De novo drug design through gradient-based regularized search in information-theoretically controlled latent space

• Published in: Journal of computer-aided molecular design 2024-12, Vol.38 (1), p.32, Article 32
• Main Authors: Jang, Hyosoon, Seo, Sangmin, Park, Sanghyun, Kim, Byung Ju, Choi, Geon-Woo, Choi, Jonghwan, Park, Chihyun
• Format: Article
• Language: English
• Subjects: Algorithms; Animal Anatomy; Chemical compounds; Chemistry; Chemistry and Materials Science; Computer Applications in Chemistry; Constraints; Correspondence; Drug Design; Histology; Humans; Information theory; Morphology; Physical Chemistry; Proto-Oncogene Proteins c-bcl-2 - antagonists & inhibitors; Proto-Oncogene Proteins c-bcl-2 - chemistry; Proto-Oncogene Proteins c-bcl-2 - metabolism; Theoretical analysis
• ISSN: 0920-654X; 1573-4951; 1573-4951
• DOI: 10.1007/s10822-024-00571-3

Over the last decade, automatic chemical design frameworks for discovering molecules with drug-like properties have significantly progressed. Among them, the variational autoencoder (VAE) is a cutting-edge approach that models the tractable latent space of the molecular space. In particular, the usage of a VAE along with a property estimator has attracted considerable interest because it enables gradient-based optimization of a given molecule. However, although successful results have been achieved experimentally, the theoretical background and prerequisites for the correct operation of this method have not yet been clarified. In view of the above, we theoretically analyze and rigorously reconstruct the entire framework. From the perspective of parameterized distribution and the information theory, we first describe how the previous model overcomes the limitations of the beta VAE in discovering molecules with the desired properties. Furthermore, we describe the prerequisites for training the above model. Next, from the log-likelihood perspective of each term, we reformulate the objectives for exploring latent space to generate drug-like molecules. The distributional constraints are defined in this study, which will break away from the invalid molecular search. We demonstrated that our model could discover a novel chemical compound for targeting BCL-2 family proteins in de novo approach. Through the theoretical analysis and practical implementation, the importance of the aforementioned prerequisites and constraints to operate the model was verified.