Quantification of contributions of molecular fragments for eye irritation of organic chemicals using QSAR study

Democratizing cheminformatics: interpretable chemical grouping using an automated KNIME workflow

With the increased availability of chemical data in public databases, innovative techniques and algorithms have emerged for the analysis, exploration, visualization, and extraction of information from these data. One such technique is chemical grouping, where chemicals with common characteristics are categorized into distinct groups based on physicochemical properties, use, biological activity, or a combination. However, existing tools for chemical grouping often require specialized programming skills or the use of commercial software packages. To address these challenges, we developed a user-friendly chemical grouping workflow implemented in KNIME, a free, open-source, low/no-code, data analytics platform. The workflow serves as an all-encompassing tool, expertly incorporating a range of processes such as molecular descriptor calculation, feature selection, dimensionality reduction, hyperparameter search, and supervised and unsupervised machine learning methods, enabling effective chemical grouping and visualization of results. Furthermore, we implemented tools for interpretation, identifying key molecular descriptors for the chemical groups, and using natural language summaries to clarify the rationale behind these groupings. The workflow was designed to run seamlessly in both the KNIME local desktop version and KNIME Server WebPortal as a web application. It incorporates interactive interfaces and guides to assist users in a step-by-step manner. We demonstrate the utility of this workflow through a case study using an eye irritation and corrosion dataset.Scientific contributionsThis work presents a novel, comprehensive chemical grouping workflow in KNIME, enhancing accessibility by integrating a user-friendly graphical interface that eliminates the need for extensive programming skills. This workflow uniquely combines several features such as automated molecular descriptor calculation, feature selection, dimensionality reduction, and machine learning algorithms (both supervised and unsupervised), with hyperparameter optimization to refine chemical grouping accuracy. Moreover, we have introduced an innovative interpretative step and natural language summaries to elucidate the underlying reasons for chemical groupings, significantly advancing the usability of the tool and interpretability of the results.

In silico prediction of the full United Nations Globally Harmonized System eye irritation categories of liquid chemicals by IATA-like bottom-up approach of random forest method

As an alternative to in vivo Draize rabbit eye irritation test, this study aimed to construct an in silico model to predict the complete United Nations (UN) Globally Harmonized System (GHS) for classification and labeling of chemicals for eye irritation category [eye damage (Category 1), irritating to eye (Category 2) and nonirritating (No category)] of liquid chemicals with Integrated approaches to testing and assessment (IATA)-like two-stage random forest approach. Liquid chemicals (n = 219) with 34 physicochemical descriptors and quality in vivo data were collected with no missing values. Seven machine learning algorithms (Naive Bayes, Logistic Regression, First Large Margin, Neural Net, Random Forest (RF), Gradient Boosted Tree, and Support Vector Machine) were examined for the ternary categorization of eye irritation potential at a single run through 10-fold cross-validation. RF, which performed best, was further improved by applying the 'Bottom-up approach' concept of IATA, namely, separating No category first, and discriminating Category 1 from 2, thereafter. The best performing training dataset achieved an overall accuracy of 73% and the correct prediction for Category 1, 2, and No category was 80%, 50%, and 77%, respectively for the test dataset. This prediction model was further validated with an external dataset of 28 chemicals, for which an overall accuracy of 71% was achieved.

Prediction of Biodegradability for Polycyclic Aromatic Hydrocarbons Using Various In Silico Modeling Methods

Polycyclic aromatic hydrocarbons (PAHs) have attracted great concern as global environmental pollutants. In this work, the quantitative structure-biodegradability relationship (QSBR) study has been done to predict the biodegradability of PAHs and develop the correlation between the biodegradability and the molecular structures. The structural chemistry and quantum chemistry descriptors were used to represent molecular structures. Three in silico modeling methods, i.e., multiple linear regression (MLR), radial basis function neural network, and back-propagation artificial neural network (BPANN), are utilized to construct the linear and nonlinear prediction models and provide some insights into the structural characteristics affecting the biodegradability of PAHs. The stability of these QSBR models was tested by leave-one-out cross-validation, and the cross-validated correlation coefficients (q²) were 0.6109, 0.6887, and 0.6586, respectively. The correlation coefficients (R²) of the three models for the training set were 0.7811, 0.8883, and 0.9667, respectively. The comparison of the three models showed that the BPANN model produced a statistically more significant model than the other two models. On the basis of molecular structure, the dominant molecular structure descriptor affecting biodegradability of PAHs were analyzed and discussed.