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Related Concept Videos

SDS-PAGE01:27

SDS-PAGE

Gel electrophoresis is a method that separates biological macromolecules like nucleic acids or proteins by forcing them to pass through a gel matrix under an electric field.
A variation of gel electrophoresis, termed  polyacrylamide gel electrophoresis (PAGE), is commonly used for separating proteins according to their molecular size by passing them through a polyacrylamide gel. Because of the varying charges associated with amino acid side chains, PAGE can be used to separate intact proteins...
Mass Spectrometry of Amines01:15

Mass Spectrometry of Amines

In mass spectroscopy, amines undergo fragmentation to give parent ions with odd molecule weights. This observed mass spectrum follows the nitrogen rule; a molecule with an odd number of nitrogen atoms produces a molecular ion with an odd molecular weight. Amines undergo fragmentation through α cleavage, producing nitrogen-containing cations—iminium ions—and alkyl radicals. Mass spectra of aromatic and cyclic aliphatic amines exhibit strong molecular ion peaks, but acyclic aliphatic amines show...
Structure of Amines01:19

Structure of Amines

The hybridized nitrogen atom in amines possesses a lone pair of electrons and is bound to three substituents with a bond angle of around 108°, which is less than the tetrahedral angle of 109.5°. However, the C–N–H bond angle is slightly larger at 112°, with a carbon–nitrogen bond length of 147 pm. This carbon–nitrogen bond length of of amines is longer than the carbon–oxygen bond of alcohols (143 pm) but shorter than alkanes’ carbon–carbon bond (154 pm). These aspects are illustrated in Figure...

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Related Experiment Video

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Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library
13:37

Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library

Published on: June 20, 2014

Efficient stacking on protein amide fragments.

Michael Harder1, Bernd Kuhn, François Diederich

  • 1Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland.

Chemmedchem
|January 29, 2013
PubMed
Summary

This study reveals how to enhance aromatic stacking interactions with protein amide groups. Optimizing dipole alignment, dipole moment, and π-electron density improves ligand binding for drug design.

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Area of Science:

  • Medicinal Chemistry
  • Computational Chemistry
  • Structural Biology

Background:

  • Protein receptor binding sites often expose less polar π-surfaces on amide groups.
  • These amide groups are present in the protein backbone and in glutamine (Gln) and asparagine (Asn) side chains.

Purpose of the Study:

  • To investigate the energetics and geometric preferences of heteroarene stacking on protein amide groups.
  • To identify guidelines for improving these stacking interactions in drug design.

Main Methods:

  • Utilized quantum chemical calculations.
  • Performed Protein Data Bank (PDB) searches on model systems.
  • Analyzed interactions between heteroarenes and amide groups relevant to medicinal chemistry.

Main Results:

  • Identified three key factors to improve aromatic stacking energy with protein amide groups.
  • Optimizing fragment dipole vector alignment (antiparallel to amide dipole) enhances binding.
  • Increasing the aromatic substituent's dipole moment and decreasing its π-electron density are beneficial.

Conclusions:

  • Provides rational guidelines for exploiting π-surface-amide group interactions in drug design.
  • Findings can aid in the development of more effective structure-based therapeutics.
  • Understanding these interactions is crucial for optimizing ligand-protein binding.