BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search
Home Forums Wiki NMR feeds Downloads Register Today's Posts



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
 
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Old 04-16-2017, 06:09 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,777
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Virtual screen to NMR (VS2NMR): Discovery of fragment hits for the CBP bromodomain.

Virtual screen to NMR (VS2NMR): Discovery of fragment hits for the CBP bromodomain.

Related Articles Virtual screen to NMR (VS2NMR): Discovery of fragment hits for the CBP bromodomain.

Bioorg Med Chem Lett. 2017 Apr 04;:

Authors: Spiliotopoulos D, Zhu J, Wamhoff EC, Deerain N, Marchand JR, Aretz J, Rademacher C, Caflisch A

Abstract
Overexpression of the CREB-binding protein (CBP), a bromodomain-containing transcription coactivator involved in a variety of cellular processes, has been observed in several types of cancer with a correlation to aggressiveness. We have screened a library of nearly 1500 fragments by high-throughput docking into the CBP bromodomain followed by binding energy evaluation using a force field with electrostatic solvation. Twenty of the 39 fragments selected by virtual screening are positive in one or more ligand-observed nuclear magnetic resonance (NMR) experiments. Four crystal structures of the CBP bromodomain in complex with in silico screening hits validate the pose predicted by docking. Thus, the success ratio of the high-throughput docking procedure is 50% or 10% if one considers the validation by ligand-observed NMR spectroscopy or X-ray crystallography, respectively. Compounds 1 and 3 show favorable ligand efficiency in two different in vitro binding assays. The structure of the CBP bromodomain in the complex with the brominated pyrrole 1 suggests fragment growing by Suzuki coupling.


PMID: 28410781 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Protein-templated fragment ligations - from molecular recognition to drug discovery
Protein-templated fragment ligations - from molecular recognition to drug discovery The understanding and manipulation of molecular recognition events is the key to modern approaches in drug discovery. Protein-templated fragment ligation is a novel concept to support drug discovery and can help to improve the efficacy of already existing protein ligands. Protein-templated fragment ligations are chemical reactions between small molecules ("fragments") that utilize a protein´s surface as a template to combine and to form a protein ligand with increased binding affinity. The...
nmrlearner Journal club 0 01-24-2017 08:12 PM
[NMR paper] Applications of (19)F-NMR in Fragment-Based Drug Discovery.
Applications of (19)F-NMR in Fragment-Based Drug Discovery. Related Articles Applications of (19)F-NMR in Fragment-Based Drug Discovery. Molecules. 2016;21(7) Authors: Norton RS, Leung EW, Chandrashekaran IR, MacRaild CA Abstract (19)F-NMR has proved to be a valuable tool in fragment-based drug discovery. Its applications include screening libraries of fluorinated fragments, assessing competition among elaborated fragments and identifying the binding poses of promising hits. By observing fluorine in both the ligand and the...
nmrlearner Journal club 0 07-22-2016 01:34 AM
[NMR paper] Process of Fragment-Based Lead Discovery-A Perspective from NMR.
Process of Fragment-Based Lead Discovery-A Perspective from NMR. Related Articles Process of Fragment-Based Lead Discovery-A Perspective from NMR. Molecules. 2016;21(7) Authors: Ma R, Wang P, Wu J, Ruan K Abstract Fragment-based lead discovery (FBLD) has proven fruitful during the past two decades for a variety of targets, even challenging protein-protein interaction (PPI) systems. Nuclear magnetic resonance (NMR) spectroscopy plays a vital role, from initial fragment-based screening to lead generation, because of its power...
nmrlearner Journal club 0 07-22-2016 01:34 AM
[NMR paper] Discovery of New E-Selectin Inhibitors by Virtual Screening, Fluorescence Binding Assays, and STD NMR Experiments.
Discovery of New E-Selectin Inhibitors by Virtual Screening, Fluorescence Binding Assays, and STD NMR Experiments. Discovery of New E-Selectin Inhibitors by Virtual Screening, Fluorescence Binding Assays, and STD NMR Experiments. ChemMedChem. 2016 Mar 21; Authors: Barra PA, Jiménez VA, Gavin JA, Daranas AH, Alderete JB Abstract E-selectin is an endothelial protein that participates in the adhesion of metastatic cancer cells, and is therefore a relevant target for antitumor therapeutic intervention. In this work, virtual...
nmrlearner Journal club 0 03-22-2016 01:46 PM
[NMR paper] Fragment-based drug discovery using NMR spectroscopy.
Fragment-based drug discovery using NMR spectroscopy. Related Articles Fragment-based drug discovery using NMR spectroscopy. J Biomol NMR. 2013 May 18; Authors: Harner MJ, Frank AO, Fesik SW Abstract Nuclear magnetic resonance (NMR) spectroscopy has evolved into a powerful tool for fragment-based drug discovery over the last two decades. While NMR has been traditionally used to elucidate the three-dimensional structures and dynamics of biomacromolecules and their interactions, it can also be a very valuable tool for the reliable...
nmrlearner Journal club 0 05-21-2013 02:34 PM
[NMR paper] HTS by NMR of Combinatorial Libraries: A Fragment-Based Approach to Ligand Discovery.
HTS by NMR of Combinatorial Libraries: A Fragment-Based Approach to Ligand Discovery. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-cellhub.gif Related Articles HTS by NMR of Combinatorial Libraries: A Fragment-Based Approach to Ligand Discovery. Chem Biol. 2013 Jan 24;20(1):19-33 Authors: Wu B, Zhang Z, Noberini R, Barile E, Giulianotti M, Pinilla C, Houghten RA, Pasquale EB, Pellecchia M Abstract Fragment-based ligand design (FBLD) approaches have become more widely used in drug discovery...
nmrlearner Journal club 0 02-03-2013 10:19 AM
[NMR in the fragment-based drug discovery].
. . Tanpakushitsu Kakusan Koso. 2009 Sep;54(12 Suppl):1617-21 Authors: Hanzawa H, Takizawa T
nmrlearner Journal club 0 01-28-2011 01:50 PM
NMR Screening and Hit Validation in Fragment Based Drug Discovery.
NMR Screening and Hit Validation in Fragment Based Drug Discovery. Related Articles NMR Screening and Hit Validation in Fragment Based Drug Discovery. Curr Top Med Chem. 2010 Sep 2; Authors: Campos-Olivas R Over the past three decades nuclear magnetic resonance spectroscopy has been developed into a mature technique for the characterization of interactions of small molecule ligands with their corresponding protein and nucleic acid receptors. In fact, a significant number of industrial and academic laboratories employ NMR for screening small...
nmrlearner Journal club 0 09-03-2010 02:30 PM



Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 12:11 AM.


Map