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PredMS: a random forest model for predicting metabolic stability of drug candidates in human liver microsomes

Jae Yong Ryu¹, Jeong Hyun Lee², Byung Ho Lee²

¹Department of Biotechnology, Duksung Women's University, Seoul 01369, Republic of Korea.

Bioinformatics (Oxford, England)

|September 13, 2021

Abstract

Motivation:

Poor metabolic stability leads to drug development failure. Therefore, it is essential to evaluate the metabolic stability of small compounds for successful drug discovery and development. However, evaluating metabolic stability in vitro and in vivo is expensive, time-consuming and laborious. In addition, only a few free software programs are available for metabolic stability data and prediction. Therefore, in this study, we aimed to develop a prediction model that predicts the metabolic stability of small compounds.

Results:

We developed a computational model, PredMS, which predicts the metabolic stability of small compounds as stable or unstable in human liver microsomes. PredMS is based on a random forest model using an in-house database of metabolic stability data of 1917 compounds. To validate the prediction performance of PredMS, we generated external test data of 61 compounds. PredMS achieved an accuracy of 0.74, Matthew's correlation coefficient of 0.48, sensitivity of 0.70, specificity of 0.86, positive predictive value of 0.94 and negative predictive value of 0.46 on the external test dataset. PredMS will be a useful tool to predict the metabolic stability of small compounds in the early stages of drug discovery and development.

Availability And Implementation:

The source code for PredMS is available at https://bitbucket.org/krictai/predms, and the PredMS web server is available at https://predms.netlify.app.

Supplementary Information:

Supplementary data are available at Bioinformatics online.

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