Predicting Volume of Distribution in Humans: Performance of in silico Methods for A Large Set of Structurally Diverse Clinical Compounds

Volume of distribution at steady state (VD,ss) is one of the key pharmacokinetic parameters estimated during the drug discovery process. Despite considerable efforts to predict VD,ss, accuracy and choice of prediction methods remain a challenge, with evaluations constrained to a small set (< 150) of compounds. To address these issues, a series of in silico methods for predicting human VD,ss directly from structure were evaluated using a large set of clinical compounds. Machine learning (ML) models were built to predict VD,ss directly, and to predict input parameters required for mechanistic and empirical VD,ss predictions. In addition, LogD, fraction unbound in plasma (fup) and blood to plasma partition ratio (BPR) were measured on 254 compounds to estimate impact of measured data on predictive performance of mechanistic models. Furthermore, impact of novel methodologies such as measuring partition (Kp) in adipocytes and myocytes (n=189) on VD,ss predictions was also investigated. In predicting VD,ss directly from chemical structures, both mechanistic or empirical scaling using a combination of predicted rat and dog VD,ss demonstrated comparable performance (62-71% within 3-fold). The direct ML model outperformed other in silico methods (75% within 3-fold, r2=0.5, AAFE=2.2) when built from a larger dataset. Scaling to human either from predicted VD,ss of rat or dog yielded poor results (< 47% within 3-fold). Measured fup and BPR improved performance of mechanistic VD,ss predictions significantly (81% within 3-fold, r2=0.6, AAFE=2.0). Adipocyte intracellular Kp showed good correlation to the VD,ss, but was limited in estimating the compounds with low VD,ssSignificance Statement This work advances the in-silico prediction of VD,ss directly from structure and with the aid of in vitro data. Rigorous and comprehensive evaluation of various methods using a large set of clinical compounds (n=956) is presented. The scale of both techniques and number of compounds evaluated is far beyond any previously presented. The novel data set (n=254) generated using a single protocol for each in vitro assay reported in this study could further aid in advancing VD,ss prediction methodologies. © 2020 The Authors. This is an open access article under the terms of the Creative Commons Attribution CC BY License, which permits use, distribution, and reproduction in any medium, provided that the original work is properly cited.

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