The binding affinity determination of protein-ligand complexes is a cornerstone of drug design. State-of-the-art techniques are limited by lengthy and expensive processes. Building upon our recently introduced novel screening method utilizing photochemically induced dynamic nuclear polarization (photo-CIDNP) NMR, we provide the methodological framework to determine binding affinities within 5-15 min using 0.1 mg of protein. The accuracy of our method is demonstrated for the affinity constants of...
[NMR paper] Fast Quantitative Validation of 3D Models of Low-Affinity Protein-Ligand Complexes by STD NMR Spectroscopy
Fast Quantitative Validation of 3D Models of Low-Affinity Protein-Ligand Complexes by STD NMR Spectroscopy
Low-affinity protein-ligand interactions are important for many biological processes, including cell communication, signal transduction, and immune responses. Structural characterization of these complexes is also critical for the development of new drugs through fragment-based drug discovery (FBDD), but it is challenging due to the low affinity of fragments for the binding site. Saturation transfer difference (STD) NMR spectroscopy has revolutionized the study of low-affinity...
[NMR paper] Imaging Saturation Transfer Difference (STD) NMR: Affinity and Specificity of Protein-Ligand Interactions from a Single NMR Sample
Imaging Saturation Transfer Difference (STD) NMR: Affinity and Specificity of Protein-Ligand Interactions from a Single NMR Sample
We have combined saturation transfer difference NMR (STD NMR) with chemical shift imaging (CSI) and controlled concentration gradients of small molecule ligands to develop imaging STD NMR, a new tool for the assessment of protein-ligand interactions. Our methodology allows the determination of protein-ligand dissociation constants (K(D)) and assessment of the binding specificity in a single NMR tube, avoiding time-consuming titrations. We demonstrate the...
nmrlearner
Journal club
0
07-25-2023 01:43 PM
[NMR paper] Determination of Ligand-Binding Affinity (Kd) Using Transverse Relaxation Rate (R2) in the Ligand-Observed 1H NMR Experiment and Applications to Fragment-Based Drug Discovery
Determination of Ligand-Binding Affinity (Kd) Using Transverse Relaxation Rate (R2) in the Ligand-Observed 1H NMR Experiment and Applications to Fragment-Based Drug Discovery
High hit rates from initial ligand-observed NMR screening can make it challenging to prioritize which hits to follow up, especially in cases where there are no available crystal structures of these hits bound to the target proteins or other strategies to provide affinity ranking. Here, we report a reproducible, accurate, and versatile quantitative ligand-observed NMR assay, which can determine K(d) values of fragments...
nmrlearner
Journal club
0
07-20-2023 06:33 AM
[NMR paper] Determination of intracellular protein-ligand binding affinity by competition binding in-cell NMR
Determination of intracellular protein-ligand binding affinity by competition binding in-cell NMR
Structure-based drug development suffers from high attrition rates due to the poor activity of lead compounds in cellular and animal models caused by low cell penetrance, off-target binding or changes in the conformation of the target protein in the cellular environment. The latter two effects cause a change in the apparent binding affinity of the compound, which is indirectly assessed by cellular activity assays. To date, direct measurement of the intracellular binding affinity remains a...
...
nmrlearner
Journal club
0
10-05-2021 05:24 PM
[NMR paper] Fast NMR-Based Determination of the 3D Structure of the Binding Site of Protein-Ligand Complexes with Weak Affinity Binders.
Fast NMR-Based Determination of the 3D Structure of the Binding Site of Protein-Ligand Complexes with Weak Affinity Binders.
Fast NMR-Based Determination of the 3D Structure of the Binding Site of Protein-Ligand Complexes with Weak Affinity Binders.
Angew Chem Int Ed Engl. 2017 Apr 07;:
Authors: Wälti MA, Riek R, Orts J
Abstract
In early drug discovery approaches, screening hits are often weak affinity binders that are difficult to characterize in structural detail, particularly towards obtaining the 3D structure of...
nmrlearner
Journal club
0
04-08-2017 10:57 AM
Direct enzyme-substrate affinity determination by real-time hyperpolarized (13)C-MRS
From The DNP-NMR Blog:
Direct enzyme-substrate affinity determination by real-time hyperpolarized (13)C-MRS
Friesen-Waldner, L.J., et al., Direct enzyme-substrate affinity determination by real-time hyperpolarized (13)C-MRS. Chem Commun (Camb), 2014. 50(89): p. 13801-4.
http://www.ncbi.nlm.nih.gov/pubmed/25253534
nmrlearner
News from NMR blogs
0
10-29-2014 03:51 PM
[NMR paper] Determination of protein-ligand binding affinity by NMR: observations from serum albu
Determination of protein-ligand binding affinity by NMR: observations from serum albumin model systems.
Related Articles Determination of protein-ligand binding affinity by NMR: observations from serum albumin model systems.
Magn Reson Chem. 2005 Jun;43(6):463-70
Authors: Fielding L, Rutherford S, Fletcher D
The usefulness of bovine serum albumin (BSA) as a model protein for testing NMR methods for the study of protein-ligand interactions is discussed. Isothermal titration calorimetry established the binding affinity and stoichiometry of the...
Rapid Protein-Ligand Affinity Determination by Photoinduced Hyperpolarized NMR
Linear Mode
