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Related Concept Videos

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...
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...
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 and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...

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Ligand-target interaction-based weighting of substructures for virtual screening.

Thomas J Crisman1, Mihiret T Sisay, Jürgen Bajorath

  • 1Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universitat, Dahlmannstrasse 2, Bonn, Germany.

Journal of Chemical Information and Modeling
|September 30, 2008
PubMed
Summary

A new method scores molecular features using 3D interaction data for virtual screening. This Interaction Annotated Structural Features (IASF) approach improves hit identification in drug discovery compared to traditional methods.

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Area of Science:

  • Computational chemistry and cheminformatics
  • Drug discovery and development
  • Structural biology

Background:

  • Virtual screening is crucial for identifying novel drug candidates.
  • Current methods like fragment-based similarity searching and docking have limitations in accuracy and efficiency.
  • Integrating 3D ligand-target interaction data can enhance the predictive power of screening methods.

Purpose of the Study:

  • To introduce a novel methodology for assigning energy-based scores to 2D structural features.
  • To leverage 3D ligand-target interaction information for improved virtual screening.
  • To develop a scoring system that enhances the identification of active compounds in large databases.

Main Methods:

  • Development of the Interaction Annotated Structural Features (IASF) method.
  • Assigning energy-based scores to 2D structural fragments based on 3D interaction data.
  • Utilizing cumulative scores of interaction-annotated features for similarity searching.
  • Application and validation of the IASF method on five high-throughput screening (HTS) datasets.

Main Results:

  • The IASF method successfully assigns scores to 2D structural features using 3D interaction data.
  • Database molecules are assigned cumulative scores reflecting similarity to active reference compounds.
  • Application to five HTS datasets demonstrated superior hit identification compared to conventional methods.
  • IASF often identified more hits than fragment-based similarity searching and ligand-protein docking.

Conclusions:

  • The Interaction Annotated Structural Features (IASF) method provides an effective approach for virtual screening.
  • Incorporating 3D ligand-target interaction information into 2D feature scoring significantly enhances hit discovery.
  • IASF offers a promising alternative to existing virtual screening techniques for identifying potential drug candidates.