Development of an in silico prediction system of human renal excretion and clearance from chemical structure information incorporating fraction unbound in plasma as a descriptor

Prediction of pharmacokinetic profiles of new chemical entities is essential in drug development to minimize the risks of potential withdrawals. The excretion of unchanged compounds by the kidney constitutes a major route in drug elimination and plays an important role in pharmacokinetics. Herein, we created in silico prediction models of the fraction of drug excreted unchanged in the urine (f(e)) and renal clearance (CL(r)), with datasets of 411 and 401 compounds using freely available software; notably, all models require chemical structure information alone. The binary classification model for f(e) demonstrated a balanced accuracy of 0.74. The two-step prediction system for CL(r) was generated using a combination of the classification model to predict excretion-type compounds and regression models to predict the CL(r) value for each excretion type. The accuracies of the regression models increased upon adding a descriptor, which was the observed and predicted fraction unbound in plasma (f(u,p)); 78.6% of the samples in the higher range of renal clearance fell within 2-fold error with predicted f(u,p) value. Our prediction system for renal excretion is freely available to the public and can be used as a practical tool for prioritization and optimization of compound synthesis in the early stage of drug discovery.