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Related Concept Videos

Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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:
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

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:
Ligand Binding Sites02:40

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...
Regulation of Metabolism01:19

Regulation of Metabolism

Cellular needs and conditions vary from cell to cell and change within individual cells over time. For example, the required enzymes and energetic demands of stomach cells are different from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive cell works much harder to process and break down nutrients during the time that closely follows a meal compared with many hours after a meal. As these cellular demands and conditions vary, so do the amounts and...

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Related Experiment Video

Updated: Jul 4, 2026

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
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Published on: December 1, 2020

Modulation of biomolecular interactions with complex-binding small molecules.

Zheng Cai1, Mark I Greene, Alan Berezov

  • 1Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, and Abramson Family Cancer Research Institute, 252 John Morgan Building, 3600 Hamilton Walk, Philadelphia, PA 19104, USA.

Methods (San Diego, Calif.)
|June 24, 2008
PubMed
Summary
This summary is machine-generated.

Designing noncompetitive small molecules offers a novel strategy to modulate biomolecular interactions. This complex-binding modulation (CBM) approach targets intermolecular complexes, overcoming limitations of traditional competitive inhibitors for drug development.

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Area of Science:

  • Biochemistry
  • Drug Discovery
  • Computational Chemistry

Background:

  • Modulating biomolecular interactions with small molecules is crucial for therapeutics but historically challenging.
  • Traditional competitive inhibition approaches often show low effectiveness.
  • Natural compounds provide precedents for complex-binding mechanisms.

Purpose of the Study:

  • To introduce a novel de novo structure-based design approach for noncompetitive small molecules.
  • To develop a computational algorithm for designing molecules that bind to intermolecular complexes.
  • To investigate the effects of these designed molecules on protein-protein and protein-small molecule interactions.

Main Methods:

  • Development of a complex-binding modulation (CBM) algorithm.
  • Structure-based de novo design of noncompetitive small molecules (CBM compounds).
  • Application of the CBM algorithm to design compounds targeting intermolecular pockets of complexes.

Main Results:

  • Successful design of CBM compounds using a novel algorithm.
  • Demonstration of CBM compounds' ability to bind to intermolecular complexes.
  • Investigation into the modulation of protein-protein and protein-small molecule interactions by CBM compounds.

Conclusions:

  • The CBM algorithm enables rational design of noncompetitive small molecules.
  • This approach offers a promising strategy for modulating biomolecular interactions.
  • The findings support CBM compounds as potential therapeutic agents targeting complex interfaces.