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



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  
Unread 01-13-2015, 02:31 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 Applications of NMR screening techniques to the pharmaceutical target Checkpoint kinase 1.

Applications of NMR screening techniques to the pharmaceutical target Checkpoint kinase 1.

Related Articles Applications of NMR screening techniques to the pharmaceutical target Checkpoint kinase 1.

J Pharm Biomed Anal. 2014 May;93:125-35

Authors: Lancelot N, Piotto M, Theret I, Lesur B, Hennig P

Abstract
Ligand screening techniques based on NMR spectroscopy are not as sensitive as other commonly used methods like fluorescence, radiolabeling and surface plasmon resonance. However, using modern NMR instrumentation, they can achieve reliable screening under near physiological condition using as little as 4.6 nmol of receptor and 100 nmol of ligand. Additionally, these NMR methods can also provide valuable and specific information on the ligand under investigation such as the dissociation constant KD, the binding epitope and most importantly some structural information on the actual conformation in the bound state. In this manuscript, we describe the use of NMR based screening techniques ("Saturation Transfer Difference" (STD) and "Water Ligand Observed via Gradient SpectroscopY" (WaterLOGSY)) to detect small therapeutic molecules that interact with the DNA damage checkpoint enzyme Checkpoint kinase 1 (Chk1). After the identification of the most potent ligand, we used specific NMR experiments to perform the epitope mapping of this ligand ("Group epitope mapping-STD" (GEM-STD), "Difference of Inversion REcovery rate with and without Target IrradiatiON" (DIRECTION)) and to characterize its bound conformation ("Transferred-Nuclear Overhauser Effect SpectroscopY" (tr-NOESY), "Transferred-Rotating frame Overhauser Effect SpectroscopY" (tr-ROESY)). Finally, we used molecular docking procedures to position the ligand within the active site of Chk1. On the experimental level, a comparison between NMR studies performed in a 90%H2O/10%D2O buffer and a 100% D2O buffer is also presented and discussed.


PMID: 24280017 [PubMed - indexed for MEDLINE]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Characterization of the Immersion Properties of the Peripheral Membrane Anchor of the FATC Domain of the Kinase 'Target of Rapamycin' by NMR, Oriented CD Spectroscopy and MD Simulations.
Characterization of the Immersion Properties of the Peripheral Membrane Anchor of the FATC Domain of the Kinase 'Target of Rapamycin' by NMR, Oriented CD Spectroscopy and MD Simulations. Characterization of the Immersion Properties of the Peripheral Membrane Anchor of the FATC Domain of the Kinase 'Target of Rapamycin' by NMR, Oriented CD Spectroscopy and MD Simulations. J Phys Chem B. 2014 Apr 11; Authors: Sommer LA, Janke JJ, Bennett WF, Bürck J, Ulrich AS, Tieleman DP, Dames SA Abstract The multidomain ser/thr kinase...
nmrlearner Journal club 0 04-15-2014 10:38 AM
[NMR paper] Characterization of residue-dependent differences in the peripheral membrane association of the FATC domain of the kinase 'target of rapamycin' by NMR and CD spectroscopy.
Characterization of residue-dependent differences in the peripheral membrane association of the FATC domain of the kinase 'target of rapamycin' by NMR and CD spectroscopy. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Characterization of residue-dependent differences in the peripheral membrane association of the FATC domain of the kinase 'target of rapamycin' by NMR and CD spectroscopy. FEBS Lett. 2014 Apr 3; Authors: Sommer LA, Dames SA ...
nmrlearner Journal club 0 04-08-2014 08:02 PM
Quantitative NMR spectroscopy in pharmaceutical applications
Quantitative NMR spectroscopy in pharmaceutical applications Publication year: 2010 Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 57, Issue 2</br> Ulrike Holzgrabe</br> </br> </br></br>
nmrlearner Journal club 0 03-09-2012 09:16 AM
Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification.
Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification. Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification. J Biomol Screen. 2010 Sep;15(8):978-89 Authors: Kobayashi M, Retra K, Figaroa F, Hollander JG, Ab E, Heetebrij RJ, Irth H, Siegal G Fragment-based drug discovery (FBDD) has become a widely accepted tool that is complementary to high-throughput screening (HTS) in developing...
nmrlearner Journal club 0 01-13-2011 12:00 PM
[NMR paper] TINS, target immobilized NMR screening: an efficient and sensitive method for ligand
TINS, target immobilized NMR screening: an efficient and sensitive method for ligand discovery. Related Articles TINS, target immobilized NMR screening: an efficient and sensitive method for ligand discovery. Chem Biol. 2005 Feb;12(2):207-16 Authors: Vanwetswinkel S, Heetebrij RJ, van Duynhoven J, Hollander JG, Filippov DV, Hajduk PJ, Siegal G We propose a ligand screening method, called TINS (target immobilized NMR screening), which reduces the amount of target required for the fragment-based approach to drug discovery. Binding is detected by...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] Application of NMR SHAPES screening to an RNA target.
Application of NMR SHAPES screening to an RNA target. Related Articles Application of NMR SHAPES screening to an RNA target. J Am Chem Soc. 2003 Dec 24;125(51):15724-5 Authors: Johnson EC, Feher VA, Peng JW, Moore JM, Williamson JR Several NMR screening techniques have been developed in recent years to aid in the identification of lead drug compounds. These NMR methods have traditionally been used for protein targets, and here we examine their applicability for an RNA target. We used the SHAPES compound library to test three different NMR...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] NMR spectroscopy techniques for screening and identifying ligand binding to protein r
NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. Related Articles NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. Angew Chem Int Ed Engl. 2003 Feb 24;42(8):864-90 Authors: Meyer B, Peters T Binding events of ligands to receptors are the key for an understanding of biological processes. Gaining insight into protein-protein and protein-ligand interactions in solution has recently become possible on an atomic level by new NMR spectroscopic techniques....
nmrlearner Journal club 0 11-24-2010 09:01 PM
Quantitative NMR Spectroscopy in Pharmaceutical Applications
Quantitative NMR Spectroscopy in Pharmaceutical Applications Publication year: 2010 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 10 May 2010</br> Ulrike, Holzgrabe</br> More...
nmrlearner Journal club 0 08-16-2010 03:50 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

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 11:15 AM.


Map