A Combination of Machine Learning and PBPK Modeling Approach for Pharmacokinetics Prediction of Small Molecules in Humans

Recently, there has been rapid development in model-induced drug development, which has the potential to reduce animal experiments and accelerate drug discovery. Physiologically based pharmacokinetic (PBPK) and machine learning (ML) models are commonly used in early drug discovery to predict drug properties. However, basic PBPK models require a large number of molecule-specific inputs from in vitro experiments, which hinders the efficiency and accuracy of these models. To address this issue, this paper introduces a new computational platform that combines ML and PBPK models. The platform predicts molecule PK profiles with high accuracy and without the need for experimental data. This study developed a whole-body PBPK model and ML models of plasma protein unbinding (fup), Caco-2 cell permeability, and total plasma clearance to predict the PK of small molecules. Pharmacokinetic profiles were simulated using a "bottom-up" PBPK modeling approach with ML inputs. Additionally, 40 compounds were used to evaluate the platform's accuracy. Results showed that the ML-PBPK model predicted the area under the concentration-time curve (AUC) with 62.5% accuracy within a 2-fold range, which was higher than using in vitro inputs with 47.5% accuracy. The ML-PBPK model platform provides high accuracy in prediction and reduces the number of experiments and time required compared to traditional PBPK approaches. The platform successfully predicts human PK parameters without in vitro and in vivo experiments and can potentially guide early drug discovery and development.