Integrating Generative Pretrained Transformer and Genetic Algorithms for Efficient and Diverse Molecular Generation

In computer-aided drug design, molecular generation models play a crucial role in accelerating the drug development process. Current models mainly fall into two categories: deep learning models with high performance but poor interpretability and heuristic algorithms with better interpretability but limited performance. In this study, we introduce an innovative molecular generation model, the compound construction model (CCMol), which integrates the powerful generative capabilities of the generative pretrained transformer (GPT) and the efficient optimization mechanisms of genetic algorithms (GA) to achieve effective and innovative molecular structures. Specifically, our approach uses structure-based drug design comprising both ligand and protein primary structure-based aspects. CCMol integrates GPT for initial molecular generation and GA for iterative optimization of physicochemical and biological properties. The model's reliability was validated by generating molecules targeting three critical disease-related proteins (GLP1, WRN, and JAK2). The results indicate that CCMol is on average with current advanced models in multiple indicators and performs better than the baseline model in terms of structure diversity and drug-related properties indicators, demonstrating that CCMol exhibits outstanding performance in developing novel and effective candidate drug molecules, particularly suitable for expanding the chemical validity of candidate structures at the early stages of drug discovery.