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Ligand Docking and Drug Discovery

Protein structure based inhibitor discovery by flexible docking of millions of available or virtual compounds has repeatedly demonstrated its great potential. Using the ICM platform, we have developed and benchmarked the docking and scoring technology and identified new inhibitors based on the three-dimensional models of proteins of interest.

Benchmarks and Comparisons

Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R
Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment.
Structure, 2011 Aug 10, 19, 1108-26, 21827947

Building ligand pocket models: alternative states, homology models

Kufareva I, Abagyan R
Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states.
J Med Chem, 2008 Dec 25, 51, 7921-32, 19053777

Improved ligand docking protocols

Bottegoni G, Kufareva I, Totrov M, Abagyan R
Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking.
J Med Chem, 2009 Jan 22, 52, 397-406, 19090659

Bottegoni G, Rocchia W, Rueda M, Abagyan R, Cavalli A
Systematic exploitation of multiple receptor conformations for virtual ligand screening.
PLoS One, 2011, 6, e18845, 21625529, pdf

Rueda M, Bottegoni G, Abagyan R
Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes.
J Chem Inf Model, 2009 Mar, 49, 716-25, 19434904

Ligand-guided optimization of binding sites in homology models

Subtype-selectivity for adenosine receptor antagonists. (see the 2011, Neuropharmacology reference below)

Katritch V, Rueda M, Lam PC, Yeager M, Abagyan R
GPCR 3D homology models for ligand screening: lessons learned from blind predictions of adenosine A2a receptor complex. Proteins, 2010 Jan, 78, 197-211

Application of ICM Docking and Collaborations

Katritch V, Kufareva I, Abagyan R
Structure based prediction of subtype-selectivity for adenosine receptor antagonists.
Neuropharmacology, 2011 Jan, 60, 108-15, 20637786

Odell LR, Howan D, Gordon CP, Robertson MJ, Chau N, Mariana A, Whiting AE, Abagyan R, Daniel JA, Gorgani NN, Robinson PJ, McCluskey A
The pthaladyns: GTP competitive inhibitors of dynamin I and II GTPase derived from virtual screening.
J Med Chem, 2010 Jul 22, 53, 5267-80, 20575553

Bowers EM, Yan G, Mukherjee C, Orry A, Wang L, Holbert MA, Crump NT, Hazzalin CA, Liszczak G, Yuan H, Larocca C, Saldanha SA, Abagyan R, Sun Y, Meyers DJ, Marmorstein R, Mahadevan LC, Alani RM, Cole PA
Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor.
Chem Biol, 2010 May 28, 17, 471-82, 20534345

Cheltsov AV, Aoyagi M, Aleshin A, Yu EC, Gilliland T, Zhai D, Bobkov AA, Reed JC, Liddington RC, Abagyan R
Vaccinia virus virulence factor N1L is a novel promising target for antiviral therapeutic intervention.
J Med Chem, 2010 May 27, 53, 3899-906, 20441222

Chan DS, Lee HM, Yang F, Che CM, Wong CC, Abagyan R, Leung CH, Ma DL
Structure-Based Discovery of Natural-Product-like TNF-alpha Inhibitors.
Angew Chem Int Ed Engl, 2010 Mar 16, 49, 2860-2864, 20235259

Chow KH, Sun RW, Lam JB, Li CK, Xu A, Ma DL, Abagyan R, Wang Y, Che CM
A gold(III) porphyrin complex with antitumor properties targets the Wnt/beta-catenin pathway.
Cancer Res, 2010 Jan 1, 70, 329-37, 19996284

Bisson WH, Koch DC, O'Donnell EF, Khalil SM, Kerkvliet NI, Tanguay RL, Abagyan R, Kolluri SK
Modeling of the aryl hydrocarbon receptor (AhR) ligand binding domain and its utility in virtual ligand screening to predict new AhR ligands.
J Med Chem, 2009 Sep 24, 52, 5635-41, 19719119

Wu P, Ma DL, Leung CH, Yan SC, Zhu N, Abagyan R, Che CM
Stabilization of G-quadruplex DNA with platinum(II) Schiff base complexes: luminescent probe and down-regulation of c-myc oncogene expression.
Chemistry, 2009 Dec 7, 15, 13008-21, 19876976

Last updated: 2013/05/31