MegaSyn: Integrating Generative Molecular Design, Automated Analog Designer, and Synthetic Viability Prediction

Generative machine learning models have become widely adopted in drug discovery and other fields to produce new molecules and explore molecular space, with the goal of discovering novel compounds with optimized properties. These generative models are frequently combined with transfer learning or scoring of the physicochemical properties to steer generative design, yet often, they are not capable of addressing a wide variety of potential problems, as well as converge into similar molecular space when combined with a scoring function for the desired properties. In addition, these generated compounds may not be synthetically feasible, reducing their capabilities and limiting their usefulness in real-world scenarios. Here, we introduce a suite of automated tools called MegaSyn representing three components: a new hill-climb algorithm, which makes use of SMILES-based recurrent neural network (RNN) generative models, analog generation software, and retrosynthetic analysis coupled with fragment analysis to score molecules for their synthetic feasibility. We show that by deconstructing the targeted molecules and focusing on substructures, combined with an ensemble of generative models, MegaSyn generally performs well for the specific tasks of generating new scaffolds as well as targeted analogs, which are likely synthesizable and druglike. We now describe the development, benchmarking, and testing of this suite of tools and propose how they might be used to optimize molecules or prioritize promising lead compounds using these RNN examples provided by multiple test case examples.