Mol-CycleGAN: a generative model for molecular optimization

• Main Authors: Łukasz Maziarka, Agnieszka Pocha, Jan Kaczmarczyk, Krzysztof Rataj, Tomasz Danel, Michał Warchoł
• Format: Article
• Language: English
• Published: BMC 2020-01-01
• Series: Journal of Cheminformatics
• Subjects: Drug design; Molecular optimization; Generative models; Deep learning
• Online Access: https://doi.org/10.1186/s13321-019-0404-1

Abstract Designing a molecule with desired properties is one of the biggest challenges in drug development, as it requires optimization of chemical compound structures with respect to many complex properties. To improve the compound design process, we introduce Mol-CycleGAN—a CycleGAN-based model that generates optimized compounds with high structural similarity to the original ones. Namely, given a molecule our model generates a structurally similar one with an optimized value of the considered property. We evaluate the performance of the model on selected optimization objectives related to structural properties (presence of halogen groups, number of aromatic rings) and to a physicochemical property (penalized logP). In the task of optimization of penalized logP of drug-like molecules our model significantly outperforms previous results.