A Deep Learning Proteomic Scale Approach for Drug Design

Abstract Computational approaches have accelerated novel therapeutic discovery in recent decades. The Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multi-target therapeutic discovery, repurposing, and design aims to improve their efficacy and safety by employing a holistic approach by computing interaction signatures between every drug/compound and a large library of non-redundant protein structures corresponding to the human proteome fold space. These signatures are compared and analyzed to determine if a given drug/compound is efficacious and safe for a given indication/disease. In this study, we used a deep learning based autoencoder to first reduce the dimensionality of CANDO computed drug-proteome interaction signatures. We then employed a reduced conditional variational autoencoder to generate novel drug-like compounds when given a target encoded “objective” signature. Using this model, we designed compounds to recreate the interaction signatures for twenty approved and experimental drugs and showed that 16/20 designed compounds are predicted to be significantly (p-value ≤ .05) more behaviorally similar relative to all corresponding controls, and 20/20 are predicted to be more behaviorally similar relative to a random control. We further observed that redesigns of objectives developed via rational drug design perform significantly better than those derived from natural sources (p-value ≤ .05), suggesting that the model has learned an abstraction of rational drug design. We also show that designed compounds are structurally diverse and synthetically feasible when compared to their respective objective drugs despite consistently high predicted behavioral similarity. Finally, we generated new designs that enhance thirteen drugs/compounds associated with non-small cell lung cancer and anti-aging properties using their predicted proteomic interaction signatures. This work represents a significant step forward in automating holistic therapeutic design with machine learning, and subsequently offers a reduction in the time needed to generate novel, effective, and safe drug leads for any indication.