that introduced a c-Myc tag to four different targets and allowed all four cell assays to be run using a standardized process. These process improvements yielded cost savings and greatly reduced the required resource, as well as reducing timelines for developing cellular assays.