Deep generative models for ligand‐based de novo design applied to multi‐parametric optimization

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Abstract
Multi‐parameter optimization (MPO) is a major challenge in new chemical entity (NCE) drug discovery. Recently, promising results were reported for deep learning generative models applied to de novo molecular design, but, to our knowledge, until now no report was made of the value of this new technology for addressing MPO in an actual drug discovery project. In this study, we demonstrate the benefit of applying AI technology in a real drug discovery project. We evaluate the potential of a ligand‐based de novo design technology using deep learning generative models to accelerate the obtention of lead compounds meeting 11 different biological activity objectives simultaneously. Using the initial dataset of the project, we built QSAR models for all the 11 objectives, with moderate to high performance (precision between 0.67 and 1.0 on an independent test set). Our DL‐based AI de novo design algorithm, combined with the QSAR models, generated 150 virtual compounds predicted as active on all objectives. Eleven were synthetized and tested. The AI‐designed compounds met 9.5 objectives on average (i.e., 86% success rate) versus 6.4 (i.e., 58% success rate) for the initial molecules measured on all objectives. One of the AI‐designed molecules was active on all 11 measured objectives, and two were active on 10 objectives while being in the error margin of the assay for the last one. The AI algorithm designed compounds with functional groups, which, although being rare or absent in the initial dataset, turned out to be highly beneficial for the MPO.

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