Assessing HTS performance using BioAssay Ontology: screening and analysis of a bacterial phospho-N-acetylmuramoyl-pentapeptide translocase campaign

Minimum Information and Quality Standards for Conducting, Reporting, and Organizing In Vitro Research

Insufficient description of experimental practices can contribute to difficulties in reproducing research findings. In response to this, "minimum information" guidelines have been developed for different disciplines. These standards help ensure that the complete experiment is described, including both experimental protocols and data processing methods, allowing a critical evaluation of the whole process and the potential recreation of the work. Selected examples of minimum information checklists with relevance for in vitro research are presented here and are collected by and registered at the MIBBI/FAIRsharing Information Resource portal.In addition, to support integrative research and to allow for comparisons and data sharing across studies, ontologies and vocabularies need to be defined and integrated across areas of in vitro research. As examples, this chapter addresses ontologies for cells and bioassays and discusses their importance for in vitro studies.Finally, specific quality requirements for important in vitro research tools (like chemical probes, antibodies, and cell lines) are suggested, and remaining issues are discussed.

A Rapid and Efficient Luminescence-based Method for Assaying Phosphoglycosyltransferase Enzymes

Phosphoglycosyltransferases (PGTs) are families of integral membrane proteins with intriguingly diverse architectures. These enzymes function to initiate many important biosynthetic pathways including those leading to peptidoglycan, N-linked glycoproteins and lipopolysaccharide O-antigen. In spite of tremendous efforts, characterization of these enzymes remains a challenge not only due to the inherent difficulties associated with the purification of integral membrane proteins but also due to the limited availability of convenient assays. Current PGT assays include radioactivity-based methods, which rely on liquid-liquid or solid-liquid extractions, multienzyme systems linked to lactate dehydrogenase and NAD⁺ generation, and HPLC-based approaches, all of which may suffer from low sensitivity and low throughput. Herein, we present the validation of a new luminescence-based assay (UMP-Glo) for measuring activities of PGT enzymes. This assay measures UMP, the by-product of PGT reactions, in a sensitive and quantitative manner by measuring the luminescence output in a discontinuous coupled assay system. The assay is rapid and robust in nature, and also compatible with microtiter plate formats. Activity and kinetic parameters of PglC, a PGT from Campylobacter jejuni, were quickly established using this assay. The efficacy of the assay was further corroborated using two different PGTs; PglC from Helicobacter pullorum and WecA from Thermatoga maritima.

Non-stoichiometric inhibition in integrated lead finding - a literature review

INTRODUCTION

Non-stoichiometric inhibition summarizes different mechanisms by which low-molecular weight compounds can reproducibly inhibit high-throughput screening (HTS) and other lead finding assays without binding to a structurally defined site on their molecular target. This disqualifies such molecules from optimization by medicinal chemistry, and therefore their rapid elimination from screening hit lists is essential for productive and effective drug discovery.

AREAS COVERED

This review covers recent literature that either investigates the various mechanisms behind non-stoichiometric inhibition or suggests assays and readouts to identify them. In addition, combination of the various methods to distill promising molecules out of raw primary hit lists step-by-step is considered. Emerging technologies to demonstrate target engagement in cells are also discussed.

EXPERT OPINION

Over the last few years, awareness of non-stoichiometric inhibitors within screening libraries and HTS hit lists has considerably increased, not only in the pharmaceutical industry but also in the academic drug discovery community. This has resulted in a variety of methods to detect and handle such compounds. These range from in silico approaches to flag suspicious compounds, and counterassays to measure non-stoichiometric inhibition, to biophysical methods that positively demonstrate stoichiometric binding. In addition, novel technologies to verify target engagement within cells are becoming available. While still a time- and resource-consuming nuisance, non-stoichiometric inhibitors therefore do not fundamentally jeopardize the discovery of low molecular weight lead and drug candidates. Rather, they should be viewed as a manageable issue that with appropriate expertise can be overcome through integration of the above-mentioned approaches.

A Modular Approach to Phosphoglycosyltransferase Inhibitors Inspired by Nucleoside Antibiotics

Phosphoglycosyltransferases (PGTs) represent "gatekeeper" enzymes in complex glycan assembly pathways by catalyzing transfer of a phosphosugar from an activated nucleotide diphosphosugar to a membrane-resident polyprenol phosphate. The unique structures of selected nucleoside antibiotics, such as tunicamycin and mureidomycin A, which are known to inhibit comparable biochemical transformations, are exploited as the foundation for the development of modular synthetic inhibitors of PGTs. Herein we present the design, synthesis, and biochemical evaluation of two readily manipulatable modular scaffolds as inhibitors of monotopic bacterial PGTs. Selected compounds show IC50 values down to the 40 μm range, thereby serving as lead compounds for future development of selective and effective inhibitors of diverse PGTs of biological and medicinal interest.

Increasing the delivery of next generation therapeutics from high throughput screening libraries

The pharmaceutical industry has historically relied on high throughput screening as a cornerstone to identify chemical equity for drug discovery projects. However, with pharmaceutical companies moving through a phase of diminished returns and alternative hit identification strategies proving successful, it is more important than ever to understand how this approach can be used more effectively to increase the delivery of next generation therapeutics from high throughput screening libraries. There is a wide literature that describes HTS and fragment based screening approaches which offer clear direction on the process for these two distinct activities. However, few people have considered how best to identify medium to low molecular weight compounds from large diversity screening sets and increase downstream success.