Designing a Prospective COVID-19 Therapeutic with Reinforcement Learning

Marcin J. Skwark, Nicolás López Carranza, Thomas Pierrot, Joe Phillips, Slim Said, Alexandre Laterre, Amine Kerkeni, Uğur Şahin, Karim Beguir

The SARS-CoV-2 pandemic has created a global race for a cure. One approach focuses on designing a novel variant of the human angiotensin-converting enzyme 2 (ACE2) that binds more tightly to the SARS-CoV-2 spike protein and diverts it from human cells. Here we formulate a novel protein design framework as a reinforcement learning problem. We generate new designs efficiently through the combination of a fast, biologically-grounded reward function and sequential action-space formulation. The use of Policy Gradients reduces the compute budget needed to reach consistent, high-quality designs by at least an order of magnitude compared to standard methods. Complexes designed by this method have been validated by molecular dynamics simulations, confirming their increased stability. This suggests that combining leading protein design methods with modern deep reinforcement learning is a viable path for discovering a Covid-19 cure and may accelerate design of peptide-based therapeutics for other diseases.

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