Binding Specificity Determines the Cytochrome P450 3A4 Mediated Enantioselective Metabolism of Metconazole

Study on the Bioactivity, Toxicity, Stereoselective Fate, and Risk Assessment of Chiral Fungicide Isopyrazam in Five Kinds of Fruits and Vegetables

Isopyrazam (IPZ) is a new chiral fungicide. For bioactivity, there was a 3.37-1578 times difference among the four stereoisomers. For Alternaria alternata and Phoma multirostrata, cis-(1S,4R,9S)-IPZ had the greatest activity. Using cis-IPZ might improve the efficacy and reduce the dosage of the racemate by 54.7-72.2% for A. alternata and P. multirostrata. To zebrafish, trans-IPZ showed the highest acute toxicity (LC50, 0.096 mg/L). The degradation half-lives of IPZ stereoisomers in the five crops ranged from 3.50 to 15.2 days. Cis-IPZ was preferentially degraded in grape, pear, and celery. The residual concentrations of IPZ in grape and celery were still higher than the maximum residue limit, and the acute and chronic dietary intake risks of IPZ in celery were unacceptable (RQa: 146-250%, HQ: 117-200%), which were worthy of further researching. Based on the research results, it is safer and more reasonable to use IPZ in the form of a racemate with a high ratio of cis-IPZ.

Computational simulations uncover enantioselective metabolism of chiral triazole fungicides by human CYP450 enzymes: A case study of tebuconazole

Tebuconazole (TEB), a prominent chiral triazole fungicide, has been extensively utilized for plant pathogen control globally. Despite experimental evidence of TEB metabolism in mammals, the enantioselectivity in the biotransformation of R- and S-TEB enantiomers by specific CYP450s remains elusive. In this work, integrated in silico simulations were employed to unveil the binding interactions and enantioselective metabolic fate of TEB enantiomers within human CYP1A2, 2B6, 2E1, and 3A4. Molecular dynamics (MD) simulations clearly delineated the binding specificity of R- and S-TEB to the four CYP450s, crucially determining their differences in metabolic activity and enantioselectivity. The primary driving force for robust ligand binding was identified as van der Waals interactions with CYP450s, particularly involving the hydrophobic residues. Mechanistic insights derived from quantum mechanics/molecular mechanics (QM/MM) calculations established C2-methyl hydroxylation as the predominant route of R-/S-TEB metabolism, while C6-hydroxylation and triazol epoxidation were deemed kinetically infeasible pathways. Specifically, the resulting hydroxy-R-TEB metabolite primarily originates from R-TEB biotransformation by 1A2, 2E1 and 3A4, whereas hydroxy-S-TEB is preferentially produced by 2B6. These findings significantly contribute to our comprehension of the binding specificity and enantioselective metabolic fate of chiral TEB by CYP450s, potentially informing further research on human health risk assessment associated with TEB exposure.

Exploring the selectivity of cytochrome P450 for enhanced novel anticancer agent synthesis

Cytochrome P450 monooxygenases are an extensive and unique class of enzymes, which can regio- and stereo-selectively functionalise hydrocarbons by way of oxidation reactions. These enzymes are naturally occurring but have also been extensively applied in a synthesis context, where they are used as efficient biocatalysts. Recently, a biosynthetic pathway where a cytochrome P450 monooxygenase catalyses a critical step of the pathway was uncovered, leading to the production of a number of products that display high antitumour potency. In this work, we use computational techniques to gain insight into the factors that determine the relative yields of the different products. We use conformational search algorithms to understand the substrate stereochemistry. On a machine-learned 3D protein structure, we use molecular docking to obtain a library of favourable poses for substrate-protein interaction. With molecular dynamics, we investigate the most favourable poses for reactivity on a molecular level, allowing us to investigate which protein-substrate interactions favour a given product and thus gain insight into the product selectivity.

Enantioselective bioaccumulation, biotransformation and spatial distribution of chiral fungicide difenoconazole in earthworms (Eisenia fetida)

The enantioselective environmental behavior of difenoconazole, a widely utilized triazole fungicide commonly detected in agricultural soils, has yet to be comprehensively explored within the earthworm-soil system. To address this research gap, we investigated the bioaccumulation and elimination kinetics, degradation pathways, biotransformation mechanisms, spatial distribution, and toxicity of chiral difenoconazole. The four stereoisomers of difenoconazole were baseline separated and analyzed using SFC-MS/MS. Pronounced enantioselectivity was observed during the uptake phase, with earthworms exhibiting a preference for (2R,4R)-difenoconazole and (2R,4S)-difenoconazole. A total of five transformation products (TPs) were detected and identified using UHPLC-QTOF/MS in the earthworm-soil system. Four of the TPs were detected in both earthworm and soil, and one TP was produced only in eaerthwroms. Hydrolysis and hydroxylation were the primary transformation pathways of difenoconazole in both earthworms and soil. Furthermore, a chiral TP, 3-chloro, 4-hydroxy difenoconazole, was generated with significant enantioselectivity, and molecular docking results indicate the greater catalytic bioactivity of (2R,4R)- and (2R,4S)-difenoconazole, leading to the preferential formation of their corresponding hydroxylated TPs. Furthermore, Mass Spectrometry Imaging (MSI) was applied for the first time to explore the spatial distribution of difenoconazole and the TPs in earthworms, and the "secretory zone" was found to be the dominant region to uptake and biodegrade difenoconazole. ECOSAR predictions highlighted the potentially hazardous impact of most difenoconazole TPs on aquatic ecosystems. These findings are important for understanding the environmental fate of difenoconazole, evaluating environmental risks, and offering valuable insights for guiding scientific bioremediation efforts.

Exploring the binding behavior mechanism of vitamin B12 to α-Casein and β-Casein: multi-spectroscopy and molecular dynamic approaches

The aim of this study was to investigate the behavior interaction of α-Casein-B12 and β-Casein-B12 complexes as binary systems through the methods of multiple spectroscopic, zeta potential, calorimetric, and molecular dynamics (MD) simulation. Fluorescence spectroscopy denoted the role ofB12as a quencher in both cases of α-Casein and β-Casein fluorescence intensities, which also verifies the existence of interactions. The quenching constants of α-Casein-B12 and β-Casein-B12 complexes at 298 K in the first set of binding sites were 2.89 × 104 and 4.41 × 104 M-1, while the constants of second set of binding sites were 8.56 × 104 and 1.58 × 105 M-1, respectively. The data of synchronized fluorescence spectroscopy at Δλ = 60 nm were indicative of the closer location of β-Casein-B12 complex to the Tyr residues. Additionally, the binding distance between B12 and the Trp residues of α-Casein and β-Casein were obtained in accordance to the Förster's theory of nonradioactive energy transfer to be 1.95 nm and 1.85 nm, respectively. Relatively, the RLS results demonstrated the production of larger particles in both systems, while the outcomes of zeta potential confirmed the formation of α-Casein-B12 and β-Casein-B12 complexes and approved the existence of electrostatic interactions. We also evaluated the thermodynamic parameters by considering the fluorescence data at three varying temperatures. According to the nonlinear Stern-Volmer plots of α-Casein and β-Casein in the presence of B12 in binary systems, the two sets of binding sites indicated the detection of two types of interaction behaviors. Time-resolved fluorescence results revealed that the fluorescence quenching of complexes are static mechanism. Furthermore, the outcomes of circular dichroism (CD) represented the occurrence of conformational changes in α-Casein and β-Casein upon their binding to B12 as the binary system. The experimental results that were obtained throughout the binding of α-Casein-B12 and β-Casein-B12 complexes were confirmed by molecular modeling.Communicated by Ramaswamy H. Sarma.

In vitro exposure to triazoles used as fungicides impairs human granulosa cells steroidogenesis

Triazoles are the main components of fungicides used in conventional agriculture. Some data suggests that they may be endocrine disruptors. Here, we found five triazoles, prothioconazole, metconazole, difenoconazole, tetraconazole, and cyproconazole, in soil or water from the Centre-Val de Loire region of France. We then studied their effects from 0.001 µM to 1000 µM for 48 h on the steroidogenesis and cytotoxicity of ovarian cells from patients in this region and the human granulosa line KGN. In addition, the expression of the aryl hydrocarbon receptor (AHR) nuclear receptor in KGN cells was studied. Overall, all triazoles reduced the secretion of progesterone, estradiol, or both at doses that were non-cytotoxic but higher than those found in the environment. This was mainly associated, depending on the triazole, with a decrease in the expression of CYP51, STAR, CYP11A1, CYP19A1, or HSD3B proteins, or a combination thereof, in hGCs and KGN cells and an increase in AHR in KGN cells.

Enantioselective metabolism of novel chiral insecticide Paichongding by human cytochrome P450 3A4: A computational insight

As a novel chiral neonicotinoid insecticide, Paichongding (IPP) has been widely applied in agriculture due to its excellent insecticidal activity. However, the enantioselective metabolism of IPP stereoisomers (5R7R-IPP, 5S7S-IPP, 5R7S-IPP, and 5S7R-IPP) mediated by enzymes in non-target organisms, especially the cytochrome P450s (CYPs), remains unknown. To address this knowledge gap, we developed an integrated computational framework to elucidate the binding interactions and enantioselective metabolism of IPP stereoisomers in human CYP3A4. The results reveal that 5R7R-IPP shows much stronger binding affinity to CYP3A4 than 5S7S-IPP, while enantiomers 5R7S-IPP and 5S7R-IPP have no essential difference in their binding potential, owing to their specific interactions with key CYP3A4 residues. Although enantiomers 5R7R-IPP and 5S7S-IPP feature distinct binding modes resulting from the chiral differences, their transformation activities are slightly different, with C5 and C13 being the primary metabolic sites, respectively. In contrast, CYP3A4 preferably metabolizes 5R7S-IPP over 5S7R-IPP. The metabolism of epimers 5R7R-IPP and 5R7S-IPP share C5-hydroxylation routes due to the conserved 5R-conformaitons, but differ with the transformation routes at C11/C13 and C3 sites. The 7R-chirality of 5S7R-IPP significantly reduces the metabolic potency compared to 5S7S-IPP. CYP3A4-catalyzed hydroxylation and desaturation of IPP stereoisomers generate various chiral metabolites, with C5- and C13-hydroxyIPPs further transforming into depropylated products. Furthermore, the toxicity assessment reveals that IPP, along with the majority of its hydroxylated, desaturated, and depropylated metabolites, can potentially induce adverse effects on human health, specifically hepatotoxicity, respiratory toxicity, and carcinogenicity. This study provides valuable insights into the enantioselective fate of chiral IPP metabolism by CYP3A4, and the identified metabolites can serve as potential biomarkers for monitoring IPP exposure and associated health risk in human body.

Enantioselective Behaviors of Chiral Pesticides and Enantiomeric Signatures in Foods and the Environment

Unreasonable application of pesticides may result in residues in the environment and foods. Chiral pesticides consist of two or more enantiomers, which may exhibit different behaviors. This Review intends to provide progress on the enantioselective residues of chiral pesticides in foods. Among the main chiral analytical methods, high performance liquid chromatography (HPLC) is the most frequently utilized. Most chiral pesticides are utilized as racemates; however, due to enantioselective dissipation, bioaccumulation, biodegradation, and chiral conversion, enantiospecific residues have been found in the environment and foods. Some chiral pesticides exhibit strong enantioselectivity, highlighting the importance of evaluation on an enantiomeric level. However, the occurrence characteristics of chiral pesticides in foods and specific enzymes or transport proteins involved in enantioselectivity needs to be further investigated. This Review could help the production of some chiral pesticides to single-enantiomer formulations, thereby reducing pesticide consumption as well as increasing food production and finally reducing human health risks.

Maternal exposure to chiral triazole fungicide tebuconazole induces enantioselective thyroid disruption in zebrafish offspring

Pesticides could induce long-term impacts on aquatic ecosystem via transgenerational toxicity. However, for many chiral pesticides, the potential enantioselectivity of transgenerational toxicity has yet to be fully understood. In this study, we used zebrafish as models to evaluate the maternal transfer risk of tebuconazole (TEB), which is a chiral triazole fungicide currently used worldwide and has been frequently detected in surface waters. After 28-day food exposure (20 and 400 ng/g) to the two enantiomers of TEB (S- and R-TEB) in adult female zebrafish (F0), increased malformation rate and decreased swimming speed were found in F1 larvae, with R-TEB showing higher impacts than S-enantiomer. Additionally, enantioselective effects on the secretion of thyroid hormones (THs) and expression of TH-related key genes along the hypothalamic-pituitary-thyroid (HPT) axis were found in both F0 and F1 after maternal exposure. Both the two enantiomers significantly disrupted the triiodothyronine (T3) and thyroxine (T4) contents in F0 with different degrees, whereas in F1, significant effects were only found in R-TEB groups with decreasing of both T3 and T4 contents. Most of the HPT axis related genes in F0 were upregulated by TEB and more sensitive to R-TEB than to S-TEB. In contrast, most of the genes in F1 were downregulated by both R- and S-TEB, especially the genes that are primarily responsible for thyroid development and growth (Nkx2-1), TH synthesis (NIS and TSHꞵ) and metabolism (Deio1). Findings from this study highlight the key role of enantioselectivity in the ecological risk assessment of chiral pesticides through maternal transfer.

Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers

It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.

Residue, dissipation and dietary intake risk assessment of tolfenpyrad in four leafy green vegetables under greenhouse conditions

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A QuEChERS-GC–MS/MS method was used to detect tolfenpyrad in leafy green vegetables.

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Half-lives of tolfenpyrad were 2.0–6.8 d in greenhouse-grown leafy green vegetables.

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PHI of tolfenpyrad was suggested as 21 d in BCL and 28 d in BBL, SOL and LSL.

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The potential health risk of tolfenpyrad was acceptable in leafy green vegetables.

A novel and accurate analytical method for the determination of tolfenpyrad in four leafy green vegetables, Brassica bara L., Spinacia oleracea L., Lactuca sativa L. and Brassica chinensis L., was developed and applied to investigate the residue distribution and dietary risk under greenhouse conditions. The established approach was determined to be adequate, with recoveries of 79.2%–92.9% and relative standard deviations < 8%. Tolfenpyrad dissipated relatively rapidly in four leafy green vegetables. Terminal residues of tolfenpyrad were below 0.5 mg/kg (maximum residue limit for Brassica bara L. set by China) in leafy green vegetables collected 28 d after the last application. Due to risk quotient values < 100%, the residue levels of tolfenpyrad in leafy green vegetables collected 21 days after the last application were deemed safe for consumers. The results provide field data for the reasonable use and dietary risk assessment of tolfenpyrad in leafy green vegetables.

Systematic investigation of stereochemistry, stereoselective bioactivity, and antifungal mechanism of chiral triazole fungicide metconazole

In this study, the stereochemistry, stereoselective fungicidal bioactivity, and antifungal mechanism of chiral triazole fungicide metconazole were investigated. The configurations of metconazole stereoisomers were determined to be (1R, 5R)-metconazole, (1R, 5S)-metconazole, (1S, 5S)-metconazole, and (1S, 5R)-metconazole through using electronic circular dichroism spectroscopy. The bioactivities of four stereoisomers and their stereoisomer mixture toward Fusarium graminearum Schw and Alternaria triticina were found to be in the following order: (1S, 5R)-metconazole > the stereoisomer mixture > (1S, 5S)-metconazole > (1R, 5R)-metconazole > (1R, 5S)-metconazole. In addition, the fungicidal activities of (1S, 5R)-metconazole against two tested pathogens was 13.9-23.4 times higher than those of (1R, 5S)-metconazole. Molecular docking methodology was applied to characterize the docking energy and distances between Cytochrome P450 CYP51B and the metconazole stereoisomers, and (1S, 5R)-metconazole showed the strongest binding energy and the shortest distance binding to CYP51B than the other three stereoisomers. Moreover, enantioselective metabolisms of (1S, 5R)-metconazole and (1R, 5S)-metconazole by Fusarium graminearum Schw were investigated through NMR-based metabolomics. The amounts of alanine, arginine, acetate, ethanol, and dimethylamine produced in the presence of (1R, 5S)-metconazole were significantly higher than corresponding amounts in the presence of (1S, 5R)-metconazole, whereas the amounts of glucose, glycerol, glutamate, methionine, and trimethylamine formed in the presence of (1R, 5S)-metconazole were much less than those in the presence of (1S, 5R)-metconazole. This systematic investigation of metconazole stereoisomers would provide a new perception of metconazole in stereoisomeric level, including bioactivities, metabolic behaviors and antifungal mechanism.

CASTELO: clustered atom subtypes aided lead optimization-a combined machine learning and molecular modeling method

Background

Drug discovery is a multi-stage process that comprises two costly major steps: pre-clinical research and clinical trials. Among its stages, lead optimization easily consumes more than half of the pre-clinical budget. We propose a combined machine learning and molecular modeling approach that partially automates lead optimization workflow in silico, providing suggestions for modification hot spots.

Results

The initial data collection is achieved with physics-based molecular dynamics simulation. Contact matrices are calculated as the preliminary features extracted from the simulations. To take advantage of the temporal information from the simulations, we enhanced contact matrices data with temporal dynamism representation, which are then modeled with unsupervised convolutional variational autoencoder (CVAE). Finally, conventional and CVAE-based clustering methods are compared with metrics to rank the submolecular structures and propose potential candidates for lead optimization.

Conclusion

With no need for extensive structure-activity data, our method provides new hints for drug modification hotspots which can be used to improve drug potency and reduce the lead optimization time. It can potentially become a valuable tool for medicinal chemists.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04214-4.

Comparison the dissipation behaviors and exposure risk of carbendazim and procymidone in greenhouse strawberries under different application method: Individual and joint applications

The dissipation behaviors and exposure risks of individual and joint application of procymidone and carbendazim in greenhouse strawberries were studied. The initial concentrations were similar after individual or joint applications, while the dissipation half-lives and finial concentrations were significantly different. After joint application, the dissipation half-lives of procymidone and carbendazim were 12.9 and 16.0 days, respectively, which were about 1.8 times higher than those after individual application. Furthermore, the final residues under joint application condition were 1.8-3.5 times higher than those under individual application condition. The joint application decreased the dissipation rates of procymidone or carbendazim in strawberries, and increased the final residue concentrations. The dietary intake risks of procymidone and carbendazim (whether applied individually or jointly) were no higher than 0.12, which were acceptable for human health. This work would shed a light for the guidance of the joint application and risk assessment of the typical fungicides in strawberry.

A review on the stereospecific fate and effects of chiral conazole fungicides

The production and use of chiral pesticides are triggered by the need for more complex molecules capable of effectively combating a greater spectrum of pests and crop diseases, while sustaining high production yields. Currently, chiral pesticides comprise about 30% of all pesticides in use; however, some pesticide groups such as conazole fungicides (CFs) consist almost exclusively of chiral compounds. CFs are produced and field-applied as racemic (1:1) mixtures of two enantiomers (one chiral center in the molecule) or four diastereoisomers, i.e., two pairs of enantiomers (two chiral centers in the molecule). Research on the stereoselective environmental behavior and effects of chiral pesticides such as CFs has become increasingly important within the fields of environmental chemistry and ecotoxicology. This is motivated by the fact that currently, the fate and effects of chiral pesticides such as CFs that arise due to their stereoselectivity are not fully understood and integrated into risk assessment and regulatory decisions. In order to fill this gap, a summary of the state-of-the-art literature related to the stereospecific fate and effects of CFs is needed. This will also benefit the agrochemistry industry as they enhance their understanding of the environmental implications of CFs which will aid future research and development of chiral products. This review provides a collection of >80 stereoselective studies for CFs related to chiral analytical methods, fungicidal activity, non-target toxicity, and behavior of this broadly used pesticide class in the soil environment. In addition, the review sheds more light on mechanisms behind stereoselectivity, considers possible agricultural and environmental implications, and suggests future directions for the safe use of chiral CFs and the reduction of their environmental footprint.

Dioxybenzone triggers enhanced estrogenic effect via metabolic activation: in silico, in vitro and in vivo investigation

Dioxybenzone is widely used in cosmetics and personal care products and frequently detected in multiple environmental media and human samples. However, the current understanding of the metabolic susceptibility of dioxybenzone and the potential endocrine disruption through its metabolites in mimicking human estrogens remains largely unclear. Here we investigated the in vitro metabolism of dioxybenzone, detected the residue of metabolites in rats, and determined the estrogenic disrupting effects of these metabolites toward estrogen receptor α (ERα). In vitro metabolism revealed two major metabolites from dioxybenzone, i.e., M1 through the demethylation of methoxy moiety and M2 through hydroxylation of aromatic carbon. M1 and M2 were both rapidly detected in rat plasma upon exposure to dioxybenzone, which were then distributed into organs of rats in the order of livers > kidneys > uteri > ovaries. The 100 ns molecular dynamics simulation revealed that M1 and M2 formed hydrogen bond to residue Leu387 and Glu353, respectively, on ERα ligand binding domain, leading to a reduced binding free energy. M1 and M2 also significantly induced estrogenic effect in comparison to dioxybenzone as validated by the recombinant ERα yeast two-hybrid assay and uterotrophic assay. Overall, our study revealed the potential of metabolic activation of dioxybenzone to induce estrogenic disrupting effects, suggesting the need for incorporating metabolic evaluation into the health risk assessment of benzophenones and their structurally similar analogs.

Computational Approaches in Preclinical Studies on Drug Discovery and Development

Because undesirable pharmacokinetics and toxicity are significant reasons for the failure of drug development in the costly late stage, it has been widely recognized that drug ADMET properties should be considered as early as possible to reduce failure rates in the clinical phase of drug discovery. Concurrently, drug recalls have become increasingly common in recent years, prompting pharmaceutical companies to increase attention toward the safety evaluation of preclinical drugs. In vitro and in vivo drug evaluation techniques are currently more mature in preclinical applications, but these technologies are costly. In recent years, with the rapid development of computer science, in silico technology has been widely used to evaluate the relevant properties of drugs in the preclinical stage and has produced many software programs and in silico models, further promoting the study of ADMET in vitro. In this review, we first introduce the two ADMET prediction categories (molecular modeling and data modeling). Then, we perform a systematic classification and description of the databases and software commonly used for ADMET prediction. We focus on some widely studied ADMT properties as well as PBPK simulation, and we list some applications that are related to the prediction categories and web tools. Finally, we discuss challenges and limitations in the preclinical area and propose some suggestions and prospects for the future.

Elucidating the potential neurotoxicity of chiral phenthoate: Molecular insight from experimental and computational studies

Chiral organophosphorus pollutants are existed ubiquitously in the ecological environment, but the enantioselective toxicities of these nerve agents to humans and their molecular bases have not been fully elucidated. Using experimental and computational approaches, this story was to explore the neurotoxic response process of the target acetylcholinesterase (AChE) to chiral phenthoate and further decipher the microscopic mechanism of such toxicological effect at the enantiomeric level. The results showed that the toxic reaction of AChE with chiral phenthoate exhibited significant enantioselectivity, and (R)-phenthoate (K＝1.486 × 10⁵ M^-1) has a bioaffinity for the nerve enzyme nearly three times that of (S)-phenthoate (K＝4.503 × 10⁴ M^-1). Dynamic research outcomes interpreted the wet experiments, and the inherent conformational flexibility of the target enzyme has a great influence on the enantioselective neurotoxicological action processes, especially reflected in the conformational changes of the three key loop regions (i.e. residues His-447, Gly-448, and Tyr-449; residues Gly-122, Phe-123, and Tyr-124; and residues Thr-75, Leu-76, and Tyr-77) around the reaction patch. This was supported by the quantitative results of conformational studies derived from circular dichroism spectroscopy (α-helix: 34.7%→30.2%/31.6%; β-sheet: 23.6%→19.5%/20.7%; turn: 19.2%→22.4%/21.9%; and random coil: 22.5%→27.9%/25.8%). Meanwhile, via analyzing the modes of toxic action and free energies, we can find that (R)-phenthoate has a strong inhibitory effect on the enzymatic activity of AChE, as compared with (S)-phenthoate, and electrostatic energy (-23.79/－17.77 kJ mol^-1) played a critical role in toxicological reactions. These points were the underlying causes of chiral phenthoate displaying different degrees of enantioselective neurotoxicity.

Structural Basis of the Potential Binding Mechanism of Remdesivir to SARS-CoV-2 RNA-Dependent RNA Polymerase

Starting from late 2019, the coronavirus disease 2019 (COVID-19) has emerged as a once-in-a-century pandemic with deadly consequences, which urgently calls for new treatments, cures, and supporting apparatuses. Recently, because of its positive results in clinical trials, remdesivir was approved by the Food and Drug Administration to treat COVID-19 through Emergency Use Authorization. Here, we used molecular dynamics simulations and free energy perturbation methods to study the inhibition mechanism of remdesivir to its target SARS-CoV-2 virus RNA-dependent RNA polymerase (RdRp). We first constructed the homology model of this polymerase based on a previously available structure of SARS-CoV NSP12 RdRp (with a sequence identity of 95.8%). We then built a putative preinsertion binding structure by aligning the remdesivir + RdRp complex to the ATP bound poliovirus RdRp without the RNA template. The putative binding structure was further optimized with molecular dynamics simulations. The resulting stable preinsertion state of remdesivir appeared to form hydrogen bonds with the RNA template when aligned with the newly solved cryo-EM structure of SARS-CoV-2 RdRp. The relative binding free energy between remdesivir and ATP was calculated to be -2.80 ± 0.84 kcal/mol, where remdesivir bound much stronger to SARS-CoV-2 RdRp than the natural substrate ATP. The ∼100-fold improvement in the K_d from remdesivir over ATP indicates an effective replacement of ATP in blocking of the RdRp preinsertion site. Key residues D618, S549, and R555 are found to be the contributors to the binding affinity of remdesivir. These findings suggest that remdesivir can potentially act as a SARS-CoV-2 RNA-chain terminator, effectively stopping its RNA replication, with key residues also identified for future lead optimization and/or drug resistance studies.

Structural Basis of the Potential Binding Mechanism of Remdesivir to SARS-CoV-2 RNA-Dependent RNA Polymerase

Starting from late 2019, the coronavirus disease 2019 (COVID-19) has emerged as a once-in-a-century pandemic with deadly consequences, which urgently calls for new treatments, cures, and supporting apparatuses. Recently, because of its positive results in clinical trials, remdesivir was approved by the Food and Drug Administration to treat COVID-19 through Emergency Use Authorization. Here, we used molecular dynamics simulations and free energy perturbation methods to study the inhibition mechanism of remdesivir to its target SARS-CoV-2 virus RNA-dependent RNA polymerase (RdRp). We first constructed the homology model of this polymerase based on a previously available structure of SARS-CoV NSP12 RdRp (with a sequence identity of 95.8%). We then built a putative preinsertion binding structure by aligning the remdesivir + RdRp complex to the ATP bound poliovirus RdRp without the RNA template. The putative binding structure was further optimized with molecular dynamics simulations. The resulting stable preinsertion state of remdesivir appeared to form hydrogen bonds with the RNA template when aligned with the newly solved cryo-EM structure of SARS-CoV-2 RdRp. The relative binding free energy between remdesivir and ATP was calculated to be -2.80 ± 0.84 kcal/mol, where remdesivir bound much stronger to SARS-CoV-2 RdRp than the natural substrate ATP. The ∼100-fold improvement in the Kd from remdesivir over ATP indicates an effective replacement of ATP in blocking of the RdRp preinsertion site. Key residues D618, S549, and R555 are found to be the contributors to the binding affinity of remdesivir. These findings suggest that remdesivir can potentially act as a SARS-CoV-2 RNA-chain terminator, effectively stopping its RNA replication, with key residues also identified for future lead optimization and/or drug resistance studies.

Enantioselective behaviors of cis-epoxiconazole in vegetables-soil-earthworms system by liquid chromatography-quadrupole-time-of-flight mass spectrometry

Cis-epoxiconazole is a widely used triazole fungicide for control and prevention of a series of fungal diseases in fruits, vegetables, teas and grains. The present work aimed at exploring enantioselective behavior of cis-epoxiconazole in the vegetable-soil-earthworm system. Firstly, the absolute configuration of cis-epoxiconazole enantiomers was ascertained. Secondly, enantioselective degradation of cis-epoxiconazole in cabbage, pakchoi and pepper were performed under field trials, which has not been previously reported. Enantioselective degradation occurred in cabbage and pepper samples. 2R, 3S-(+)-cis-epoxiconazole was degraded faster than 2S, 3R-(-)-cis-epoxiconazole in cabbage, while the reversed results were obtained in pepper. No enantioselective degradation was observed in pakchoi. Finally, soil is the principal reservoir of environmental pesticides, so the enantioselective behaviors of cis-epoxiconazole in soil and soil organism (earthworm, Eisenia fetida) were evaluated. Similar bioaccumulation curves in earthworms and degradation curves in soil were observed under the exposure levels of 1 and 10 mg/kg. Accumulation factors (AFs) indicated earthworms had weak bioaccumulation potential to cis-epoxiconazole in the contaminated soil, and no obvious enantioselectivity was observed. The different enantioselectivities in different vegetables illuminated that preferentially enriched enantiomer might impose higher risk on human health than the other one, and the high risk enantiomer required further assessment. These results may reduce the uncertainty of cis-epoxiconazole to the environmental risk assessment.

Enantioselective Olfactory Effects of the Neonicotinoid Dinotefuran on Honey Bees (Apis mellifera L.)

Sublethal exposure to neonicotinoids affects honey bee olfaction, but few studies have investigated the sublethal effects of the enantioselective neonicotinoid dinotefuran on honey bee olfaction. This study assessed the sublethal olfactory toxicity of dinotefuran enantiomers to honey bees. Compared to R-dinotefuran, S-dinotefuran had higher acute oral toxicity, sucrose sensitivity effects, octopamine concentrations, lower learning ability, and memory effects on honey bees. High-throughput circular RNA sequencing of the honey bee brain revealed that R-dinotefuran caused more gene regulatory changes than S-dinotefuran. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses demonstrated that the SERCA, Kca, and Maxik genes may be related to the enantioselective effects of dinotefuran isomers on honey bee olfaction. These results indicated that the current ecotoxicological safety knowledge about chiral dinotefuran effects on honey bees should be amended.

Evaluation of the toxicity of 5-fluorouracil on three digestive enzymes from the view of side effects

Among the side effects of 5-fluorouracil (5-FU), the performance of the gastrointestinal reactions is faster and more obvious than others. In this work, the effects of 5-FU on the activities and conformational structures of the important digestive enzymes including α-amylase, pepsin and trypsin were studied to analyze the mechanism of the gastrointestinal adverse effects causing by 5-FU binding. The results showed that the enzymatic activity of pepsin was obviously reduced by the presence of 5-FU that bound directly to the enzyme activity cavity site. The molecular modeling and fluorescence quenching data indicated that the hydrophobic, polar and hydrogen bonding forces were involved in the ground state complex formation between proteases and 5-FU. In addition, 5-FU changed the tertiary structures of α-amylase, pepsin, and trypsin.

Parameterization of Molybdenum Disulfide Interacting with Water Using the Free Energy Perturbation Method

Water contact angles (WCA) are often used to parametrize force field parameters of novel 2D nanomaterials, such as molybdenum disulfide (MoS₂), which has emerged as a promising nanomaterial in many biomedical applications due to its unique and impressive properties. However, there is a wide range of water-MoS₂ contact angles in the literature depending on the aging process on the surface of a MoS₂ nanosheet and/or substrate material. In this study, we revisit and optimize existing parameters for the basal plane of MoS₂ with two popular water models, TIP3P and SPC/E, using the wide range of WCAs from various experiments. We develop and deploy the free energy perturbation method for parametrizing MoS₂ with experimentally determined WCAs for both fresh and aged surfaces. Energy decomposition analysis on the simulation trajectories reveals that MoS₂-water interaction is dominated by van der Waals interaction, which mainly comes from the top layer of MoS₂. We conclude that to describe both fresh and aged MoS₂ surfaces it is convenient to only adjust the Lennard-Jones parameter ε_S (the depth of the potential well of a sulfur atom), which displays a surprisingly linear correlation with WCAs.

Stereoselective toxicity of metconazole to the antioxidant defenses and the photosynthesis system of Chlorella pyrenoidosa

Metconazole (MEZ) is a broad-spectrum fungicide with four optical stereoisomers. Compared to traditional fungicides, it achieves better control effect at lower dosages. However, its toxicity to non-target organisms has rarely been investigated. This study investigated the stereoselective toxicity of metconazole to Chlorella pyrenoidosa (C. pyrenoidosa). The results indicate that the presence of the racemate and four stereoisomers of MEZ caused a sudden increase of reactive oxygen species (ROS). This in turn stimulated antioxidant defense, impaired photosynthesis and responses of subcellular structure, and eventually inhibited cell growth. The 96 h-EC₅₀ of the racemate, cis-1R,5S-MEZ, cis-1S,5R-MEZ, trans-1S,5S-MEZ, and trans-1R,5R-MEZ were 0.058, 0.182, 0.129, 0.032, and 0.038 mg/L, respectively. Furtheromre, the generation of ROS, antioxidant response, and the loss of photosynthetic function in C. pyrenoidosa were all preferentially trans-1S,5S-MEZ induced. These results aid the understanding of the stereoselective effects of chiral pesticides on C. pyrenoidosa. Such stereoselective differences must be considered when assessing the risk of metconazole to environment.

Mechanistic understanding and binding analysis of two-dimensional MoS2 nanosheets with human serum albumin by the biochemical and biophysical approach

With the advent of molybdenum disulfide nanosheets (MoS₂ NSs) for biological applications, their complex interactions with human serum albumin (HSA) need to be understood in great detail for the molecular mechanisms of protein structure and activity. It was observed that MoS₂ NSs quench the intrinsic fluorescence of HSA as a consequence of ground-state complex formation by the electron transfer, van der Waals, and hydrophobic forces. The presence of MoS₂ NSs partly altered the conformation of HSA and destroyed the binding domain of HSA with bilirubin. In addition, MoS₂ NSs can decrease the rate of the formation of beta sheet structures of HSA, reduce the non-enzymatic glycosylation, and increase the esterase-like activity of HSA. We hope that the present study will be helpful to understand the fundamental interactions of the two-dimensional materials with various biomacromolecules in human blood.

Enantioselective thyroid disruption in zebrafish embryo-larvae via exposure to environmental concentrations of the chloroacetamide herbicide acetochlor

Acetochlor (ACT) is a chiral chloroacetamide pesticide that has been heavily used around the world, resulting in its residues being frequently found in surface waters. It has been reported that ACT is an endocrine disrupting chemical (EDC) with strong thyroid hormone-disrupting activity in aquatic organisms. However, the enantioselectivity underlying thyroid disruption has yet to be understood. In this study, using a zebrafish embryo-larvae model, the enantioselective thyroid disruption of ACT was investigated at a series of environmentally relevant concentrations (1, 2, 10 and 50 μg/L). Our results showed that both racemic ACT and its enantiomers significantly increased the malformation rates of embryos at 72 h postfertilization (hpf). Decreased thyroxine (T₄) contents and increased triiodothyronine (T₃) contents were found in larvae at 120 hpf, with (+)-S-ACT exhibiting a greater effect than (-)-R-enantiomer. Similarly, (+)-S-ACT also showed a stronger effect on the mRNA expressions of thyroid hormone receptors (TRα and TRβ), deiodinase2 (Dio2) and thyroid-stimulating hormone-β (TSHβ) genes. The observed enantioselectivity in TR expressions was consistent with that of in silico binding analysis, which suggested that (+)-S-enantiomer binds more potently to the TRs than (-)-R-enantiomer. In general, ACT enantiomers showed different influences on the secretion of THs, expression of TH-related key genes and binding affinity to TRs. Considering the different toxicity of different enantiomers, our study highlights the importance of enantioselectivity in understanding of thyroid disruption effects of chiral pesticides.

Molecular characterization of the effects of Ganoderma Lucidum polysaccharides on the structure and activity of bovine serum albumin

The investigation about polysaccharides-protein system is attributed to numerous very important applications for pharmaceutical, food, chemical and other industries. In the present work, multi-spectral methods and molecular docking were used to analyze the molecular interactions of polysaccharides from Ganoderma Lucidum (GLP) with bovine serum albumin (BSA). The nonenzymatic glucosylation, fibrillation, thermal stability, and structure information of GLP-BSA system were also studied. The results showed that the formation of GLP-BSA complex by mainly hydrogen-bonding forces resulted in the conformational changes of protein. GLP acted as a stabilizer to increase the thermal stability of BSA solution having a novel and more stable conformational state during the thermal denaturation process. 8-anilino-1-naphthalenesulfonic acid (ANS) fluorescence spectral results suggested that there exist some intermediate state which has low binding ability with ANS in the presence of GLP. The presence of GLP caused a decrease in the formation of beta sheet structures with a lower rate. The fluorescence spectra of BSA glycosylated by GLP confirmed the formation of covalent bonds between BSA and GLP through the Maillard reaction which was also confirmed by using thermogravimetric (TGA) and Fourier transform infrared (FTIR) analysis. In addition, BSA still maintains the esterase-like good activity in the presence of GLP. These results provide a basis for screening the molecular interactions of polysaccharides with protein from the perspective of important food active ingredients.

Ligand Access Channels in Cytochrome P450 Enzymes: A Review

Quantitative structure-activity relationships may bring invaluable information on structural elements of both enzymes and substrates that, together, govern substrate specificity. Buried active sites in cytochrome P450 enzymes are connected to the solvent by a network of channels exiting at the distal surface of the protein. This review presents different in silico tools that were developed to uncover such channels in P450 crystal structures. It also lists some of the experimental evidence that actually suggest that these predicted channels might indeed play a critical role in modulating P450 functions. Amino acid residues at the entrance of the channels may participate to a first global ligand recognition of ligands by P450 enzymes before they reach the buried active site. Moreover, different P450 enzymes show different networks of predicted channels. The plasticity of P450 structures is also important to take into account when looking at how channels might play their role.