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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

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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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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.
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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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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
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DiPPI: A Curated Data Set for Drug-like Molecules in Protein-Protein Interfaces.

Fatma Cankara1, Simge Senyuz1, Ahenk Zeynep Sayin2

  • 1Graduate School of Sciences and Engineering, Koç University, İstanbul 34450, Turkey.

Journal of Chemical Information and Modeling
|June 22, 2024
PubMed
Summary

This study introduces DiPPI, a web resource detailing drug-like molecules interacting with protein interfaces. It aids drug repurposing by providing curated data on protein interfaces and drug properties, facilitating disease-related PPI investigation.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Pharmacology and Drug Discovery
  • Bioinformatics

Background:

  • Protein-protein interactions (PPIs) are crucial in biological processes, and their dysfunction is linked to various diseases.
  • Targeting PPIs offers a promising therapeutic strategy, necessitating a deeper understanding of drug-modulated PPIs.
  • Identifying small molecules that modulate PPIs is essential for developing novel therapeutics.

Purpose of the Study:

  • To curate a comprehensive dataset of drug-like molecules that bind to protein interfaces.
  • To develop DiPPI, a web-based resource for exploring protein-protein interface and drug-like molecule properties.
  • To facilitate drug repurposing studies by providing structured data on interface-binding drugs.

Main Methods:

  • Compiled a large dataset of protein structures and their interfaces, identifying drug-binding sites.
  • Developed a web server (DiPPI) with two modules: one for interface properties and another for drug-like molecules.
  • Integrated data on interface characteristics (e.g., amino acid properties, conservation) and drug properties (e.g., Lipinski's rules, molecular fingerprints).

Main Results:

  • The dataset includes 534,203 interfaces from 98,632 protein structures, with 55,135 interfaces binding drug-like molecules.
  • DiPPI hosts 2,214 drug-like molecules, including 335 FDA-approved drugs, clustered by molecular fingerprints.
  • The web resource provides detailed properties of both interfaces and drugs, enabling efficient searching and analysis.

Conclusions:

  • DiPPI offers a valuable, freely accessible resource for researchers investigating drug-protein interface interactions.
  • The platform streamlines drug repurposing efforts by providing curated and analyzed data on interface-targeting molecules.
  • This resource supports the development of new therapeutic strategies by elucidating the landscape of drug-modulated protein-protein interactions.