Leveraging language model for advanced multiproperty molecular optimization via prompt engineering

Optimizing a candidate molecule’s physiochemical and functional properties has been a critical task in drug and material design. Although the non-trivial task of balancing multiple (potentially conflicting) optimization objectives is considered ideal for artificial intelligence, several technical challenges such as the scarcity of multiproperty-labelled training data have hindered the development of a satisfactory AI solution for a long time. Prompt-MolOpt is a tool for molecular optimization; it makes use of prompt-based embeddings, as used in large language models, to improve the transformer’s ability to optimize molecules for specific property adjustments. Notably, Prompt-MolOpt excels in working with limited multiproperty data (even under the zero-shot setting) by effectively generalizing causal relationships learned from single-property datasets. In comparative evaluations against established models such as JTNN, hierG2G and Modof, Prompt-MolOpt achieves over a 15% relative improvement in multiproperty optimization success rates compared with the leading Modof model. Furthermore, a variant of Prompt-MolOpt, named Prompt-MolOpt^P, can preserve the pharmacophores or any user-specified fragments under the structural transformation, further broadening its application scope. By constructing tailored optimization datasets, with the protocol introduced in this work, Prompt-MolOpt steers molecular optimization towards domain-relevant chemical spaces, enhancing the quality of the optimized molecules. Real-world tests, such as those involving blood–brain barrier permeability optimization, underscore its practical relevance. Prompt-MolOpt offers a versatile approach for multiproperty and multi-site molecular optimizations, suggesting its potential utility in chemistry research and drug and material discovery.