Identification of potent CypD inhibitors via pharmacophore based virtual screening, docking and molecular dynamics simulation

被引：4

作者：

Chen, Xiao-Zhong ^{[1
]}

Yu, Xiu-Yan ^{[1
]}

Dai, Chen ^{[1
]}

Huang, Qiu-Yang ^{[2
]}

Shen, Yan ^{[1
,2
]}

Wang, Juan ^{[1
]}

Hu, Yong ^{[1
]}

Lin, Zhi-Hua ^{[1
,2
,3
]}

机构：

[1] Chongqing Univ Technol, Dept Pharm & Bioengn, Chongqing 405400, Peoples R China

[2] Chongqing Univ Technol, Chongqing Key Lab Med Chem & Mol Pharmacol, Chongqing 405400, Peoples R China

[3] Chongqing Key Lab Targeted Drug Screening & Act E, Chongqing 400054, Peoples R China

来源：

JOURNAL OF MOLECULAR STRUCTURE | 2022年 / 1247卷

基金：

中国国家自然科学基金;

关键词：

Cyclophilin D; Virtual screening; 3D-QSAR pharmacophore; Docking; Molecular dynamics; Binding free energy calculations; 3D-QSAR;

D O I：

10.1016/j.molstruc.2021.131355

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

Cyclophilin D (CypD) is a mitochondrial matrix peptidyl prolidase that has been identified as a target for the treatment of acute pancreatitis. However, only a few compounds have been reported as CypD inhibitors. To discover novel CypD inhibitors, a ZINC database including 206,724 compounds was screened through 3D-QSAR pharmacophore model and molecular docking in sequence. After an in-depth analysis of the docking results obtained, ZINC161011368, ZINC664707610 and ZINC665010466 were selected for the molecular dynamics simulations and the binding free energy calculations. On this basis, ZINC161011368 was identified as having the potential of application as a novel CypD inhibitor. This study provides a basis for screening highly active CypD inhibitors for the treatment of acute pancreatitis. (c) 2021 Elsevier B.V. All rights reserved.

引用

页数：8

共 50 条

[1] Pharmacophore-based virtual screening, molecular docking and molecular dynamics simulation for identification of potential ERK inhibitors
Tian, Yafeng
Zhang, Mi
Heng, Panpan
Hou, Hua
Wang, Baoshan
[J]. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2024, 42 (04): : 2153 - 2161
[2] Identification of HDAC6 selective inhibitors: pharmacophore based virtual screening, molecular docking and molecular dynamics simulation
Yan, Guoyi
Li, Dongxiao
Zhong, Xinxin
Liu, Ge
Wang, Xueqin
Lu, Yuanxiang
Qin, Fangyuan
Guo, Yuqi
Duan, Shaofeng
Li, Deyu
[J]. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2021, 39 (06): : 1928 - 1939
[3] Identification of Novel Src Inhibitors: Pharmacophore-Based Virtual Screening, Molecular Docking and Molecular Dynamics Simulations
Zhang, Yi
Zhang, Ting-jian
Tu, Shun
Zhang, Zhen-hao
Meng, Fan-hao
[J]. MOLECULES, 2020, 25 (18):
[4] Pharmacophore-enabled virtual screening, molecular docking and molecular dynamics studies for identification of potent and selective histone deacetylase 8 inhibitors
Kashyap, Kriti
Kakkar, Rita
[J]. COMPUTERS IN BIOLOGY AND MEDICINE, 2020, 123
[5] Multidimensional Criteria for Virtual Screening of PqsR Inhibitors Based on Pharmacophore, Docking, and Molecular Dynamics
Xiao, Haichuan
Li, Jiahao
Yang, Dongdong
Du, Jiarui
Li, Jie
Lin, Shuqi
Zhou, Haibo
Sun, Pinghua
Xu, Jun
[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2024, 25 (03)
[6] Identification of Novel Inhibitors of Mycobacterium tuberculosis PknG Using Pharmacophore Based Virtual Screening, Docking, Molecular Dynamics Simulation, and Their Biological Evaluation
Singh, Nidhi
Tiwari, Sameer
Srivastava, Kishore K.
Siddiqi, Mohammad Imran
[J]. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2015, 55 (06) : 1120 - 1129
[7] Identification of novel BRD4 inhibitors by pharmacophore screening, molecular docking, and molecular dynamics simulation
Dong, Junmin
Wang, Xinghe
[J]. JOURNAL OF MOLECULAR STRUCTURE, 2023, 1274
[8] Identification of promising DNA GyrB inhibitors for Tuberculosis using pharmacophore-based virtual screening, molecular docking and molecular dynamics studies
Islam, Md Ataul
Pillay, Tahir S.
[J]. CHEMICAL BIOLOGY & DRUG DESIGN, 2017, 90 (02) : 282 - 296
[9] Pharmacophore-based virtual screening, molecular docking and molecular dynamics simulations study for the identification of LIM kinase-1 inhibitors
Singh, Ravi
Pokle, Ankit Vyankatrao
Ghosh, Powsali
Ganeshpurkar, Ankit
Swetha, Rayala
Singh, Sushil Kumar
Kumar, Ashok
[J]. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2023, 41 (13): : 6089 - 6103
[10] Pharmacophore based virtual screening, molecular docking studies to design potent heat shock protein 90 inhibitors
Sakkiah, Sugunadevi
Thangapandian, Sundarapandian
John, Shalini
Lee, Keun Woo
[J]. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 2011, 46 (07) : 2937 - 2947

← 1 2 3 4 5 →