Prediction of the Relative Free Energies of Drug Polymorphs above Zero Kelvin

Yang Mingjun; Dybeck Eric; Sun Guangxu; Peng Chunwang; Samas Brian; Burger Virginia M.; Zeng Qun; Jin Yingdi; Bellucci Michael A.; Liu Yang; Zhang Peiyu; Ma Jian; Jiang Yide Alan; Hancock Bruno C.; Wen Shuhao; Wood Geoffrey P. F.

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Prediction of the Relative Free Energies of Drug Polymorphs above Zero Kelvin

机译：预测Zelvin高于Zellvin的药物多晶型物的相对能量

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Crystal structure prediction (CSP) calculations can reduce risk and improve efficiency during drug development. Traditionally, CSP calculations use lattice energies computed through density functional theory. While this approach is often successful in predicting the low energy structures, it neglects the crucial role of thermal effects on polymorph stabilities. In the present study, we develop a robust and efficient protocol for predicting the relative stability of polymorphs at different temperatures. The protocol is executed on a highly parallel cloud computing infrastructure to produce results at time scales useful for drug development timelines. We demonstrate this protocol on molecule XXIII from the sixth crystal structure prediction blind test. Our results predict that Form D is the most stable experimentally observed polymorph at ambient temperature and Form C is the most stable at low temperature consistent with experiments also conducted in the present study.

机译：晶体结构预测（CSP）计算可以降低风险，提高药物开发期间的效率。传统上，CSP计算使用通过密度泛函理论计算的晶格能量。虽然这种方法在预测低能量结构方面往往是成功的，但它忽略了热效应对多晶型稳定性的关键作用。在本研究中，我们开发了一种稳健而有效的方案，用于预测不同温度的多晶型物的相对稳定性。该协议在高度平行的云计算基础设施上执行，以产生适用于药物开发时间表的时间尺度的结果。我们在第六晶体结构预测盲试验中展示了本分子XXIII的该方案。我们的结果预测，形式D是环境温度下最稳定的实验观察到的多晶型物，而形式C是在本研究中也进行的实验中的低温下最稳定的。

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《Crystal growth & design》 |2020年第8期|共14页
作者
Yang Mingjun; Dybeck Eric; Sun Guangxu; Peng Chunwang; Samas Brian; Burger Virginia M.; Zeng Qun; Jin Yingdi; Bellucci Michael A.; Liu Yang; Zhang Peiyu; Ma Jian; Jiang Yide Alan; Hancock Bruno C.; Wen Shuhao; Wood Geoffrey P. F.;
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XtalPi Inc Shenzhen Jingtai Technol Co Ltd Shenzhen 518100 Peoples R China;

Pfizer Worldwide R&

D Groton CT 06340 USA;

XtalPi Inc Shenzhen Jingtai Technol Co Ltd Shenzhen 518100 Peoples R China;

XtalPi Inc Shenzhen Jingtai Technol Co Ltd Shenzhen 518100 Peoples R China;

Pfizer Worldwide R&

D Groton CT 06340 USA;

XtalPi Inc Cambridge MA 02142 USA;

XtalPi Inc Shenzhen Jingtai Technol Co Ltd Shenzhen 518100 Peoples R China;

XtalPi Inc Shenzhen Jingtai Technol Co Ltd Shenzhen 518100 Peoples R China;

XtalPi Inc Cambridge MA 02142 USA;

XtalPi Inc Shenzhen Jingtai Technol Co Ltd Shenzhen 518100 Peoples R China;

XtalPi Inc Shenzhen Jingtai Technol Co Ltd Shenzhen 518100 Peoples R China;

XtalPi Inc Shenzhen Jingtai Technol Co Ltd Shenzhen 518100 Peoples R China;

XtalPi Inc Cambridge MA 02142 USA;

Pfizer Worldwide R&

D Groton CT 06340 USA;

XtalPi Inc Cambridge MA 02142 USA;

Pfizer Worldwide R&

D Groton CT 06340 USA;

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正文语种 eng
中图分类晶体学;
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专利

1. Prediction of the Relative Free Energies of Drug Polymorphs above Zero Kelvin [J] . Yang Mingjun, Dybeck Eric, Sun Guangxu, Crystal growth & design . 2020,第8期

机译：预测Zelvin高于Zellvin的药物多晶型物的相对能量
2. QTAIM application in drug development: Prediction of relative stability of drug polymorphs from experimental crystal structures [J] . Abramov Y.A. The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory . 2011,第45期

机译：QTAIM在药物开发中的应用：根据实验晶体结构预测药物多晶型物的相对稳定性
3. Toward Accurate Relative Energy Predictions of the Bioactive Conformation of Drugs [J] . Butler KT, Luque FJ, Barril X Journal of Computational Chemistry: Organic, Inorganic, Physical, Biological . 2009,第4期

机译：对药物生物活性构象的准确相对能量预测
4. Prediction of anti-EGFR drug resistance base on binding free energy and hydrogen bond analysis [C] . Zhou Weiqiang, Wang Debby D., Yan Hong, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology . 2013

机译：基于结合自由能和氢键分析的抗EGFR药物耐药性预测
5. Membrane Permeability Prediction of Drug-like Molecules with Molecular Dynamics and Free Energy Calculations =基於分子動力學和自由能計算的藥物分子膜滲透性預測 [D] . Tse, Chi Hang. 2020

机译：Membrane Permeability Prediction of Drug-like Molecules with Molecular Dynamics and Free Energy Calculations =基于分子动力学和自由能计算的药物分子膜渗透性预测
6. D3R Grand Challenge 2: Blind Prediction of Protein-Ligand Poses Affinity Rankings and Relative Binding Free Energies [O] . Zied Gaieb, Shuai Liu, Symon Gathiaka, -1

机译：D3R大挑战2：蛋白质配体姿势亲和力排名和相对结合自由能的盲目预测
7. Prediction of the Relative Free Energies of Drug Polymorphs above Zero Kelvin [O] . -1

机译：预测Zellvin高于Zellvin的药物多晶型物的相对能量

Prediction of the Relative Free Energies of Drug Polymorphs above Zero Kelvin

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