Abstract:Rational design of covalent inhibitors requires simultaneously optimizing multiple properties, such as binding affinity, target selectivity, or electrophilic reactivity. This presents a multi-objective problem not easily addressed by screening alone. Here we present a machine learning pipeline for generating covalent inhibitor candidates using multi-objective reinforcement learning (RL), applied to two targets: epidermal growth factor receptor (EGFR) and acetylcholinesterase (ACHE). A SMILES-based pretrained LSTM serves as the generative model, optimized via policy gradient RL with Pareto crowding distance to balance competing scoring functions including synthetic accessibility, predicted covalent activity, residue affinity, and an approximated docking score. The pipeline rediscovers known covalent inhibitors at rates of up to 0.50% (EGFR) and 0.74% (ACHE) in 10,000-structure runs, with candidate structures achieving warhead-to-residue distances as short as 5.5 angstrom (EGFR) and 3.2 angstrom (ACHE) after further docking-based screening. More notably, the pipeline spontaneously generates structures bearing warhead motifs absent from the training data - including allenes, 3-oxo-$\beta$-sultams, and $\alpha$-methylene-$\beta$-lactones - all of which have independent literature support as covalent warheads. These results suggest that RL-guided generation can explore covalent chemical space beyond its training distribution, and may be useful as a tool for medicinal chemists working on covalent drug discovery.
| Subjects: | Machine Learning (cs.LG) |
| Cite as: | arXiv:2604.20019 [cs.LG] |
| (or arXiv:2604.20019v1 [cs.LG] for this version) | |
| https://doi.org/10.48550/arXiv.2604.20019 arXiv-issued DOI via DataCite (pending registration) |
From: Renee Gil [view email]
[v1]
Tue, 21 Apr 2026 21:54:53 UTC (5,821 KB)
此内容由惯性聚合(RSS阅读器)自动聚合整理，仅供阅读参考。 原文来自 — 版权归原作者所有。