embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules

Al‐Jarf, Raghad; Tang, Simon; Pires, Douglas E V; Ascher, David B.

doi:10.1021/acs.jcim.2c00824

Cited by 10 publications

(7 citation statements)

References 52 publications

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“…The datasets are internally and externally validated via different cross-validation schemes and low-redundancy blind sets, respectively. The embryoTox (Aljarf et al, 2023) webserver is used to predict and classify molecules which are likely to be safe to use during pregnancy in women. The webserver is trained and validated using in vitro bioactivity data of over 700 small molecules.…”

Section: Methodsmentioning

confidence: 99%

Tracing the pathways and mechanisms involved in medicinal uses of flaxseed with computational methods and bioinformatics tools

Joshi,

Srivastava

2024

Front. Chem.

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Pharmacological drugs targeting specific pathways involved in various diseases have seen recent advancement with newer and more efficient emerging drug targets, but these drugs are limited in terms of their side effects and patient adherence. The potential of plant-based diets in the form of functional foods is increasingly being realized as an option to treat and/or prevent several diseases. In this work, we have selected flaxseed (Linum usitatissimum), also known as linseed, to study its pharmacological efficacy and proposed mechanisms of action for medicinal purposes. The target genes of linseed with Disease Specificity Index (DSI >0.6) are compared to the associated genes of diabetes mellitus, decrease in appetite, addictive behavior, cardiovascular diseases (CVDs), inflammatory bowel diseases (IBDs), and Polycystic Ovary Syndrome (PCOS), and the selected genes are further evaluated using in silico methods. The binding affinity of flaxseed to three common target proteins (CCDC28b, PDCD6IP, and USP34) is assessed by docking and molecular dynamics (MD) simulations. The results show that linseed is safe to use for mutagenic toxicity and other cardiotoxicity measures, but linseed is unsafe for embryotoxicity, hERG toxicity, and cardiac failure. The analysis of the protein–protein interaction (PPI) network, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicates that flaxseed can be used as a medicinal herb for treatment of diabetes mellitus, cardiovascular diseases, IBDs, and PCOS.

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Section: Methodsmentioning

confidence: 99%

Tracing the pathways and mechanisms involved in medicinal uses of flaxseed with computational methods and bioinformatics tools

Joshi,

Srivastava

2024

Front. Chem.

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“…Therefore, in Silico in Adsorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) is out-lab experiment as mathematical calculations of Quantitative Structure -Activity Relationship (QSAR) [14]. Several research groups designed online computer simulation websites as free structural based prediction technique of chemical before accessing in complications of experiments and their results [15,16,17].…”

Section: In Silico -Toxicity Predictionmentioning

confidence: 99%

“…In this article, a new Iraqi attempt to present in Silicoonline website prediction of seven chemicals randomly selected from IASJ website related to corrosion inhibitor and introduced in free online Biosig -Lab/ tool website [15,17,18] to get knowledge about their effects on foetus's health (teratogenic risk [17]), cardiac [18]: Arrhythmia, Cardiac Failure, Heart Block, hERG toxicity, Hypertension, and Myocardial Infarction beside honey bee (A. mellifera), mallard and flathead minnow, human health: AMES, rat LD50 and oral chronic toxicities [15] as shown in Figure (1).…”

Section: In Silico -Toxicity Predictionmentioning

confidence: 99%

Assessing the Environmental Safety of Corrosion Inhibitors in Iraqi Studies: A Predictive Analysis

Hammud

2024

IJOIR

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Corrosion inhibitors play a crucial role in mitigating the detrimental effects of chemical and electrochemical interactions over time. This phenomenon poses significant threats to structural integrity, strength, and has far-reaching economic implications across various industries such as construction, petrochemicals, mining, fertilizer, and energy units. The environmental repercussions, including toxic outflows and plant failures, underscore the need for comprehensive assessments. Despite the commendable contributions of Iraqi researchers in developing organic, inorganic, natural, and nano-corrosion inhibitors, there is a critical gap in considering potential side effects. This study explores a pioneering approach to evaluating the toxicity of corrosion inhibitors on both human health and the environment. Leveraging mathematical modeling and mechanisms, we present a mimic estimation of environmental factors influencing corrosion phenomena. The out-lab experimental calculations employ Quantitative Structure-Activity Relationship (QSAR) techniques, providing a structural-based predictive model for assessing the potential impact of chemicals before embarking on experimental complexities. Drawing from Iraqi journals, seven corrosion inhibitors with diverse chemical structures, experimental conditions, and publishing sources were selected. These compounds were subjected to scrutiny using online prediction websites that evaluate Embro-toxicity, Cardio-toxicity, and crop-toxicity. Each inhibitor underwent screening by specific toxicological web servers. The findings revealed that all studied compounds posed moderate to extremely unsafe risks to fetal health during pregnancy, potentially categorizing them as teratogens with elevated risks of preterm labor, miscarriage, or stillbirth. Additionally, none of the tested materials exhibited herbicidal activity.

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“…[ 2 ] This process pertains to the capacity of specific substances or agents to induce congenital malformations or anomalies in a developing embryo or fetus upon exposure to them during gestation. [ 3 ] Teratogenicity is frequently linked to chemical or drug exposure, but it can also arise from the ingestion of botanical substances. Botanical products comprise diverse chemical constituents, encompassing innate compounds, secondary metabolites, and probable hazardous substances.…”

Section: Introductionmentioning

confidence: 99%

Exploration of Teratogenic Effects of Bambusa vulgaris on Wistar Rats by Evaluating Morphological and Skeletal Parameters

Acharya,

Behera,

Chowdhury

et al. 2024

Macromolecular Symposia

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Bambusa vulgaris is a commonly consumable plant, which is widely utilized by indigenous peoples as a source of food. Consumption of these plant products in various forms is typically acceptable due to their distinct tastes, and aromatic flavor. However, there is little information on the plant's safety and toxicity profile. Although toxicity information on B. vulgaris is readily available, the impact of plants during pregnancy has yet to be fully explored. To determine the possible mechanism behind teratogenicity, pregnant albino Wistar rats are administered aqueous extracts of B. vulgaris in a dose‐dependent manner. For determining the structural malformations, Teratogenicity indices include maternal common physiological parameters, number of implantations and fetal indices, number of live, resorpsed, and dead somites, morphological malformations, and skeletal malformations of different organs are evaluated by comparing different test groups with control groups. Most developmental indices, including implantation and fetalindices, vertebral, organ, and skeletal structures are significantly altered by the crude extract at higher dosages in treated as compared to control animals. The administration of aqueous extract of B. vulgaris during the organogenesis phase in rats has a considerable deleterious effect on embryonic and fetal developmental indices. It ruthlessly impacts the embryo's numerous organs as well as their typical physiological processes in a dose‐dependent way. The present investigation validates the capacity of B. vulgaris to cause developmental toxicity in Wistar rats, as evidenced by significant alterations in their gestational morphological, structural, and skeletal anatomy and physiology. It is recommended that further scientific studies be conducted to evaluate the more advanced mechanisms of teratogenicity associated with B. vulgaris.

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embryoTox: Using Graph-Based Signatures to Predict the Teratogenicity of Small Molecules

Cited by 10 publications

References 52 publications

Tracing the pathways and mechanisms involved in medicinal uses of flaxseed with computational methods and bioinformatics tools

Tracing the pathways and mechanisms involved in medicinal uses of flaxseed with computational methods and bioinformatics tools

Assessing the Environmental Safety of Corrosion Inhibitors in Iraqi Studies: A Predictive Analysis

Exploration of Teratogenic Effects of Bambusa vulgaris on Wistar Rats by Evaluating Morphological and Skeletal Parameters

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