Design of a Lead-Like Cysteine-Targeting Covalent Library and the Identification of Hits to Cys55 of Bfl-1.

Covalent hit identification is a viable approach to identify chemical starting points against difficult-to-drug targets. While most researchers screen libraries of <2k electrophilic fragments, focusing on lead-like compounds can be advantageous in terms of finding hits with improved affinity and with a better chance of identifying cryptic pockets. However, due to the increased molecular complexity, larger numbers of compounds (>10k) are desirable to ensure adequate coverage of chemical space. Herein, the approach taken to build a library of 12k covalent lead-like compounds is reported, utilizing legacy compounds, robust library chemistry, and acquisitions. The lead-like covalent library was screened against the antiapoptotic protein Bfl-1, and six promising hits that displaced the BIM peptide from the PPI interface were identified. Intriguingly, X-ray crystallography of lead-like compound 8 showed that it binds to a previously unobserved conformation of the Bfl-1 protein and is an ideal starting point for the optimization of Bfl-1 inhibitors.

Rapid screening of riot control agents using DART-TD-HRMS.

PURPOSE: Riot Control Agents (RCAs) are chemicals used in law enforcement for non-lethal riot control and use in conflicts between states that violates the Chemical Weapons Convention. OPCW's Scientific Advisory Board has identified sixteen potential RCAs including capsaicinoids, CS, and CR. RCAs may be misused for criminal purposes, so methods for detecting such misuse are needed. This study therefore evaluates the feasibility of a rapid, high throughput screening method of RCAs on surfaces (particularly clothing surfaces) by Direct Analysis in Real Time with a thermal desorption unit coupled to high-resolution mass spectrometry (DART-TD-HRMS). METHODS: A broadly applicable method for detecting potential RCAs was developed and tested on cotton fabric samples sprayed with self-defence sprays from an in-house reference stock. The feasibility of detecting RCAs by direct analysis of surface wipe samples placed in the DART source was also investigated. RESULTS: The method detected all sixteen RCAs and contaminated clothing were successfully screened for active agents in a reference collection of self-defence sprays. A pilot study also showed that RCAs can be detected by holding a sample directly in front of the DART source. CONCLUSION: DART-TD-HRMS enables rapid and simple screening of RCAs on fabric samples enabling a high sample throughput.

The potential of thermal desorption-GC/MS-based analytical methods for the unambiguous identification and quantification of perfluoroisobutene and carbonyl fluoride in air samples.

The reactive gases perfluoroisobutene and carbonyl fluoride are highly toxic and difficult to analyze in air. For this paper, the available sampling and analysis methods involving gas chromatography/mass spectrometry were investigated for their potential to give unambiguous identification and quantification of perfluoroisobutene and carbonyl fluoride, for which no such methods exist. Although high concentrations of perfluoroisobutene could be analyzed directly by manual split injection, sorbent sampling followed by thermal desorption GC/MS allowed lower concentrations to be analyzed. However, a significant degradation of perfluoroisobutene observed after thermal desorption analysis inspired the use of derivatization of perfluoroisobutene with 3,4-dimercaptotoluene. The use of Tenax TA sorbent tubes spiked with 3,4-dimercaptotoluene and trimethylamine in a molar ratio of 1:8 proved successful for the quantification of a unique perfluoroisobutene derivative, and the method was validated for atmospheres in the range of 0.13-152 ppb with a relative standard deviation of less than 20% and an accuracy of 90%. Although carbonyl fluoride was less stable than perfluoroisobutene, direct analysis was possible at high concentrations but the response was not linear. The 3,4-dimercaptotoluene derivatization method developed was also applicable for quantification of carbonyl fluoride atmospheres.

Route Determination of Sulfur Mustard Using Nontargeted Chemical Attribution Signature Screening.

Route determination of sulfur mustard was accomplished through comprehensive nontargeted screening of chemical attribution signatures. Sulfur mustard samples prepared via 11 different synthetic routes were analyzed using gas chromatography/high-resolution mass spectrometry. A large number of compounds were detected, and multivariate data analysis of the mass spectrometric results enabled the discovery of route-specific signature profiles. The performance of two supervised machine learning algorithms for retrospective synthetic route attribution, orthogonal partial least squares discriminant analysis (OPLS-DA) and random forest (RF), were compared using external test sets. Complete classification accuracy was achieved for test set samples (2/2 and 9/9) by using classification models to resolve the one-step routes starting from ethylene and the thiodiglycol chlorination methods used in the two-step routes. Retrospective determination of initial thiodiglycol synthesis methods in sulfur mustard samples, following chlorination, was more difficult. Nevertheless, the large number of markers detected using the nontargeted methodology enabled correct assignment of 5/9 test set samples using OPLS-DA and 8/9 using RF. RF was also used to construct an 11-class model with a total classification accuracy of 10/11. The developed methods were further evaluated by classifying sulfur mustard spiked into soil and textile matrix samples. Due to matrix effects and the low spiking level (0.05% w/w), route determination was more challenging in these cases. Nevertheless, acceptable classification performance was achieved during external test set validation: chlorination methods were correctly classified for 12/18 and 11/15 in spiked soil and textile samples, respectively.

In Situ Assembly of Choline Acetyltransferase Ligands by a Hydrothiolation Reaction Reveals Key Determinants for Inhibitor Design.

The potential drug target choline acetyltransferase (ChAT) catalyses the production of the neurotransmitter acetylcholine in cholinergic neurons, T-cells, and B-cells. Herein, we show that arylvinylpyridiniums (AVPs), the most widely studied class of ChAT inhibitors, act as substrate in an unusual coenzyme A-dependent hydrothiolation reaction. This in situ synthesis yields an adduct that is the actual enzyme inhibitor. The adduct is deeply buried in the active site tunnel of ChAT and interactions with a hydrophobic pocket near the choline binding site have major implications for the molecular recognition of inhibitors. Our findings clarify the inhibition mechanism of AVPs, establish a drug modality that exploits a target-catalysed reaction between exogenous and endogenous precursors, and provide new directions for the development of ChAT inhibitors with improved potency and bioactivity.

Radical Functionalization of Unsaturated Amino Acids: Synthesis of Side-Chain-Fluorinated, Azido-Substituted, and Hydroxylated Amino Acids.

A range of enantiomerically pure protected side-chain-fluorinated amino acids has been prepared (13 examples) by treatment of protected amino acids containing unsaturated side chains with a combination of Fe(III)/NaBH4 and Selectfluor. The modification of the conditions by replacement of Selectfluor with NaN3 allowed the preparation of side-chain azido-substituted amino acids (five examples), which upon catalytic hydrogenation gave the corresponding amines, isolated as lactams (four examples). Radical hydration of the unsaturated side chains leading to side-chain-hydroxylated protected amino acids has also been demonstrated.

Synthesis route attribution of sulfur mustard by multivariate data analysis of chemical signatures.

A multivariate model was developed to attribute samples to a synthetic method used in the production of sulfur mustard (HD). Eleven synthetic methods were used to produce 66 samples for model construction. Three chemists working in both participating laboratories took part in the production, with the aim to introduce variability while reducing the influence of laboratory or chemist specific impurities in multivariate analysis. A gas chromatographic/mass spectrometric data set of peak areas for 103 compounds was subjected to orthogonal partial least squares - discriminant analysis to extract chemical attribution signature profiles and to construct multivariate models for classification of samples. For one- and two-step routes, model quality allowed the classification of an external test set (16/16 samples) according to synthesis conditions in the reaction yielding sulfur mustard. Classification of samples according to first-step methodology was considerably more difficult, given the high purity and uniform quality of the intermediate thiodiglycol produced in the study. Model performance in classification of aged samples was also investigated.

On the use of spectra from portable Raman and ATR-IR instruments in synthesis route attribution of a chemical warfare agent by multivariate modeling.

Collecting data under field conditions for forensic investigations of chemical warfare agents calls for the use of portable instruments. In this study, a set of aged, crude preparations of sulfur mustard were characterized spectroscopically without any sample preparation using handheld Raman and portable IR instruments. The spectral data was used to construct Random Forest multivariate models for the attribution of test set samples to the synthetic method used for their production. Colored and fluorescent samples were included in the study, which made Raman spectroscopy challenging although fluorescence was diminished by using an excitation wavelength of 1064 nm. The predictive power of models constructed with IR or Raman data alone, as well as with combined data was investigated. Both techniques gave useful data for attribution. Model performance was enhanced when Raman and IR spectra were combined, allowing correct classification of 19/23 (83%) of test set spectra. The results demonstrate that data obtained with spectroscopy instruments amenable for field deployment can be useful in forensic studies of chemical warfare agents.

Transient replication of a hepatitis C virus genotype 1b replicon chimera encoding NS5A-5B from genotype 3a.

Although hepatitis C virus (HCV) is a pathogen of global significance, experimental therapies in current clinical development include highly efficacious all-oral combinations of HCV direct-acting antivirals (DAAs). If approved for use, these new treatment regimens will impact dramatically upon our capacity to eradicate HCV in the majority of virus-infected patients. However, recent data from late-stage clinical evaluations demonstrated that individuals infected with HCV genotype (GT) 3 responded less well to all-oral DAA combinations than patients infected with other HCV GTs. In light of these observations, the present study sought to expand the number of molecular tools available to investigate small molecule-mediated inhibition of HCV GT3 NS5A and NS5B proteins in preclinical tissue-culture systems. Accordingly, a novel subgenomic HCV replicon chimera was created by utilizing a GT1b backbone modified to produce NS5A and NS5B proteins from a consensus sequence generated from HCV GT3a genomic sequences deposited online at the European Hepatitis C Virus database. This approach avoided the need to isolate and amplify HCV genomes from sera derived from HCV-infected patients. The replicon chimera, together with a version engineered to express NS5A encoding a Y93H mutation, demonstrated levels of replication in transient assays robust enough to assess accurate antiviral activities of inhibitors representing different HCV DAA classes. Thus, the replicon chimera represents a new simple molecular tool suitable for drug discovery programmes aimed at investigating, understanding, and improving GT3a activities of HCV DAAs targeting NS5A or NS5B.

Design and synthesis of potent macrocyclic renin inhibitors.

Two types of P1-P3-linked macrocyclic renin inhibitors containing the hydroxyethylene isostere (HE) scaffold just outside the macrocyclic ring have been synthesized. An aromatic or aliphatic substituent (P3sp) was introduced in the macrocyclic ring aiming at the S3 subpocket (S3sp) in order to optimize the potency. A 5-6-fold improvement in both the K(i) and the human plasma renin activity (HPRA)IC(50) was observed when moving from the starting linear peptidomimetic compound 1 to the most potent macrocycle 42 (K(i) = 3.3 nM and HPRA IC(50) = 7 nM). Truncation of the prime side of 42 led to 8-10-fold loss of inhibitory activity in macrocycle 43 (K(i) = 34 nM and HPRA IC(50) = 56 nM). All macrocycles were epimeric mixtures in regard to the P3sp substituent and X-ray crystallographic data of the representative renin macrocycle 43 complex showed that only the S-isomer buried the substituent into the S3sp. Inhibitory selectivity over cathepsin D (Cat-D) and BACE-1 was also investigated for all the macrocycles and showed that truncation of the prime side increased selectivity of inhibition in favor of renin.

Taking control of P1, P1' and double bond stereochemistry in the synthesis of Phe-Phe (E)-alkene amide isostere dipeptidomimetics.

A protocol for the stereocontrolled independent preparation of both C-2 epimers of Phe-Phe trans-vinyl amide isostere dipeptidomimetics has been devised based on a Wittig-type reaction, in which two chiral building blocks were joined with excellent E-selectivity to give compounds of the type PhePsi[(E)-CH[double bond, length as m-dash]CH]-PheOH.

Modulation of peripheral inflammation by the substance P N-terminal metabolite substance P1-7.

The N-terminal metabolite of the undecapeptide substance P (SP), substance P1-7 (SP1-7), is known to modulate nociception in the central nervous system (CNS) and often has opposite effects from SP. This study investigated the ability of SP(1-7) to modulate the vasodilatation response to SP in anaesthetized rats under different injury conditions using a blister model of inflammation on the hind footpad. The results indicated that SP1-7 inhibited the vascular response to SP in a dose-dependent manner. The putative antagonists naloxone and D-Pro2-D-Phe7-SP1-7 (D-SP1-7) reversed the effect of SP1-7. D-SP1-7 improved the responsiveness to SP under chronic nerve injury, which suggests a role for endogenous SP1-7 in this model. SP1-7 did not inhibit the response to electrical stimulation of the sciatic nerve, which indicates that the heptapeptide interacts at a post-terminal binding site. The current results suggest that SP1-7 may have inhibitory properties in inflammation, analogous to its antinociceptive role in the central nervous system.

A biocatalytic route to P-chirogenic compounds by lipase-catalyzed desymmetrization of a prochiral phosphine-borane.

[reaction: see text] Available methods for synthesis of P-chirogenic compounds are limited. We set out to find biocatalytical means to introduce asymmetry in a phosphine-borane. After screening different lipases, Candida antarctica lipase B was found to give excellent results in the desymmetrization of prochiral phosphine-boranes. Both enantiomers can be obtained in up to >98% optical purity via acetylation or hydrolysis in processes that allow recycling of the substrates.

Azadirachtin-impregnated traps for the control of Dermanyssus gallinae.

The effect of neem oil (azadirachtin), originating from the tree Azadirachta indica, was investigated as a potential compound to control the poultry red mite, Dermanyssus gallinae. In vitro tests were performed to determine the most appropriate formulation of neem extracts and concentration of the substance to be used. Cardboard traps containing 20% neem oil were placed at the mites' aggregation sites, out of reach of the hens, in a floor system for layers containing approximately 2400 birds. Treated traps were replaced every week for 4 weeks. Throughout the study, the parasite population was monitored by collections of mites with untreated plastic traps. A 92% reduction of D. gallinae was recorded.