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一种强大的晶体结构预测方法,用于支持小分子药物开发,并进行大规模验证和盲法研究。

A robust crystal structure prediction method to support small molecule drug development with large scale validation and blind study.

作者信息

Zhou Dong, Bier Imanuel, Santra Biswajit, Jacobson Leif D, Wu Chuanjie, Garaizar Suarez Adiran, Almaguer Barbara Ramirez, Yu Haoyu, Abel Robert, Friesner Richard A, Wang Lingle

机构信息

Schrödinger Inc., New York: 1540 Broadway, 24th Floor, 10036, New York, NY, USA.

Atommap Inc. 450 Lexington Avenue, 4th floor, 10017, New York, NY, USA.

出版信息

Nat Commun. 2025 Mar 5;16(1):2210. doi: 10.1038/s41467-025-57479-1.

Abstract

Crystal polymorphism is an important and fascinating aspect of solid state chemistry with far reaching implications in the pharmaceuticals, agrisciences, nutraceuticals, battery and aviation industries. Late appearing more stable polymorphs have caused numerous issues in the pharmaceutical industry. Experimental polymorph screening can be very expensive and time consuming, and sometimes may miss important low energy polymorphs due to an inability to exhaust all crystallization conditions. In this paper, we report a crystal structure prediction (CSP) method with state of the art accuracy and efficiency, validated on a large and diverse dataset including 66 molecules with 137 experimentally known polymorphic forms. The method combines a novel systematic crystal packing search algorithm and the use of machine learning force fields in a hierarchical crystal energy ranking. Our method not only reproduces all the experimentally known polymorphs, but also suggests new low energy polymorphs yet to be discovered by experiment that might pose potential risks to development of the currently known forms of these compounds. In addition, we report the prediction results of a blinded study, results for Target XXXI from the seventh CSP blind test, and demonstrate how the method can be used to accelerate clinical formulation design and derisk downstream processing.

摘要

晶体多晶型现象是固态化学中一个重要且引人入胜的方面,在制药、农业科学、营养保健品、电池和航空工业等领域有着深远的影响。后期出现的更稳定的多晶型物在制药行业引发了诸多问题。实验性多晶型筛选可能非常昂贵且耗时,有时由于无法穷尽所有结晶条件,可能会遗漏重要的低能量多晶型物。在本文中,我们报告了一种具有先进准确性和效率的晶体结构预测(CSP)方法,该方法在一个大型且多样的数据集上得到了验证,该数据集包括66个分子的137种实验已知的多晶型形式。该方法结合了一种新颖的系统晶体堆积搜索算法,并在分层晶体能量排序中使用机器学习力场。我们的方法不仅重现了所有实验已知的多晶型物,还提出了尚未被实验发现的新的低能量多晶型物,这些多晶型物可能会对这些化合物目前已知形式的开发构成潜在风险。此外,我们报告了一项盲测的预测结果、第七届CSP盲测中目标XXXI的结果,并展示了该方法如何用于加速临床制剂设计和降低下游加工风险。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f371/11882951/578cb8171800/41467_2025_57479_Fig1_HTML.jpg

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