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Article(id=1236689047532392856, tenantId=1146029695717560320, journalId=1235980733773295621, issueId=1236689043514257626, articleNumber=null, orderNo=null, doi=null, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=null, receivedDateStr=null, revisedDate=null, revisedDateStr=null, acceptedDate=1662048000000, acceptedDateStr=2022-09-02, onlineDate=1772779245503, onlineDateStr=2026-03-06, pubDate=1680105600000, pubDateStr=2023-03-30, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1772779245503, onlineIssueDateStr=2026-03-06, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1772779245503, creator=13701087609, updateTime=1772779245503, updator=13701087609, issue=Issue{id=1236689043514257626, tenantId=1146029695717560320, journalId=1235980733773295621, year='2023', volume='32', issue='6', pageStart='553', pageEnd='656', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1772779244545, creator=13701087609, updateTime=1772779562627, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1236690377705575144, tenantId=1146029695717560320, journalId=1235980733773295621, issueId=1236689043514257626, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1236690377705575145, tenantId=1146029695717560320, journalId=1235980733773295621, issueId=1236689043514257626, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=610, endPage=617, ext={EN=ArticleExt(id=1236689048174121372, articleId=1236689047532392856, tenantId=1146029695717560320, journalId=1235980733773295621, language=EN, title=Molecular dynamics simulation study of IDH1R132H mutant protein and its inhibitor AG-881, columnId=null, journalTitle=Chinese Journal of New Drugs, columnName=null, runingTitle=null, highlight=null, articleAbstract=
Objective:

To investigate the mechanism of compound AG-881 on inhibiting IDH1R132H mutant protein by molecular dynamics method.

Methods:

The activated IDH1R132H protein structure and inactivated AG-881-IDH1R132H protein structure were constructed respectively and placed in a stereoscopic box. Molecular dynamics simulations were carried out on each system for 100 ns. The protein conformations of different systems were compared, and hydrogen bond analysis, energy analysis and principal component analysis (PCA), etc. were performed.

Results:

Substrate α-KG could stabilize IDH1R132H protein in the activated closed conformation. After AG-881 acted on the allosteric site of the protein at dimer interface, it made IDH1R132H in the open conformation of inactive state. In this process, amino acid residue Gln277 participated into the binding of AG-881. At the same time, hydrophobic occupation and hydrogen bond contributed mainly to the binding of AG-881 to IDH1R132H. In addition, halogen bond also played a certain role.

Conclusion:

Molecular dynamics simulation can be used as an effective aid for allosteric inhibitor design, and the potential mechanism of AG-881 inhibiting IDH1R132H activity can be studied, which can further provide theoretical guidance for the development of new drugs targeting IDH1 mutant proteins.

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目的：

采用分子动力学模拟方法研究化合物AG-881（vorasidenib）抑制IDH1R132H突变蛋白的作用机制。

方法：

分别构建激活态的IDH1R132H突变蛋白结构和失活态的AG-881-IDH1R132H突变蛋白结构，置于立体水盒子内，进行100 ns的分子动力学模拟，比较不同体系的蛋白构象并分析氢键、能量和主成分等性质。

结果：

底物α-KG可使IDH1R132H突变蛋白稳定在活化状态的闭合构象。AG-881作用于蛋白二聚体界面的变构位点后，使IDH1R132H突变蛋白处于非活化状态的开放构象，发挥抑制作用。在作用过程中，氨基酸残基Gln277在AG-881的结合中起重要作用。同时，疏水作用和氢键在AG-881与IDH1R132H突变蛋白的结合中也做出重要贡献。此外，卤键也起到一定作用。

结论：

分子动力学模拟可以作为变构抑制剂设计的有效辅助手段，探索研究AG-881抑制IDH1R132H突变蛋白活性的潜在作用机制，进一步为以IDH1突变蛋白为靶点的新药研发提供一定的理论指导。

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孟凡翠，女，研究员，主要从事计算机辅助药物设计与虚拟筛选研究。E-mail: 。
刘巍，男，研究员，主要从事新药筛选与评价研究。E-mail: 。
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邵婷婷，女，硕士研究生，主要从事药理学研究。E-mail: 。

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邵婷婷，女，硕士研究生，主要从事药理学研究。E-mail: 。

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邵婷婷，女，硕士研究生，主要从事药理学研究。E-mail: 。

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IDH1R132H突变蛋白与其抑制剂AG-881的分子动力学模拟研究
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邵婷婷 1, 2 , 孔晓华 2 , 靳京 2, 3 , 孟凡翠 2, 3, 4 , 刘巍 2, 3, 4
中国新药杂志 | 实验研究 2023,32(6): 610-617
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中国新药杂志 | 实验研究 2023, 32(6): 610-617
IDH1R132H突变蛋白与其抑制剂AG-881的分子动力学模拟研究
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邵婷婷1, 2 , 孔晓华2, 靳京2, 3, 孟凡翠2, 3, 4 , 刘巍2, 3, 4
作者信息
  • 1天津医科大学药学院，天津 300070
  • 2天津药物研究院有限公司天津市新药设计与发现重点实验室，天津 300450
  • 3释药技术与药动学国家重点实验室，天津 300301
  • 4天津药物研究院中国医学科学院药物代谢新技术创新单元，天津 300301

    • 邵婷婷，女，硕士研究生，主要从事药理学研究。E-mail: 。

通讯作者:

孟凡翠，女，研究员，主要从事计算机辅助药物设计与虚拟筛选研究。E-mail: 。
刘巍，男，研究员，主要从事新药筛选与评价研究。E-mail: 。
Molecular dynamics simulation study of IDH1R132H mutant protein and its inhibitor AG-881
Ting-ting SHAO1, 2 , Xiao-hua KONG2, Jing JIN2, 3, Fan-cui MENG2, 3, 4 , Wei LIU2, 3, 4
Affiliations
  • 1Pharmacy College, Tianjin Medical University, Tianjin 300070, China
  • 2Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300450, China
  • 3State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin 300301, China
  • 4Tianjin Institute of Pharmaceutical Research, Research Unit for Drug Metabolism, Chinese Academy of Medical Sciences, Tianjin 300301, China
出版时间: 2023-03-30
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目的：

采用分子动力学模拟方法研究化合物AG-881（vorasidenib）抑制IDH1R132H突变蛋白的作用机制。

方法：

分别构建激活态的IDH1R132H突变蛋白结构和失活态的AG-881-IDH1R132H突变蛋白结构，置于立体水盒子内，进行100 ns的分子动力学模拟，比较不同体系的蛋白构象并分析氢键、能量和主成分等性质。

结果：

底物α-KG可使IDH1R132H突变蛋白稳定在活化状态的闭合构象。AG-881作用于蛋白二聚体界面的变构位点后，使IDH1R132H突变蛋白处于非活化状态的开放构象，发挥抑制作用。在作用过程中，氨基酸残基Gln277在AG-881的结合中起重要作用。同时，疏水作用和氢键在AG-881与IDH1R132H突变蛋白的结合中也做出重要贡献。此外，卤键也起到一定作用。

结论：

分子动力学模拟可以作为变构抑制剂设计的有效辅助手段，探索研究AG-881抑制IDH1R132H突变蛋白活性的潜在作用机制，进一步为以IDH1突变蛋白为靶点的新药研发提供一定的理论指导。

异柠檬酸脱氢酶1  /  分子动力学  /  AG-881  /  氨基酸残基  /  变构位点
Objective:

To investigate the mechanism of compound AG-881 on inhibiting IDH1R132H mutant protein by molecular dynamics method.

Methods:

The activated IDH1R132H protein structure and inactivated AG-881-IDH1R132H protein structure were constructed respectively and placed in a stereoscopic box. Molecular dynamics simulations were carried out on each system for 100 ns. The protein conformations of different systems were compared, and hydrogen bond analysis, energy analysis and principal component analysis (PCA), etc. were performed.

Results:

Substrate α-KG could stabilize IDH1R132H protein in the activated closed conformation. After AG-881 acted on the allosteric site of the protein at dimer interface, it made IDH1R132H in the open conformation of inactive state. In this process, amino acid residue Gln277 participated into the binding of AG-881. At the same time, hydrophobic occupation and hydrogen bond contributed mainly to the binding of AG-881 to IDH1R132H. In addition, halogen bond also played a certain role.

Conclusion:

Molecular dynamics simulation can be used as an effective aid for allosteric inhibitor design, and the potential mechanism of AG-881 inhibiting IDH1R132H activity can be studied, which can further provide theoretical guidance for the development of new drugs targeting IDH1 mutant proteins.

isocitrate dehydrogenase 1  /  molecular dynamics  /  AG-881  /  amino acid residue  /  allosteric site
邵婷婷, 孔晓华, 靳京, 孟凡翠, 刘巍. IDH1R132H突变蛋白与其抑制剂AG-881的分子动力学模拟研究. 中国新药杂志, 2023 , 32 (6) : 610 -617 .
Ting-ting SHAO, Xiao-hua KONG, Jing JIN, Fan-cui MENG, Wei LIU. Molecular dynamics simulation study of IDH1R132H mutant protein and its inhibitor AG-881[J]. Chinese Journal of New Drugs, 2023 , 32 (6) : 610 -617 .
基金
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  • 中国医学科学院医学与健康科技创新工程项目(2019-I2M-5-020)
2023年第32卷第6期
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  • 首发时间：2026-03-06
  • 出版时间：2023-03-30
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  • 录用日期：2022-09-02
基金
中国医学科学院医学与健康科技创新工程项目(2019-I2M-5-020)
作者信息
    1天津医科大学药学院，天津 300070
    2天津药物研究院有限公司天津市新药设计与发现重点实验室，天津 300450
    3释药技术与药动学国家重点实验室，天津 300301
    4天津药物研究院中国医学科学院药物代谢新技术创新单元，天津 300301

通讯作者:

孟凡翠，女，研究员，主要从事计算机辅助药物设计与虚拟筛选研究。E-mail: 。
刘巍，男，研究员，主要从事新药筛选与评价研究。E-mail: 。
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2种不同金属材料的力学参数
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Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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