Protein-based NMR spectroscopy has proven to be a very robust method for finding fragment leads to protein targets. However, one limitation of protein-based NMR is that the data acquisition and analysis can be time consuming. In order to streamline the scoring of protein-based NMR fragment screening data and the determination of ligand affinities using 2D NMR experiments we have developed a data analysis workflow based on principal component analysis (PCA) within the TREND NMR Pro software package. We illustrate this using four different proteins and sets of ligands which interact with these proteins over a range of affinities. Also, these PCA-based methods can be successfully applied even to systems where ligand binding to target proteins is in intermediate or even slow exchange on the NMR time scale. Finally, these methods will work for scoring of fragment binding data using protein spectra that are either highly overlapped or lower in resolution.
[NMR paper] Fast and Efficient Fragment-Based Lead Generation by Fully Automated Processing and Analysis of Ligand-Observed NMR Binding Data.
Fast and Efficient Fragment-Based Lead Generation by Fully Automated Processing and Analysis of Ligand-Observed NMR Binding Data.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Fast and Efficient Fragment-Based Lead Generation by Fully Automated Processing and Analysis of Ligand-Observed NMR Binding Data.
J Med Chem. 2016 Apr 14;59(7):3303-10
Authors: Peng C, Frommlet A, Perez M, Cobas C, Blechschmidt A, Dominguez S, Lingel A
Abstract
NMR...
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[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...
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[NMR paper] NMR-based platform for fragment-based lead discovery used in screening BRD4-targeted compounds.
NMR-based platform for fragment-based lead discovery used in screening BRD4-targeted compounds.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.nature.com-images-lo_npg.gif Related Articles NMR-based platform for fragment-based lead discovery used in screening BRD4-targeted compounds.
Acta Pharmacol Sin. 2016 May 30;
Authors: Yu JL, Chen TT, Zhou C, Lian FL, Tang XL, Wen Y, Shen JK, Xu YC, Xiong B, Zhang NX
Abstract
AIM: Fragment-based lead discovery (FBLD) is a complementary approach in drug...
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[NMR paper] Protein-RNA specificity by high-throughput principal component analysis of NMR spectra.
Protein-RNA specificity by high-throughput principal component analysis of NMR spectra.
Related Articles Protein-RNA specificity by high-throughput principal component analysis of NMR spectra.
Nucleic Acids Res. 2015 Jan 13;
Authors: Collins KM, Oregioni A, Robertson LE, Kelly G, Ramos A
Abstract
Defining the RNA target selectivity of the proteins regulating mRNA metabolism is a key issue in RNA biology. Here we present a novel use of principal component analysis (PCA) to extract the RNA sequence preference of RNA binding...
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01-15-2015 06:10 PM
Fragment-based discovery of novel thymidylate synthase leads by NMR screening and group epitope mapping.
Fragment-based discovery of novel thymidylate synthase leads by NMR screening and group epitope mapping.
Fragment-based discovery of novel thymidylate synthase leads by NMR screening and group epitope mapping.
Chem Biol Drug Des. 2010 Sep 1;76(3):218-33
Authors: Begley DW, Zheng S, Varani G
Solution-state nuclear magnetic resonance (NMR) is a versatile tool for the study of binding interactions between small molecules and macromolecular targets. We applied ligand-based NMR techniques to the study of human thymidylate synthase (hTS) using known...
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[NMR paper] NMR-based screening methods for lead discovery.
NMR-based screening methods for lead discovery.
Related Articles NMR-based screening methods for lead discovery.
EXS. 2003;(93):183-202
Authors: Vogtherr M, Fiebig K
Diversity and robustness of NMR based screening methods make these techniques highly attractive as tools for drug discovery. Although not all screening techniques discussed here may be applicable to any given target, there is however a good chance that at least one of the described methods will prove productive in finding several medium affinity ligands. A comparison of each of...
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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...
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[BMNRC community] NMR-based screening: a powerful tool in fragment-based drug discovery
NMR-based screening: a powerful tool in fragment-based drug discovery
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NMR-based fragment screening and lead discovery accelerated by principal component analysis
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