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Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Conserved Binding Sites

Conserved Binding Sites

Conjugate Addition (1,4-Addition) vs Direct Addition (1,2-Addition)

Conjugate Addition (1,4-Addition) vs Direct Addition (1,2-Addition)

α,β-Unsaturated carbonyl compounds with two electrophilic sites, the carbonyl carbon, and the β carbon, are susceptible to nucleophilic attack via two modes: conjugate or 1,4-addition and direct or 1,2-addition.
Conjugate addition results in a thermodynamically stable product. The reaction retains the stronger C=O bond at the expense of the weaker C=C π bond. The process is slow as the β carbon is less electrophilic than the carbonyl carbon.
Direct addition products are...

Ligand Binding Sites

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

Ligand Binding Sites

Ligand Binding Sites

Additional Subnuclear Structures

Additional Subnuclear Structures

The eukaryotic nucleus is a double membrane-bound organelle that contains nearly all of the cell’s genetic material in the form of chromosomes. It is rightly called the “brain” of the cell as it shoulders the responsibility of responding to various physiological processes, stress, altered metabolic conditions, and other cellular signals.
The nucleus contains many membrane-less subnuclear organelles or nuclear bodies, such as nucleoli, Cajal bodies, speckles,...

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Related Experiment Video

Updated: Feb 7, 2026

Engineering Molecular Recognition with Bio-mimetic Polymers on Single Walled Carbon Nanotubes

Engineering Molecular Recognition with Bio-mimetic Polymers on Single Walled Carbon Nanotubes

Published on: January 10, 2017

Molecular Tweezers with Additional Recognition Sites.

Christian Heid¹, Andrea Sowislok¹, Torsten Schaller¹

¹Faculty of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.

Chemistry (Weinheim an Der Bergstrasse, Germany)

|July 18, 2018

Summary

Researchers developed new synthetic methods for molecular tweezers, versatile tools for chemical biology. These novel structures with clickable alkynyl phosphates can bind amino acids and peptides.

Keywords:

alkynols amino acids esters molecular tweezers peptides

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Last Updated: Feb 7, 2026

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Area of Science:

Supramolecular Chemistry
Organic Synthesis
Chemical Biology

Background:

Molecular tweezers are crucial host molecules in supramolecular chemistry.
Developing versatile synthetic routes for functionalized molecular tweezers is essential for expanding their applications.

Purpose of the Study:

To present novel synthetic strategies for molecular tweezers with aliphatic phosphate ester groups.
To enable the attachment of functional units via click chemistry for broader applications.

Main Methods:

Trichloroacetonitrile method: Activation of hydroxyl groups via trichloroacetimidate intermediates.
Phosphoramidite strategy: Activation of hydroquinone precursors followed by coupling and oxidation.
Both methods utilize mild conditions for synthesis.

Main Results:

Successful synthesis of mono- and disubstituted molecular tweezers.
Introduction of alkynyl ester groups for click chemistry functionalization.
Demonstrated binding of lysine, arginine, and peptides by the synthesized tweezers.

Conclusions:

The developed synthetic routes provide convenient access to novel molecular tweezers.
Clickable alkynyl phosphates enhance the versatility of molecular tweezers for chemical biology.
The synthetic concept is transferable to other macrocyclic host classes.