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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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Large-scale bioactivity analysis of the small-molecule assayed proteome.

Tyler William H Backman1,2, Daniel S Evans3, Thomas Girke2

  • 1Department of Bioengineering, University of California Riverside, Riverside, California, United States of America.

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|February 9, 2017
PubMed
Summary

This study analyzed drug bioactivity in PubChem, revealing FDA-approved drugs often show cross-reactivity within protein families, not across them. It identified novel drug targets and compounds, with over half of new findings being reproducible.

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Area of Science:

  • Drug discovery and development
  • Computational chemistry
  • Pharmacology

Background:

  • Small molecule bioactivity profiling is crucial for identifying potential drug candidates and understanding drug mechanisms.
  • FDA-approved drugs and non-FDA approved compounds exhibit distinct bioactivity patterns.
  • Target promiscuity, or activity against multiple targets, is a key characteristic influencing drug efficacy and safety.

Purpose of the Study:

  • To analyze and compare small molecule bioactivity profiles of FDA-approved drugs versus non-FDA approved compounds across diverse protein families.
  • To identify novel protein targets for existing drugs and novel compounds with potential therapeutic applications.
  • To characterize compound promiscuity and evaluate methods for its detection.

Main Methods:

  • Analysis of small molecule bioactivity data from PubChem BioAssay.
  • Comparison of bioactivity profiles between FDA-approved and non-FDA approved compounds.
  • Biclustering and Bayesian statistical modeling to identify drug-target relationships and compound promiscuity.
  • Evaluation of aggregator assays and PAINS substructures for promiscuity assessment.

Main Results:

  • FDA-approved drugs exhibit target promiscuity primarily through cross-reactivity within protein families.
  • Identified 804 novel protein targets for FDA-approved drugs and 901 for non-FDA approved compounds.
  • Discovered over 486,000 novel compounds active against known drug targets and over 153,000 against novel targets.
  • Estimated over half of novel outcomes are reproducible based on replicated screen agreement.
  • Aggregator assays and PAINS substructures show varying accuracy in identifying promiscuous compounds.

Conclusions:

  • The study provides a comprehensive reference for novel drug and target identification.
  • Findings aid in selecting promising candidates and eliminating unselective compounds.
  • Understanding target cross-reactivity within protein families is essential for drug development.