In silico evaluation of pesticides as potential modulators of human DNA methyltransferases

Fragment-based discovery of new potential DNMT1 inhibitors integrating multiple pharmacophore modeling, 3D-QSAR, virtual screening, molecular docking, ADME, and molecular dynamics simulation approaches

DNA methyl transferases (DNMTs) are one of the crucial epigenetic modulators associated with a wide variety of cancer conditions. Among the DNMT isoforms, DNMT1 is correlated with bladder, pancreatic, and breast cancer, as well as acute myeloid leukemia and esophagus squamous cell carcinoma. Therefore, the inhibition of DNMT1 could be an attractive target for combating cancers and other metabolic disorders. The disadvantages of the existing nucleoside and non-nucleoside DNMT1 inhibitors are the main motive for the discovery of novel promising inhibitors. Here, pharmacophore modeling, 3D-QSAR, and e-pharmacophore modeling of DNMT1 inhibitors were performed for the large fragment database screening. The resulting fragments with high dock scores were combined into molecules. The current study revealed several constitutional pharmacophoric features that can be essential for selective DNMT1 inhibition. The fragment docking and virtual screening identified 10 final hit molecules that exhibited good binding affinities in terms of docking score, binding free energies, and acceptable ADME properties. Also, the modified lead molecules (GL1b and GL2b) designed in this study showed effective binding with DNMT1 confirmed by their docking scores, binding free energies, 3D-QSAR predicted activities and acceptable drug-like properties. The MD simulation studies also suggested that leads (GL1b and GL2b) formed stable complexes with DNMT1. Therefore, the findings of this study can provide effective information for the development/identification of novel DNMT1 inhibitors as effective anticancer agents.

Toxicology of chemical biocides: Anticoagulant rodenticides - Beyond hemostasis disturbance

The use of anticoagulant rodenticides (ARs) is one of the most commonly employed management methods for pest rodents. ARs compete with vitamin K (VK) required for the synthesis of blood clotting factors in the liver, resulting in inhibition of blood coagulation and often animal death due to hemorrhage. Besides rodents (target species), ARs may affect non-target animal species and humans. Out of hemostasis disturbance, the effects of ARs may be related to the inhibition of proteins that require VK for their synthesis but are not involved in the coagulation process, to their direct cytotoxicity, and their pro-oxidant/proinflammatory activity. A survey of the cellular and molecular mechanisms of these sublethal/asymptomatic AR effects is given in this review. Data from field, clinical, and experimental studies are presented. Knowledge of these mechanisms might improve hazard characterization and identification of potential ecotoxicological risks associated with ARs, contributing to a safer use of these chemicals.

Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications

Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.

In Silico Analysis to Identify Molecular Targets for Chemicals of Concern: The Case Study of Flocoumafen, an Anticoagulant Pesticide

Rodenticides are pesticides used worldwide, with little information available regarding health consequences in wildlife and humans. The aim of the present study was to use virtual screening to identify potential targets for flocoumafen, a superwarfarin rodenticide. Blind docking of more than 841 human proteins was carried out employing AutoDock Vina. The strength of the ligand interaction with the proteins was quantified based on the binding affinity score (kcal/mol). Results indicate that flocoumafen could be a promiscuous ligand for diversity of cellular protein targets. The best complexes were obtained for prostaglandin F synthase (-14.2 kcal/mol) and serum albumin (-14.0 kcal/mol) followed by glucocorticoid receptor 2, matrix metalloproteinase-9, nuclear receptor ROR-alpha, and activin receptor type-1, all with values equal or better than -13.5 kcal/mol. Docking method validation based on the root-mean-square deviation showed that flocoumafen had good capability to predict corresponding co-crystallized poses; and molecular dynamics simulations suggested the complex with greater binding affinity was thermodynamically stable. Protein-protein interaction networks built with main protein targets revealed that protein kinase B (AKT1), ribosomal protein S6 kinase B1 (RPS6KB1), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), retinoid X receptor alpha (RXRA), and protein phosphatase 2 catalytic subunit alpha (PPP2CA) were major hub proteins, whereas the gene ontology analysis reported that cellular response to endogenous stimulus, protein binding, and the TOR complex were the biological processes, molecular function, and cell component enrichments, respectively. These results should motivate more ecotoxicity testing for flocoumafen and other superwarfarins, as well as precautionary legislation to minimize exposure to these highly toxic chemicals. Environ Toxicol Chem 2021;40:2034-2043. © 2021 SETAC.

Cytogenetic toxicity from pesticide and trace element mixtures in soils used for conventional and organic crops of Allium cepa L

Pesticides and trace elements occur in complex mixtures in agroecosystems, affecting soil health and food security. Hence, it is necessary to determine their toxicity in field conditions and to develop monitoring approaches to assess conventional and organic agriculture. The aim of this research was to evaluate the associations between Allium cepa L. cytogenetic biomarkers and the realistic mixture of pesticides and trace elements found in soils of conventional, conversion, and organic crops in an intensive agricultural region in Colombia. Pesticide screening was conducted using GC-MS/MS and LC-MS/MS methods. Arsenic, cadmium, lead, and zinc were analyzed by ICP-MS; chromium, copper, nickel, and selenium by ICP-OES; and mercury by a direct analyzer. The meristematic cells in roots of Allium cepa L. were analyzed through microscopic observations to quantify cytogenetic effects. In conventional crops, 26 pesticides were detected in the soil samples, and those were below the limit of quantification in organic crops. The mean levels of As, Cd, Cr, Ni, Pb, and Se were also greater in soils of conventional crops compared to the organics. In addition, the biomarkers of cytotoxicity and genotoxicity appeared augmented in conventional samples, and those were correlated with pesticide and trace element concentrations, pollution indices, and hazard quotients. Subsequently, a discriminant function based on the mitotic index, chromosomal aberrations, and nuclear abnormalities was suitable to classify the samples by crop type. These results demonstrate the sensitivity of Allium cepa L. to the toxicity of complex mixtures in field crops and its potential as an in-situ approach for soil health monitoring in organic and conventional crop systems.

Glyphosate and AMPA Induce Alterations in Expression of Genes Involved in Chromatin Architecture in Human Peripheral Blood Mononuclear Cells (In Vitro)

We have determined the effect of glyphosate and aminomethylphosphonic acid (AMPA) on expression of genes involved in chromatin architecture in human peripheral blood mononuclear cells (PBMCs). The cells were incubated with glyphosate and AMPA in the concentrations ranging from 0.5 to 100 μM and from 0.5, to 250 μM, respectively. The expression profile of the following genes by quantitative Real-Time PCR was evaluated: Genes involved in the DNA methylation (DNMT1, DNMT3A) and DNA demethylation process (TET3) and those involved in chromatin remodeling: genes involved in the modification of histone methylation (EHMT1, EHMT2) and genes involved in the modification of histone deacetylation (HDAC3, HDAC5). Gene profiling showed that glyphosate changed the expression of DNMT1, DMNT3A, and HDAC3, while AMPA changed the expression of DNMT1 and HDAC3. The results also revealed that glyphosate at lower concentrations than AMPA upregulated the expression of the tested genes. Both compounds studied altered expression of genes, which are characteristic for the regulation of transcriptionally inactive chromatin. However, the unknown activity of many other proteins involved in chromatin structure regulation prevents to carry out an unambiguous evaluation of the effect of tested xenobiotics on the studied process. Undoubtedly, we have observed that glyphosate and AMPA affect epigenetic processes that regulate chromatin architecture.