Molecular docking: a potential tool to aid ecotoxicity testing in environmental risk assessment of pharmaceuticals

Nanoengineering of mono (Au, Ag) and bimetallic (Ag-Au) alloy nanoparticles for dye degradation and toxicity assessment

This research entails the synthesis and catalytic exploration of bimetallic nanoparticles combining silver (Ag) and gold (Au). The Au concentration was systematically varied (20%, 40%, 60%, and 80%), alongside the utilization of CTAB surfactant for nanoparticle stabilization. UV visible spectroscopic analysis confirmed the formation and stability of synthesized Au, Ag and bimetallic (Ag-Au) nanoparticles. FESEM further confirmed the formation of uniform sized Au and Ag nanoparticles. Integration of Au into Ag resulted in bimetallic (Ag-Au) alloy nanoparticles with smaller dimensions as compared to individual Au and Ag nanoparticles. EDX spectra and mapping verified the composition of each synthesized bimetallic nanoparticle variant. The catalytic potential of the synthesized nanoparticles was methodically explored using UV-visible spectroscopy. All the synthesized nanoparticles showcased excellent catalytic efficacy. The synergistic effect of the alloyed bimetallic nanoparticles was found promising. Assessment of dye toxicity pre- and post-degradation was conducted using the ECOSAR program, indicating a reduction in dye toxicity following degradation.

From Protein Sequence to Structure: The Next Frontier in Cross-Species Extrapolation for Chemical Safety Evaluations

Computational screening for potentially bioactive molecules using advanced molecular modeling approaches including molecular docking and molecular dynamic simulation is mainstream in certain fields like drug discovery. Significant advances in computationally predicting protein structures from sequence information have also expanded the availability of structures for nonmodel species. Therefore, the objective of the present study was to develop an analysis pipeline to harness the power of these bioinformatics approaches for cross-species extrapolation for evaluating chemical safety. The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool compares protein-sequence similarity across species for conservation of known chemical targets, providing an initial line of evidence for extrapolation of toxicity knowledge. However, with the development of structural models from tools like the Iterative Threading ASSEmbly Refinement (ITASSER), analyses of protein structural conservation can be included to add further lines of evidence and generate protein models across species. Models generated through such a pipeline could then be used for advanced molecular modeling approaches in the context of species extrapolation. Two case examples illustrating this pipeline from SeqAPASS sequences to I-TASSER-generated protein structures were created for human liver fatty acid-binding protein (LFABP) and androgen receptor (AR). Ninety-nine LFABP and 268 AR protein models representing diverse species were generated and analyzed for conservation using template modeling (TM)-align. The results from the structural comparisons were in line with the sequence-based SeqAPASS workflow, adding further evidence of LFABL and AR conservation across vertebrate species. The present study lays the foundation for expanding the capabilities of the web-based SeqAPASS tool to include structural comparisons for species extrapolation, facilitating more rapid and efficient toxicological assessments among species with limited or no existing toxicity data. Environ Toxicol Chem 2023;42:463-474. © 2022 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Theoretical evaluation of the malathion and its chemical derivatives interaction with cytosolic phospholipase A2 from zebrafish

Cytosolic phospholipase A2 (cPLA2) belongs to a large family of proteins and plays a crucial role in the regulation of arachidonic acid metabolism and inflammation cascade in zebrafish (Danio rerio). This enzyme with a molecular weight of 85 kDa, has two distinct domains. One is the regulatory and calcium-dependent (Ca²⁺) domain called C2, the other is the catalytic α/β hydrolase Ca²⁺-independent domain, where serine and aspartic acid catalytic dyad residues are present. We investigated the interaction of malathion and their organophosphate metabolites in the cPLA2 using in silico tools. Molecular docking results showed hydrophobic interactions with the paraoxon and catalytic site residue (Ser 223). Malathion increases intracellular Ca²⁺ due to endoplasmic reticulum influx which in turn activities phospholipase A2 and arachidonic acid release. Molecular docking and homology modelling of proteins and ligands could be a complementary tool for ecotoxicology and environment pollution assessment.

A holistic comparison of flavor signature and chemical profile in different harvesting periods of Chrysanthemum morifolium Ramat. based on metabolomics combined with bioinformatics and molecular docking strategy

Taiju and Duoju are products of Hangbaiju (HJ) obtained during different collection periods, and they have been commonly used as ingredients in tea beverages and dietary traditional Chinese medicine. This study reports an integrated strategy based on metabolomics, bioinformatics and molecular docking to further explore the effect of the harvesting period on the metabolic profile and clinical efficacy of HJ. Firstly, gas chromatography-mass spectrometry (GC-MS) and ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF/MS) were employed for non-targeted metabolomics profiling of essential oils and flavonoids. A sequential window acquisition of all theoretical fragment-ion spectra information-dependent acquisition (SWATH-IDA) bi-directionally verified (SIBDV) method was developed that integrates the advantages of both SWATH and IDA in characterizing flavonoids. Chemometric methods were then used to screen potential chemical markers. Furthermore, HJ is effective in hepatoprotective functions. Therefore, hepatocellular-carcinoma-related differentially expressed genes were obtained using bioinformatics, and the corresponding proteins were molecularly docked with diagnostic chemical markers. In total, 78 volatile oils and 63 flavonoids were tentatively identified. The results allowed the selection of 11 metabolites (5 volatile oils and 6 flavonoids), which are nominated as novel markers for material authentication of Taiju and Duoju. Additionally, two proteins associated with hepatoma were screened using bioinformatics. All six flavonoid markers with binding energies of <-5 kcal mol-1 were considered to be anti-hepatoma biomarkers. Noticeably, in Taiju, the content of hydroxygenkwanin showed a downward trend, but the content of the other five flavonoids and the five flavored volatile difference compounds had an upward trend. This bestows a unique flavor profile on Taiju, leading to differences in sensory aroma and clinical efficacy in Taiju and Duoju. In conclusion, the transformation of secondary metabolites was the dominant trend during HJ growth. These findings lay the foundation for food development and distinguishing clinical applications.

In Silico Conformation of the Drug Colchicine into Tubulin Models and Acute Phytotoxic Activity on Cucumis sativus Radicles

Many tests are used to determine the toxic activity of miscellaneous substances, and those that are simple, fast, and inexpensive are useful for screening compounds with applications in different fields. The Cucumis sativus root growth inhibition test is an example of acute toxicity determinations. On the other hand, colchicine has been used as a herbicide to generate polyploids in plant species finally reaching the environment; for this reason, colchicine could become a point of attention in ecotoxicology. This work established that Cucumis sativus, at the colchicine binding site (CBS) in tubulin, shares 100% similarity with humans. Colchicine was docked on seven Cucumis sativus computational models of the αβ-tubulin heterodimer, allowing us to understand a possible conformation in tubulin to trigger its antimitotic effect. Furthermore, an in vitro phytotoxicity assay of colchicine-treated cucumber radicles indicated a hormetic-type concentration-dependent response with macroscopic changes in radicles and hypocotyl. These results support the highly preserved grade of tubulins in several species, and using microtubule inhibitors could require attention in ecotoxicological issues. The Cucumis sativus root growth test could help evaluate small molecules (colchicine analogs), chiefly by CBS interactions, a known druggable site, still a target in the search for antimitotic compounds.

Bioactivity-guided separation of potential α-glycosidase inhibitor from clerodendranthus spicatus based on HSCCC coupled with molecular docking

Clerodendranthus Spicatus is a traditional Dais medi-edible plant and it has been proven to have good blood glucose-lowering efficacy. However, the material basis of Clerodendranthus Spicatus has not been clarified yet and therefore needs to be determined. In this paper, the effective ingredients of this medicine were purified by high-speed counter-current chromatography. Alongside, their potential hypoglycemic activity was determined by α-glucosidase inhibitory activities in vitro and molecular docking. Finally, five compounds were purified and identified as 2-caffeoyl-L-tartaric acid (1), N-(E)-caffeoyldopamine (2), rosmarinc acid (3), methyl rosmarinate (4), 6,7,8,3',4'-Pentamethoxyflavone (5). Examination of α-glucosidase inhibitory activity in vitro showed that 2-caffeoyl-L-tartaric acid and rosmarinic acid had a higher inhibitory activity than acarbose. Molecular docking indicated that the affinity energy of the identified compounds ranged from - 7.6 to - 8.6 kcal/mol, a more desirable result than acarbose (- 6.6 kcal/mol). Particularly, rosmarinc acid with the lowest affinity energy of - 8.6 kcal/mol was wrapped with 6 hydrogen bonds. Overall, α-glucosidase inhibitory activities and molecular docking suggested that rosmarinc acid was likely to be a promising hypoglycemic drug.

Molecular interactions of vinclozolin metabolites with human estrogen receptors 1GWR-α and 1QKM and androgen receptor 2AM9-β: Implication for endocrine disruption

Background: Vinclozolin (VCZ) is a widely used antifungal agent with capability to enter into the human food chain. VCZ metabolizes into seven metabolites M1-M7. Several studies have shown its effects on reprotoxicity. However, there is limited information available on the interaction of VCZ metabolites with nuclear receptors. In silico studies aimed at identifying interaction of endocrine disruptor with nuclear receptors serve a prescreening framework in risk assessment.Methods: We studied interactive potential of VCZ and its metabolites with human estrogen (ER) and androgen receptor (AR) using molecular docking method. Binding potential of VCZ and its metabolites with estrogen receptors 1GWR-α, 1QKM and androgen receptor 2AM9-β was checked by using Schrodinger Maestro 10.5. Estradiol (E2), a natural ligand of ER and AR was taken as a reference.Results: VCZ and its metabolites showed higher or similar binding efficiency on interaction with target proteins when compared with E2. VCZ and its metabolites also exhibited agonistic effect against 1GWR-α, 1QKM and 2AM9-β with strong binding potential to them.Conclusion: Some VCZ metabolites such as M4 and M5 showed higher binding potencies with 1GWR-α, 1QKM and 2AM9-β than E2. Toxicity data of VCZ is well endowed. However, endocrine disrupting potential of VCZ via nuclear receptor mediated pathway is less understood. This in silico study revealing that not only VCZ but its metabolites have potential to interact with 1GWR-α, 1QKM and 2AM9-β offers a platform for further exploration of VCZ in this direction.

Vision of a near future: Bridging the human health-environment divide. Toward an integrated strategy to understand mechanisms across species for chemical safety assessment

There is a growing recognition that application of mechanistic approaches to understand cross-species shared molecular targets and pathway conservation in the context of hazard characterization, provide significant opportunities in risk assessment (RA) for both human health and environmental safety. Specifically, it has been recognized that a more comprehensive and reliable understanding of similarities and differences in biological pathways across a variety of species will better enable cross-species extrapolation of potential adverse toxicological effects. Ultimately, this would also advance the generation and use of mechanistic data for both human health and environmental RA. A workshop brought together representatives from industry, academia and government to discuss how to improve the use of existing data, and to generate new NAMs data to derive better mechanistic understanding between humans and environmentally-relevant species, ultimately resulting in holistic chemical safety decisions. Thanks to a thorough dialogue among all participants, key challenges, current gaps and research needs were identified, and potential solutions proposed. This discussion highlighted the common objective to progress toward more predictive, mechanistically based, data-driven and animal-free chemical safety assessments. Overall, the participants recognized that there is no single approach which would provide all the answers for bridging the gap between mechanism-based human health and environmental RA, but acknowledged we now have the incentive, tools and data availability to address this concept, maximizing the potential for improvements in both human health and environmental RA.

In Silico 3D Modeling of Binding Activities

In silico three-dimensional (3D) molecular modeling tools based upon the receptor/enzyme-ligand docking simulation in protein crystal structures and/or homology modeling of receptors have been reliably used in pharmacological research and development for decades. Molecular docking methodologies are helpful for revealing facets of activation and inactivation, thus improving mechanistic understanding and predicting molecular ligand binding activity, and they can have a high level of accuracy, and have also been explored and applied in chemical risk assessment. This computational approach is, however, only applicable for chemical hazard identification situations where the specific target receptor for a given chemical is known and the crystal structure/homology model of the receptor is available.

Modification of S-Adenosyl-l-Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation

Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world's population in tropical and subtropical countries. Nonstructural protein 5 (NS5) methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S-adenosyl-l-methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2'OH, resulting in S-adenosyl-l-homocysteine (SAH). The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity) test. The 2 simulations were performed using Molecular Operating Environment (MOE) 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356) based on ΔG_binding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever.

Comparative study of diclofenac-induced embryotoxicity and teratogenesis in Xenopus laevis and Lithobates catesbeianus, using the frog embryo teratogenesis assay: Xenopus (FETAX)

Water is an increasingly deteriorated, limited natural resource due to population increase and industrialization. Also, the widespread use of pharmaceuticals in modern society leads to their presence in domestic, hospital and industrial effluents. Due to their analgesic properties, some of the most commonly used pharmaceuticals are nonsteroidal anti-inflammatory drugs (NSAIDs). High concentrations of one these products, diclofenac (DCF), have been detected in effluents and water bodies of different countries, including Mexico. Diverse studies show that trace amounts (ngL^-1 to μgL^-1) of this compound induce toxicity on aquatic organisms such as algae, microcrustaceans and fish. However, studies on its potential toxicity during development in species of commercial interest such as the American bullfrog Lithobates catesbeianus are scarce. The present study aimed to evaluate DCF-induced teratogenesis and embryotoxicity in Xenopus laevis and L. catesbeianus, a species marketed as a nutritional meat source in Mexico, using the frog embryo teratogenesis assay: Xenopus (FETAX). Oocytes in mid-blastula transition were exposed for 96h to 1, 4, 8, 16, 32 and 62.5mgDCFL^-1. The criteria evaluated were mortality, malformation and growth inhibition. The teratogenic index was 4.2 in L. catesbeianus, three-fold higher than the reference limit (1.5), and 3.9 in X. laevis. Diclofenac induced diverse malformations in both species, the most frequent of these being axial malformations in the tail and notochord, edema and stunted growth. Results indicate that DCF is a potentially teratogenic compound and is toxic during development in X. laevis and L. catesbeianus, a species which, due to its sensitivity, can be used to evaluate the toxicity of pharmaceutical products, using FETAX.

Hormesis of some organic solvents on Vibrio qinghaiensis sp.-Q67 from first binding to the β subunit of luciferase

Hormesis is a biphasic concentration–response relationship. During the luminescence inhibition test ofVibrio qinghaiensissp.-Q67 (Q67), some organic solvents display the hormesis phenomenon.

Isolation of Compounds from Sargassum wightii by GCMS and the Molecular Docking against Anti-Inflammatory Marker COX2

The study focused on the molecular docking of GC-MS isolated compounds from theSargassum wightiiagainst inflammatory marker Cycloxigenase-2 (COX2). Seven compounds isolated by GC-MS were tested for their anti-inflammatory action using insilico analysis. The crystal structure obtained from the protein data bank was docked against seven compounds and the glide score as well as glide energy were determined using Schrödinger Maestro software (version 2013.1). The results of molecular docking showed that out of the seven bioactive compounds tested, methyl salicylate, benzoic acid, 2-hydroxy-,ethyl ester, diethyl phthalate, hexadecanoic acid, ethyl ester and (E) -9-octadecenoic acid ethyl ester were effectively inhibited the COX2 protein. The ADME properties of the compounds analyzed using Qikprop version 3.6 software of Schrodinger suite and the results showed that all the compounds were biologically active and the scores were within the acceptable range. This study revealed that the possibility of using these compounds against COX2 to treat inflammation.

Application of in silico and in vitro methods in the development of adverse outcome pathway constructs in wildlife

There is a long history of using both in silico and in vitro methods to predict adverse effects in humans and environmental species where toxicity data are lacking. Currently, there is a great deal of interest in applying these methods to the development of so-called 'adverse outcome pathway' (AOP) constructs. The AOP approach provides a framework for organizing information at the chemical and biological level, allowing evidence from both in silico and in vitro studies to be rationally combined to fill gaps in knowledge concerning toxicological events. Fundamental to this new paradigm is a greater understanding of the mechanisms of toxicity and, in particular, where these mechanisms may be conserved across taxa, such as between model animals and related wild species. This presents an opportunity to make predictions across diverse species, where empirical data are unlikely to become available as is the case for most species of wildlife.

Leveraging existing data for prioritization of the ecological risks of human and veterinary pharmaceuticals to aquatic organisms

Medicinal innovation has led to the discovery and use of thousands of human and veterinary drugs. With this comes the potential for unintended effects on non-target organisms exposed to pharmaceuticals inevitably entering the environment. The impracticality of generating whole-organism chronic toxicity data representative of all species in the environment has necessitated prioritization of drugs for focused empirical testing as well as field monitoring. Current prioritization strategies typically emphasize likelihood for exposure (i.e. predicted/measured environmental concentrations), while incorporating only rather limited consideration of potential effects of the drug to non-target organisms. However, substantial mammalian pharmacokinetic and mechanism/mode of action (MOA) data are produced during drug development to understand drug target specificity and efficacy for intended consumers. An integrated prioritization strategy for assessing risks of human and veterinary drugs would leverage available pharmacokinetic and toxicokinetic data for evaluation of the potential for adverse effects to non-target organisms. In this reiview, we demonstrate the utility of read-across approaches to leverage mammalian absorption, distribution, metabolism and elimination data; analyse cross-species molecular target conservation and translate therapeutic MOA to an adverse outcome pathway(s) relevant to aquatic organisms as a means to inform prioritization of drugs for focused toxicity testing and environmental monitoring.

Occurrence, ecotoxicological effects and risk assessment of antihypertensive pharmaceutical residues in the aquatic environment--A review

This study presents a review of the investigated antihypertensives in different aquatic compartments. It aims to compare these data with those regarding ecotoxicity effects in order to find out ecotoxicological data gaps for these pharmaceuticals and to point out the need for future studies. In addition, part of this article is dedicated to the risk assessment of the parent compounds atenolol, metoprolol, propranolol and verapamil, which are of great environmental concern in terms of contamination levels and for which there are sufficient ecotoxicological data available. 79 articles were retrieved presenting quantization data for 34 different antihypertensives and/or their metabolites. Only 43 articles were found regarding acute and chronic ecotoxicological effects of antihypertensive drugs. The results indicated that the beta-blockers atenolol, metoprolol and propranolol are the antihypertensives most frequently detected in the aquatic environment. They are also the drugs which reached the highest maximum concentrations in surface waters in the data reported in the literature. The highest percentages of ecotoxicity data regarding antihypertensives were also related to these beta-blockers. On the other hand, there is clearly a lack of ecotoxicity data, especially the chronic ones, regarding other antihypertensives. The environmental risk assessment (ERA) showed that all three of the evaluated beta-blockers can pose a potential long-term risk for non-target organisms of both fresh and marine water species. However, more meaningful ecotoxicity data for antihypertensives, including saltwater species, are required to refine and enlarge these results. Additional studies focusing on potential interactions between pharmaceutical mixtures, including antihypertensives, are also an urgent need.

Are pharmaceuticals with evolutionary conserved molecular drug targets more potent to cause toxic effects in non-target organisms?

The ubiquitous use of pharmaceuticals has resulted in a continuous discharge into wastewater and pharmaceuticals and their metabolites are found in the environment. Due to their design towards specific drug targets, pharmaceuticals may be therapeutically active already at low environmental concentrations. Several human drug targets are evolutionary conserved in aquatic organisms, raising concerns about effects of these pharmaceuticals in non-target organisms. In this study, we hypothesized that the toxicity of a pharmaceutical towards a non-target invertebrate depends on the presence of the human drug target orthologs in this species. This was tested by assessing toxicity of pharmaceuticals with (miconazole and promethazine) and without (levonorgestrel) identified drug target orthologs in the cladoceran Daphnia magna. The toxicity was evaluated using general toxicity endpoints at individual (immobility, reproduction and development), biochemical (RNA and DNA content) and molecular (gene expression) levels. The results provide evidence for higher toxicity of miconazole and promethazine, i.e. the drugs with identified drug target orthologs. At the individual level, miconazole had the lowest effect concentrations for immobility and reproduction (0.3 and 0.022 mg L-1, respectively) followed by promethazine (1.6 and 0.18 mg L-1, respectively). At the biochemical level, individual RNA content was affected by miconazole and promethazine already at 0.0023 and 0.059 mg L-1, respectively. At the molecular level, gene expression for cuticle protein was significantly suppressed by exposure to both miconazole and promethazine; moreover, daphnids exposed to miconazole had significantly lower vitellogenin expression. Levonorgestrel did not have any effects on any endpoints in the concentrations tested. These results highlight the importance of considering drug target conservation in environmental risk assessments of pharmaceuticals.