Chemistry or biology: which comes first after the genome is sequenced?

In drug discovery, chemical screening is performed after a protein's function has been determined. By screening for ligands that alter the function of a cell or an organism, new proteins that participate in poorly understood biological processes can be identified. Genomic and expression-cloning technologies can rapidly identify the protein targets of these ligands, enhancing the power of chemical screening as a tool for the initial stages of biological discovery.     

A False‐Positive Screening Hit in Fragment‐Based Lead Discovery: Watch out for the Red Herring

With the rising popularity of fragment‐based approaches in drug development, more and more attention has to be devoted to the detection of false‐positive screening results. In particular, the small size and low affinity of fragments drives screening techniques to their limit. The pursuit of a false‐positive hit can cause significant loss of time and resources. Here, we present an instructive and intriguing investigation into the origin of misleading assay results for a fragment that emerged as the most potent binder for the aspartic protease endothiapepsin (EP) across multiple screening assays. This molecule shows its biological effect mainly after conversion into another entity through a reaction cascade that involves major rearrangements of its heterocyclic scaffold. The formed ligand binds EP through an induced‐fit mechanism involving remarkable electrostatic interactions. Structural information in the initial screening proved to be crucial for the identification of this false‐positive hit.     

In search of novel inhibitors of anti-cancer drug target fibroblast growth factor receptors: Insights from virtual screening,molecular docking,and molecular dynamics

Fibroblast growth factor receptors (FGFR) are an essential player in oncogenesis and tumor progression. LY2874455 was identified as a pan-FGFR inhibitor and has gone through phase I clinical trial. In the current study, virtual screening was conducted against the PubChem database using a pharmacophore model generated from the crystal structure of FGFR4 inhibited by LY2874455. PubChem 137300327 was identified as the most suitable compound from this screening. Later, molecular docking and molecular dynamics studies conducted with FGFRs corroborated the initial finding. Analysis of ADMET properties disclosed that LY2874455 and PubChem 137300327 share alike properties. Our study suggests that PubChem 137300327 is a potential pan-FGFR inhibitor and can be exploited to treat different cancers following validation in proper wet-lab experiments and study in animal cancer models. This compound also follows Lipinski’s rules and can be used as a lead compound to synthesize more effective anticancer compounds.     

Practical aspects of chemometrics for oil spill fingerprinting

Tiered approaches for oil spill fingerprinting have evolved rapidly since the 1990s. Chemometrics provides a large number of tools for pattern recognition, calibration and classification that can increase the speed and the objectivity of the analysis and allow for more extensive use of the available data in this field. However, although the chemometric literature is extensive, it does not focus on practical issues that are relevant to oil spill fingerprinting. The aim of this review is to provide a framework for the use of chemometric approaches in tiered oil spill fingerprinting and to provide clear-cut practical details and experiences that can be used by the forensic chemist. The framework is based on methods for initial screening, which include classification of samples into oil type, detection of non matches and of weathering state, and detailed oil spill fingerprinting, in which a more rigorous matching of an oil spill sample to suspected source oils is obtained. This review is intended as a tutorial, and is based on two examples of initial screening using respectively gas chromatography with flame ionization detection and fluorescence spectroscopy; and two of detailed oil spill fingerprinting where gas chromatography-mass spectrometry data are analyzed according to two approaches: The first relying on sections of processed chromatograms and the second on diagnostic ratios.     

An efficient use of the WATERGATE W5 sequence for observing a ligand binding with a protein receptor

An efficient pulse sequence for observing a ligand binding with a receptor has been developed by incorporating the WATERGATE W5 sequence. In the conventional water ligand observed via gradient spectroscopy (WaterLOGSY) techniques, the water resonance is selectively excited using, e.g. the double-pulsed field gradient spin-echo (DPFGSE) sequence at the initial portion of pulse sequence. In the current version, the modified WATERGATE W5 sequence is incorporated at the initial portion of the pulse sequence, and the resonance at the water frequency can be selectively reserved by the modified WATERGATE W5 sequence. The efficiency of ligand-observed NMR screening techniques has been demonstrated using the human serum albumin (HSA)-tryptophan complex.     

PowerMV: a software environment for molecular viewing, descriptor generation, data analysis and hit evaluation

Ideally, a team of biologists, medicinal chemists and information specialists will evaluate the hits from high throughput screening. In practice, it often falls to nonmedicinal chemists to make the initial evaluation of HTS hits. Chemical genetics and high content screening both rely on screening in cells or animals where the biological target may not be known. There is a need to place active compounds into a context to suggest potential biological mechanisms. Our idea is to build an operating environment to help the biologist make the initial evaluation of HTS data. To this end the operating environment provides viewing of compound structure files, computation of basic biologically relevant chemical properties and searching against biologically annotated chemical structure databases. The benefit is to help the nonmedicinal chemist, biologist and statistician put compounds into a potentially informative biological context. Although there are several similar public and private programs used in the pharmaceutical industry to help evaluate hits, these programs are often built for computational chemists. Our program is designed for use by biologists and statisticians.     

Evaluations of molecular docking programs for virtual screening

Structure-based virtual screening is carried out using molecular docking programs. A number of such docking programs are currently available, and the selection of docking program is difficult without knowing the characteristics or performance of each program. In this study, the screening performances of three molecular docking programs, DOCK, AutoDock, and GOLD, were evaluated with 116 target proteins. The screening performances were validated using two novel standards, along with a traditional enrichment rate measurement. For the evaluations, each docking run was repeated 1000 times with three initial conformations of a ligand. While each docking program has some merit over the other docking programs in some aspects, DOCK showed an unexpectedly better screening performance in the enrichment rates. Finally, we made several recommendations based on the evaluation results to enhance the screening performances of the docking programs.     

Photostimulated luminescence detection of irradiated shellfish: international interlaboratory trial

An interlaboratory trial was conducted to validate photostimulated luminescence (PSL) detection of irradiated shellfish. Five species of shellfish (Nephrops norvegicus, mussels, black tiger prawns, brown shrimps, and king scallops) were presented blind as nonirradiated and irradiated to 0.5 and 2.5 kGy. Precharacterization analysis of each product and treatment was performed on both whole (including shell) and intestinal samples. The results for whole samples (including shell) confirmed that the method was able to distinguish between nonirradiated and irradiated samples, regardless of dose. Intestinal data have identified that the method is dependent on the quantity and sensitivity of grits present within the intestinal tract, which can be assessed using calibration by normalization to 1 kGy. Five laboratories returned both initial screening and calibrated data and sample classification. All laboratories correctly identified all irradiated products using the screening criteria. There were no false positives. The results confirm the validity of the PSL method for shellfish, which has been adopted as a European standard method and by the Codex Alimentarius Commission. Calibration is required where only intestinal material is available. For whole samples with shell, screening alone is sufficient.     

Peptide‐Stabilized,Fluorescent Silver Nanoclusters: Solid‐Phase Synthesis and Screening

Few‐atom silver nanoclusters (AgNCs) can exhibit strong fluorescence; however, they require ligands to prevent aggregation into larger nanoparticles. Fluorescent AgNCs in biopolymer scaffolds have so far mainly been synthesized in solution, and peptides have only found limited use compared to DNA. Herein, we demonstrate how solid‐phase methods can increase throughput dramatically in peptide ligand screening and in initial evaluation of fluorescence intensity and chemical stability of peptide‐stabilized AgNCs (P‐AgNCs). 9‐Fluorenylmethyloxycarbonyl (Fmoc) solid‐phase peptide synthesis on a hydroxymethyl‐benzoic acid (HMBA) polyethylene glycol polyacrylamide copolymer (PEGA) resin enabled on‐resin screening and evaluation of a peptide library, leading to identification of novel peptide‐stabilized, fluorescent AgNCs. Using systematic amino acid substitutions, we synthesized and screened a 144‐member library. This allowed us to evaluate the effect of length, charge, and Cys content in peptides used as ligands for AgNC stabilization. The results of this study will enable future spectroscopic studies of these peptide‐stabilized AgNCs for bioimaging and other applications.     

Determination of initial reaction rates using wilkinson's relation

Uncertainty sometimes exists in determining initial reaction rates from experimental data. A method, originally proposed by Wilkinson [9] for estimating orders and rate constants for simple batch nth order reactions, has been generalized to complex kinetic systems. This method yields very accurate initial rates for all systems and extends the conversion range of experimental investigation of initial rates well beyond the “zero-order” region. Accurate initial rates are required in analytical methods used for screening alternate reaction mechanisms.     

Automated and Efficient Generation of General Molecular Aggregate Structures

Modeling intermolecular interactions of complex non-covalent structures is important in many areas of chemistry. To facilitate the generation of reasonable dimer, oligomer, and general aggregate geometries, we introduce an automated computational interaction site screening (aISS) workflow. This easy-to-use tool combines a genetic algorithm employing the intermolecular force-field xTB-IFF for initial search steps with the general force-field GFN-FF and the semi-empirical GFN2-xTB method for geometry optimizations. Compared with the alternative CREST program, aISS yields similar results but with computer time savings of 1–3 orders of magnitude. This allows for the treatment of systems with thousands of atoms composed of elements up to radon, e.g., metal-organic complexes, or even polyhedra and zeolite cut-outs which were not accessible before. Moreover, aISS can identify reactive sites and provides options like site-directed (user-guided) screening.     

Accelerated Discovery in Photocatalysis using a Mechanism‐Based Screening Method

Herein, we report a conceptually novel mechanism‐based screening approach to accelerate discovery in photocatalysis. In contrast to most screening methods, which consider reactions as discrete entities, this approach instead focuses on a single constituent mechanistic step of a catalytic reaction. Using luminescence spectroscopy to investigate the key quenching step in photocatalytic reactions, an initial screen of 100 compounds led to the discovery of two promising substrate classes. Moreover, a second, more focused screen provided mechanistic insights useful in developing proof‐of‐concept reactions. Overall, this fast and straightforward approach both facilitated the discovery and aided the development of new light‐promoted reactions and suggests that mechanism‐based screening strategies could become useful tools in the hunt for new reactivity.     

Substrate binding and activation via pendant hydrogen-bonding groups as an approach to biomimetic homogeneous catalysis

In a biomimetic approach to organometallic catalysis, pendant hydrogen-bonding groups are shown to influence the chemistry of ligand binding and activation in an iridium complex. Such groups can bind a substrate by hydrogen bonding and so offer the possibility of a biomimetic approach to catalysis where binding is controlled via molecular recognition. Because catalyst design in this area may be challenging, combinatorial and rapid screening methods may be needed to assay potential catalysts and initial progress on developing these methods for hydrosilation of alkenes and imines is described. Catalysis of aldehyde imination and the origin of pK_a changes of bound H₂ are discussed.     

Enzyme assays with boronic acid appended bipyridinium salts

In-vitro fluorescent enzyme assays have been developed for sucrose phosphorylase (SPO) and phosphoglucomutase (PGM). These assays make use of a selective carbohydrate sensing system that detects the unlabeled enzymatic products fructose and glucose-6-phosphate. The system comprises 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt as the reporter unit and boronic acid appended viologens as selective receptors with working ranges from 70 μM to 1.0 mM for fructose (SPO) and 190 μM to 2.0 mM for glucose-6-phosphate (PGM). The change in fluorescence can be converted into product concentration, allowing initial reaction velocities and Michaelis-Menten kinetics to be calculated. The assays are also carried out in multiwell plate formats, making them suitable for high-throughput screening of enzyme inhibitors. Rapid PGM inhibition screening is demonstrated with EDTA and LiCl. The PGM assay can also be used for enzyme quantification with a detection limit of 50 ng mL⁻¹.     

Agonists of the follicle stimulating hormone receptor from an encoded thiazolidinone library

The design, synthesis, characterization, and screening of a large, encoded thiazolidinone library are described. Three sets of 35 building blocks were combined by encoded split-pool synthesis to give a library containing more than 42 000 members. Building block selection was based in part on a novel small molecule follicle stimulating hormone receptor agonist hit and in part for diversity. HPLC/MS techniques were applied at the single-bead level to build confidence in the reliability of library construction. Application of two distinct screening strategies resulted in the identification of compounds with significantly improved potency over the initial hit. This work demonstrates the versatility of encoded libraries for preparing a large number of analogues of a given hit while simultaneously generating a large collection of compounds for screening against other targets.     

Rapid screening of pesticides from fruit surfaces: preliminary examinations using a laser desorption—differential mobility spectrometry coupling

A procedure based on the coupling of pulsed laser desorption and differential mobility spectrometry is described which allows the fast screening of surfaces in respect to organic contaminations, in particular pesticides. We investigated the general capability of this technique for the rapid screening of pesticides from fruit surfaces. Although the coupling presented requires further optimization, the method developed permits the fast detection of pesticides from the surfaces of apples, grapes, tomatoes and pepper in the ng range. The initial results regarding the detection and quantification of a few prominent pesticides on different materials are presented.