ReBADD-SE: Multi-objective molecular optimisation using SELFIES fragment and off-policy self-critical sequence training
Jonghwan Choi, Sangmin Seo, Seungyeon Choi, Shengmin Piao, Chihyun Park, Sung Jin Ryu, Byung Ju Kim, Sanghyun Park
Abstract
The discovery of drugs to selectively remove disease-related cells is challenging in computer-aided drug design. Many studies have proposed multi-objective molecular generation methods and demonstrated their superiority using the public benchmark dataset for kinase inhibitor generation tasks. However, the dataset does not contain many molecules that violate Lipinski's rule of five. Thus, it remains unclear whether existing methods are effective in generating molecules violating the rule, such as navitoclax. To address this, we analysed the limitations of existing methods and propose a multi-objective molecular generation method with a novel parsing algorithm for molecular string representation and a modified reinforcement learning method for the efficient training of multi-objective molecular optimisation. The proposed model had success rates of 84% in GSK3b+JNK3 inhibitor generation and 99% in Bcl-2 family inhibitor generation tasks.