Target-specific novel molecules with their recipe: Incorporating synthesizability in the design process

Abstract

Application of Artificial intelligence (AI) in drug discovery has led to several success stories in recent times. While traditional methods mostly relied upon screening large chemical libraries for early-stage drug-design, de novo design can help identify novel target-specific molecules by sampling from a much larger chemical space. Although this has increased the possibility of finding diverse and novel molecules from previously unexplored chemical space, this has also posed a great challenge for medicinal chemists to synthesize at least some of the de novo designed novel molecules for experimental validation. To address this challenge, in this work, we propose a novel forward synthesis-based generative AI method, which is used to explore the synthesizable chemical space. The method uses a structure-based drug design framework, where the target protein structure and a target-specific seed fragment from co-crystal structures can be the initial inputs. A random fragment from a purchasable fragment library can also be the input if a target-specific fragment is unavailable. Then a template-based forward synthesis route prediction and molecule generation is performed in parallel using the Monte Carlo Tree Search (MCTS) method where, the subsequent fragments for molecule growth can again be obtained from a purchasable fragment library. The rewards for each iteration of MCTS are computed using a drug-target affinity (DTA) model based on the docking pose of the generated reaction intermediates at the binding site of the target protein of interest. With the help of the proposed method, it is now possible to overcome one of the major obstacles posed to the AI-based drug design approaches through the ability of the method to design novel target-specific synthesizable molecules.

Keywords: Drug design; Forward synthesis; Generative model; Monte Carlo tree search; Structure-based framework.