Machine Learning Small Molecule Properties in Drug Discovery
Nikolai Schapin Maciej Majewski Alejandro Varela Carlos Arroniz Gianni De Fabritiis
Machine learning (ML) is a promising approach for predicting small molecule
properties in drug discovery. Here, we provide a comprehensive overview of
various ML methods introduced for this purpose in recent years. We review a
wide range of properties, including binding affinities, solubility, and ADMET
(Absorption, Distribution, Metabolism, Excretion, and Toxicity). We discuss
existing popular datasets and molecular descriptors and embeddings, such as
chemical fingerprints and graph-based neural networks. We highlight also
challenges of predicting and optimizing multiple properties during hit-to-lead
and lead optimization stages of drug discovery and explore briefly possible
multi-objective optimization techniques that can be used to balance diverse
properties while optimizing lead candidates. Finally, techniques to provide an
understanding of model predictions, especially for critical decision-making in
drug discovery are assessed. Overall, this review provides insights into the
landscape of ML models for small molecule property predictions in drug
discovery. So far, there are multiple diverse approaches, but their
performances are often comparable. Neural networks, while more flexible, do not
always outperform simpler models. This shows that the availability of
high-quality training data remains crucial for training accurate models and
there is a need for standardized benchmarks, additional performance metrics,
and best practices to enable richer comparisons between the different
techniques and models that can shed a better light on the differences between
the many techniques.