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Title: Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1

Journal Article · · eLife
DOI:https://doi.org/10.7554/eLife.25541· OSTI ID:1368344

Overexpression of anti-apoptotic Bcl-2 family proteins contributes to cancer progression and confers resistance to chemotherapy. Small molecules that target Bcl-2 are used in the clinic to treat leukemia, but tight and selective inhibitors are not available for Bcl-2 paralog Bfl-1. Guided by computational analysis, we designed variants of the native BH3 motif PUMA that are > 150-fold selective for Bfl-1 binding. The designed peptides potently trigger disruption of the mitochondrial outer membrane in cells dependent on Bfl-1, but not in cells dependent on other anti-apoptotic homologs. High-resolution crystal structures show that designed peptide FS2 binds Bfl-1 in a shifted geometry, relative to PUMA and other binding partners, due to a set of epistatic mutations. FS2 modified with an electrophile reacts with a cysteine near the peptide-binding groove to augment specificity. Designed Bfl-1 binders provide reagents for cellular profiling and leads for developing enhanced and cell-permeable peptide or small-molecule inhibitors.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities Division; National Inst. of General Medical Sciences; National Inst. of Health; NIH-ORIP HEI; National Science Foundation (NSF); MIT School of Science Ludwig Fund for Cancer Research; Koch Institute/MIT - Dana-Farber/Harvard Cancer Center Bridge Project
Grant/Contract Number:
AC02-06CH11357; P41 GM103403; S10 RR029205; R01-GM110048
OSTI ID:
1368344
Journal Information:
eLife, Vol. 6, Issue 2017; ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.Copyright Statement
Country of Publication:
United States
Language:
ENGLISH
Citation Metrics:
Cited by: 27 works
Citation information provided by
Web of Science

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Cited By (12)

BH3 profiling discriminates on-target small molecule BH3 mimetics from putative mimetics journal July 2019
Prediction of venetoclax activity in precursor B-ALL by functional assessment of apoptosis signaling journal July 2019
Advances in protein structure prediction and design journal August 2019
Molecular evolution of peptides by yeast surface display technology journal January 2019
Iterative optimization yields Mcl-1–targeting stapled peptides with selective cytotoxicity to Mcl-1–dependent cancer cells journal January 2018
Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations journal December 2018
Peptide design by optimization on a data-parameterized protein interaction landscape journal October 2018
N‐locking stabilization of covalent helical peptides: Application to Bfl‐1 antagonists journal April 2020
Splicing modulation sensitizes chronic lymphocytic leukemia cells to venetoclax by remodeling mitochondrial apoptotic dependencies journal October 2018
Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level journal December 2019
Sabutoclax (BI97C1) and BI112D1, Putative Inhibitors of MCL-1, Induce Mitochondrial Fragmentation Either Upstream of or Independent of Apoptosis journal May 2013
Prediction of venetoclax activity in precursor B-ALL by functional assessment of apoptosis signaling text January 2019

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