用神经网络势实现全自动药物晶型预测,大幅降低计算成本与人力需求。
Toward Routine CSP of Pharmaceuticals: A Fully Automated Protocol Using Neural Network Potentials
- 基于专为药物晶型设计的神经网络势,实现全自动结构生成与排序。
- 在49个药物分子上成功复现110种实验晶型,平均耗时仅8.4千核时。
- 可并行运行于实验筛选中,助力药物研发早期快速决策。
晶型预测(CSP)是制药开发中识别和评估多晶型风险的重要工具,但其广泛应用受限于高计算成本及对人工干预和专家知识的依赖。本文提出一种完全自动化的高通量CSP流程,核心为专为药物晶型生成与排序设计的新型神经网络势(Lavo-NN)。该方法集成于可扩展的云工作流中。在包含49种独特分子(几乎全为类药分子)的回溯性基准测试中,成功生成了全部110种$Z' = 1$的实验晶型。该基准的平均计算量约为8.4千核时,显著低于其他协议。通过案例研究解决了实验数据歧义,并在半盲挑战中仅凭粉末X射线衍射图谱成功识别并排序三种现代药物的晶型。该流程显著降低时间和成本,使CSP可提前部署于药物发现阶段,如先导化合物优化。快速响应与高通量特性支持与实验筛选并行运行,为化学家提供实时指导。
原文摘要 · Abstract (English)
Crystal structure prediction (CSP) is a useful tool in pharmaceutical development for identifying and assessing risks associated with polymorphism, yet widespread adoption has been hindered by high computational costs and the need for both manual specification and expert knowledge to achieve useful results. Here, we introduce a fully automated, high-throughput CSP protocol designed to overcome these barriers. The protocol's efficiency is driven by Lavo-NN, a novel neural network potential (NNP) architected and trained specifically for pharmaceutical crystal structure generation and ranking. This NNP-driven crystal generation phase is integrated into a scalable cloud-based workflow. We validate this CSP protocol on an extensive retrospective benchmark of 49 unique molecules, almost all of which are drug-like, successfully generating structures that match all 110 $Z' = 1$ experimental polymorphs. The average CSP in this benchmark is performed with approximately 8.4k CPU hours, which is a significant reduction compared to other protocols. The practical utility of the protocol is further demonstrated through case studies that resolve ambiguities in experimental data and a semi-blinded challenge that successfully identifies and ranks polymorphs of three modern drugs from powder X-ray diffraction patterns alone. By significantly reducing the required time and cost, the protocol enables CSP to be routinely deployed earlier in the drug discovery pipeline, such as during lead optimization. Rapid turnaround times and high throughput also enable CSP that can be run in parallel with experimental screening, providing chemists with real-time insights to guide their work in the lab.
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