Browse
Submit Data
Databases
API
Help

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Theoretical study on the toxicity of 'Novichok' agent candidates.

ABSTRACT: The identities and properties of 'Novichok' (Russian for 'newcomer' or 'novice') agents allegedly used in the recent terrorist attack in the UK have not been well documented. Although several people previously involved in the synthesis of these materials claimed Novichok agents to be five to eight times more potent than VX, a deadly nerve agent, no open data on these species are currently available. To bridge this gap, we herein performed a theoretical study on several Novichok agent candidates and conducted natural population charge analysis to evaluate the possible mechanisms of their toxicity, suggesting that these agents might promote the ageing and deformation of acetylcholinesterase. Moreover, the reaction of Novichok agents with acetylcholinesterase serine was calculated to be most thermodynamically favoured for Novichok candidate A234. Thus, this work is believed to provide a basis for finding Novichok antidotes and should inspire further detoxification studies to prepare for possible terrorist attacks in the future.

SUBMITTER: Jeong K

PROVIDER: S-EPMC6731729 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Theoretical study on the toxicity of 'Novichok' agent candidates.

Jeong Keunhong K Choi Junwon J

Royal Society open science 20190807 8

The identities and properties of 'Novichok' (Russian for 'newcomer' or 'novice') agents allegedly used in the recent terrorist attack in the UK have not been well documented. Although several people previously involved in the synthesis of these materials claimed Novichok agents to be five to eight times more potent than VX, a deadly nerve agent, no open data on these species are currently available. To bridge this gap, we herein performed a theoretical study on several Novichok agent candidates ...[more]

PMID: 31598242

Similar Datasets

Theoretical study of the molecular aspect of the suspected novichok agent A234 of the Skripal poisoning.

Project description:Novichoks are the suspected nerve agents in the March 2018 Skripal poisoning. In this context, the novichok agent A234 (chemical structure proposed by Mirzayanov) was studied using computational methods to shed light on its molecular, electronic, spectroscopic, thermodynamic and toxicity parameters as well as on potential thermal and hydrolysis degradation pathways. The poisoning action and antidote of A234 were also investigated. Some of these parameters were compared to three common G- and V-series nerve agents, namely GB, VR and VX. The research findings should be useful towards the detection, development of antidotes and destruction of A234.

| S-EPMC6408395 | biostudies-literature

Characterization and Study on Fragmentation Pathways of a Novel Nerve Agent, 'Novichok (A234)', in Aqueous Solution by Liquid Chromatography-Tandem Mass Spectrometry.

Project description:As a first step toward studying the properties of Novichok (ethyl (1-(diethylamino)ethylidene)phosphoramidofluoridate (A234)), we investigated its degradation products and fragmentation pathways in aqueous solution at different pH levels by liquid chromatography-tandem mass spectrometry. A234 was synthesized in our laboratory and characterized by nuclear magnetic resonance spectroscopy. Three sets of aqueous samples were prepared at different pH levels. A stock solution of A234 was prepared in acetonitrile at a concentration of 1 mg/mL and stored at -20 °C until use. Aqueous samples (0.1 mg/mL) were prepared by diluting the stock solution with deionized water. The acidic aqueous sample (pH = 3.5) and basic aqueous sample (pH = 9.4) were prepared using 0.01 M acetic acid and 0.01 M potassium carbonate, respectively. The analysis of the fragmentation patterns and degradation pathways of A234 showed that the same degradation products were formed at all pH levels. However, the hydrolysis rate of A234 was fastest under acidic conditions. In all three conditions, the fragmentation pattern and the major degradation product of A234 were determined. This information will be applicable to studies regarding the decontamination of Novichok and the trace analysis of its degradation products in various environmental matrices.

| S-EPMC7923011 | biostudies-literature

Theoretical Study of the Microhydration the Chemical Warfare Agent Sulfur Mustard.

Project description:A microhydration study of sulfur mustard (SM) was carried out using M06-2X, B3LYP, B3LYP-D3, and MP2 levels of theory with the 6-311++G(2d,2p) basis set. The changes in energetics, structural parameters and vibrational wavenumbers following the addition of up to three discrete water molecules to SM were analyzed. We observed slight changes in the geometry of SM upon microhydration. The stability of hydrated clusters is due to weak C-H···O-H hydrogen bonds. The free energy change for the formation of the clusters is positive at room temperature and becomes exergonic when the temperature decreases. The infrared stretchings of C-Cl of SM and O-H of water are redshifted upon the addition of water molecules. The findings from this work add to the literature of hydrated SM and can be useful in its detection and subsequent destruction.

| S-EPMC7003240 | biostudies-literature

Identification and Study of Biomarkers from Novichok-Inhibited Butyrylcholinesterase in Human Plasma.

Project description:To identify biomarkers of ethyl (1-(diethylamino)ethylidene)phosphoramidofluoridate (A234)- or methyl (1-(diethylamino)ethylidene)phosphoramidofluoridate (A232)-inhibited butyrylcholinesterase (BChE), we investigated nonapeptide adducts containing the active site serine, which plays a key role in enzyme activity, using LC-MS/HRMS. Biomarkers were acquired as expected, and they exhibited a significant amount of fragment ions from the inhibiting agent itself, in contrast to the MS2 spectra of conventional nerve agents. These biomarkers had a higher abundance of [M+2H]2+ ions than [M+H]+ ions, making doubly charged ions more suitable for trace analysis.

| S-EPMC8270327 | biostudies-literature

Synthesis, structure and toxicity evaluation of ethanolamine nitro/chloronitrobenzoates: a combined experimental and theoretical study.

Project description:BACKGROUND:Nitroaromatic and chloronitroaromatic compounds have been a subject of great interest in industry and recently in medical-pharmaceutic field. 2-Chloro-4-nitro/2-chloro-5-nitrobenzoic acids and 4-nitrobenzoic acid are promising new agents for the treatment of main infectious killing diseases in the world: immunodeficiency diseases and tuberculosis. RESULTS:New ethanolamine nitro/chloronitrobenzoates were synthesized and characterized by X-ray crystallography, UV-vis, FT-IR and elementary analysis techniques. The toxicity of the compounds prepared and correspondent components was evaluated using Hydractinia echinata as test system. A significant lower toxicity was observed for nitro-derivative compared with chloronitro-derivatives and individual components. Crystallographic studies, together with the chemical reactivity and stability profiles resulted from density functional theory and ab initio molecular orbital calculations, explain the particular behavior of ethanolamine 4-nitrobenzoate in biological test. CONCLUSIONS:The experimental and theoretical data reveal the potential of these compounds to contribute to the design of new active pharmaceutical ingredients with lower toxicity.

| S-EPMC5718998 | biostudies-literature

Hydrolysis and enzymatic degradation of Novichok nerve agents.

Project description:Several parameters of the Novichok nerve agents A230, A232 and A234 were determined. Hydrolysis rates were approximately one to three orders of magnitude slower than G-type nerve agents and approximately zero to two orders of magnitude slower than V-type nerve agents. A230 was the most labile Novichok compound followed by A232 then A234. Activation energies (Ea) and frequency factors (A) were determined for all three compounds. The organophosphorus acid anhydrolase (OPAA) enzyme had catalytic efficiencies on the Novichok compounds ranging between 104 and 105 M-1 min-1 with the highest k cat/Km value for A230, then A232 and lastly, A234.

| S-EPMC7002793 | biostudies-literature

Effective Drug Delivery in Diffuse Intrinsic Pontine Glioma: A Theoretical Model to Identify Potential Candidates.

Project description:Despite decades of clinical trials for diffuse intrinsic pontine glioma (DIPG), patient survival does not exceed 10% at two years post-diagnosis. Lack of benefit from systemic chemotherapy may be attributed to an intact bloodbrain barrier (BBB). We aim to develop a theoretical model including relevant physicochemical properties in order to review whether applied chemotherapeutics are suitable for passive diffusion through an intact BBB or whether local administration via convection-enhanced delivery (CED) may increase their therapeutic potential. Physicochemical properties (lipophilicity, molecular weight, and charge in physiological environment) of anticancer drugs historically and currently administered to DIPG patients, that affect passive diffusion over the BBB, were included in the model. Subsequently, the likelihood of BBB passage of these drugs was ascertained, as well as their potential for intratumoral administration via CED. As only non-molecularly charged, lipophilic, and relatively small sized drugs are likely to passively diffuse through the BBB, out of 51 drugs modeled, only 8 (15%)-carmustine, lomustine, erlotinib, vismodegib, lenalomide, thalidomide, vorinostat, and mebendazole-are theoretically qualified for systemic administration in DIPG. Local administration via CED might create more therapeutic options, excluding only positively charged drugs and drugs that are either prodrugs and/or only available as oral formulation. A wide variety of drugs have been administered systemically to DIPG patients. Our model shows that only few are likely to penetrate the BBB via passive diffusion, which may partly explain the lack of efficacy. Drug distribution via CED is less dependent on physicochemical properties and may increase the therapeutic options for DIPG.

| S-EPMC5670105 | biostudies-literature

Discovering mycobacterial lectins as potential drug targets and vaccine candidates for tuberculosis treatment: a theoretical approach.

Project description:M. tuberculosis proliferates within the macrophages during infection and they are bounded by carbohydrates in the cell wall, called lectins. Despite their surface localization, the studies on exact functions of lectins are unexplored. Hence, in our study, using insilico approaches, 11 potential lectins of Mtb was explored as potential drug targets and vaccine candidates. Initially, a gene interaction network was constructed for the 11 potential lectins and identified its functional partners. A gene ontology analysis was also performed for the 11 mycobacterial lectins along with its functional partners and found most of the proteins are present in the extracellular region of the bacterium and belongs to the PE/PPE family of proteins. Further, molecular docking studies were performed for two of the potential lectins (Rv2075c and Rv1917c). A novel series of quinoxalinone and fucoidan derivatives have been made to dock against these selected lectins. Molecular docking study reveals that quinoxalinone derivatives showed better affinity against Rv2075c, whereas fucoidan derivatives have good binding affinity against Rv1917c. Moreover, the mycobacterial lectins can interact with the host and they are considered as potential vaccine candidates. Hence, immunoinformatics study was carried out for all the 11 potential lectins. B-cell and T-cell binding epitopes were predicted using insilico tools. Further, an immunodominant epitope 1062SIPAIPLSVEV1072 of Rv1917c was identified, which was predicted to bind B-cell and most of the MHC alleles. Thus, the study has explored that mycobacterial lectins could be potentially used as drug targets and vaccine candidates for tuberculosis treatment.Supplementary informationThe online version contains supplementary material available at 10.1007/s42485-021-00065-y.

| S-EPMC8129965 | biostudies-literature

Enzymatic Decontamination of G-Type, V-Type and Novichok Nerve Agents.

Project description:Organophosphorus nerve agents (OPNAs) are highly toxic compounds inhibiting cholinergic enzymes in the central and autonomic nervous systems and neuromuscular junctions, causing severe intoxications in humans. Medical countermeasures and efficient decontamination solutions are needed to counteract the toxicity of a wide spectrum of harmful OPNAs including G, V and Novichok agents. Here, we describe the use of engineered OPNA-degrading enzymes for the degradation of various toxic agents including insecticides, a series of OPNA surrogates, as well as real chemical warfare agents (cyclosarin, sarin, soman, tabun, VX, A230, A232, A234). We demonstrate that only two enzymes can degrade most of these molecules at high concentrations (25 mM) in less than 5 min. Using surface assays adapted from NATO AEP-65 guidelines, we further show that enzyme-based solutions can decontaminate 97.6% and 99.4% of 10 g∙m-2 of soman- and VX-contaminated surfaces, respectively. Finally, we demonstrate that these enzymes can degrade ethyl-paraoxon down to sub-inhibitory concentrations of acetylcholinesterase, confirming their efficacy from high to micromolar doses.

| S-EPMC8347808 | biostudies-literature

Anti-HCV and anti-malaria agent, potential candidates to repurpose for coronavirus infection: Virtual screening, molecular docking, and molecular dynamics simulation study.

Project description:AIMS:Coronavirus disease 2019 (COVID-19) has appeared in Wuhan, China but the fast transmission has led to its widespread prevalence in various countries, which has made it a global concern. Another concern is the lack of definitive treatment for this disease. The researchers tried different treatment options which are not specific. The current study aims to identify potential small molecule inhibitors against the main protease protein of SARS-CoV-2 by the computational approach. MAIN METHODS:In this study, a virtual screening procedure employing docking of the two different datasets from the ZINC database, including 1615 FDA approved drugs and 4266 world approved drugs were used to identify new potential small molecule inhibitors for the newly released crystal structure of main protease protein of SARS-CoV-2. In the following to validate the docking result, molecular dynamics simulations were applied on selected ligands to identify the behavior and stability of them in the binding pocket of the main protease in 150 nanoseconds (ns). Furthermore, binding energy using the MMPBSA approach was also calculated. KEY FINDINGS:The result indicates that simeprevir (Hepatitis C virus NS3/4A protease inhibitor) and pyronaridine (antimalarial agent) could fit well to the binding pocket of the main protease and because of some other beneficial features including broad-spectrum antiviral properties and ADME profile, they might be a promising drug candidate for repurposing to the treatment of COVID-19. SIGNIFICANCE:Simeprevir and pyronaridine were selected by the combination of virtual screening and molecular dynamics simulation approaches as a potential candidate for treatment of COVID-19.

| S-EPMC7413873 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data