Developing Robust Human Liver Microsomal Stability Prediction Models: Leveraging Inter-Species Correlation with Rat Data

Abstract

Objectives: Pharmacokinetic issues were the leading cause of drug attrition, accounting for approximately 40% of all cases before the turn of the century. To this end, several high-throughput in vitro assays like microsomal stability have been developed to evaluate the pharmacokinetic profiles of compounds in the early stages of drug discovery. At NCATS, a single-point rat liver microsomal (RLM) stability assay is used as a Tier I assay, while human liver microsomal (HLM) stability is employed as a Tier II assay. We experimentally screened and collected data on over 30,000 compounds for RLM stability and over 7000 compounds for HLM stability. Although HLM stability screening provides valuable insights, the increasing number of hits generated, along with the time- and resource-intensive nature of the assay, highlights the need for alternative strategies. One promising approach is leveraging in silico models trained on these experimental datasets. Methods: We describe the development of an HLM stability prediction model using our in-house HLM stability dataset. Results: Employing both classical machine learning methods and advanced techniques, such as neural networks, we achieved model accuracies exceeding 80%. Moreover, we validated our model using external test sets and found that our models are comparable to some of the best models in literature. Additionally, the strong correlation observed between our RLM and HLM data was further reinforced by the fact that our HLM model performance improved when using RLM stability predictions as an input descriptor. Conclusions: The best model along with a subset of our dataset (PubChem AID: 1963597) has been made publicly accessible on the ADME@NCATS website for the benefit of the greater drug discovery community. To the best of our knowledge, it is the largest open-source model of its kind and the first to leverage cross-species data.

Keywords

• metabolic stability
• human liver microsomes
• rat liver microsomes
• quantitative structure activity relationships
• in silico ADME