Accurate prediction of molecular properties and drug targets using a self-supervised image representation learning framework

The clinical efficacy and safety of a drug is determined by its molecular properties and targets in humans. However, proteome-wide evaluation of all compounds in humans, or even animal models, is challenging. In this study, we present an unsupervised pretraining deep learning framework, named ImageMol, pretrained on 10 million unlabelled drug-like, bioactive molecules, to predict molecular targets of candidate compounds. The ImageMol framework is designed to pretrain chemical representations from unlabelled molecular images on the basis of local and global structural characteristics of molecules from pixels. We demonstrate high performance of ImageMol in evaluation of molecular properties (that is, the drug's metabolism, brain penetration and toxicity) and molecular target profiles (that is, beta-secretase enzyme and kinases) across 51 benchmark datasets. ImageMol shows high accuracy in identifying anti-SARS-CoV-2 molecules across 13 high-throughput experimental datasets from the National Center for Advancing Translational Sciences. Via ImageMol, we identified candidate clinical 3C-like protease inhibitors for potential treatment of COVID-19. Predicting the properties of a molecule from its structure with high accuracy is a crucial problem in digital drug design. Instead of sequence features, Zeng and colleagues use an image representation of a large collection of bioactive molecules to pretrain a model that can be fine-tuned on specific property prediction tasks.

Deep learning for drug repurposing: Methods, databases, and applications

Drug development is time-consuming and expensive. Repurposing existing drugs for new therapies is an attractive solution that accelerates drug development at reduced experimental costs, specifically for Coronavirus Disease 2019 (COVID-19), an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, comprehensively obtaining and productively integrating available knowledge and big biomedical data to effectively advance deep learning models is still challenging for drug repurposing in other complex diseases. In this review, we introduce guidelines on how to utilize deep learning methodologies and tools for drug repurposing. We first summarized the commonly used bioinformatics and pharmacogenomics databases for drug repurposing. Next, we discuss recently developed sequence-based and graph-based representation approaches as well as state-of-the-art deep learning-based methods. Finally, we present applications of drug repurposing to fight the COVID-19 pandemic and outline its future challenges. This article is categorized under: Data Science > Artificial Intelligence/Machine Learning