Multi-objective de novo drug design with conditional graph generative model

Recently, deep generative models have revealed itself as a promising way of performing de novo molecule design. However, previous research has focused mainly on generating SMILES strings instead of molecular graphs. Although available, current graph generative models are are often too general and computationally expensive. In this work, a new de novo molecular design framework is proposed based on a type of sequential graph generators that do not use atom level recurrent units. Compared with previous graph generative models, the proposed method is much more tuned for molecule generation and has been scaled up to cover significantly larger molecules in the ChEMBL database. It is shown that the graph-based model outperforms SMILES based models in a variety of metrics, especially in the rate of valid outputs. For the application of drug design tasks, conditional graph generative model is employed. This method offers highe flexibility and is suitable for generation based on multiple objectives. The results have demonstrated that this approach can be effectively applied to solve several drug design problems, including the generation of compounds containing a given scaffold, compounds with specific drug-likeness and synthetic accessibility requirements, as well as dual inhibitors against JNK3 and GSK-3β. [Image: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13321-018-0287-6) contains supplementary material, which is available to authorized users.