Explore drug-like space with deep generative models

作者:Wang, Jianmin; Mao, Jiashun; Wang, Meng; Le, Xiangyang; Wang, Yunyun*
来源:Methods, 2023, 210: 52-59.
DOI:10.1016/j.ymeth.2023.01.004

摘要

The process of design/discovery of drugs involves the identification and design of novel molecules that have the desired properties and bind well to a given disease-relevant target. One of the main challenges to effectively identify potential drug candidates is to explore the vast drug-like chemical space to find novel chemical struc-tures with desired physicochemical properties and biological characteristics. Moreover, the chemical space of currently available molecular libraries is only a small fraction of the total possible drug-like chemical space. Deep molecular generative models have received much attention and provide an alternative approach to the design and discovery of molecules. To efficiently explore the drug-like space, we first constructed the drug-like dataset and then performed the generative design of drug-like molecules using a Conditional Randomized Transformer approach with the molecular access system (MACCS) fingerprint as a condition and compared it with previously published molecular generative models. The results show that the deep molecular generative model explores the wider drug-like chemical space. The generated drug-like molecules share the chemical space with known drugs, and the drug-like space captured by the combination of quantitative estimation of drug-likeness (QED) and quantitative estimate of protein-protein interaction targeting drug-likeness (QEPPI) can cover a larger drug-like space. Finally, we show the potential application of the model in design of inhibitors of MDM2-p53 protein- -protein interaction. Our results demonstrate the potential application of deep molecular generative models for guided exploration in drug-like chemical space and molecular design.

  • 单位
    南通大学; 哈尔滨医科大学