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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...
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...
Conserved Binding Sites01:49

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 analyses 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...
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:

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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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Computational multiscale modeling in protein--ligand docking.

Michela Taufer1, Roger Armen, Jianhan Chen

  • 1Department of Computer and Information Sciences, University of Delaware, Newark, 19716, USA. taufer@cis.udel.edu

IEEE Engineering in Medicine and Biology Magazine : the Quarterly Magazine of the Engineering in Medicine & Biology Society
|April 8, 2009
PubMed
Summary

Small molecule ligands targeting enzymes are crucial for biological processes. Inhibiting specific enzymes offers a therapeutic strategy for infectious and noninfectious diseases by modulating biochemical pathways.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Pharmacology

Background:

  • Enzyme activity is fundamental to biological systems, regulating complex biochemical pathways.
  • Small molecule ligands can bind to and modulate enzyme function.
  • Enzyme inhibition is a key mechanism for many existing drugs.

Purpose of the Study:

  • To highlight the critical role of enzyme-ligand interactions in biological regulation.
  • To underscore the therapeutic potential of enzyme inhibitors in disease treatment.
  • To provide an overview of enzyme targeting in both infectious and noninfectious diseases.

Main Methods:

  • Review of biochemical principles governing enzyme-ligand binding.
  • Analysis of the mechanism of enzyme inhibition.
  • Examination of therapeutic strategies targeting enzymes in disease.

Main Results:

  • Enzyme inhibition by small molecules can control biochemical pathways.
  • Targeting pathogen or human enzymes offers disease treatment avenues.
  • Enzyme inhibitors are effective against a range of infectious and noninfectious diseases.

Conclusions:

  • Enzyme inhibition is a validated therapeutic strategy.
  • Targeting specific enzymes provides a precise approach to disease intervention.
  • Further research into enzyme-ligand interactions can yield novel therapeutics.