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In this work, we combined Deep Docking and free energy MD simulations for the in silico screening and experimental validation for potential inhibitors of leucine rich repeat kinase 2 (LRRK2) targeting the WD40 repeat (WDR) domain. 

Abstract The development of high‐performance elastomers for additive manufacturing requires overcoming complex property trade‐offs that challenge conventional material discovery pipelines. Here, a human‐in‐the‐loop reinforcement learning (RL) approach is used to discover polyurethane elastomers that overcome pervasive stress–strain property tradeoffs. Starting with a diverse training set of 92 formulations, a coupled multi‐component reward system was identified that guides RL agents toward materials with both high strength and extensibility. Through three rounds of iterative optimization combining RL predictions with human chemical intuition, we identified elastomers with more than double the average toughness compared to the initial training set. The final exploitation round, aided by solubility prescreening, predicted twelve materials exhibiting both high strength (>10 MPa) and high strain at break (>200%). Analysis of the high‐performing materials revealed structure‐property insights, including the benefits of high molar mass urethane oligomers, a high density of urethane functional groups, and incorporation of rigid low molecular weight diols and unsymmetric diisocyanates. These findings demonstrate that machine‐guided, human‐augmented design is a powerful strategy for accelerating polymer discovery in applications where data is scarce and expensive to acquire, with broad applicability to multi‐objective materials optimization. 

The CACHE challenges are a series of prospective benchmarking exercises to evaluate progress in the field of computational hit-finding. Here we report the results of the inaugural CACHE challenge in which 23 computational teams each selected up to 100 commercially available compounds that they predicted would bind to the WDR domain of the Parkinson’s disease target LRRK2, a domain with no known ligand and only an apo structure in the PDB. The lack of known binding data and presumably low druggability of the target is a challenge to computational hit finding methods. Of the 1955 molecules predicted by participants in Round 1 of the challenge, 73 were found to bind to LRRK2 in an SPR assay with a KD lower than 150 μM. These 73 molecules were advanced to the Round 2 hit expansion phase, where computational teams each selected up to 50 analogs. Binding was observed in two orthogonal assays for seven chemically diverse series, with affinities ranging from 18 to 140 μM. The seven successful computational workflows varied in their screening strategies and techniques. Three used molecular dynamics to produce a conformational ensemble of the targeted site, three included a fragment docking step, three implemented a generative design strategy and five used one or more deep learning steps. CACHE #1 reflects a highly exploratory phase in computational drug design where participants adopted strikingly diverging screening strategies. Machine learning-accelerated methods achieved similar results to brute force (e.g., exhaustive) docking. First-in-class, experimentally confirmed compounds were rare and weakly potent, indicating that recent advances are not sufficient to effectively address challenging targets.