Suppr超能文献

通过沉积/升华炼金术路径在集合中进行晶体多晶型搜索。

Crystal Polymorph Search in the Ensemble via a Deposition/Sublimation Alchemical Path.

作者信息

Nessler Aaron J, Okada Okimasa, Kinoshita Yuya, Nishimura Koki, Nagata Hiroomi, Fukuzawa Kaori, Yonemochi Etsuo, Schnieders Michael J

机构信息

Department of Biomedical Engineering, University of Iowa, 103 South Capitol Street, 5601 Seamans Center for the Engineering Arts and Sciences, Iowa City, Iowa 52242, United States.

Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan.

出版信息

Cryst Growth Des. 2024 Mar 9;24(8):3205-3217. doi: 10.1021/acs.cgd.3c01358. eCollection 2024 Apr 17.

Abstract

The formulation of active pharmaceutical ingredients involves discovering stable crystal packing arrangements or polymorphs, each of which has distinct pharmaceutically relevant properties. Traditional experimental screening techniques utilizing various conditions are commonly supplemented with in silico crystal structure prediction (CSP) to inform the crystallization process and mitigate risk. Predictions are often based on advanced classical force fields or quantum mechanical calculations that model the crystal potential energy landscape but do not fully incorporate temperature, pressure, or solution conditions during the search procedure. This study proposes an innovative alchemical path that utilizes an advanced polarizable atomic multipole force field to predict crystal structures based on direct sampling of the ensemble. The use of alchemical (i.e., nonphysical) intermediates, a novel Monte Carlo barostat, and an orthogonal space tempering bias combine to enhance the sampling efficiency of the deposition/sublimation phase transition. The proposed algorithm was applied to 2-((4-(2-(3,4-dichlorophenyl)ethyl)phenyl)amino)benzoic acid (Cambridge Crystallography Database Centre ID: XAFPAY) as a case study to showcase the algorithm. Each experimentally determined polymorph with one molecule in the asymmetric unit was successfully reproduced via approximately 1000 short 1 ns simulations per space group where each simulation was initiated from random rigid body coordinates and unit cell parameters. Utilizing two threads of a recent Intel CPU (a Xeon Gold 6330 CPU at 2.00 GHz), 1 ns of sampling using the polarizable AMOEBA force field can be acquired in 4 h (equating to more than 300 ns/day using all 112 threads/56 cores of a dual CPU node) within the Force Field X software (https://ffx.biochem.uiowa.edu). These results demonstrate a step forward in the rigorous use of the ensemble during the CSP search process and open the door to future algorithms that incorporate solution conditions using continuum solvation methods.

摘要

活性药物成分的制剂涉及发现稳定的晶体堆积排列或多晶型物,每种多晶型物都具有独特的与药学相关的性质。利用各种条件的传统实验筛选技术通常辅以计算机晶体结构预测(CSP),以指导结晶过程并降低风险。预测通常基于先进的经典力场或量子力学计算,这些计算对晶体势能面进行建模,但在搜索过程中并未充分考虑温度、压力或溶液条件。本研究提出了一种创新的炼金术路径,该路径利用先进的可极化原子多极子力场,通过对系综的直接采样来预测晶体结构。炼金术(即非物理)中间体的使用、一种新型蒙特卡洛恒压器以及正交空间回火偏差相结合,提高了沉积/升华相变的采样效率。将所提出的算法应用于2-((4-(2-(3,4-二氯苯基)乙基)phenyl)氨基)苯甲酸(剑桥晶体学数据库中心编号:XAFPAY)作为案例研究,以展示该算法。每个不对称单元中有一个分子的每个实验确定的多晶型物,通过每个空间群约1000次短的1纳秒模拟成功再现,其中每次模拟均从随机刚体坐标和晶胞参数开始。利用英特尔最新款CPU的两个线程(2.00 GHz的至强金牌6330 CPU),在Force Field X软件(https://ffx.biochem.uiowa.edu)中,使用可极化AMOEBA力场进行1纳秒的采样可在4小时内完成(相当于使用双CPU节点的所有112个线程/56个核心时每天超过300纳秒)。这些结果表明在CSP搜索过程中严格使用系综方面向前迈进了一步,并为未来使用连续溶剂化方法纳入溶液条件开了先河。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7dfb/11036363/05f021af2dd4/cg3c01358_0001.jpg

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验