Unveiling BCL-xL-specific PROTAC efficiency and dissociation pathways using native mass spectrometry.

Area of Science:

• Biochemistry
• Chemical Biology
• Mass Spectrometry

Background:

• Overexpression of anti-apoptotic proteins like BCL-xL drives cancer and chemotherapy resistance.
• Small-molecule BCL-xL inhibitors face toxicity issues, particularly thrombocytopenia.
• Proteolysis-targeting chimeras (PROTACs) offer an alternative by degrading target proteins via the ubiquitin-proteasome system.

Purpose of the Study:

• To utilize native mass spectrometry (MS) as a platform for screening and characterizing PROTACs targeting BCL-xL.
• To investigate the formation, stability, and dissociation pathways of ternary complexes involving BCL-xL, PROTACs, and the VHL E3 ligase complex (VCB).
• To assess the utility of native MS techniques, including collision-induced dissociation (CID), ultraviolet photodissociation (UVPD), and variable-temperature electrospray ionization MS (vT-ESI-MS), for PROTAC analysis.

Main Methods:

• Native mass spectrometry (MS) was employed for label-free screening and characterization.
• Direct detection of binary (BCL-xL·PROTAC) and ternary (BCL-xL·PROTAC·VCB) complexes.
• Analysis of complex dissociation pathways using collision-induced dissociation (CID) and ultraviolet photodissociation (UVPD).
• Assessment of thermal stability in solution using variable-temperature ESI-MS (vT-ESI-MS).

Main Results:

• Native MS successfully detected and semi-quantified PROTAC binding affinities and cooperativity in both binary and ternary complexes.
• CID and UVPD revealed distinct fragmentation patterns, providing insights into the structural organization and gas-phase stability of the complexes.
• vT-ESI-MS allowed for the evaluation of the thermal stabilities of these complexes in solution.
• The study confirmed the effectiveness of native MS in analyzing PROTAC-induced ternary complex formation.

Conclusions:

• Native MS is a powerful, rapid, and label-free tool for screening and mechanistic characterization of PROTACs.
• This approach provides valuable insights into ternary complex formation and stability, crucial for PROTAC design and optimization.
• Native MS facilitates the development of novel PROTAC-based therapeutics for cancers driven by proteins like BCL-xL.