Exploring fragment adding strategies to enhance molecule pretraining in AI-driven drug discovery

The effectiveness of AI-driven drug discovery can be enhanced by pretraining on small molecules. However, the conventional masked language model pretraining techniques are not suitable for molecule pretraining due to the limited vocabulary size and the non-sequential structure of molecules. To overcome these challenges, we propose FragAdd, a strategy that involves adding a chemically implausible molecular fragment to the input molecule. This approach allows for the incorporation of rich local information and the generation of a high-quality graph representation, which is advantageous for tasks like virtual screening. Consequently, we have developed a virtual screening protocol that focuses on identifying estrogen receptor alpha binders on a nucleus receptor. Our results demonstrate a significant improvement in the binding capacity of the retrieved molecules. Additionally, we demonstrate that the FragAdd strategy can be combined with other self-supervised methods to further expedite the drug discovery process.