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PatchSearch: a web server for off-target protein identification.

Julien Rey1,2, Inès Rasolohery1, Pierre Tufféry1,2

  • 1Université Paris Diderot, Sorbonne Paris Cité, INSERM UMRS-973, Molécules Thérapeutiques in silico (MTi), F-75205 Paris, France.

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Summary
This summary is machine-generated.

PatchSearch identifies potential drug off-target proteins by finding compatible binding sites on protein surfaces. This tool aids in drug discovery and repurposing by detecting unexpected protein interactions.

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Area of Science:

  • Computational biology
  • Drug discovery
  • Bioinformatics

Background:

  • Drugs can interact with unintended proteins (off-targets) due to the vast number of proteins in the human body.
  • Identifying these off-target interactions is crucial for drug safety and efficacy.

Purpose of the Study:

  • To introduce the PatchSearch web server for identifying potential off-target proteins.
  • To provide a tool for detecting structurally conserved binding sites compatible with known ligands.

Main Methods:

  • PatchSearch utilizes a non-sequential local alignment of surface patches to compare protein structures.
  • It analyzes geometric and physicochemical properties of binding sites to assess ligand compatibility.
  • Ligand binding modes and estimated affinities (using Vinardo scoring) are proposed for potential off-targets.

Main Results:

  • The web server efficiently detects potential interactions between ligands and distant off-target proteins.
  • It identifies proteins with binding sites structurally conserved and compatible with user-supplied ligands.
  • PatchSearch successfully predicts potential off-target binding sites and ligand interactions.

Conclusions:

  • PatchSearch is a novel tool for detecting potential off-target proteins and their interactions.
  • This web server can facilitate drug repurposing by uncovering unexpected drug-target interactions.
  • The tool aids in understanding drug behavior and improving drug development strategies.