Learning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning

• URL: http://arxiv.org/abs/2004.12485v2
• Date: Wed, 20 May 2020 03:28:15 GMT
• Title: Learning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning
• Authors: Sai Krishna Gottipati, Boris Sattarov, Sufeng Niu, Yashaswi Pathak, Haoran Wei, Shengchao Liu, Karam M. J. Thomas, Simon Blackburn, Connor W. Coley, Jian Tang, Sarath Chandar, Yoshua Bengio
• Abstract summary: We propose a novel forward synthesis framework powered by reinforcement learning (RL) for de novo drug design. In this setup, the agent learns to navigate through the immense synthetically accessible chemical space. We describe how the end-to-end training in this study represents an important paradigm in radically expanding the synthesizable chemical space.
• Score: 75.95376096628135
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Over the last decade, there has been significant progress in the field of machine learning for de novo drug design, particularly in deep generative models. However, current generative approaches exhibit a significant challenge as they do not ensure that the proposed molecular structures can be feasibly synthesized nor do they provide the synthesis routes of the proposed small molecules, thereby seriously limiting their practical applicability. In this work, we propose a novel forward synthesis framework powered by reinforcement learning (RL) for de novo drug design, Policy Gradient for Forward Synthesis (PGFS), that addresses this challenge by embedding the concept of synthetic accessibility directly into the de novo drug design system. In this setup, the agent learns to navigate through the immense synthetically accessible chemical space by subjecting commercially available small molecule building blocks to valid chemical reactions at every time step of the iterative virtual multi-step synthesis process. The proposed environment for drug discovery provides a highly challenging test-bed for RL algorithms owing to the large state space and high-dimensional continuous action space with hierarchical actions. PGFS achieves state-of-the-art performance in generating structures with high QED and penalized clogP. Moreover, we validate PGFS in an in-silico proof-of-concept associated with three HIV targets. Finally, we describe how the end-to-end training conceptualized in this study represents an important paradigm in radically expanding the synthesizable chemical space and automating the drug discovery process.

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