Covalent docking using autodock: Two-point attractor and flexible side chain methods

被引：173

作者：

Bianco, Giulia ^{[1
]}

Forli, Stefano ^{[2
]}

Goodsell, David S. ^{[2
]}

Olson, Arthur J. ^{[2
]}

机构：

[1] Univ Cagliari, Drug Sci Sect, Dept Life & Environm Sci, Via Osped 72, I-09124 Cagliari, Italy

[2] Scripps Res Inst, Mol Graph Lab, Dept Integrat Struct & Computat Biol, MB 112,10550 North Torrey Pines Rd, La Jolla, CA 92037 USA

来源：

PROTEIN SCIENCE | 2016年 / 25卷 / 01期

基金：

美国国家卫生研究院;

关键词：

computational docking; computer-aided drug design; covalent inhibitors; ligand-protein interactions; PROTEIN-LIGAND DOCKING; AUTOMATED DOCKING; CRYSTAL-STRUCTURE; FORCE-FIELD; INHIBITORS; COMPLEXES; ALGORITHM; DISCOVERY;

D O I：

10.1002/pro.2733

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We describe two methods of automated covalent docking using Autodock4: the two-point attractor method and the flexible side chain method. Both methods were applied to a training set of 20 diverse protein-ligand covalent complexes, evaluating their reliability in predicting the crystallographic pose of the ligands. The flexible side chain method performed best, recovering the pose in 75% of cases, with failures for the largest inhibitors tested. Both methods are freely available at the AutoDock website (http://autodock.scripps.edu).

引用

页码：295 / 301

页数：7

共 23 条

[1] Lennard-Jones potential and dummy atom settings to overcome the AUTODOCK limitation in treating flexible ring systems [J].

Forli, Stefano ;

Botta, Maurizio .

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2007, 47 (04) :1481-1492

[2] A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking [J].

Forli, Stefano ;

Olson, Arthur J. .

JOURNAL OF MEDICINAL CHEMISTRY, 2012, 55 (02) :623-638

[3] Strategies for discovering and derisking covalent, irreversible enzyme inhibitors [J].

Johnson, Douglas S. ;

Weerapana, Eranthie ;

Cravatt, Benjamin F. .

FUTURE MEDICINAL CHEMISTRY, 2010, 2 (06) :949-964

[4] Characterization of Irreversible Kinase Inhibitors by Directly Detecting Covalent Bond Formation: A Tool for Dissecting Kinase Drug Resistance [J].

Klueter, Sabine ;

Simard, Jeffrey R. ;

Rode, Haridas B. ;

Gruetter, Christian ;

Pawar, Vijaykumar ;

Raaijmakers, Hans C. A. ;

Barf, Tjeerd A. ;

Rabiller, Matthias ;

van Otterlo, Willem A. L. ;

Rauh, Daniel .

CHEMBIOCHEM, 2010, 11 (18) :2557-2566

[5]

Kramer B, 1999, PROTEINS, V37, P228, DOI 10.1002/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO

[6]

2-8

[7] Covalent docking of large libraries for the discovery of chemical probes [J].

London, Nir ;

Miller, Rand M. ;

Krishnan, Shyam ;

Uchida, Kenji ;

Irwin, John J. ;

Eidam, Oliv ;

Gibold, Lucie ;

Cimermancic, Peter ;

Bonnet, Richard ;

Shoichet, Brian K. ;

Taunton, Jack .

NATURE CHEMICAL BIOLOGY, 2014, 10 (12) :1066-+

[8] Drug discovery considerations in the development of covalent inhibitors [J].

Mah, Robert ;

Thomas, Jason R. ;

Shafer, Cynthia M. .

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 2014, 24 (01) :33-39

[9] Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go [J].

Moitessier, N. ;

Englebienne, P. ;

Lee, D. ;

Lawandi, J. ;

Corbeil, C. R. .

BRITISH JOURNAL OF PHARMACOLOGY, 2008, 153 :S7-S26

[10] AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility [J].

Morris, Garrett M. ;

Huey, Ruth ;

Lindstrom, William ;

Sanner, Michel F. ;

Belew, Richard K. ;

Goodsell, David S. ;

Olson, Arthur J. .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2009, 30 (16) :2785-2791

← 1 2 3 →