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Related Concept Videos

Drug Discovery: Overview01:26

Drug Discovery: Overview

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Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...
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Cooperative Allosteric Transitions01:58

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Cooperative Allosteric Transitions01:58

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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...
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Allosteric Proteins-ATCase01:19

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Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
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Allosteric Regulation01:08

Allosteric Regulation

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Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
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Ligand Binding and Linkage00:49

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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...
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Updated: Dec 29, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Integrated Computational Approaches and Tools forAllosteric Drug Discovery.

Olivier Sheik Amamuddy1, Wayde Veldman1, Colleen Manyumwa1

  • 1Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University,Grahamstown 6140, South Africa.

International Journal of Molecular Sciences
|February 5, 2020
PubMed
Summary

Computational methods enhance allosteric drug discovery by predicting interactions and identifying sites. Integrating these tools with experimental data improves efficiency and reliability for developing targeted therapies.

Keywords:
AllosteryMD-TASKallosteric modulatorsdrug resistancenetwork analysisprecision medicine

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Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Chemistry and Cheminformatics
  • Pharmacology and Drug Discovery

Background:

  • Allosteric regulation in proteins is crucial for drug discovery, offering targeted modulation with reduced toxicity.
  • Allosteric modulators provide selectivity and minimize side effects compared to traditional drugs.
  • Understanding allosteric mechanisms is key to developing novel therapeutic strategies.

Purpose of the Study:

  • To review computational approaches for allosteric drug discovery.
  • To discuss the integration of computational tools into robust workflows for identifying allosteric sites and modulators.
  • To explore applications in pathogen resistance and precision medicine.

Main Methods:

  • Review of existing computational approaches for predicting ligand-protein interactions and binding.
  • Focus on dynamic and network-centric perspectives for understanding allosteric mechanisms.
  • Integration of computational pipelines with experimental feedback.

Main Results:

  • Novel computational approaches provide new insights into allosteric mechanisms.
  • Computer-based discovery of allosteric drugs is facilitated by these methods.
  • Current methods are continuously being improved for greater accuracy and reliability.

Conclusions:

  • Integrating computational and experimental approaches enhances the efficiency and reliability of allosteric drug discovery.
  • Allosteric modulators offer opportunities for targeted protein modulation and improved therapeutic indices.
  • These strategies can be applied to combat pathogen resistance and advance precision medicine.