Ligand Screening by Saturation-Transfer Difference (STD) NMR Spectroscopy

Abstract

NMR based methods to screen for high-affinity ligands have become an indispensable tool for designing rationalized drugs, as these offer a combination of good experimental design of the screening process and data interpretation methods, which together provide unprecedented information on the complex nature of protein-ligand interactions. These methods rely on measuring direct changes in the spectral parameters, that are often simpler than the complex experimental procedures used to study structure and dynamics of proteins. The goal of this review article is to provide the basic details of NMR based ligand-screening methods, with particular focus on the saturation transfer difference (STD) experiment. In addition, we provide an overview of other NMR experimental methods and a practical guide on how to go about designing and implementing them.

Smelling Sulfur: Copper and Silver Regulate the Response of Human Odorant Receptor OR2T11 to Low-Molecular-Weight Thiols

“…The amplification factor ( A STD ) is obtained by multiplying the relative STD effect of a given signal (the intensity of a signal in the difference spectrum divided by its intensity in the reference spectrum, I STD / I 0 ) with the molar ratio of ligand relative to the protein, [odorant]/[OR]. − The concentration of OR was taken to be 13 nmol/L, and the concentration of odorant was taken to be the average of the ERETIC (electronic reference to access in vivo concentrations) values for the samples with and without the metal salts. Previously, we have shown that for the three independent experiments with TBM, CuCl 2 , and MOR244-3, I STD / I O was equal to 0.002 with a relative standard deviation of 13%.…”

A dual drug regimen synergistically blocks human parainfluenza virus infection

“…To-date, only a closed-216 loop structure of hPIV-3 HN has been observed in complex with zanamivir ( 3 ) 25 38 . Since we observe an increase in STD-NMR signals for zanamivir ( 3 ) in the presence of suramin ( 7 ) and hPIV-3 HN, it suggests that a faster exchange of zanamivir ( 3 ) from bound- to free-form occurs 41 . A possible explanation of this outcome is that suramin ( 7 ) induces the 216 loop to open enabling this faster exchange.…”

Integration of NMR studies, computational predictions, and in vitro assays in the search of marine diterpenes with antitumor activity

“…In order to understand the molecular‐level interactions of the active compounds with tubulin, those were analyzed by the NMR saturation transfer difference experiment (NMR‐STD). This pulse sequence allows the identification of the hydrogen atoms of the ligand that participate in interactions with tubulin (Krishnan, 2005).…”

“…This demonstrated that all signals in the STD spectra in the presence of the protein correspond to the hydrogens from the ligand structure that were involved in the interaction with the protein. These protons suffered interference of protein magnetization, induced by saturation NMR radio frequency pulse-a process that allows the characterization of groupspecific epitopes of the ligands (Krishnan, 2005;Monaco et al, 2017). Compounds 1, 17, and 26 showed interaction with the protein in the STD spectra (Figures S8 and S9).…”