Dataset Information

A Hybrid Machine Learning Approach for Structure Stability Prediction in Molecular Co-crystal Screenings.

ABSTRACT: Co-crystals are a highly interesting material class as varying their components and stoichiometry in principle allows tuning supramolecular assemblies toward desired physical properties. The in silico prediction of co-crystal structures represents a daunting task, however, as they span a vast search space and usually feature large unit cells. This requires theoretical models that are accurate and fast to evaluate, a combination that can in principle be accomplished by modern machine-learned (ML) potentials trained on first-principles data. Crucially, these ML potentials need to account for the description of long-range interactions, which are essential for the stability and structure of molecular crystals. In this contribution, we present a strategy for developing Δ-ML potentials for co-crystals, which use a physical baseline model to describe long-range interactions. The applicability of this approach is demonstrated for co-crystals of variable composition consisting of an active pharmaceutical ingredient and various co-formers. We find that the Δ-ML approach offers a strong and consistent improvement over the density functional tight binding baseline. Importantly, this even holds true when extrapolating beyond the scope of the training set, for instance in molecular dynamics simulations under ambient conditions.

SUBMITTER: Wengert S

PROVIDER: S-EPMC9281391 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Different types of chemicals and products may exhibit various health risks when administered into the human body. For toxicity reasons, the number of new drugs entering the market through the conventional drug development process has been reduced over the years. However, with the advent of big data and artificial intelligence, machine learning techniques have emerged as a potential solution for predicting toxicity and ensuring efficient drug development and chemical safety. An ML model for toxicity prediction can reduce experimental costs and time while addressing ethical concerns by drastically reducing the need for animals and clinical trials. Herein, MolToxPred, an ML-based tool, has been developed using a stacked model approach to predict the potential toxicity of small molecules and metabolites. The stacked model consists of random forest, multi-layer perceptron, and LightGBM as base classifiers and Logistic Regression as the meta classifier. For training and validation purposes, a comprehensive set of toxic and non-toxic molecules is curated. Different structural and physicochemical-based features in the form of molecular descriptors and fingerprints were employed. MolToxPred utilizes a comprehensive feature selection process and optimizes its hyperparameters through Bayesian optimization with stratified 5-fold cross-validation. In the evaluation phase, MolToxPred achieved an AUROC of 87.76% on the test set and 88.84% on an external validation set. The McNemar test was used as the post-hoc test to determine if the stacked models' performance was significantly different compared to the base learners. The developed stacked model outperformed its base classifiers and an existing tool in the literature, reaffirming its better performance. The hypothesis is that the incorporation of a diverse set of data, the subsequent feature selection, and a stacked ensemble approach give MolToxPred the edge over other methods. In addition to this, an attempt has been made to identify structural alerts responsible for endpoints of the Tox21 data to determine the association of a molecule with a plausible downstream pathway of action. MolToxPred may be helpful for drug discovery and regulatory pipelines in pharmaceutical and other industries for in silico toxicity prediction of small molecule candidates.

Dataset Information

A Hybrid Machine Learning Approach for Structure Stability Prediction in Molecular Co-crystal Screenings.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets