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Related Concept Videos

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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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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Conserved Binding Sites01:49

Conserved Binding Sites

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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.
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The Equilibrium Binding Constant and Binding Strength02:18

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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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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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G Protein–Coupled Receptors (GPCRs) are membrane-bound receptors that transiently associate with heterotrimeric G proteins and induce an appropriate response to various stimuli. GPCRs regulate critical physiological pathways and are excellent drug targets for treating diseases such as diabetes, cancer, obesity, depression, or Alzheimer's. Nearly 35% of approved drugs implement their therapeutic effects by selectively interacting with specific GPCRs.
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GPER binding site detection and description: A flavonoid-based docking and molecular dynamics simulations study.

David Méndez-Luna1, Sonia Guzmán-Velázquez2, Itzia-Irene Padilla-Martínez3

  • 1Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Alcaldía Miguel Hidalgo, C.P. 11340 Ciudad de México, Mexico; Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Zacatenco, Av. Wilfrido Massieu 399, Col. Nueva Industrial Vallejo, Alcaldía Gustavo A. Madero, C.P. 07738 Ciudad de México, Mexico.

The Journal of Steroid Biochemistry and Molecular Biology
|February 2, 2024
PubMed
Summary

Flavonoids show promise as adjuvant cancer treatments by interacting with the G-protein coupled estrogen receptor (GPER). Specific flavonoids like Puerarin may modulate GPER, offering potential anti-cancer effects.

Keywords:
Binding SiteDockingFlavonoidsGPERMolecular Dynamics simulations

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Pharmacology

Background:

  • Flavonoids are plant-derived phenolic compounds with significant health implications.
  • Dietary intake of flavonoids (approx. 1g/day) supports human homeostasis.
  • Flavonoids are being investigated for their role as adjuvant cancer therapies.

Purpose of the Study:

  • To investigate the potential of specific flavonoids as ligands for the G-protein coupled estrogen receptor (GPER).
  • To elucidate the mechanism of GPER activation by flavonoids and identify key interacting residues.
  • To explore the anti-cancer potential of selected flavonoids through GPER modulation.

Main Methods:

  • Computational analysis including pocket detection, docking, and molecular dynamics simulations.
  • Screening of 39 flavonoids to identify potential GPER ligands.
  • Identification of a novel sugar-acceptor sub-cavity within the GPER binding site.

Main Results:

  • Four flavonoids (Puerarin, Isoquercetin, Kaempferol 3-O-glucoside, Petunidin 3-O-glucoside) were identified as potential GPER ligands.
  • The sugar moiety of these flavonoids defines a new sub-cavity in the GPER binding site.
  • Key residues involved in GPER activation by these flavonoids were identified.

Conclusions:

  • The studied flavonoids show potential as GPER ligands, suggesting a mechanism for their anti-cancer effects.
  • Further in vitro and in vivo studies are warranted to validate these findings.
  • This research highlights flavonoids as promising candidates for novel anti-cancer drug development targeting GPER.