DARC: Mapping Surface Topography by Ray-Casting for Effective Virtual Screening at Protein Interaction Sites.

PubWeight™: 0.82‹?›

🔗 View Article (PMID 26126123)

Published in J Med Chem on July 10, 2015

Authors

Ragul Gowthaman1, Sven A Miller1, Steven Rogers1, Jittasak Khowsathit1, Lan Lan1, Nan Bai1, David K Johnson1, Chunjing Liu1, Liang Xu1, Asokan Anbanandam1, Jeffrey Aubé1, Anuradha Roy1, John Karanicolas1

Author Affiliations

1: Center for Computational Biology, ‡Department of Molecular Biosciences, §Center of Biomedical Research Excellence, Center for Cancer Experimental Therapeutics, ∥Department of Radiation Oncology, ⊥Biomolecular NMR Laboratory, #Department of Medicinal Chemistry, and ∇High Throughput Screening Laboratory University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66045-7534, United States.

Articles cited by this

(truncated to the top 100)

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem (2009) 23.19

An inhibitor of Bcl-2 family proteins induces regression of solid tumours. Nature (2005) 22.40

The BH3 mimetic ABT-737 targets selective Bcl-2 proteins and efficiently induces apoptosis via Bak/Bax if Mcl-1 is neutralized. Cancer Cell (2006) 10.19

Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature (2007) 9.12

ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor activity while sparing platelets. Nat Med (2013) 8.89

Mechanisms of apoptosis sensitivity and resistance to the BH3 mimetic ABT-737 in acute myeloid leukemia. Cancer Cell (2006) 8.59

PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res (2005) 7.66

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol (2011) 7.33

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A (1992) 6.86

Relating protein pharmacology by ligand chemistry. Nat Biotechnol (2007) 6.61

ZINC: a free tool to discover chemistry for biology. J Chem Inf Model (2012) 6.57

New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem (2010) 6.54

Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol (1997) 4.69

Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database. J Chem Inf Model (2010) 4.38

Mcl-1 down-regulation potentiates ABT-737 lethality by cooperatively inducing Bak activation and Bax translocation. Cancer Res (2007) 3.92

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model (1997) 3.59

The MCL-1 BH3 helix is an exclusive MCL-1 inhibitor and apoptosis sensitizer. Nat Chem Biol (2010) 3.17

Comparison of shape-matching and docking as virtual screening tools. J Med Chem (2007) 3.09

Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem (2007) 3.03

Privileged scaffolds for library design and drug discovery. Curr Opin Chem Biol (2010) 3.01

Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem (2012) 2.86

RosettaLigand docking with full ligand and receptor flexibility. J Mol Biol (2008) 2.86

DOCK 6: combining techniques to model RNA-small molecule complexes. RNA (2009) 2.75

Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol (2004) 2.65

Identification of a chemical probe for NAADP by virtual screening. Nat Chem Biol (2009) 2.54

A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. J Med Chem (2005) 2.52

The rise of fragment-based drug discovery. Nat Chem (2009) 2.46

Empirical scoring functions for advanced protein-ligand docking with PLANTS. J Chem Inf Model (2009) 2.42

Structure-based design of potent small-molecule inhibitors of anti-apoptotic Bcl-2 proteins. J Med Chem (2006) 2.35

Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc (2005) 2.32

Discovery of potent myeloid cell leukemia 1 (Mcl-1) inhibitors using fragment-based methods and structure-based design. J Med Chem (2012) 2.23

Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14

Effect of detergent on "promiscuous" inhibitors. J Med Chem (2003) 2.08

FlexE: efficient molecular docking considering protein structure variations. J Mol Biol (2001) 2.05

Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins (2007) 2.03

Interpreting steep dose-response curves in early inhibitor discovery. J Med Chem (2006) 2.00

Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics (2005) 1.97

Small-molecule inhibitors of protein-protein interactions: progressing toward the reality. Chem Biol (2014) 1.95

Conformer generation with OMEGA: learning from the data set and the analysis of failures. J Chem Inf Model (2012) 1.86

Privileged structures: applications in drug discovery. Comb Chem High Throughput Screen (2004) 1.82

Nucleoside and nucleotide HIV reverse transcriptase inhibitors: 25 years after zidovudine. Antiviral Res (2009) 1.77

Between a rock and a hard place? Nat Chem Biol (2006) 1.77

A unique inhibitor binding site in ERK1/2 is associated with slow binding kinetics. Nat Chem Biol (2014) 1.76

Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem (2003) 1.70

What do we know and when do we know it? J Comput Aided Mol Des (2008) 1.68

Promiscuous aggregate-based inhibitors promote enzyme unfolding. J Med Chem (2009) 1.68

A small-molecule inhibitor of Bcl-XL potentiates the activity of cytotoxic drugs in vitro and in vivo. Cancer Res (2006) 1.67

Atomic interactions and profile of small molecules disrupting protein-protein interfaces: the TIMBAL database. Chem Biol Drug Des (2009) 1.64

Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists. PLoS One (2012) 1.60

Small molecular weight protein-protein interaction antagonists: an insurmountable challenge? Curr Opin Chem Biol (2008) 1.53

Surface plasmon resonance based assay for the detection and characterization of promiscuous inhibitors. J Med Chem (2008) 1.52

Disrupting protein-protein interactions with non-peptidic, small molecule alpha-helix mimetics. Curr Opin Chem Biol (2010) 1.47

Similarity-based approaches to virtual screening. Biochem Soc Trans (2003) 1.45

A novel small-molecule inhibitor of mcl-1 blocks pancreatic cancer growth in vitro and in vivo. Mol Cancer Ther (2013) 1.42

The BH3 alpha-helical mimic BH3-M6 disrupts Bcl-X(L), Bcl-2, and MCL-1 protein-protein interactions with Bax, Bak, Bad, or Bim and induces apoptosis in a Bax- and Bim-dependent manner. J Biol Chem (2010) 1.39

Characterization of local geometry of protein surfaces with the visibility criterion. Proteins (2008) 1.39

Structural biology in fragment-based drug design. Curr Opin Struct Biol (2010) 1.36

Multiple solvent crystal structures: probing binding sites, plasticity and hydration. J Mol Biol (2006) 1.35

FLEXS: a method for fast flexible ligand superposition. J Med Chem (1998) 1.32

Rational design of proteolytically stable, cell-permeable peptide-based selective Mcl-1 inhibitors. J Am Chem Soc (2012) 1.24

Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes. Protein Sci (2010) 1.24

Therapeutic window for melanoma treatment provided by selective effects of the proteasome on Bcl-2 proteins. Cell Death Differ (2007) 1.24

Small molecule Mcl-1 inhibitors for the treatment of cancer. Pharmacol Ther (2014) 1.23

Evaluation of DOCK 6 as a pose generation and database enrichment tool. J Comput Aided Mol Des (2012) 1.22

Structure-guided design of a series of MCL-1 inhibitors with high affinity and selectivity. J Med Chem (2015) 1.22

Structure-activity relationship studies of chalcone leading to 3-hydroxy-4,3',4',5'-tetramethoxychalcone and its analogues as potent nuclear factor kappaB inhibitors and their anticancer activities. J Med Chem (2009) 1.16

Evaluation and critical assessment of putative MCL-1 inhibitors. Cell Death Differ (2013) 1.16

A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction. BMC Bioinformatics (2010) 1.15

Real-time ligand binding pocket database search using local surface descriptors. Proteins (2010) 1.12

Structure-based druggability assessment--identifying suitable targets for small molecule therapeutics. Curr Opin Chem Biol (2011) 1.08

The novel BH3 α-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein-protein interactions with Bak. Mol Cancer (2013) 1.04

Inhibitors of the anti-apoptotic Bcl-2 proteins: a patent review. Expert Opin Ther Pat (2011) 1.04

Discovery of novel inhibitors of the ZipA/FtsZ complex by NMR fragment screening coupled with structure-based design. Bioorg Med Chem (2006) 1.03

Discovery of a potent and selective Bcl-2 inhibitor using SAR by NMR. Bioorg Med Chem Lett (2010) 1.02

Protein-ligand recognition using spherical harmonic molecular surfaces: towards a fast and efficient filter for large virtual throughput screening. J Mol Graph Model (2002) 1.01

rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids. PLoS Comput Biol (2014) 1.01

How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis. Eur Biophys J (2010) 0.99

Exploring protein flexibility: incorporating structural ensembles from crystal structures and simulation into virtual screening protocols. J Phys Chem B (2012) 0.99

Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. Bioinformatics (2011) 0.99

SAR by interligand nuclear overhauser effects (ILOEs) based discovery of acylsulfonamide compounds active against Bcl-x(L) and Mcl-1. J Med Chem (2011) 0.98

Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface. PLoS Comput Biol (2013) 0.98

Fragment-based discovery of potent inhibitors of the anti-apoptotic MCL-1 protein. Bioorg Med Chem Lett (2014) 0.96

Potential and limitations of ensemble docking. J Chem Inf Model (2012) 0.96

How far can virtual screening take us in drug discovery? Expert Opin Drug Discov (2013) 0.95

Structure-based approaches to ligands for G-protein-coupled adenosine and P2Y receptors, from small molecules to nanoconjugates. J Med Chem (2013) 0.94

Comprehensive peptidomimetic libraries targeting protein-protein interactions. Acc Chem Res (2012) 0.93

Discovery of a potent inhibitor of replication protein a protein-protein interactions using a fragment-linking approach. J Med Chem (2013) 0.93

Protein flexibility in virtual screening: the BACE-1 case study. J Chem Inf Model (2012) 0.90

TIMBAL v2: update of a database holding small molecules modulating protein-protein interactions. Database (Oxford) (2013) 0.89

Targeting protein-protein interactions in hematologic malignancies: still a challenge or a great opportunity for future therapies? Immunol Rev (2015) 0.88

High-quality NMR structure of human anti-apoptotic protein domain Mcl-1(171-327) for cancer drug design. PLoS One (2014) 0.86

Discovery of potent Mcl-1/Bcl-xL dual inhibitors by using a hybridization strategy based on structural analysis of target proteins. J Med Chem (2013) 0.86

Synthesis of cell-permeable stapled BH3 peptide-based Mcl-1 inhibitors containing simple aryl and vinylaryl cross-linkers. Tetrahedron (2014) 0.84

Chemical approaches towards unravelling kinase-mediated signalling pathways. Chem Soc Rev (2010) 0.84

Tailoring peptidomimetics for targeting protein-protein interactions. Mol Cancer Res (2014) 0.84

Ligand efficiency driven design of new inhibitors of Mycobacterium tuberculosis transcriptional repressor EthR using fragment growing, merging, and linking approaches. J Med Chem (2014) 0.84

Structure-based virtual screening for drug discovery: principles, applications and recent advances. Curr Top Med Chem (2014) 0.84

Purported Mcl-1 inhibitor marinopyrrole A fails to show selective cytotoxicity for Mcl-1-dependent cell lines. Cell Death Dis (2013) 0.83

Structural properties of non-traditional drug targets present new challenges for virtual screening. J Chem Inf Model (2013) 0.83

Improving virtual screening performance against conformational variations of receptors by shape matching with ligand binding pocket. J Chem Inf Model (2009) 0.83