基于丙氨酸扫描与相互作用熵方法的PARP1与配体的结合自由能计算

Youzi Zhang; Xiao Liu; Yifan Zhou; John Z.H. Zhang

doi:10.1360/N032017-00161

基于丙氨酸扫描与相互作用熵方法的PARP1与配体的结合自由能计算

Translated title of the contribution: Calculation of PARP1-ligand binding free energy using alanine scanning and interaction entropy method

Youzi Zhang, Xiao Liu, Yifan Zhou, John Z.H. Zhang

Chemistry

Research output: Contribution to journal › Article › peer-review

Abstract

Poly(ADP-ribose) polymerase 1 (PARP1) is a novel target of cancer medication for its important role in DNA repair. In this article, we use interaction entropy (IE) approach combined with the MM/GBSA method to compute residue-specific protein-ligand binding free energies for ten ligands and these residue-specific binding free energies are combined to produce total protein-ligand binding free energy. Our calculated binding free energies are in much better agreement with the corresponding experimental data than those using standard MM/GBSA approach.

Translated title of the contribution	Calculation of PARP1-ligand binding free energy using alanine scanning and interaction entropy method
Original language	Chinese (Traditional)
Pages (from-to)	204-209
Number of pages	6
Journal	Scientia Sinica Chimica
Volume	48
Issue number	2
DOIs	https://doi.org/10.1360/N032017-00161
State	Published - 2018

Keywords

Binding free energies
Inhibitor
Interaction entropy
MD simulation
MM/GBSA
PARP1

ASJC Scopus subject areas

General Chemistry
Biochemistry
General Chemical Engineering
Materials Chemistry

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title = "基于丙氨酸扫描与相互作用熵方法的PARP1与配体的结合自由能计算",

abstract = "Poly(ADP-ribose) polymerase 1 (PARP1) is a novel target of cancer medication for its important role in DNA repair. In this article, we use interaction entropy (IE) approach combined with the MM/GBSA method to compute residue-specific protein-ligand binding free energies for ten ligands and these residue-specific binding free energies are combined to produce total protein-ligand binding free energy. Our calculated binding free energies are in much better agreement with the corresponding experimental data than those using standard MM/GBSA approach.",

keywords = "Binding free energies, Inhibitor, Interaction entropy, MD simulation, MM/GBSA, PARP1",

author = "Youzi Zhang and Xiao Liu and Yifan Zhou and Zhang, {John Z.H.}",

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year = "2018",

doi = "10.1360/N032017-00161",

language = "Chinese (Traditional)",

volume = "48",

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AU - Zhang, Youzi

AU - Liu, Xiao

AU - Zhou, Yifan

AU - Zhang, John Z.H.

PY - 2018

Y1 - 2018

N2 - Poly(ADP-ribose) polymerase 1 (PARP1) is a novel target of cancer medication for its important role in DNA repair. In this article, we use interaction entropy (IE) approach combined with the MM/GBSA method to compute residue-specific protein-ligand binding free energies for ten ligands and these residue-specific binding free energies are combined to produce total protein-ligand binding free energy. Our calculated binding free energies are in much better agreement with the corresponding experimental data than those using standard MM/GBSA approach.

AB - Poly(ADP-ribose) polymerase 1 (PARP1) is a novel target of cancer medication for its important role in DNA repair. In this article, we use interaction entropy (IE) approach combined with the MM/GBSA method to compute residue-specific protein-ligand binding free energies for ten ligands and these residue-specific binding free energies are combined to produce total protein-ligand binding free energy. Our calculated binding free energies are in much better agreement with the corresponding experimental data than those using standard MM/GBSA approach.

KW - Binding free energies

KW - Inhibitor

KW - Interaction entropy

KW - MD simulation

KW - MM/GBSA

KW - PARP1

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基于丙氨酸扫描与相互作用熵方法的PARP1与配体的结合自由能计算

Abstract

Keywords

ASJC Scopus subject areas

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