Xenobiotic Molecules Research Articles

XenoBug: machine learning-based tool to predict pollutant-degrading enzymes from environmental metagenomes.

Application of machine learning-based methods to identify novel bacterial enzymes capable of degrading a wide range of xenobiotics offers enormous potential for bioremediation of toxic and carcinogenic recalcitrant xenobiotics such as pesticides, plastics, petroleum, and pharmacological products that adversely impact ecology and health. Using 6814 diverse substrates involved in ∼141200 biochemical reactions, we have developed 'XenoBug', a machine learning-based tool that predicts bacterial enzymes, enzymatic reaction, the species capable of biodegrading xenobiotics, and the metagenomic source of the predicted enzymes. For training, a hybrid feature set was used that comprises 1603 molecular descriptors and linear and circular fingerprints. It also includes enzyme datasets consisting of ∼3.3 million enzyme sequences derived from an environmental metagenome database and ∼16 million enzymes from ∼38000 bacterial genomes. For different reaction classes, XenoBug shows very high binary accuracies (>0.75) and F1 scores (>0.62). XenoBug is also validated on a set of diverse classes of xenobiotics such as pesticides, environmental pollutants, pharmacological products, and hydrocarbons known to be degraded by the bacterial enzymes. XenoBug predicted known as well as previously unreported metabolic enzymes for the degradation of molecules in the validation set, thus showing its broad utility to predict the metabolism of any input xenobiotic molecules. XenoBug is available on: https://metabiosys.iiserb.ac.in/xenobug.

GutBugDB: a web resource to predict the human gut microbiome-mediated biotransformation of biotic and xenobiotic molecules.

There has been a growing recognition of the significant role played by the human gut microbiota in altering the bioavailability as well as the pharmacokinetic and pharmacodynamic aspects of orally ingested xenobiotic and biotic molecules. The determination of species-specific contributions to the metabolism of biotic and xenobiotic molecules has the potential to aid in the development of new therapeutic and nutraceutical molecules that can modulate human gut microbiota. Here we present "GutBugDB," an open-access digital repository that provides information on potential gut microbiome-mediated biotransformation of biotic and xenobiotic molecules using the predictions from the GutBug tool. This database is constructed using metabolic proteins from 690 gut bacterial genomes and 363,872 protein enzymes assigned with their EC numbers (with representative Expasy ID and domains present). It provides information on gut microbiome enzyme-mediated metabolic biotransformation for 1439 FDA-approved drugs and nutraceuticals. GutBugDB is publicly available at https://metabiosys.iiserb.ac.in/gutbugdb/.

Cyanobacterial based bioremediation of xenobiotics compounds

Cyanobacterial based bioremediation of xenobiotics compounds

In Vitro Effects of Some Chemotherapeutic Drugs on Rat Erythrocytes Glutathione S-transferase (GST) Enzyme

After heart disease, cancer is the leading cause of death worldwide. Currently, breast, lung, bowel, and prostate cancer are the most common cancers in the worldwide. By stopping cancer cells from dividing, spreading, growing, making more cells, and then destroying them, chemotherapy drugs are used to treat diseases caused by cancer. The glutathione S-transferase enzyme is responsible for the detoxification of xenobiotic molecules produced by the body during cancer treatment. In this study, glutathione S-transferase enzyme (GST, EC: 2.5.1.18) was extracted from the erythrocytes of rats by affinity column chromatography in one step. The gel electrophoresis (SDS-PAGE) was used to verify the GST enzyme's purity, A single protein band was obtained. The GST enzyme was purified with 22.5 EU/mg specific activity, 237.14 purification-fold, and 48.98% purification yield. The subsequently investigation study into the in vitro effects of 5-fluorouracil (5-FU) and cyclophosphamide (CP) chemotherapy drugs on purified GST enzyme activity revealed that both 5-fluorouracil and cyclophosphamide increased GST activity at a concentration range of (0.385 to 15.4 mM, and 19.15 to 191.5 mM) respectively.

Investigating the crosstalk between ABCC4 and ABCC5 in 3T3-L1 adipocyte differentiation

IntroductionThe plasma membrane-bound protein, multi-drug resistance-associated protein 4 (MRP4/ABCC4), has gained attention for its pivotal role in facilitating the efflux of a wide range of endogenous and xenobiotic molecules. Its significance in adipogenesis and fatty acid metabolism has been brought to light by recent studies. Notably, research on ABCC4 knockout (ABCC4−/−) mice has established a link between the absence of ABCC4 and the development of obesity and diabetes. Nevertheless, the specific contribution of ABCC4 within adipose tissue remains largely unexplored.MethodsTo address this gap, we conducted a study to elucidate the role of the ABCC4 transporter in mature adipocytes, using siRNA constructs to silence its gene function.ResultsThe successful knockdown of ABCC4 significantly altered lipid status and adipogenic gene expression in mature 3T3-L1 adipocytes. Intriguingly, this knockdown also altered the gene expression patterns of other ABCC transporter family members in 3T3-L1 cells. The downregulation of ABCC5 expression was particularly noteworthy, suggesting potential crosstalk between ABCC transporters in mature adipocytes. Additionally, knocking down ABCC5 resulted in significantly higher adipogenic and lipogenic gene expression levels. Oil Red O staining confirmed increased lipid accumulation following the knockdown of ABCC4 and ABCC5. Surprisingly, the simultaneous knockdown of both transporters did not show a cumulative effect on adipogenesis, rather it led to higher levels of intracellular cAMP and extracellular prostaglandin metabolite, both of which are essential signaling molecules in adipogenesis.ConclusionThese results highlight the complex interplay between ABCC4 and ABCC5 transporters in adipocyte function and suggest their individual contributions toward obesity and related disorders.

Deorphanizing solute carriers in Saccharomyces cerevisiae for secondary uptake of xenobiotic compounds.

The exchange of small molecules between the cell and the environment happens through transporter proteins. Besides nutrients and native metabolic products, xenobiotic molecules are also transported, however it is not well understood which transporters are involved. In this study, by combining exo-metabolome screening in yeast with transporter characterization in Xenopus oocytes, we mapped the activity of 30 yeast transporters toward six small non-toxic substrates. Firstly, using LC-MS, we determined 385 compounds from a chemical library that were imported and exported by S. cerevisiae. Of the 385 compounds transported by yeast, we selected six compounds (viz. sn-glycero-3-phosphocholine, 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, acrylic acid, 2-benzoxazolol) for characterization against 30 S. cerevisiae xenobiotic transport proteins expressed in Xenopus oocytes. The compounds were selected to represent a diverse set of chemicals with a broad interest in applied microbiology. Twenty transporters showed activity toward one or more of the compounds. The tested transporter proteins were mostly promiscuous in equilibrative transport (i.e., facilitated diffusion). The compounds 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, and sn-glycero-3-phosphocholine were transported equilibratively by transporters that could transport up to three of the compounds. In contrast, the compounds acrylic acid and 2-benzoxazolol, were strictly transported by dedicated transporters. The prevalence of promiscuous equilibrative transporters of non-native substrates has significant implications for strain development in biotechnology and offers an explanation as to why transporter engineering has been a challenge in metabolic engineering. The method described here can be generally applied to study the transport of other small non-toxic molecules. The yeast transporter library is available at AddGene (ID 79999).

Reusable porous chromium- zinc oxide nano-sheets for efficient detoxification of xenobiotics through integrated advanced oxidation water clean-up process

Reusable porous chromium- zinc oxide nano-sheets for efficient detoxification of xenobiotics through integrated advanced oxidation water clean-up process

Signatures of Co-evolution and Co-regulation in the CYP3A and CYP4F Genes in Humans.

Cytochromes P450 (CYP450) are hemoproteins generally involved in the detoxification of the body of xenobiotic molecules. They participate in the metabolism of many drugs and genetic polymorphisms in humans have been found to impact drug responses and metabolic functions. In this study, we investigate the genetic diversity of CYP450 genes. We found that two clusters, CYP3A and CYP4F, are notably differentiated across human populations with evidence for selective pressures acting on both clusters: we found signals of recent positive selection in CYP3A and CYP4F genes and signals of balancing selection in CYP4F genes. Furthermore, an extensive amount of unusual linkage disequilibrium is detected in this latter cluster, indicating co-evolution signatures among CYP4F genes. Several of the selective signals uncovered co-localize with expression quantitative trait loci (eQTL), which could suggest epistasis acting on co-regulation in these gene families. In particular, we detected a potential co-regulation event between CYP3A5 and CYP3A43, a gene whose function remains poorly characterized. We further identified a causal relationship between CYP3A5 expression and reticulocyte count through Mendelian randomization analyses, potentially involving a regulatory region displaying a selective signal specific to African populations. Our findings linking natural selection and gene expression in CYP3A and CYP4F subfamilies are of importance in understanding population differences in metabolism of nutrients and drugs.

Application of artificial intelligence approaches to predict the metabolism of xenobiotic molecules by human gut microbiome.

A highly complex, diverse, and dense community of more than 1,000 different gut bacterial species constitutes the human gut microbiome that harbours vast metabolic capabilities encoded by more than 300,000 bacterial enzymes to metabolise complex polysaccharides, orally administered drugs/xenobiotics, nutraceuticals, or prebiotics. One of the implications of gut microbiome mediated biotransformation is the metabolism of xenobiotics such as medicinal drugs, which lead to alteration in their pharmacological properties, loss of drug efficacy, bioavailability, may generate toxic byproducts and sometimes also help in conversion of a prodrug into its active metabolite. Given the diversity of gut microbiome and the complex interplay of the metabolic enzymes and their diverse substrates, the traditional experimental methods have limited ability to identify the gut bacterial species involved in such biotransformation, and to study the bacterial species-metabolite interactions in gut. In this scenario, computational approaches such as machine learning-based tools presents unprecedented opportunities and ability to predict the gut bacteria and enzymes that can potentially metabolise a candidate drug. Here, we have reviewed the need to identify the gut microbiome-based metabolism of xenobiotics and have provided comprehensive information on the available methods, tools, and databases to address it along with their scope and limitations.

Improved methods for the detection of heme and protoporphyrin IX adducts and quantification of heme B from cytochrome P450 containing systems

Improved methods for the detection of heme and protoporphyrin IX adducts and quantification of heme B from cytochrome P450 containing systems

Nuclear receptor superfamily structural diversity in pacific oyster: In silico identification of estradiol binding candidates

Nuclear receptor superfamily structural diversity in pacific oyster: In silico identification of estradiol binding candidates

Iron Load Toxicity in Medicine: From Molecular and Cellular Aspects to Clinical Implications.

Iron is essential for all organisms and cells. Diseases of iron imbalance affect billions of patients, including those with iron overload and other forms of iron toxicity. Excess iron load is an adverse prognostic factor for all diseases and can cause serious organ damage and fatalities following chronic red blood cell transfusions in patients of many conditions, including hemoglobinopathies, myelodyspasia, and hematopoietic stem cell transplantation. Similar toxicity of excess body iron load but at a slower rate of disease progression is found in idiopathic haemochromatosis patients. Excess iron deposition in different regions of the brain with suspected toxicity has been identified by MRI T2* and similar methods in many neurodegenerative diseases, including Alzheimer's disease and Parkinson's disease. Based on its role as the major biological catalyst of free radical reactions and the Fenton reaction, iron has also been implicated in all diseases associated with free radical pathology and tissue damage. Furthermore, the recent discovery of ferroptosis, which is a cell death program based on free radical generation by iron and cell membrane lipid oxidation, sparked thousands of investigations and the association of iron with cardiac, kidney, liver, and many other diseases, including cancer and infections. The toxicity implications of iron in a labile, non-protein bound form and its complexes with dietary molecules such as vitamin C and drugs such as doxorubicin and other xenobiotic molecules in relation to carcinogenesis and other forms of toxicity are also discussed. In each case and form of iron toxicity, the mechanistic insights, diagnostic criteria, and molecular interactions are essential for the design of new and effective therapeutic interventions and of future targeted therapeutic strategies. In particular, this approach has been successful for the treatment of most iron loading conditions and especially for the transition of thalassemia from a fatal to a chronic disease due to new therapeutic protocols resulting in the complete elimination of iron overload and of iron toxicity.

Systemic Exposure, Metabolism, and Elimination of [14C]-Labeled Amino Lipid, Lipid 5, after a Single Administration of mRNA Encapsulating Lipid Nanoparticles to Sprague-Dawley Rats.

The emerging therapeutic modality of lipid nanoparticle (LNP)-encapsulated mRNAs has demonstrated promising clinical results when used as vaccines and is currently being tested in formulations for a wide range of targeted chronic disease treatments. These therapeutics are multicomponent assemblages of well-characterized naturally occurring molecules in addition to xenobiotic molecules, whose in vivo distributions are poorly understood. Here, the metabolic outcome and in vivo elimination of heptadecan-9-yl 8-((2-hydroxyethyl) (8-(nonyloxy)-8-oxooctyl)amino)octanoate (Lipid 5), a key xenobiotic amino lipid in LNP formulations, were assessed after intravenous administration of 14C-labeled Lipid 5 to Sprague-Dawley rats. Intact Lipid 5 was predominantly cleared from plasma within 10 hour after dosing, with only small quantities (<1% of 14C dose) of a single diacid metabolite detected after 10 hour. Lipid 5 was rapidly metabolized via ester hydrolysis into aliphatic alcohols and diacidic amino head group moieties, which were further metabolized via β-oxidation. Overall, >90% of the administered Lipid 5-derived 14C was recovered in urine (65%) and feces (35%), predominantly as oxidative metabolites, within 72 hour after dosing, indicating rapid renal and hepatic elimination. In vitro metabolite identification after incubation with human, nonhuman primate, and rat hepatocytes showed similar metabolites to those found in vivo. No meaningful differences were observed in Lipid 5 metabolism or elimination by sex. In conclusion, Lipid 5, a critical amino lipid component of LNPs for mRNA therapeutic delivery, showed minimal exposure, rapid metabolism, and near-complete elimination of 14C metabolites in rats. SIGNIFICANCE STATEMENT: Heptadecan-9-yl 8-((2-hydroxyethyl) (8-(nonyloxy)-8-oxooctyl)amino)octanoate (Lipid 5) is a key component of lipid nanoparticles used for the delivery of mRNA-based medicines; understanding the rates and routes of its clearance is crucial to assessing its long-term safety in lipid nanoparticle technology. This study conclusively established the rapid metabolism, and near-complete elimination of intravenously administered [14C]Lipid 5 in rats via both liver and kidney as oxidative metabolites derived from ester hydrolysis and subsequent β-oxidation.

Evaluation of Hepatoprotective and Nephroprotective Effect of Α- Pinene on Wistar Albino Rat

Introduction: Hepato-renal toxicity is a devastating, non-communicable disease. Because of a lack of information on low-cost management to combat the disease, this study postulates the ameliorative effect of selected phytoconstituents against toxicity. Aim and Objective: The current study reveals an active phytoconstituent, α- Pinene, that has the ability to combat the degenerative effects of CCl4. Methodology: Carbon tetrachloride (CCl4) is an organic xenobiotic molecule as well as the most potent hepatotoxic agent used (1200 mg/kg body weight; i.p.) to induce hepato-renal toxicity in experimental rats. To determine in vivo hepato-renal toxicity, three different doses (0.05 ml/kg body weight, 0.1 ml/kg body weight, and 0.15 ml/kg body weight; intraperitoneally) were chosen. Vitamin C at the dose of 250 mg/kg/p.o. was used as a standard, due to its maximum ameliorative activity against oxidative damage in CCl4-induced hepato-renal toxicity in rats. For 7 days, the animals were pre-treated with α-pinene and Vitamin C. CCl4 was charged only on the 7th day. Result and Conclusion: The related biochemical tests were studied. CCl4 intoxication reduces mitochondrial membrane potential in liver and kidney cells, which accelerates excessive intracellular ROS production, but α-pinene pretreatment successfully restores it in both liver and kidney cells. Pretreatment with α-pinene and vitamin C for 7 days increased intracellular ameliorative capability in hepatic and renal cells significantly (p 0.01). In conclusion, α-pinene is capable of restoring antioxidant status by quenching intracellular ROS. As a result, α-pinene has the potential to provide hepatoprotective and nephroprotective effects against CCl4-induced toxicity in rats.

Potential Toxic Mechanisms of Neonicotinoid Insecticides in Rice: Inhibiting Auxin-Mediated Signal Transduction.

Inappropriate application of pesticides not only causes sub-lethal effects on ecosystem service providers but also reduces crop yield and quality. As a xenobiotic signal molecule, pesticides may interact with signal transduction receptors in crops, resulting in oxidative damage and even metabolic perturbations. We discovered that three neonicotinoid insecticides (NIs), namely, imidacloprid, thiamethoxam, and clothianidin, at 0.06-0.12 kg ai/ha significantly inhibited the auxin signal pathway in rice leaves, thereby reducing the intracellular auxin (IAA) content. Molecular simulation further confirmed that NIs occupied the binding site where auxin transporter-like proteins 1 (LAX11) and 2 (LAX12), in which Thr253 and Asn66 of LAX11, as well as Thr244 and Asn57 of LAX12, were bound to the nitroguanidine of NIs via H-bonds. Meanwhile, Asn66 of LAX11 and Asn57 of LAX12 interacted with nitroguanidine via aromatic H-bonds. Moreover, phenylpropanoid biosynthesis was significantly disturbed because of the inhibited auxin signal pathway. Notably, peroxidase-coding genes were downregulated with a maximum value greater than 10-fold, resulting in decreased antioxidant metabolites flavone (37.82%) and lignin content (20.15%). Ultimately, rice biomass was reduced by up to 25.41% due to the decline in IAA content and antioxidant capacity. This study deeply explored the molecular mechanism of metabolic perturbations in crops stressed by pesticides, thus providing a scientific basis for pesticide environmental risk assessment and agricultural product safety.

Residues forming the gating regions of asymmetric multidrug transporter Pdr5 also play roles in conformational switching and protein folding

Residues forming the gating regions of asymmetric multidrug transporter Pdr5 also play roles in conformational switching and protein folding

Dermatokinetics: Advances and Experimental Models, Focus on Skin Metabolism

Numerous dermal contact products, such as drugs or cosmetics, are applied on the skin, the first protective barrier to their entrance into the organism. These products contain various xenobiotic molecules that can penetrate the viable epidermis. Many studies have shown that keratinocyte metabolism could affect their behavior by biotransformation. While aiming for detoxification, toxic metabolites can be produced. These metabolites may react with biological macromolecules often leading to sensitization reactions. After passing through the epidermis, xenobiotics can reach the vascularized dermis and therefore, be bioavailable and distributed into the entire organism. To highlight these mechanisms, dermatokinetics, based on the concept of pharmacokinetics, has been developed recently. It provides information on the action of xenobiotics that penetrate the organism through the dermal route. The purpose of this review is first to describe and synthesize the dermatokinetics mechanisms to consider when assessing the absorption of a xenobiotic through the skin. We focus on skin absorption and specifically on skin metabolism, the two main processes involved in dermatokinetics. In addition, experimental models and methods to assess dermatokinetics are described and discussed to select the most relevant method when evaluating, in a specific context, dermatokinetics parameters of a xenobiotic. We also discuss the limits of this approach as it is notably used for risk assessment in the industry where scenario studies generally focus only on one xenobiotic and do not consider interactions with the rest of the exposome. The hypothesis of adverse effects due to the combination of chemical substances in contact with individuals and not to a single molecule, is being increasingly studied and embraced in the scientific community.

The adult horn fly transcriptome and its complement of transcripts encoding cytochrome P450s, glutathione S-transferases, and esterases

The adult horn fly transcriptome and its complement of transcripts encoding cytochrome P450s, glutathione S-transferases, and esterases

Identification and Functional Analysis of Glutathione S-Transferases from Sitophilus zeamais in Olfactory Organ.

Simple SummarySitophilus zeamais is a worldwide pest that destroys many grain products, causing a loss of cereal quality and quantity resulting from its metabolites and behavior. Glutathione S-transferases (GSTs), as a group of odorant-degrading enzymes (ODEs), play an important role in degrading xenobiotic odorant molecules in insect olfactory sensing systems. However, there have been few reports about the function of the GST genes of S. zeamais in the odorant-degrading process. In this study, we characterized 13 full-length genes encoding GST sequences from S. zeamais and analyzed the expression pattern in different tissues of SzeaGSTd1. In addition, we investigated the ability of recombinant SzeaGSTd1 to degrade the volatile molecules of the host, and the data indicated that the content of capryl alcohol significantly decreased in the system. In summary, we believe SzeaGSTd1 plays a key role in the olfactory sensing system of S. zeamais.Odorant-degrading enzymes (ODEs) play an important role in rapidly degrading and inactivating odorant molecules that have completed information transmission, as well as in maintaining the stability and sensitivity of insect olfactory sensing systems. Glutathione S-transferases (GSTs), as a group of ODEs, supposedly bear the ability to catalyze the conjugation of glutathione (GSH) and xenobiotic odorant molecules in the degrading process. However, there are few reports regarding the role of the GST genes of Sitophilus zeamais in the degrading process. Thus, we characterized 13 full-length genes encoding GST sequences from S. zeamais, of which only SzeaGSTd1 contained a high abundance in the antennae. Ligand-binding assays implied that SzeaGSTd1 was able to catalyze the conjugation of GSH with 2, 4-dinitrochlorobenzene (CDNB). We investigated whether recombinant SzeaGSTd1 bears the ability to degrade the volatile molecules of the host; among the host volatiles, and found capryl alcohol to be a suitable substrate for SzeaGSTd1. These results strongly suggest that SzeaGSTd1 probably plays a role in auxiliary host location by degrading the host volatiles of capryl alcohol and exhibits a potential biological function in the olfactory sensing system of S. zeamais. Knowledge of the potential functions of SzeaGSTd1 will provide new ideas for biological control strategies for S. zeamais.

Regulation of the pleiotropic drug resistance transcription factors Pdr1 and Pdr3 in yeast

Aim: To understand how transcriptional factors Pdr1 and Pdr3, belonging to the pleiotropic drug resistance system, are activated, and regulated after introducing chemical tox- ins to the cell in the model organism Saccharomyces cere-visiae. Methods: Series of molecular methods were applied using different strains ofS. cerevisiae over-expressing proteins of interest as a eukaryotic cell model. The chemical stress in- troduced to the cell is represented by menadione. Results were obtained performing protein detection and analysis. Additionally, the regulation of the DNA binding of the tran- scriptional activators after stimulation is quantified using chromatin immunoprecipitation, employing epitope-tagged factors and real-time qPCR. Results: Our results indicated higher expression levels of the Pdr1 transcriptional factor, compared to its homolo- gous Pdr3 after treatment with menadione. The yeast-cell defence system was tested against various organic solvents to exclude the possibility of their presence potentially af- fecting the results. The results indicate that Pdr1 is most abundant after 30 minutes from the beginning of the treat- ment, compared with 240 minutes after the treatment when the function of the transcription factor is faded. It appears that Pdr1 binding to the PDR5 and SNQ2 promoters, which are both activated by Pdr1, peaks around the same time, or more precisely after 40 minutes from the start of the treatment. Conclusion: The tendency of Pdr1 reduction after its activa- tion by menadione is detected. One possibility is that Pdr1, after recognizing the xenobiotic menadione, is removed by a degradation mechanism. Given the fact that Pdr1 directly binds the xenobiotic molecule, its destruction might help the cells to remove toxic levels of menadione. It is possible that overexpressing the part of Pdr1 which recognizes me- nadione alone was sufficient to detoxify and hence produce a tolerance towards menadione.