Few-shot molecular property optimization via a domain-specialized large language model

Abstract

Large language models (LLMs) have revolutionized machine learning with their few-shot learning and reasoning capabilities, demonstrating impressive results in fields like natural language processing and computer vision. However, when applied to the domains of biology and chemistry, current LLMs face substantial limitations, particularly in capturing the nuanced relationships between the molecular structure and pharmacochemical properties. This challenge has constrained the application of few-shot learning for small-molecule generation and optimization in drug discovery. Here, we introduce DrugLLM, a novel LLM tailored specifically for molecular optimization. DrugLLM leverages Functional Group Tokenization (FGT), which effectively tokenizes molecules for LLM learning, achieving over 53% token compression compared to SMILES. Besides, we propose a new pre-training strategy that enables DrugLLM to iteratively predict and modify molecular structures based on a few prior modifications, aligning each modification toward optimizing a specified pharmacological property. In multiple computational experiments, DrugLLM achieved state-of-the-art performance in few-shot molecular generation, surpassing all the mainstream LLMs including GPT-4. Furthermore, by applying DrugLLM to optimize HCN2 inhibitors, two bioactive compounds were obtained and successfully validated through wet-lab experiments. These results highlight the robust potential of DrugLLM in accelerating the optimization of molecules and AI-driven drug discovery.