8VWZ

Human Bcl-2 (G101V Mutant)/Bcl-xL Chimera Fused to MBP in Complex with Inhibitor S55746

Summary for 8VWZ

• Entry DOI: 10.2210/pdb8vwz/pdb
• Related: 8VWX 8VXM 8VXN
• Descriptor: Maltose/maltodextrin-binding periplasmic protein fused to apoptosis regulator Bcl-2/Bcl-xL chimera, ~{N}-(4-hydroxyphenyl)-3-[6-[[(3~{S})-3-(morpholin-4-ylmethyl)-3,4-dihydro-1~{H}-isoquinolin-2-yl]carbonyl]-1,3-benzodioxol-5-yl]-~{N}-phenyl-5,6,7,8-tetrahydroindolizine-1-carboxamide, DI(HYDROXYETHYL)ETHER, ... (4 entities in total)
• Functional Keywords: apoptosis, bcl-2, g101v mutant, mbp fusion, bcl-xl chimera, s55746, complex, protein-protein interface inhibitor
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 1
• Total formula weight: 62119.83

Authors

Baird, J.,Holliday, M. (deposition date: 2024-02-02, release date: 2024-10-02, Last modification date: 2025-03-12)

Primary citation

Sun, Y.,Houde, D.,Iacob, R.E.,Baird, J.,Swift, R.V.,Holliday, M.,Shi, X.,Sidoli, S.,Brenowitz, M.
Hydrogen/Deuterium Exchange and Protein Oxidative Footprinting with Mass Spectrometry Collectively Discriminate the Binding of Small-Molecule Therapeutics to Bcl-2.
Anal.Chem., 97:4329-4340, 2025

PubMed Abstract: Characterizing protein-ligand interactions is crucial to understanding cellular metabolism and guiding drug discovery and development. Herein, we explore complementing hydrogen/deuterium exchange mass spectrometry (HDX-MS) with a recently developed Fenton chemistry-based approach to protein oxidative footprinting mass spectrometry (OX-MS) to discriminate the binding of small-molecule therapeutics. Using drug-dependent perturbation as the experimental report, this combination of techniques more clearly differentiates the in-solution binding profiles of Venetoclax (ABT-199, GDC-0199-AbbVie and Genentech) and a drug candidate S55746 (Servier) to the apoptotic regulatory protein Bcl-2 than either technique alone. These results highlight the value of combining these methods to compare compounds in drug discovery and development. To better understand the structural context of the HDX-MS and OX-MS drug-dependent perturbations, we mapped these data on Bcl-2-Venetoclax and Bcl-2-S55746 cocrystal structures and compared these results with the structure of apo Bcl-2. HDX-MS shows that Venetoclax more strongly impacts the protein backbone compared to S55746. OX-MS reveals oxidation perturbations rationalized by direct side-chain protection as well as by crystallographically observed drug-induced protein restructuring. Both methods report the perturbation of some, but not all, residues mapped within 4 Å of the bound drugs in the crystal structures. Concordant characterization of backbone and side-chain accessibility will enhance our understanding of in-solution protein structure dynamics and protein-ligand interactions during drug discovery, development, and characterization, particularly when high-resolution structures are lacking.

PubMed: 39969248
DOI: 10.1021/acs.analchem.4c04516

Experimental method

X-RAY DIFFRACTION (2.33 Å)