Related ArticlesDevelopment and Validation of 2D Difference Intensity Analysis for Chemical Library Screening by Protein-Detected NMR.
Chembiochem. 2017 Dec 13;:
Authors: Egner JM, Jensen DR, Olp MD, Kennedy NW, Volkman BF, Peterson FC, Smith BC, Hill RB
Abstract
An academic chemical screening approach was developed and a 352-chemical fragment library screened against 3 different protein targets using 2D protein-detected NMR. The approach was optimized against 2 protein targets with known ligands, CXCL12 and BRD4. Principal component analysis reliably identified compounds that induced NMR crosspeak broadening, but did not unambiguously identify ligands with specific affinity (hits). For improved hit detection, a novel scoring metric - difference intensity analysis (DIA) -*was devised that sums all positive and negative intensities from 2D difference spectra. Applying DIA quickly discriminated potential ligands from compounds inducing NMR crosspeak broadening and other nonspecific effects. Subsequent NMR titrations validated chemotypes important for binding to CXCL12 and BRD4. A novel target, mitochondrial fission protein Fis1, was screened and 6 hits were identified using DIA. Screening these diverse protein targets identified quinones and catechols that induced NMR crosspeak broadening, hampered NMR analyses, but are currently not computationally identified as pan-assay interference compounds. The results establish a streamlined screening workflow that can easily be scaled and adapted as part of a larger screening pipeline to identify fragment hits and assess relative binding affinities in the range of 0.3 - 1.6 mM. DIA may prove useful in library screening and other applications where NMR chemical shift perturbations are measured.
PMID: 29239081 [PubMed - as supplied by publisher]
[NMR paper] Probabilistic validation of protein NMR chemical shift assignments.
Probabilistic validation of protein NMR chemical shift assignments.
Probabilistic validation of protein NMR chemical shift assignments.
J Biomol NMR. 2016 Jan 2;
Authors: Dashti H, Tonelli M, Lee W, Westler WM, Cornilescu G, Ulrich EL, Markley JL
Abstract
Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments....
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01-05-2016 08:23 PM
Probabilistic validation of protein NMR chemical shift assignments
Probabilistic validation of protein NMR chemical shift assignments
Abstract
Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data . ARECA has been evaluated through its application to 26...
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01-03-2016 01:25 AM
[NMR paper] Identification of Small-Molecule Inhibitors of the HuR/RNA Interaction Using a Fluorescence Polarization Screening Assay Followed by NMR Validation.
Identification of Small-Molecule Inhibitors of the HuR/RNA Interaction Using a Fluorescence Polarization Screening Assay Followed by NMR Validation.
Related Articles Identification of Small-Molecule Inhibitors of the HuR/RNA Interaction Using a Fluorescence Polarization Screening Assay Followed by NMR Validation.
PLoS One. 2015;10(9):e0138780
Authors: Wang Z, Bhattacharya A, Ivanov DN
Abstract
The human antigen R (HuR) stabilizes many mRNAs of proto-oncogene, transcription factors, cytokines and growth factors by recognizing...
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09-22-2015 06:40 PM
[NMR paper] Saturation transfer difference NMR for fragment screening.
Saturation transfer difference NMR for fragment screening.
Related Articles Saturation transfer difference NMR for fragment screening.
Curr Protoc Chem Biol. 2013 Dec 1;5(4):251-68
Authors: Begley DW, Moen SO, Pierce PG, Zartler ER
Abstract
Fragment screening by saturation transfer difference nuclear magnetic resonance (STD-NMR) is a robust method for identifying small molecule binders and is well suited to a broad set of biological targets. STD-NMR is exquisitely sensitive for detecting weakly binding compounds (a common characteristic of...
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01-07-2014 11:16 PM
[NMR paper] Specific RNA-protein interactions detected with saturation transfer difference NMR.
Specific RNA-protein interactions detected with saturation transfer difference NMR.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.landesbioscience.com-icon-pubmed-Landesbioscience2.jpg Specific RNA-protein interactions detected with saturation transfer difference NMR.
RNA Biol. 2013 Jul 30;10(8)
Authors: Harris KA, Shekhtman A, Agris PF
Abstract
RNA, at the forefront of biochemical research due to its central role in biology, is recognized by proteins through various mechanisms. Analysis of the...
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...
Development and Validation of 2D Difference Intensity Analysis for Chemical Library Screening by Protein-Detected NMR.
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