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Related Experiment Video

Updated: Jul 6, 2025

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Advancing PROTAC Characterization: Structural Insights through Adducts and Multimodal Tandem-MS Strategies.

Mohammed Rahman1,2, Bryan Marzullo1, Stephen W Holman3

  • 1Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.

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|January 10, 2024
PubMed
Summary

This study pioneers tandem mass spectrometry (MS) analysis for proteolysis targeting chimeras (PROTACs), revealing fragmentation patterns crucial for characterizing these therapeutic molecules.

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Area of Science:

  • Analytical Chemistry
  • Chemical Biology
  • Drug Discovery

Background:

  • Proteolysis targeting chimeras (PROTACs) are emerging therapeutics that induce targeted protein degradation.
  • Native PROTACs lack comprehensive tandem mass spectrometry (MS) analysis, hindering detailed structural characterization.
  • Understanding PROTAC fragmentation is vital for their development and quality control.

Purpose of the Study:

  • To investigate the tandem mass spectrometry (MS/MS) fragmentation patterns of two PROTACs, dBET1 and VZ185.
  • To enhance structural characterization of PROTACs using various cations and MS techniques.
  • To identify optimal MS approaches for elucidating PROTAC structures.

Main Methods:

  • Tandem mass spectrometry (MS/MS) analysis of dBET1 and VZ185 using sodium, lithium, and silver cations.
  • Positive and negative polarity mode MS analysis.
  • De novo structure determination using 2DMS data from degradation studies.
  • Analysis of charge-state dependent fragmentation.

Main Results:

  • Lithium cations improved positive-mode coverage for dBET1; negative mode provided richer data.
  • Charge-related factors influenced moiety observation in VZ185, with [M + 2H]2+ showing fewer fragments than [M + H]+.
  • Silver adducts indicated both charge-directed and charge-remote fragmentation mechanisms.
  • Frequently dissociated bonds were identified across multiple fragmentation techniques.

Conclusions:

  • This study provides the first detailed MS/MS fragmentation analysis of native PROTACs.
  • Optimal MS strategies for PROTAC structural elucidation were identified.
  • Findings advance the understanding and development of PROTACs as therapeutic agents.