文献检索文档翻译深度研究
Suppr Zotero 插件Zotero 插件
邀请有礼套餐&价格历史记录

新学期,新优惠

限时优惠:9月1日-9月22日

30天高级会员仅需29元

1天体验卡首发特惠仅需5.99元

了解详情
不再提醒
插件&应用
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
高级版
套餐订阅购买积分包
AI 工具
文献检索文档翻译深度研究
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利:CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2025

Diversity of Long-Lived Intermediates along the Binding Pathway of Imatinib to Abl Kinase Revealed by MD Simulations.

作者信息

Paul Fabian, Thomas Trayder, Roux Benoît

机构信息

Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States.

出版信息

J Chem Theory Comput. 2020 Dec 8;16(12):7852-7865. doi: 10.1021/acs.jctc.0c00739. Epub 2020 Nov 4.


DOI:10.1021/acs.jctc.0c00739
PMID:33147951
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8288498/
Abstract

Imatinib, a drug used for the treatment of chronic myeloid leukemia and other cancers, works by blocking the catalytic site of pathological constitutively active Abl kinase. While the binding pose is known from X-ray crystallography, the different steps leading to the formation of the complex are not well understood. The results from extensive molecular dynamics simulations show that imatinib can primarily exit the known crystallographic binding pose through the cleft of the binding site or by sliding under the αC helix. Once displaced from the crystallographic binding pose, imatinib becomes trapped in intermediate states. These intermediates are characterized by a high diversity of ligand orientations and conformations, and relaxation timescales within this region may exceed 3-4 ms. Analysis indicates that the metastable intermediate states should be spectroscopically indistinguishable from the crystallographic binding pose, in agreement with tryptophan stopped-flow fluorescence experiments.

摘要

相似文献

[1]
Diversity of Long-Lived Intermediates along the Binding Pathway of Imatinib to Abl Kinase Revealed by MD Simulations.

J Chem Theory Comput. 2020-12-8

[2]
Drug repurposing for chronic myeloid leukemia: in silico and in vitro investigation of DrugBank database for allosteric Bcr-Abl inhibitors.

J Biomol Struct Dyn. 2017-6

[3]
Dual-specific Src and Abl kinase inhibitors, PP1 and CGP76030, inhibit growth and survival of cells expressing imatinib mesylate-resistant Bcr-Abl kinases.

Blood. 2003-1-15

[4]
Molecular dynamics simulations provide insights into the origin of gleevec's selectivity toward human tyrosine kinases.

J Biomol Struct Dyn. 2018-11-1

[5]
The First Pentacyclic Triterpenoid Gypsogenin Derivative Exhibiting Anti-ABL1 Kinase and Anti-chronic Myelogenous Leukemia Activities.

Biol Pharm Bull. 2018-4-1

[6]
Dynamics of human protein kinase Aurora A linked to drug selectivity.

Elife. 2018-6-14

[7]
Expanding the structural diversity of Bcr-Abl inhibitors: Hybrid molecules based on GNF-2 and Imatinib.

Bioorg Med Chem Lett. 2015-10-1

[8]
K356dup--an in-frame insertion in the BCR-ABL gene in an imatinib-resistant chronic myeloid leukemia.

Int J Lab Hematol. 2012-12

[9]
A molecular mechanics model for imatinib and imatinib:kinase binding.

J Comput Chem. 2010-5

[10]
Cumulative mechanism of several major imatinib-resistant mutations in Abl kinase.

Proc Natl Acad Sci U S A. 2020-7-27

引用本文的文献

[1]
Probing Functional Allosteric States and Conformational Ensembles of the Allosteric Protein Kinase States and Mutants: Atomistic Modeling and Comparative Analysis of AlphaFold2, OmegaFold, and AlphaFlow Approaches and Adaptations.

J Phys Chem B. 2024-11-14

[2]
Predicting Mutation-Induced Allosteric Changes in Structures and Conformational Ensembles of the ABL Kinase Using AlphaFold2 Adaptations with Alanine Sequence Scanning.

Int J Mol Sci. 2024-9-19

[3]
In silico docking and molecular dynamics for the discovery of inhibitors of enteric methane production in ruminants - A review.

Anim Biosci. 2025-1

[4]
Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of Conformational Ensembles and Detection of Hidden Allosteric States in the ABL1 Protein Kinase.

J Chem Theory Comput. 2024-6-25

[5]
Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics.

Sci Rep. 2024-5-7

[6]
Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib.

J Chem Inf Model. 2024-4-22

[7]
Markov State Models: To Optimize or Not to Optimize.

J Chem Theory Comput. 2024-1-23

[8]
Structural mechanism of a drug-binding process involving a large conformational change of the protein target.

Nat Commun. 2023-4-5

[9]
A Guide to In Silico Drug Design.

Pharmaceutics. 2022-12-23

[10]
Probing conformational landscapes and mechanisms of allosteric communication in the functional states of the ABL kinase domain using multiscale simulations and network-based mutational profiling of allosteric residue potentials.

J Chem Phys. 2022-12-28

本文引用的文献

[1]
Identification of Druggable Kinase Target Conformations Using Markov Model Metastable States Analysis of apo-Abl.

J Chem Theory Comput. 2020-2-13

[2]
Variational selection of features for molecular kinetics.

J Chem Phys. 2019-5-21

[3]
What Makes a Kinase Promiscuous for Inhibitors?

Cell Chem Biol. 2019-1-3

[4]
Optimized Lennard-Jones Parameters for Druglike Small Molecules.

J Chem Theory Comput. 2018-5-7

[5]
Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models.

J Chem Theory Comput. 2018-4-3

[6]
VAMPnets for deep learning of molecular kinetics.

Nat Commun. 2018-1-2

[7]
Tyrosine Kinase Activation and Conformational Flexibility: Lessons from Src-Family Tyrosine Kinases.

Acc Chem Res. 2017-4-20

[8]
Classifying kinase conformations using a machine learning approach.

BMC Bioinformatics. 2017-2-2

[9]
CHARMM36m: an improved force field for folded and intrinsically disordered proteins.

Nat Methods. 2017-1

[10]
Structural propensities of kinase family proteins from a Potts model of residue co-variation.

Protein Sci. 2016-8

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

推荐工具

医学文档翻译智能文献检索