QSAR Toolbox Research Articles

Safety evaluation and modulatory effects on innate immune system of pyrazoline-derived compounds.

Pyrazolines are compounds that have been studied for their strong biological potential and structure diversity. Several studies demonstrated their biological effectiveness, highlighting their anti-inflammatory potential. This study aimed to evaluate the physicochemical profile, the safety, and the anti-inflammatory effects of four pyrazolines (PH0, PH3, PH4, and PH7). Initially, in silico analysis were performed on SwissADME and QSAR Toolbox platforms. The anti-inflammatory activity was assessed by in vitro and in vivo methodologies. Neutrophils collected from mice peritoneum and macrophages immortalized cell line (Raw 264.7) were stimulated with lipopolysaccharide (LPS), and subsequent measurement of nitric oxide (NO) and IL-1β, TNF, and IL-6 cytokines were performed by ELISA method. The effect on cell migration was evaluated by chemotaxis assay. The effect on efferocytosis was investigated using senescent neutrophils and macrophages from mice's bone marrow. The in silico results suggest suitable properties for a pharmacological prototype for oral administration, with no significant toxic effects. All compounds significantly reduced NO levels, as well as levels of IL-1β, TNF, and IL-6 cytokines. Also, they were able to reduce cell migration and increase efferocytosis. The in vivo air pouch model confirmed the effects of pyrazolines on cell kinetics and on the levels of cytokines (IL-1β and TNF) on the air pouch lavage. All of the pyrazolines evaluated showed to have positive effects on mechanisms that modulate the inflammatory response. Furthermore, the in silico analysis suggests that chemical changes in the structure can lead to improvement of the biological and pharmacokinetics proprieties.

Physicochemical, medicinal chemistry, and ADMET characteristics of bee antimicrobial peptides as natural bio-preservatives to extend food shelf life: a roadmap for food safety regulation

Antimicrobial peptides (AMPs) are gaining popularity as potential substitutes for conventional antibiotics and bio-preservatives in response to an increase in antimicrobial resistance cases. However, their poor pharmacokinetic profiles limit their applicability. This study using ADMETlab, OECD QSAR toolbox, and VEGA HUB virtual environments profiled 82 peptide sequences of seven bee antimicrobial peptides (BAMPs: abaecin, apamin, apisimin, apidaecin, defensin, hymenoptaecin, and melittin) using 81 descriptors combining physicochemical, medicinal chemistry, ADMET, and toxicophore criteria. BAMPs adhere to key drug-like physicochemical features and drug-ability regulations set forth by pharmaceutical giants, including Lipinski, Pfizer, and GlaxoSmithKline. BAMPs have been predicted to demonstrate favorable cell permeability, high water solubility, oral bioavailability, no blood-brain barrier penetration, oral and intestinal absorption, excretion, and a high therapeutic index. They function as non-substrates of p-glycoprotein and do not alter the pharmacokinetic effects of P-gp substrates. None of BAMPs were found to inhibit cytochrome P450 enzymes, indicating their potential to promote drug clearance and metabolism. BAMPs are safe from adverse reactions, free of respiratory toxicity, hERG blockers, hepatotoxicity, sensitizers, carcinogens, and mutagens. They are non-corrosive, non-irritating to the eyes, non-bioaccumulative, non-ecotoxic, antibacterial, antifungal, and antiviral, low toxic with no toxicophore or PAINS alerts recorded. They are non-toxic to various receptors, including gonadal and stress receptors, PPAR-γ, mitochondrial membrane receptor, heat shock element, and p53. Seven BAMPs have been tested for their drug-like properties, supporting their potential as potential leads for the pharmaceutical and food industries as antimicrobial agents and bio-preservatives. Future studies should optimize bee peptide expression in biological systems.

A novel integrated testing strategy (ITS) for evaluating acute fish toxicity with new approach methodologies (NAMs)

Acute fish toxicity (AFT) tests are performed in aquatic risk assessments of chemical compounds globally. However, the specific endpoint of in vivo AFT is based on the lethal concentration 50 (LC50), which is a serious challenge in terms of animal welfare. To support the 3Rs principle of replacing, reducing, and refining use of animals, integrated testing strategies (ITS) have recently been developed for environmental risk assessment. ITS efficiently integrates multiple types of information, especially new approach methodologies (NAMs), and further supports regulatory decision-making. Currently, an effective ITS framework for evaluating aquatic toxicity is lacking. Therefore, we aimed to develop a promising ITS for AFT using in silico, in vitro, and in vivo data. We established the ITS via in silico (OECD QSAR Toolbox 4.6), fish cell line acute toxicity (FCT), and fish embryo acute toxicity (FET) tests and then validated the NAMs with AFT testing. The NAM data were derived from the European Chemicals Agency (ECHA) dossier, toxicology databases, peer-reviewed research articles, and this study. For the first step in the ITS process, we aimed to design a high-throughput screening tool to identify non-toxic and toxic chemicals. We found that results of in silico, FCT, and FET tests alone were strongly correlated with AFT. Among the models, the in silico model was most suitable for identifying toxicants due to its high sensitivity and minimal animal use. Next, considering regulatory purposes and flexibility, we determined the predictive LC50 of toxic chemicals by pursuing a preference-dependent strategy, sequential testing strategy, and sensitivity-dependent strategy. All the strategies demonstrated a predictive power equal to or greater than 73%. In addition, to meet user preferences, our ITS approach has high flexibility and supports animal welfare and environmental protection. We have therefore developed multiple powerful, flexible, and more humane ITS methods for acute fish toxicity assessment by integrating NAMs.

Evaluating the consistency of judgments derived through both in silico and expert application of the Cramer classification scheme

The Cramer classification scheme has emerged as one of the most extensively-adopted predictive toxicology tools, owing in part to its employment for chemical categorisation within threshold of toxicological concern evaluation. The characteristics of several of its rules have contributed to inconsistencies with respect to degree of hazard attributed to common (particularly food-relevant) substances. This investigation examines these discrepancies, and their origins, raising awareness of such issues amongst users seeking to apply and/or adapt the rule-set.A dataset of over 3000 compounds was assembled, each with Cramer class assignments issued by up to four groups of industry and academic experts. These were complemented by corresponding outputs from in silico implementations of the scheme present within Toxtree and OECD QSAR Toolbox software, including a working of a “Revised Cramer Decision Tree”. Consistency between judgments was assessed, revealing that although the extent of inter-expert agreement was very high (≥97%), general concordance between expert and in silico calls was more modest (∼70%). In particular, 22 chemical groupings were identified to serve as prominent sources of disagreement, the origins of which could be attributed either to differences in subjective interpretation, to software coding anomalies, or to reforms introduced by authors of the revised rules.

In Silico Identification of Potential Inhibitors of SARS-CoV-2 Main Protease (Mpro).

The ongoing Coronavirus Disease 19 (COVID-19) pandemic has had a profound impact on the global healthcare system. As the SARS-CoV-2 virus, responsible for this pandemic, continues to spread and develop mutations in its genetic material, new variants of interest (VOIs) and variants of concern (VOCs) are emerging. These outbreaks lead to a decrease in the efficacy of existing treatments such as vaccines or drugs, highlighting the urgency of new therapies for COVID-19. Therefore, in this study, we aimed to identify potential SARS-CoV-2 antivirals using a virtual screening protocol and molecular dynamics simulations. These techniques allowed us to predict the binding affinity of a database of compounds with the virus Mpro protein. This in silico approach enabled us to identify twenty-two chemical structures from a public database (QSAR Toolbox Ver 4.5 ) and ten promising molecules from our in-house database. The latter molecules possess advantageous qualities, such as two-step synthesis, cost-effectiveness, and long-lasting physical and chemical stability. Consequently, these molecules can be considered as promising alternatives to combat emerging SARS-CoV-2 variants.

Assessment of performance of the profilers provided in the OECD QSAR toolbox for category formation of chemicals

Growing restrictions and bans on animal testing for chemical safety assessment under different regulations have led to an increasing use of alternative methods. Read-across is one of the major approaches used for this purpose, which relies on the identification of toxicological hazards of a data-poor or untested (target) chemical from data on other already-tested (source) similar chemicals. This requires the target substance to be first assigned to a group or category of ‘similar’ chemicals. The ‘similarity’ may be in terms of structural features alone, or in combination with certain rules that are based on mechanistic and/or toxicological aspects. In this regard, the OECD QSAR toolbox—a major free-access in silico platform—is widely used to derive toxicity predictions for a range of (eco) toxicological endpoints. The Toolbox allows the user to identify a set of similar chemicals (analogues) by computational ‘profilers’ that incorporate different structural alerts, or a combination of structural alerts and physicochemical and/or toxicokinetic rules relevant to a specific toxicological endpoint. The overall aim of this study was to assess the performance of the in silico profilers provided in the OECD QSAR Toolbox for reliability for identifying chemical analogues for category formation in a number of high-quality databases on mutagenicity, carcinogenicity, and skin sensitisation. The study also aimed to identify the reasons for any limitations in the performance of the profilers, and propose ways to improve their overall accuracy. The results showed that whilst some structural alerts are fit-for-purpose as such within the acceptable limits, others need refinement or a consideration for their possible exclusion from the profiler. Such refinements are imperative for a reliable use of the profilers in read-across and grouping/categorisation for classification, labelling and risk assessment of chemicals.

Combining QSAR and SSD to predict aquatic toxicity and species sensitivity of pyrethroid and organophosphate pesticides

ABSTRACT The widespread use of pyrethroid and organophosphate pesticides necessitates accurate toxicity predictions for regulatory compliance. In this study QSAR and SSD models for six pyrethroid and four organophosphate compounds using QSAR Toolbox and SSD Toolbox have been developed. The QSAR models, described by the formula 48 h-EC50 or 96 h-LC50 = x + y * log Kow, were validated for predicting 48 h-EC50 values for acute Daphnia toxicity and 96 h-LC50 values for acute fish toxicity, meeting criteria of n ≥10, r 2 ≥0.7, and Q 2 >0.5. Predicted 48 h-EC50 values for pyrethroids ranged from 3.95 × 10−5 mg/L (permethrin) to 8.21 × 10−3 mg/L (fenpropathrin), and 96 h-LC50 values from 3.89 × 10−5 mg/L (permethrin) to 1.68 × 10−2 mg/L (metofluthrin). For organophosphates, 48 h-EC50 values ranged from 2.00 × 10−5 mg/L (carbophenothion) to 3.76 × 10−2 mg/L (crufomate) and 96 h-LC50 values from 3.81 × 10−3 mg/L (carbophenothion) to 12.3 mg/L (crufomate). These values show a good agreement with experimental data, though some, like Carbophenothion, overestimated toxicity. HC05 values, indicating hazardous concentrations for 5% of species, range from 0.029 to 0.061 µg/L for pyrethroids and 0.030 to 0.072 µg/L for organophosphates. These values aid in establishing environmental quality standards (EQS). Compared to existing EQS, HC05 values for pyrethroids were less conservative, while those for organophosphates were comparable.

In Silico Phototoxicity Prediction of Drugs and Chemicals by using Derek Nexus and QSAR Toolbox.

Phototoxicity testing is crucial for evaluating the potential harmful effects of pharmaceuticals and chemicals on human skin when exposed to sunlight. Traditional in vivo models involving mice, rats, guinea pigs, as well as in vitro assays such as the 3T3 Neutral Red Uptake phototoxicity assay and methods based on the use of reconstructed human epidermis, have been established for phototoxicity testing. While these approaches are extremely valuable, they are costly in terms of both time and resources. Consequently, in silico approaches based on the use of predictive software tools can offer more rapid and cost-effective phototoxicity screening solutions. With this goal in mind, the current study evaluated two in silico tools - Derek Nexus 6.1.0/Derek Knowledge Base 2020 1.0 (Lhasa Limited, UK) and the QSAR Toolbox (v 4.5) developed by the Organisation for Economic Co-operation and Development (OECD) - for their capacity to predict the phototoxicity of several substances from diverse classes. Derek Nexus and the QSAR Toolbox were both found to be very useful for predicting the phototoxicity of drugs and other chemicals. Derek Nexus predicted phototoxicity of the compounds, with a sensitivity of 63%, specificity of 93%, Positive Predictive Values of 90% and Negative Predictive Value of 69%, overall accuracy of 77% and balanced accuracy of 78%. The QSAR Toolbox achieved sensitivity of 73%, specificity of 85%, Positive Predictive Value of 85% and Negative Predictive Value of 74%, overall accuracy of 79% and balanced accuracy of 79%. The results show that Derek Nexus and the QSAR Toolbox can be usefully incorporated in the workflow of phototoxicity testing for pharmaceuticals and chemicals.

Metabolism of alcohol ethoxylates (AEs) in rat, hamster, and human hepatocytes and liver S9: a pilot study for metabolic stability, metabolic pathway, and metabolites identification in vitro and in silico

Alcohol ethoxylates (AEs) are a well-known class of non-ionic surfactants widely used by the personal care market. The aim of this study was to evaluate and characterize the in vitro metabolism of AEs and identify metabolites. Five selected individual homologue AEs (C8EO4, C10EO5, C12EO4, C16EO8, and C18EO3) were incubated using human, rat, and hamster liver S9 fraction and cryopreserved hepatocytes. LC–MS was used to identify metabolites following the incubation of AEs by liver S9 and hepatocytes of all three species. All AEs were metabolized in these systems with a half-life ranging from 2 to 139 min. In general, incubation of AE with human liver S9 showed a shorter half-life compared to rat liver S9. While rat hepatocytes metabolized AEs faster than human hepatocytes. Both hydrophobic alkyl chain and hydrophilic EO head group groups of AEs were found to be target sites of metabolism. Metabolites were identified that show primary hydroxylation and dehydrogenation, followed by O-dealkylation (shortening of EO head groups) and glucuronidation. Additionally, the detection of whole EO groups indicates the cleavage of the ether bond between the alkyl chain and the EO groups as a minor metabolic pathway in the current testing system. Furthermore, no difference in metabolic patterns of each individual homologue AE investigated was observed, regardless of alkyl chain length or the number of EO groups. Moreover, there is an excellent agreement between the in vitro experimental data and the metabolite profile simulations using in silico approaches (OECD QSAR Toolbox). Altogether, these data indicate fast metabolism of all AEs with a qualitatively similar metabolic pathway with some quantitative differences observed in the metabolite profiles. These metabolic studies using different species can provide important reference values for further safety evaluation.

The evaluation of skin sensitization potential of the UVCB substance diisopentyl phthalate by in silico and in vitro methods

Diisopentyl phthalate (DiPeP) is primarily used as a plasticizer or additive within the production of polyvinyl chloride (PVC), and has many additional industrial applications. Its metabolites were recently found in urinary samples of pregnant women; thus, this substance is of concern as relates to human exposure. Depending upon the nature of the alcohol used in its synthesis, DiPeP may exist either as a mixture consisting of several branched positional isomers, or as a single defined structure. This article investigates the skin sensitization potential and immunomodulatory effects of DiPeP CAS No. 84777-06-0, which is currently marketed and classified as a UVCB substance, by in silico and in vitro methods. Our findings showed an immunomodulatory effect for DiPeP in LPS-induced THP-1 activation assay (increased CD54 expression). In silico predictions using QSAR TOOLBOX 4.5, ToxTree, and VEGA did not identify DiPeP, in the form of a discrete compound, as a skin sensitizer. The keratinocyte activation (Key Event 2 (KE2) of the adverse outcome pathway (AOP) for skin sensitization) was evaluated by two different test methods (HaCaT assay and RHE assay), and results were discordant. While the HaCaT assay showed that DiPeP can activate keratinocytes (increased levels of IL-6, IL-8, IL-1α, and ILA gene expression), in the RHE assay, DiPeP slightly increased IL-6 release. Although inconclusive for KE2, the role of DiPeP in KE3 (dendritic cell activation) was demonstrated by the increased levels of CD54 and IL-8 and TNF-α in THP-1 cells (THP-1 activation assay). Altogether, findings were inconclusive regarding the skin sensitization potential of the UVCB DiPeP—disagreeing with the results of DiPeP in the form of discrete compound (skin sensitizer by the LLNA assay). Additional studies are needed to elucidate the differences between DiPeP isomer forms, and to better understand the applicability domains of non-animal methods in identifying skin sensitization hazards of UVCB substances.

Information technologies as a tool for identification of endocrine disrupting chemicals

Background: A multitude of chemicals possess the ability to disrupt nuclear receptors, leading to adverse effects on human health. Evidences indicated that various agricultural, industrial, and household chemicals can directly or indirectly impede the endocrine system of both wildlife species and humans. These substances, defined as endocrine disrupting chemicals (EDCs), pose a potential threat to male and female reproductive functions, prompting high scientific and regulatory attention towards their identification. Aim of the study: The aim of this study is to outline a logic for identification of endocrine-disrupting chemicals, applied with non-commercial software tool. Material and methods: The analysis was conducted using the non-commercial software platform QSAR Toolbox. This platform enables the utilization of a range of pre-existing models for diverse biological/toxic effects. Moreover, it facilitates the integration of new models for various effects.Results: The estrogenic effect of a target chemical is evaluated by making use of a non-commercial software tool. The predicted result is in agreement with literature published findings on the estrogenic effect of similar to the target chemicals.Conclusions: In the current study a sequence of steps is presented in order to assess the estrogenic effect of a target chemical. Each step is explained and discussed in the light of logic incorporated in non-commercial software tool. It is expected that the results could be of help for researchers in the field of receptor binding or other similar studies.

The estimation of acute oral toxicity (LD50) of G-series organophosphorus-based chemical warfare agents using quantitative and qualitative toxicology in silico methods.

The idea of this study was the estimation of the theoretical acute toxicity (t-LD50, rat, oral dose) of organophosphorus-based chemical warfare agents from the G-series (n = 12) using different in silico methods. Initially identified in Germany, the G-type nerve agents include potent compounds such as tabun, sarin, and soman. Despite their historical significance, there is a noticeable gap in acute toxicity data for these agents. This study employs qualitative (STopTox and AdmetSAR) and quantitative (TEST; CATMoS; ProTox-II and QSAR Toolbox) in silico methods to predict LD50 values, offering an ethical alternative to animal testing. Additionally, we conducted quantitative extrapolation from animals, and the results of qualitative tests confirmed the acute toxicity potential of these substances and enabled the identification of toxicophoric groups. According to our estimations, the most lethal agents within this category were GV, soman (GD), sarin (GB), thiosarin (GBS), and chlorosarin (GC), with t-LD50 values (oral administration, extrapolated from rat to human) of 0.05mg/kg bw, 0.08mg/kg bw, 0.12mg/kg bw, 0.15mg/kg bw, and 0.17mg/kg bw, respectively. On the contrary, compounds with a cycloalkane attached to the phospho-oxygen linkage, specifically methyl cyclosarin and cyclosarin, were found to be the least toxic, with values of 2.28mg/kg bw and 3.03mg/kg bw. The findings aim to fill the knowledge gap regarding the acute toxicity of these agents, highlighting the need for modern toxicological methods that align with ethical considerations, next-generation risk assessment (NGRA) and the 3Rs (replacement, reduction and refinement) principles.

Advancing ocular safety research: A comprehensive examination of benzocaine acute exposure without animal testing

Benzocaine is a widely employed local anaesthetic; however, there is a notable dearth of preclinical and clinical evidence regarding its safety in ophthalmological products. To address this, a comprehensive strategy incorporating in silico and in vitro methodologies was proposed for assessing benzocaine's ocular toxicity without animal testing. To collect the in silico evidence, the QSAR Toolbox (v4.5) was used. A single exposure to two benzocaine concentrations (2% and 20%) was evaluated by in vitro methods. Hen’s Egg Chorioallantoic Membrane Test (HET-CAM) was performed to evaluate the effects on the conjunctiva. To study corneal integrity, Short Time Exposure test (STE) and Bovine Corneal Opacity and Permeability (BCOP) assay, followed by histopathological analysis, were carried out. Results from both in silico and in vitro methodologies categorize benzocaine as non-irritating. The histopathological analysis further affirms the safety of using benzocaine in eye drops, as no alterations were observed in evaluated corneal strata. This research proposes a useful combined strategy to provide evidence on the safety of local anaesthetics and particularly show that 2% and 20% benzocaine solutions do not induce eye irritation or corneal damage, supporting the potential use of benzocaine in the development of ophthalmic anesthetic products.

The acute toxicity of Novichok's degradation products using quantitative and qualitative toxicology in silico methods.

The emergence of Novichok agents, potent organophosphorus nerve agents, has spurred the demand for advanced analytical methods and toxicity assessments as a result of their involvement in high-profile incidents. This study focuses on the degradation products of Novichok agents, particularly their potential toxic effects on biological systems. Traditional in vivo methods for toxicity evaluation face ethical and practical constraints, prompting a shift toward in silico toxicology research. In this context, we conducted a comprehensive qualitative and quantitative analysis of acute oral toxicity (AOT) for Novichok degradation products, using various in silico methods, including TEST, CATMoS, ProTox-II, ADMETlab, ACD/Labs Percepta, and QSAR Toolbox. Adopting these methodologies aligns with the 3Rs principle, emphasising Replacement, Reduction, and Refinement in the realm of toxicological studies. Qualitative assessments with STopTox and admetSAR revealed toxic profiles for all degradation products, with predicted toxicophores highlighting structural features responsible for toxicity. Quantitative predictions yielded varied estimates of acute oral toxicity, with the most toxic degradation products being EOPAA, MOPGA, MOPAA, MPGA, EOPGA, and MPAA, respectively. Structural modifications common to all examined hydrolytic degradation products involve substituting the fluorine atom with a hydroxyl group, imparting consequential effects on toxicity. The need for sophisticated analytical techniques for identifying and quantifying Novichok degradation products is underscored due to their inherent reactivity. This study represents a crucial step in unravelling the complexities of Novichok toxicity, highlighting the ongoing need for research into its degradation processes to refine analytical methodologies and fortify readiness against potential threats.

Prediction of the biodegradation of chemicals using OECD QSAR Toolbox software

Introduction. The development of integrated approaches to testing, assessment of the hazard and exposure risk of chemicals on human health and the environment is one of the priorities of preventive toxicology. An integrated approach involves various combinations of methods in silico, in chemico, in vitro, ex vivo, in vivo for hazard assessment. In the Russian Federation, in silico methods are often perceived with skepticism, mainly due to the lack of their legal status, weak methodological base and insufficient training of specialists. In order to expand the methodological base, the possibility of predicting the stability of chemicals in biotic conditions using the OECD QSAR Toolbox software was studied.
 Material and methods. The OECD QSAR Toolbox software version 4.4.1., OECD guidelines on the assessment of biodegradation of chemicals.
 Results. The world community and the OECD have developed and implemented a three-level system for chemicals biodegradation testing, which includes tests for readily biodegradation (OECD Guidelines 301 A, 301 B, 301 C, 301 D, 301 E, 301 F, 306, 310), tests to determine the potential biodegradability (OECD Guidelines 302 A, 302 B, 302 C, 304 A) and model systems tests (OECD Guidelines 303 A, 303 B).
 To test the capabilities of the program, 24 endpoints were selected. They are the determination of biodegradability (%) by BOD, DOC, CO2, CH4 releases in OECD tests 301 A, 301 B, 301 C, 301 D, 
 302 C, 302 B, biodegradability (%) in sediments and soil, bioconcentration factors for more than 100 organic chemicals of various structures.
 The parameters were calculated using the analog method, followed by mandatory interpretation of the data obtained by an expert. When predicting the biodegradability of chemicals, it is necessary to perform a series of calculations using different tests (OECD tests 301 A, 301 B, 301 C, 301 D, 301 E, 302 B are preferred) and grouping methods followed by a comprehensive assessment of the results obtained, taking into account not only the structural similarity of substances and analogues, but also the quality of the experimental data used. When predicting biodegradability by BOD values, it is advisable to use the OECD 301 C test. The proportion of tested substances whose biodegradability could be estimated by BOD values is about 50% in the OECD 301 C test, which is primarily due to the presence of a significant amount of experimental data. The calculation of bioconcentration factors seems to be promising. For about 45% of the tested substances, it was possible to calculate bioconcentration coefficients with good correlation with experimental data. Biodegradation in soil (% and half-life) can be predicted only for a very limited range of compounds (10% of the tested substances), which is due to the difficulty of selecting structurally similar analogues with experimental data. The method is not applicable for predicting the biodegradation of salts, organometallic compounds, polymer molecules and mixed products.
 Conclusion. The Russian Register of Potentially Hazardous Chemical and Biological Substances has developed a methodological guide for predicting the stability of chemicals in biotic conditions using the OECD QSAR Toolbox software. The document presents algorithms for calculating biodegradability (%) according to OECD tests 301, 302, 303; BOD, bioconcentration factors and biodegradability (%) in soil.

The comprehensive prediction of carcinogenic potency and tumorigenic dose (TD50) for two problematic N-nitrosamines in food: NMAMPA and NMAMBA using toxicology in silico methods

The identification and toxicological assessment of potential carcinogens is of paramount importance for public health and safety. This study aimed to predict the carcinogenic potency and tumorigenic dose (TD50) for two problematic N-nitrosamines (N–NAs) commonly found in food: N-2-methylpropyl-N-1-methylacetonylnitrosamine (NMAMPA, CAS: 93755-83-0) and N-3-Methylbutyl-N-1-methylacetonylnitrosamine (NMAMBA, CAS: 71016-15-4). To achieve this goal, in silico toxicology methods were employed due to their practical applications and potential in risk assessment. The justification for conducting these studies was incoherent results published by the European Food Safety Authority (EFSA). For this purpose, we applied various in silico tools, including qualitative methods (ToxTree, ProTox II and CarcinoPred-EL) and quantitative methods (QSAR Toolbox and LAZAR) were applied to predict the carcinogenic potency. These tools leverage computational approaches to analyze chemical structures for finding toxicophores and generating predictions, making them efficient alternatives to traditional in vivo experiments. The results obtained indicated that N–NAs are carcinogenic compounds, and quantitative data was obtained in the form of estimated doses of TD50 for the compounds tested.

In silico methods for predicting physico-chemical properties and biological activity of newly synthesized esters of Bexarotene

The synthetic retinoid analogue Bexarotene (Targretin®, Ligand Pharmaceuticals Inc.) belongs to a group of compounds called rexinoids. They possess a specific affinity for the retinoid X receptor. The latter plays a role in the regulation of cell growth and differentiation through their ability to regulate transcription. Bexarotene is approved for the treatment of cutaneous T-cell lymphoma (CTCL), both as an oral and dermal dosage form. A total of 4 new Bexarotene esters were synthesized and an in silico analysis was performed using the OECD QSAR Toolbox, Molinspiration, PreADME/Tox and SwissADME software. The QSAR Toolbox results show that Bexarotene esters possess high metabolic activity with metabolites similar to those of Bexarotene. Alsom a hydrolysis process is observed making the esters act as prodrugs. According to Lipinski’s rule of 5 all four Bexarotene derivatives give 1 violation and therefore have drug-like properties. The Molinspiration and SwissADME software showed affinity of the newly synthesized molecules for nuclear receptors which partly rejects the prodrug theory. After evaluating the pharmacokinetic profile of the esters, it was observed that the molecules present promising intestinal absorption, distribution, metabolism, excretion and toxicity (ADME/T) characteristics. Even though the in silico analysis gave promising results, further investigation is needed.

Skin sensitization evaluation of a flavanol from processed rose wastewater for cosmetic application

Flavanols are extremely relevant for application and study due to the beneficial effect they have for humans when used internally or externally. They are identified in almost all plant cultures, as their metabolic products. Their pronounced benefit for protecting and restoring the skin in case of mechanical damage, radiation, allergens, chemicals and infections has been proven. Due to their natural origin, their dermatological application is also preferred. In such a case, the action of the chemical compounds and the generated skin metabolites have different mechanisms of action with respect to DNA and binding to proteins. The preliminary assessment of skin sensitization is a complex and lengthy task. Depending on the results, it is necessary to have an efficient technological approach for the isolation of flavanols with skin sensitization. Evaluation of the probable skin metabolic activity of cosmetic products containing flavanol (Luteolin) from processed rose wastewater is the aim of the conducted research, as well as prediction of protein and DNA binding of its metabolites by in silico methods (OECD QSAR Toolbox). The parent structure of the compound, as well as some of its generated metabolites, exhibit reactivity, i.e. they have different mechanisms of action in terms of DNA and protein binding.

The prediction of acute toxicity (LD50) for organophosphorus-based chemical warfare agents (V-series) using toxicology in silico methods.

Nerve agents are organophosphate chemical warfare agents that exert their toxic effects by irreversibly inhibiting acetylcholinesterase, affecting the breakdown of the neurotransmitter acetylcholine in the synaptic cleft. Due to the risk of exposure to dangerous nerve agents and for animal welfare reasons, in silico methods have been used to assess acute toxicity safely. The next-generation risk assessment (NGRA) is a new approach for predicting toxicological parameters that can meet modern requirements for toxicological research. The present study explains the acute toxicity of the examined V-series nerve agents (n = 9) using QSAR models. Toxicity Estimation Software Tool (ver. 4.2.1 and ver. 5.1.2), QSAR Toolbox (ver. 4.6), and ProTox-II browser application were used to predict the median lethal dose. The Simplified Molecular Input Line Entry Specification (SMILES) was the input data source. The results indicate that the most deadly V-agents were VX and VM, followed by structural VX analogues: RVX and CVX. The least toxic turned out to be V-sub x and Substance 100A. In silico methods for predicting various parameters are crucial for filling data gaps ahead of experimental research and preparing for the upcoming use of nerve agents.

Reconstructed human epidermis-based testing strategy of skin sensitization potential and potency classification using epidermal sensitization assay and in silico data.

The hazards and potency of skin sensitizers are traditionally determined using animal tests such as the local lymph node assay (LLNA); however, significant progress has been made in the development of non-animal test methods addressing the first three mechanistic key events of adverse outcome pathway in skin sensitization. We developed the epidermal sensitization assay (EpiSensA), which is a reconstructed human epidermis-based assay, by measuring four genes related to critical keratinocyte responses during skin sensitization. Four in vitro skin sensitization test methods (EpiSensA, direct peptide reactivity assay [DPRA], KeratinoSens™, and human cell line activation test [h-CLAT]) were systematically evaluated using 136 chemicals including lipophilic chemicals and pre/pro-haptens, which may be related to assay-specific limitations. The constructed database included existing and newly generated data. The EpiSensA showed a broader applicability domain and predicted the hazards with 82.4% and 78.8% accuracy than LLNA and human data. The EpiSensA could detect 76 out of 88 sensitizers at lower concentrations than the LLNA, indicating that the EpiSensA has higher sensitivity for the detection of minor sensitizing constituents. These results confirmed the potential use of the EpiSensA in evaluating a mixture of unknown compositions that can be evaluated by animal tests. To combine different information sources, the reconstructed human epidermis-based testing strategy (RTS) was developed based on weighted multiple information from the EpiSensA and TImes MEtabolism Simulator platform for predicting Skin Sensitization (TIMES-SS; RTSv1) or Organization for Economic Cooperation and Development (OECD) QSAR Toolbox automated workflow (RTSv2). The predictivities of the hazards and Globally Harmonized System (GHS) subcategories were equal to or better than the defined approaches (2 out of 3, integrated testing strategy [ITS]v1, and ITSv2) adopted as OECD Guideline 497.