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When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...
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Amines can be identified using mass spectroscopy based on their characteristic fragmentation patterns. The molecular ions of amines undergo fragmentation via ⍺-cleavage. The ⍺-cleavage of the carbon-carbon bonds in amines generates an alkyl radical and resonance-stabilized nitrogen-containing cation.
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NMR Spectroscopy: Chemical Shift Overview01:15

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The position of the absorption signal of a sample is reported relative to the position of the signal of tetramethylsilane (TMS), which is added as an internal reference while recording spectra. The difference between the absorption frequencies of the sample and TMS (in Hz) is divided by the spectrometer operating frequency (in MHz) to obtain a dimensionless quantity called the chemical shift. It is reported on the δ (delta) scale and expressed in parts per million.
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Mass Spectrometry: Aromatic Compound Fragmentation01:23

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Upon ionization, aromatic compounds generate a molecular ion that is observed as a prominent peak in their mass spectra. For example, the molecular ion peak for benzene appears at a mass-to-charge ratio of 78, while toluene is observed at a mass-to-charge ratio of 92. The molecular ion benzene is highly stable and does not readily undergo further fragmentation due to the significant amount of energy required to disrupt the aromatic stability of the benzene ring. In contrast, the molecular ion...
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2D NMR: Heteronuclear Single-Quantum Correlation Spectroscopy (HSQC)01:19

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Heteronuclear single-quantum correlation spectroscopy (HSQC) is a 2D NMR technique that reveals one-bond correlations between hydrogen and a heteronucleus. The HSQC experiment is similar to the heteronuclear correlation experiment (HETCOR) but is more sensitive. In the HSQC spectrum, the proton chemical shift is plotted on the horizontal F2 axis, while the 13C chemical shift is plotted on the vertical F1 axis. The corresponding proton and 13C spectra are also shown. The HSQC contour plot does...
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Chemical Shift: Internal References and Solvent Effects01:17

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In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
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NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode
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Saturation transfer difference NMR for fragment screening.

Darren W Begley1, Spencer O Moen1, Phillip G Pierce1

  • 1Emerald Bio, Bainbridge Island, Washington.

Current Protocols in Chemical Biology
|January 7, 2014
PubMed
Summary
This summary is machine-generated.

Saturation transfer difference nuclear magnetic resonance (STD-NMR) screening identifies small molecule binders for drug discovery. This method is sensitive to weakly binding fragments, crucial for finding drug leads.

Keywords:
NMRSTDfragment screeningfragment-based hit generationsaturation transfer difference

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Drug Discovery

Background:

  • Fragment-based drug discovery (FBDD) relies on identifying low-affinity binders.
  • Saturation Transfer Difference Nuclear Magnetic Resonance (STD-NMR) is a sensitive biophysical technique for detecting ligand-target interactions.
  • Developing robust screening protocols is essential for FBDD success.

Purpose of the Study:

  • To detail a comprehensive protocol for STD-NMR fragment screening.
  • To enable the identification of small molecule binders for diverse biological targets.
  • To provide a framework for optimizing STD-NMR experiments and data analysis.

Main Methods:

  • Development of a compound library specifically designed for STD-NMR screening.
  • Preparation and characterization of protein samples for binding assays.
  • Optimization of STD-NMR experimental parameters (e.g., relaxation delays, Watergate settings).
  • Standardized procedures for data collection and spectral analysis.

Main Results:

  • A validated protocol for STD-NMR fragment screening is presented.
  • The method demonstrates high sensitivity for detecting weak fragment binders.
  • The protocol is applicable to a wide range of protein targets.
  • Guidelines for library preparation and experimental optimization are provided.

Conclusions:

  • STD-NMR is a powerful and versatile technique for fragment screening in drug discovery.
  • This protocol facilitates the identification of initial fragment hits.
  • The described methods support the advancement of fragment-based lead discovery campaigns.