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A Quantum-Inspired Approach to De-Novo Drug Design
preprintrevised on 18.05.2020, 09:37 and posted on 18.05.2020, 10:43 by David Snelling, Ganesh Shahane, William Shipman, Alexander Balaeff, Mark Pearce, Shahar Keinan
Design and optimization of targeted drug-like compounds is an important part of the early stage drug discovery process. In this paper, we describe the use of a novel technique for rapid design of lead-like compounds for the Dengue viral RNA-dependent-RNA polymerase (RdRp). Initially, a large (>billions) fragment-based chemical library is designed by mapping relevant pharmacophores to the target binding pocket. The de-novo synthesis of molecules from fragments is formulated as a quadratic unconstrained binary optimization problem that can be solved using the quantum-inspired Digital Annealer (DA), providing an opportunity to take advantage of this fledgling, groundbreaking technology. The DA constrains the search space of molecules with drug-like properties that match the binding pocket and then optimizes for synthetic feasibility and novelty, thus offering significant commercial advantages over existing techniques.