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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Targets for Drug Action: Overview01:26

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Drugs target macromolecules to modify ongoing cellular processes. Primary drug targets include receptors, ion channels, transporters, and enzymes.
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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Drug-Receptor Bonds01:25

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Drug-receptor bonds are formed through various chemical forces when drugs interact with target cells. Covalent bonds, strong and irreversible, are exemplified by DNA-alkylating anticancer agents that inhibit cell division. However, such irreversible drug binding lacks selectivity and can modify the DNA of the surrounding healthy cells. Covalent binding often contributes to tissue toxicity, as seen with chloroform and paracetamol metabolites binding to the liver, causing hepatotoxicity.
In...
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Ligand Binding Sites02:40

Ligand Binding Sites

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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...
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The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
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Novel approaches to map small molecule-target interactions.

Shobhna Kapoor1, Herbert Waldmann2, Slava Ziegler1

  • 1Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund, Germany.

Bioorganic & Medicinal Chemistry
|June 1, 2016
PubMed
Summary

Identifying the molecular targets of small molecules is crucial for chemical biology and drug discovery. This work reviews new methods combining omics and bioinformatics to find these targets, addressing a key research gap.

Keywords:
Bioactive small moleculesCETSA, transcriptome sequencingCRISPR/Cas9Chem-seqProfilingTarget identificationTarget prediction

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Area of Science:

  • Chemical biology
  • Pharmaceutical research
  • Molecular pharmacology

Background:

  • Small molecules are vital tools for probing protein function and cellular processes.
  • Characterizing bioactive compounds in living systems is essential to confirm their mechanism of action.
  • A significant challenge in chemical biology is the lack of a universal method for identifying the molecular targets of small molecules.

Discussion:

  • Recent advances in omics technologies (genomics, proteomics, etc.) have revolutionized target identification.
  • Chemo- and bioinformatics analysis provide powerful computational tools to interpret complex biological data.
  • Integrating omics data with chemical information facilitates the discovery of small molecule-protein interactions.

Key Insights:

  • Novel methodologies are emerging for the systematic identification of small molecule targets.
  • The synergy between high-throughput omics and advanced bioinformatics is accelerating target discovery.
  • These approaches are critical for validating drug candidates and understanding drug action.

Outlook:

  • Future research will likely focus on refining and integrating these techniques for greater efficiency and accuracy.
  • Developing standardized protocols for target identification will benefit the broader research community.
  • These advancements hold promise for accelerating drug development and personalized medicine.