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Sun Y, Houde D, Iacob RE, Baird J, Swift RV, 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 2025; 97:4329-4340. [PMID: 39969248 PMCID: PMC11887655 DOI: 10.1021/acs.analchem.4c04516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 12/13/2024] [Accepted: 01/09/2025] [Indexed: 02/20/2025]
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.
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Affiliation(s)
- Yan Sun
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Damian Houde
- Relay
Therapeutics, Cambridge, Massachusetts 02139, United States
| | - Roxana E. Iacob
- Relay
Therapeutics, Cambridge, Massachusetts 02139, United States
| | - Jason Baird
- Relay
Therapeutics, Cambridge, Massachusetts 02139, United States
| | - Robert V. Swift
- Relay
Therapeutics, Cambridge, Massachusetts 02139, United States
| | - Michael Holliday
- Relay
Therapeutics, Cambridge, Massachusetts 02139, United States
| | - Xuyan Shi
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Simone Sidoli
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Michael Brenowitz
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
- Department
of Molecular Pharmacology, Albert Einstein
College of Medicine, Bronx, New York 10461, United States
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2
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Vafaeian A, Vafaei A, Parvizi MR, Chamanara M, Mehriardestani M, Hosseini Y. Molecular assessment of NMDAR subunits and neuronal apoptosis in the trigeminal ganglion in a model of male migraine-induced rats following Moringa oleifera alcoholic extract administration. BMC Neurosci 2025; 26:9. [PMID: 39905292 PMCID: PMC11796011 DOI: 10.1186/s12868-025-00928-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 01/17/2025] [Indexed: 02/06/2025] Open
Abstract
INTRODUCTION Migraine, a common disorder marked by severe and repetitive headaches, has been linked to the involvement of the NMDA receptor (NMDAR), a receptor responsible for glutamate signaling. Moringa oleifera (M. oleifera), recognized for its anti-inflammatory properties and therapeutic potential in various conditions, has been investigated. This study aims to assess the efficacy and precise mechanisms of M. oleifera for the treatment of migraine, for which evidence is limited. METHODS Rats were stratified into four distinct groups. The control group did not undergo the migraine-induction protocol. Post-induction, the "sumatriptan" group was administered sumatriptan injections, the "treatment" group received oral M. oleifera extract, and the "vehicle" group was provided with oral solvent treatment. Behavioral evaluations encompassing Von Frey's and hot plate assessments, in addition to qPCR analysis targeting Nr2a, Nr2b, Bax, Bcl-2, and Caspase-3, were conducted. RESULTS Von Fery's and hot plate tests revealed a notable decrease in triggering pressure and temperature within the vehicle group when compared to the other groups (both ps < 0.001). The Nr2a expression levels in both the vehicle and treatment cohorts exhibited significantly higher values than those observed in the control group (p < 0.001, p = 0.001) and the sumatriptan group (p < 0.001, p = 0.002). Conversely, no substantial alterations in Nr2b or Bcl-2 expression levels were observed across the study groups (p = 0.404, p = 0.976). Notably, heightened expressions of Caspase-3 and Bax were evident in the vehicle group relative to the other groups (p = 0.013, p = 0.010). CONCLUSIONS Moringa oleifera extract appears to mitigate symptoms of migraine by inhibiting apoptosis, suggesting potential efficacy in migraine treatment; however, additional research investigating a wider range of pathways is necessary. CLINICAL TRIAL NUMBER Not applicable.
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Affiliation(s)
- Ahmad Vafaeian
- Toxicology Research Center, AJA University of Medical Sciences, Tehran, Iran
| | - Ali Vafaei
- Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Parvizi
- Department of Physiology, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Mohsen Chamanara
- Toxicology Research Center, AJA University of Medical Sciences, Tehran, Iran
| | - Mojgan Mehriardestani
- Department of Persian Medicine, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Yasaman Hosseini
- Toxicology Research Center, AJA University of Medical Sciences, Tehran, Iran.
- Cognitive and Behavioral Research Center, AJA University of Medical Sciences, Tehran, Iran.
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3
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Moreno-Vargas LM, Prada-Gracia D. Exploring the Chemical Features and Biomedical Relevance of Cell-Penetrating Peptides. Int J Mol Sci 2024; 26:59. [PMID: 39795918 PMCID: PMC11720145 DOI: 10.3390/ijms26010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 11/27/2024] [Accepted: 11/28/2024] [Indexed: 01/13/2025] Open
Abstract
Cell-penetrating peptides (CPPs) are a diverse group of peptides, typically composed of 4 to 40 amino acids, known for their unique ability to transport a wide range of substances-such as small molecules, plasmid DNA, small interfering RNA, proteins, viruses, and nanoparticles-across cellular membranes while preserving the integrity of the cargo. CPPs exhibit passive and non-selective behavior, often requiring functionalization or chemical modification to enhance their specificity and efficacy. The precise mechanisms governing the cellular uptake of CPPs remain ambiguous; however, electrostatic interactions between positively charged amino acids and negatively charged glycosaminoglycans on the membrane, particularly heparan sulfate proteoglycans, are considered the initial crucial step for CPP uptake. Clinical trials have highlighted the potential of CPPs in diagnosing and treating various diseases, including cancer, central nervous system disorders, eye disorders, and diabetes. This review provides a comprehensive overview of CPP classifications, potential applications, transduction mechanisms, and the most relevant algorithms to improve the accuracy and reliability of predictions in CPP development.
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4
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Tang SX, Camara CM, Franco JA, Pazyra-Murphy MF, Li Y, Godes M, Moyer BM, Bird GH, Segal RA, Walensky LD. Dissecting the neuroprotective interaction between the BH4 domain of BCL-w and the IP3 receptor. Cell Chem Biol 2024; 31:1815-1826.e5. [PMID: 39067448 PMCID: PMC11490406 DOI: 10.1016/j.chembiol.2024.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 04/19/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024]
Abstract
BCL-w is a BCL-2 family protein that promotes cell survival in tissue- and disease-specific contexts. The canonical anti-apoptotic functionality of BCL-w is mediated by a surface groove that traps the BCL-2 homology 3 (BH3) α-helices of pro-apoptotic members, blocking cell death. A distinct N-terminal portion of BCL-w, termed the BCL-2 homology 4 (BH4) domain, selectively protects axons from paclitaxel-induced degeneration by modulating IP3 receptors, a noncanonical BCL-2 family target. Given the potential of BCL-w BH4 mimetics to prevent or mitigate chemotherapy-induced peripheral neuropathy, we sought to characterize the interaction between BCL-w BH4 and the IP3 receptor, combining "staple" and alanine scanning approaches with molecular dynamics simulations. We generated and identified stapled BCL-w BH4 peptides with optimized IP3 receptor binding and neuroprotective activities. Point mutagenesis further revealed the sequence determinants for BCL-w BH4 specificity, providing a blueprint for therapeutic targeting of IP3 receptors to achieve neuroprotection.
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Affiliation(s)
- Sophia X Tang
- Departments of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Christina M Camara
- Departments of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Joy A Franco
- Departments of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Maria F Pazyra-Murphy
- Departments of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Yihang Li
- Departments of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Marina Godes
- Departments of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Benjamin M Moyer
- Departments of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Gregory H Bird
- Departments of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Rosalind A Segal
- Departments of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Loren D Walensky
- Departments of Cancer Biology and Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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5
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McHenry MW, Shi P, Camara CM, Cohen DT, Rettenmaier TJ, Adhikary U, Gygi MA, Yang K, Gygi SP, Wales TE, Engen JR, Wells JA, Walensky LD. Covalent inhibition of pro-apoptotic BAX. Nat Chem Biol 2024; 20:1022-1032. [PMID: 38233584 PMCID: PMC11252247 DOI: 10.1038/s41589-023-01537-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024]
Abstract
BCL-2-associated X protein (BAX) is a promising therapeutic target for activating or restraining apoptosis in diseases of pathologic cell survival or cell death, respectively. In response to cellular stress, BAX transforms from a quiescent cytosolic monomer into a toxic oligomer that permeabilizes the mitochondria, releasing key apoptogenic factors. The mitochondrial lipid trans-2-hexadecenal (t-2-hex) sensitizes BAX activation by covalent derivatization of cysteine 126 (C126). In this study, we performed a disulfide tethering screen to discover C126-reactive molecules that modulate BAX activity. We identified covalent BAX inhibitor 1 (CBI1) as a compound that selectively derivatizes BAX at C126 and inhibits BAX activation by triggering ligands or point mutagenesis. Biochemical and structural analyses revealed that CBI1 can inhibit BAX by a dual mechanism of action: conformational constraint and competitive blockade of lipidation. These data inform a pharmacologic strategy for suppressing apoptosis in diseases of unwanted cell death by covalent targeting of BAX C126.
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Affiliation(s)
- Matthew W McHenry
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Peiwen Shi
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christina M Camara
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Daniel T Cohen
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - T Justin Rettenmaier
- Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Utsarga Adhikary
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Micah A Gygi
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ka Yang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - James A Wells
- Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Loren D Walensky
- Department of Pediatric Oncology and Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
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6
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Rouchidane Eyitayo A, Daury L, Priault M, Manon S. The membrane insertion of the pro-apoptotic protein Bax is a Tom22-dependent multi-step process: a study in nanodiscs. Cell Death Discov 2024; 10:335. [PMID: 39043635 PMCID: PMC11266675 DOI: 10.1038/s41420-024-02108-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/11/2024] [Accepted: 07/17/2024] [Indexed: 07/25/2024] Open
Abstract
Membrane insertion of the pro-apoptotic protein Bax was investigated by setting up cell-free synthesis of full-length Bax in the presence of pre-formed nanodiscs. While Bax was spontaneously poorly inserted in nanodiscs, co-synthesis with the mitochondrial receptor Tom22 stimulated Bax membrane insertion. The initial interaction of Bax with the lipid bilayer exposed the hydrophobic GALLL motif in Hα1 leading to Bax precipitation through hydrophobic interactions. The same motif was recognized by Tom22, triggering conformational changes leading to the extrusion and the ensuing membrane insertion of the C-terminal hydrophobic Hα9. Tom22 was also required for Bax-membrane insertion after Bax was activated either by BH3-activators or by its release from Bcl-xL by WEHI-539. The effect of Tom22 was impaired by D154Y substitution in Bax-Hα7 and T174P substitution in Bax-Hα9, which are found in several tumors. Conversely, a R9E substitution promoted a spontaneous insertion of Bax in nanodiscs, in the absence of Tom22. Both Tom22-activated Bax and BaxR9E alone permeabilized liposomes to dextran-10kDa and formed ~5-nm-diameter pores in nanodiscs. The concerted regulation of Bax membrane insertion by Tom22 and BH3-activators is discussed.
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Affiliation(s)
| | - Laetitia Daury
- CNRS, Université de Bordeaux, UMR 5248, CBMN, Pessac, France
| | - Muriel Priault
- CNRS, Université de Bordeaux, UMR 5095, IBGC, Bordeaux, France
| | - Stéphen Manon
- CNRS, Université de Bordeaux, UMR 5095, IBGC, Bordeaux, France.
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7
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Zhang Z, Hou L, Liu D, Luan S, Huang M, Zhao L. Directly targeting BAX for drug discovery: Therapeutic opportunities and challenges. Acta Pharm Sin B 2024; 14:2378-2401. [PMID: 38828138 PMCID: PMC11143528 DOI: 10.1016/j.apsb.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/25/2024] [Accepted: 02/04/2024] [Indexed: 06/05/2024] Open
Abstract
For over two decades, the development of B-cell lymphoma-2 (Bcl-2) family therapeutics has primarily focused on anti-apoptotic proteins, resulting in the first-in-class drugs called BH3 mimetics, especially for Bcl-2 inhibitor Venetoclax. The pro-apoptotic protein Bcl-2-associated X protein (BAX) plays a crucial role as the executioner protein of the mitochondrial regulated cell death, contributing to organismal development, tissue homeostasis, and immunity. The dysregulation of BAX is closely associated with the onset and progression of diseases characterized by pathologic cell survival or death, such as cancer, neurodegeneration, and heart failure. In addition to conducting thorough investigations into the physiological modulation of BAX, research on the regulatory mechanisms of small molecules identified through biochemical screening approaches has prompted the identification of functional and potentially druggable binding sites on BAX, as well as diverse all-molecule BAX modulators. This review presents recent advancements in elucidating the physiological and pharmacological modulation of BAX and in identifying potentially druggable binding sites on BAX. Furthermore, it highlights the structural and mechanistic insights into small-molecule modulators targeting diverse binding surfaces or conformations of BAX, offering a promising avenue for developing next-generation apoptosis modulators to treat a wide range of diseases associated with dysregulated cell death by directly targeting BAX.
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Affiliation(s)
- Zhenwei Zhang
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Linghui Hou
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Dan Liu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shenglin Luan
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd., Shenzhen 518000, China
| | - Min Huang
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Linxiang Zhao
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
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8
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Gitego N, Agianian B, Mak OW, Kumar Mv V, Cheng EH, Gavathiotis E. Chemical modulation of cytosolic BAX homodimer potentiates BAX activation and apoptosis. Nat Commun 2023; 14:8381. [PMID: 38104127 PMCID: PMC10725471 DOI: 10.1038/s41467-023-44084-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
The BCL-2 family protein BAX is a major regulator of physiological and pathological cell death. BAX predominantly resides in the cytosol in a quiescent state and upon stress, it undergoes conformational activation and mitochondrial translocation leading to mitochondrial outer membrane permeabilization, a critical event in apoptosis execution. Previous studies reported two inactive conformations of cytosolic BAX, a monomer and a dimer, however, it remains unclear how they regulate BAX. Here we show that, surprisingly, cancer cell lines express cytosolic inactive BAX dimers and/or monomers. Expression of inactive dimers, results in reduced BAX activation, translocation and apoptosis upon pro-apoptotic drug treatments. Using the inactive BAX dimer structure and a pharmacophore-based drug screen, we identify a small-molecule modulator, BDM19 that binds and activates cytosolic BAX dimers and prompts cells to apoptosis either alone or in combination with BCL-2/BCL-XL inhibitor Navitoclax. Our findings underscore the role of the cytosolic inactive BAX dimer in resistance to apoptosis and demonstrate a strategy to potentiate BAX-mediated apoptosis.
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Affiliation(s)
- Nadege Gitego
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bogos Agianian
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Oi Wei Mak
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Vasantha Kumar Mv
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Emily H Cheng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Evripidis Gavathiotis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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9
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Chen Y, Gelles JD, Mohammed JN, Chipuk JE. An optimized protocol for expression and purification of monomeric full-length BAX protein for functional interrogations. Front Cell Dev Biol 2023; 11:1322816. [PMID: 38143925 PMCID: PMC10748421 DOI: 10.3389/fcell.2023.1322816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023] Open
Abstract
Diverse developmental signals and pro-death stresses converge on the regulation of the mitochondrial pathway of apoptosis. BAX, a proapoptotic BCL-2 effector, directly forms proteolipid pores in the outer mitochondrial membrane to activate the mitochondrial pathway of apoptosis. BAX is a viable pharmacological target for various human diseases, and increasing efforts have been made to study the molecular regulation of BAX while identifying small molecules selectively targeting BAX. However, generating large quantities of monomeric and functionally competent BAX has been challenging due to its aggregation-prone nature. Additionally, there is a lack of detailed and instructional protocols available for investigators who are not already familiar with recombinant BAX production. Here, we present a comprehensive protocol for expressing, purifying, and storing functional monomeric recombinant BAX protein. We use an intein-chitin binding domain-tagged BAX-expressing construct and employ a two-step chromatography strategy to capture and purify BAX. We also provide examples of standard assays to observe BAX activation, and highlight the best practices for handling and storing BAX to effectively preserve its quality, shelf life, and function.
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Affiliation(s)
- Yiyang Chen
- Laboratory of Mitochondrial Biology in Human Health and Disease, Icahn School of Medicine at Mount Sinai, New York,NY, United States
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jesse D. Gelles
- Laboratory of Mitochondrial Biology in Human Health and Disease, Icahn School of Medicine at Mount Sinai, New York,NY, United States
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jarvier N. Mohammed
- Laboratory of Mitochondrial Biology in Human Health and Disease, Icahn School of Medicine at Mount Sinai, New York,NY, United States
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jerry Edward Chipuk
- Laboratory of Mitochondrial Biology in Human Health and Disease, Icahn School of Medicine at Mount Sinai, New York,NY, United States
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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10
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Chen Y, Gelles JD, Mohammed JN, Chipuk JE. An optimized high-yield protocol for expression and purification of monomeric full-length BAX protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562589. [PMID: 37905126 PMCID: PMC10614868 DOI: 10.1101/2023.10.16.562589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Diverse developmental signals and pro-death stresses converge on regulation of the mitochondrial pathway of apoptosis. BAX, a pro-apoptotic BCL-2 effector, directly forms proteolipid pores in the outer mitochondrial member to activate the mitochondrial pathway of apoptosis. BAX is a viable pharmacological target for various human diseases, and increasing efforts have been made to study the molecular regulation of BAX and identify small molecules selectively targeting BAX. However, generating large quantities of monomeric and functionally-competent BAX has been challenging due to its aggregation-prone nature. Additionally, there is a lack of detailed and instructional protocols available for investigators who are not already familiar with recombinant BAX production. Here, we present a comprehensive high-yield protocol for expressing, purifying, and storing functional recombinant BAX protein. We utilize an intein-tagged BAX construct and employ a two-step chromatography strategy to capture and purify BAX, and provide example standard assays to observe BAX activation. We also highlight best practices for handling and storing BAX to effectively preserve its quality, shelf-life, and function.
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Affiliation(s)
- Yiyang Chen
- Laboratory of Mitochondrial Biology in Human Health and Disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Jesse D. Gelles
- Laboratory of Mitochondrial Biology in Human Health and Disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Jarvier N. Mohammed
- Laboratory of Mitochondrial Biology in Human Health and Disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Jerry Edward Chipuk
- Laboratory of Mitochondrial Biology in Human Health and Disease, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- The Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
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11
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Czabotar PE, Garcia-Saez AJ. Mechanisms of BCL-2 family proteins in mitochondrial apoptosis. Nat Rev Mol Cell Biol 2023; 24:732-748. [PMID: 37438560 DOI: 10.1038/s41580-023-00629-4] [Citation(s) in RCA: 221] [Impact Index Per Article: 110.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/14/2023]
Abstract
The proteins of the BCL-2 family are key regulators of mitochondrial apoptosis, acting as either promoters or inhibitors of cell death. The functional interplay and balance between the opposing BCL-2 family members control permeabilization of the outer mitochondrial membrane, leading to the release of activators of the caspase cascade into the cytosol and ultimately resulting in cell death. Despite considerable research, our knowledge about the mechanisms of the BCL-2 family of proteins remains insufficient, which complicates cell fate predictions and does not allow us to fully exploit these proteins as targets for drug discovery. Detailed understanding of the formation and molecular architecture of the apoptotic pore in the outer mitochondrial membrane remains a holy grail in the field, but new studies allow us to begin constructing a structural model of its arrangement. Recent literature has also revealed unexpected activities for several BCL-2 family members that challenge established concepts of how they regulate mitochondrial permeabilization. In this Review, we revisit the most important advances in the field and integrate them into a new structure-function-based classification of the BCL-2 family members that intends to provide a comprehensive model for BCL-2 action in apoptosis. We close this Review by discussing the potential of drugging the BCL-2 family in diseases characterized by aberrant apoptosis.
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Affiliation(s)
- Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
| | - Ana J Garcia-Saez
- Membrane Biophysics, Institute of Genetics, CECAD, University of Cologne, Cologne, Germany.
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12
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Gonzalo Ó, Benedi A, Vela L, Anel A, Naval J, Marzo I. Study of the Bcl-2 Interactome by BiFC Reveals Differences in the Activation Mechanism of Bax and Bak. Cells 2023; 12:cells12050800. [PMID: 36899936 PMCID: PMC10000386 DOI: 10.3390/cells12050800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Evasion of apoptosis is one of the hallmarks of cancer cells. Proteins of the Bcl-2 family are key regulators of the intrinsic pathway of apoptosis, and alterations in some of these proteins are frequently found in cancer cells. Permeabilization of the outer mitochondrial membrane, regulated by pro- and antiapoptotic members of the Bcl-2 family of proteins, is essential for the release of apoptogenic factors leading to caspase activation, cell dismantlement, and death. Mitochondrial permeabilization depends on the formation of oligomers of the effector proteins Bax and Bak after an activation event mediated by BH3-only proteins and regulated by antiapoptotic members of the Bcl-2 family. In the present work, we have studied interactions between different members of the Bcl-2 family in living cells via the BiFC technique. Despite the limitations of this technique, present data suggest that native proteins of the Bcl-2 family acting inside living cells establish a complex network of interactions, which would fit nicely into "mixed" models recently proposed by others. Furthermore, our results point to differences in the regulation of Bax and Bak activation by proteins of the antiapoptotic and BH3-only subfamilies. We have also applied the BiFC technique to explore the different molecular models proposed for Bax and Bak oligomerization. Bax and Bak's mutants lacking the BH3 domain were still able to associate and give BiFC signals, suggesting the existence of alternative surfaces of interaction between two Bax or Bak molecules. These results agree with the widely accepted symmetric model for the dimerization of these proteins and also suggest that other regions, different from the α6 helix, could be involved in the oligomerization of BH3-in groove dimers.
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13
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Kyrychenko A, Ladokhin AS. Membrane interactions of apoptotic inhibitor Bcl-xL: What can be learned using fluorescence spectroscopy. BBA ADVANCES 2023; 3:100076. [PMID: 37082264 PMCID: PMC10074936 DOI: 10.1016/j.bbadva.2023.100076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
Permeabilization of the mitochondrial outer membrane-a point of no return in apoptotic regulation-is tightly controlled by proteins of the Bcl-2 family. Apoptotic inhibitor Bcl-xL is an important member of this family, responsible for blocking the permeabilization, and is also a promising target for anti-cancer drugs. Bcl-xL exists in the following conformations, each believed to play a role in the inhibition of apoptosis: (i) a soluble folded conformation, (ii) a membrane-anchored (by its C-terminal α8 helix) form, which retains the same fold as in solution and (iii) refolded membrane-inserted conformations, for which no structural data are available. In this review, we present the summary of the application of various methods of fluorescence spectroscopy for studying membrane interaction of Bcl-xL, and specifically the formation of the refolded inserted conformation. We discuss the application of environment-sensitive probes, Förster resonance energy transfer, fluorescence correlation spectroscopy, and fluorescent quenching for structural, thermodynamic, and functional characterization of protein-lipid interactions, which can benefit studies of other members of Bcl-2 (e.g., Bax, BAK, Bid). The conformational switching between various conformations of Bcl-xL depends on the presence of divalent cations, pH and lipid composition. This insertion-refolding transition also results in the release of the BH4 regulatory domain from the folded structure of Bcl-xL, which is relevant to the lipid-regulated conversion between canonical and non-canonical modes of apoptotic inhibition.
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Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, Kharkiv 61022, Ukraine
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160-7421, United States
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14
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Ma C, Xiang Q, Song G, Wang X. Quercetin and polycystic ovary syndrome. Front Pharmacol 2022; 13:1006678. [PMID: 36588716 PMCID: PMC9800798 DOI: 10.3389/fphar.2022.1006678] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is a reproductive endocrine disease, and results to opsomenorrhea or amenorrhea, hairy, acne, acanthosis, infertility, abortion. In the long term, PCOS may also increase the risk of endometrial cancer, diabetes, hypertension, dyslipidemia and other diseases. Till now there is no specific drug for PCOS due to the unclearness of the cause and pathogenesis, as current treatments for PCOS only target certain symptoms. Quercetin (QUR) is a flavonoid drug widely found in Chinese herbal medicines, fruits, leaves, vegetables, seeds and plants roots. Studies on other diseases have found that QUR has anti-oxidant, anti-inflammatory, anti-insulin resistance, anti-cancer and other effects. Some studies have shown that serum testosterone (T), luteinizing hormone (LH), the LH/follicule-stimulating hormone (FSH) ratio, fasting glucose, fasting insulin, HOMA-IR and lipid levels are reduced in PCOS patients with QUR treatment. However, the mechanisms of QUR in PCOS patients have not been completely elucidated. In this review, we retrospect the basic characteristics of QUR, and in vitro studies, animal experiments and clinical trials of QUR and plant extracts containing QUR in the treatment of PCOS. We also summarized the effects and mechanism of QUR in ovarian cells in vitro and PCOS model rats, the changes in relevant parameters after QUR administration in PCOS patients, and its potentially therapeutic applications.
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Affiliation(s)
- Congshun Ma
- NHC Key Laboratory of Male Reproduction and Genetics, Guangzhou, China,Department of Reproductive Medicine Center, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, China
| | - Qianru Xiang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Nutrition and Food Hygiene, School of Public Health, Southern Medical University, Guangzhou, China
| | - Ge Song
- NHC Key Laboratory of Male Reproduction and Genetics, Guangzhou, China,Department of Reproductive Medicine Center, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, China,*Correspondence: Ge Song, ; Xuefei Wang,
| | - Xuefei Wang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China,*Correspondence: Ge Song, ; Xuefei Wang,
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15
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Mushtaq AU, Ådén J, Ali K, Gröbner G. Domain-specific insight into the recognition of BH3-death motifs by the pro-survival Bcl-2 protein. Biophys J 2022; 121:4517-4525. [PMID: 36325615 PMCID: PMC9748362 DOI: 10.1016/j.bpj.2022.10.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 10/09/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022] Open
Abstract
Programmed mammalian cell death (apoptosis) is an essential mechanism in life that tightly regulates embryogenesis and removal of dysfunctional cells. In its intrinsic (mitochondrial) pathway, opposing members of the Bcl-2 (B cell lymphoma 2) protein family meet at the mitochondrial outer membrane (MOM) to control its integrity. Any imbalance can cause disorders, with upregulation of the cell-guarding antiapoptotic Bcl-2 protein itself being common in many, often incurable, cancers. Normally, the Bcl-2 protein itself is embedded in the MOM where it sequesters cell-killing apoptotic proteins such as Bax (Bcl-2-associated X protein) that would otherwise perforate the MOM and subsequently cause cell death. However, the molecular basis of Bcl-2's ability to recognize those apoptotic proteins via their common BH3 death motifs remains elusive due to the lack of structural insight. By employing nuclear magnetic resonance on fully functional human Bcl-2 protein in membrane-mimicking micelles, we identified glycine residues across all functional domains of the Bcl-2 protein and could monitor their residue-specific individual response upon the presence of a Bax-derived 36aa long BH3 domain. The observed chemical shift perturbations allowed us to determine the response and individual affinity of each glycine residue and provide an overall picture of the individual roles by which Bcl-2's functional domains engage in recognizing and inhibiting apoptotic proteins via their prominent BH3 motifs. This way, we provide a unique residue- and domain-specific insight into the molecular functioning of Bcl-2 at the membrane level, an insight also opening up for interfering with this cell-protecting mechanism in cancer therapy.
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Affiliation(s)
| | - Jörgen Ådén
- Department of Chemistry, University of Umeå, Umeå, Sweden
| | - Katan Ali
- Department of Chemistry, University of Umeå, Umeå, Sweden
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16
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Rosa N, Speelman-Rooms F, Parys JB, Bultynck G. Modulation of Ca 2+ signaling by antiapoptotic Bcl-2 versus Bcl-xL: From molecular mechanisms to relevance for cancer cell survival. Biochim Biophys Acta Rev Cancer 2022; 1877:188791. [PMID: 36162541 DOI: 10.1016/j.bbcan.2022.188791] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022]
Abstract
Members of the Bcl-2-protein family are key controllers of apoptotic cell death. The family is divided into antiapoptotic (including Bcl-2 itself, Bcl-xL, Mcl-1, etc.) and proapoptotic members (Bax, Bak, Bim, Bim, Puma, Noxa, Bad, etc.). These proteins are well known for their canonical role in the mitochondria, where they control mitochondrial outer membrane permeabilization and subsequent apoptosis. However, several proteins are recognized as modulators of intracellular Ca2+ signals that originate from the endoplasmic reticulum (ER), the major intracellular Ca2+-storage organelle. More than 25 years ago, Bcl-2, the founding member of the family, was reported to control apoptosis through Ca2+ signaling. Further work elucidated that Bcl-2 directly targets and inhibits inositol 1,4,5-trisphosphate receptors (IP3Rs), thereby suppressing proapoptotic Ca2+ signaling. In addition to Bcl-2, Bcl-xL was also shown to impact cell survival by sensitizing IP3R function, thereby promoting prosurvival oscillatory Ca2+ release. However, new work challenges this model and demonstrates that Bcl-2 and Bcl-xL can both function as inhibitors of IP3Rs. This suggests that, depending on the cell context, Bcl-xL could support very distinct Ca2+ patterns. This not only raises several questions but also opens new possibilities for the treatment of Bcl-xL-dependent cancers. In this review, we will discuss the similarities and divergences between Bcl-2 and Bcl-xL regarding Ca2+ homeostasis and IP3R modulation from both a molecular and a functional point of view, with particular emphasis on cancer cell death resistance mechanisms.
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Affiliation(s)
- Nicolas Rosa
- KU Leuven, Laboratory of Molecular & Cellular Signaling, Department of Cellular & Molecular Medicine, Campus Gasthuisberg O/N-I bus 802, Herestraat 49, BE-3000 Leuven, Belgium
| | - Femke Speelman-Rooms
- KU Leuven, Laboratory of Molecular & Cellular Signaling, Department of Cellular & Molecular Medicine, Campus Gasthuisberg O/N-I bus 802, Herestraat 49, BE-3000 Leuven, Belgium
| | - Jan B Parys
- KU Leuven, Laboratory of Molecular & Cellular Signaling, Department of Cellular & Molecular Medicine, Campus Gasthuisberg O/N-I bus 802, Herestraat 49, BE-3000 Leuven, Belgium
| | - Geert Bultynck
- KU Leuven, Laboratory of Molecular & Cellular Signaling, Department of Cellular & Molecular Medicine, Campus Gasthuisberg O/N-I bus 802, Herestraat 49, BE-3000 Leuven, Belgium.
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17
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Prew MS, Camara CM, Botzanowski T, Moroco JA, Bloch NB, Levy HR, Seo HS, Dhe-Paganon S, Bird GH, Herce HD, Gygi MA, Escudero S, Wales TE, Engen JR, Walensky LD. Structural basis for defective membrane targeting of mutant enzyme in human VLCAD deficiency. Nat Commun 2022; 13:3669. [PMID: 35760926 PMCID: PMC9237092 DOI: 10.1038/s41467-022-31466-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/17/2022] [Indexed: 12/03/2022] Open
Abstract
Very long-chain acyl-CoA dehydrogenase (VLCAD) is an inner mitochondrial membrane enzyme that catalyzes the first and rate-limiting step of long-chain fatty acid oxidation. Point mutations in human VLCAD can produce an inborn error of metabolism called VLCAD deficiency that can lead to severe pathophysiologic consequences, including cardiomyopathy, hypoglycemia, and rhabdomyolysis. Discrete mutations in a structurally-uncharacterized C-terminal domain region of VLCAD cause enzymatic deficiency by an incompletely defined mechanism. Here, we conducted a structure-function study, incorporating X-ray crystallography, hydrogen-deuterium exchange mass spectrometry, computational modeling, and biochemical analyses, to characterize a specific membrane interaction defect of full-length, human VLCAD bearing the clinically-observed mutations, A450P or L462P. By disrupting a predicted α-helical hairpin, these mutations either partially or completely impair direct interaction with the membrane itself. Thus, our data support a structural basis for VLCAD deficiency in patients with discrete mutations in an α-helical membrane-binding motif, resulting in pathologic enzyme mislocalization.
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Affiliation(s)
- Michelle S. Prew
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Christina M. Camara
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Thomas Botzanowski
- grid.261112.70000 0001 2173 3359Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA USA
| | - Jamie A. Moroco
- grid.261112.70000 0001 2173 3359Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA USA
| | - Noah B. Bloch
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Hannah R. Levy
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Hyuk-Soo Seo
- grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Sirano Dhe-Paganon
- grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Gregory H. Bird
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Henry D. Herce
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Micah A. Gygi
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Silvia Escudero
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Thomas E. Wales
- grid.261112.70000 0001 2173 3359Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA USA
| | - John R. Engen
- grid.261112.70000 0001 2173 3359Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA USA
| | - Loren D. Walensky
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
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18
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Zhou X, Zhao S, Liu T, Yao L, Zhao M, Ye X, Zhang X, Guo Q, Tu P, Zeng K. Schisandrol A protects AGEs-induced neuronal cells death by allosterically targeting ATP6V0d1 subunit of V-ATPase. Acta Pharm Sin B 2022; 12:3843-3860. [PMID: 36213534 PMCID: PMC9532558 DOI: 10.1016/j.apsb.2022.06.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/30/2022] [Accepted: 05/24/2022] [Indexed: 12/26/2022] Open
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19
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Bultynck G. Introducing the Special Issue on "Death mechanisms in cellular homeostasis" in honor of Dr. Peter Ruvolo. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119213. [PMID: 34998920 DOI: 10.1016/j.bbamcr.2022.119213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Geert Bultynck
- KU Leuven, Laboratory of Molecular & Cellular Signaling, Department of Cellular and Molecular Medicine, Campus Gasthuisberg O/N-I bus 802, Herestraat 49, BE-3000 Leuven, Belgium.
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20
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Physiological and pharmacological modulation of BAX. Trends Pharmacol Sci 2022; 43:206-220. [PMID: 34848097 PMCID: PMC8840970 DOI: 10.1016/j.tips.2021.11.001] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 01/29/2023]
Abstract
Bcl-2-associated X protein (BAX) is a critical executioner of mitochondrial regulated cell death through its lethal activity of permeabilizing the mitochondrial outer membrane (MOM). While the physiological function of BAX ensures tissue homeostasis, dysregulation of BAX leads to aberrant cell death. Despite BAX being a promising therapeutic target for human diseases, historically the development of drugs has focused on antiapoptotic BCL-2 proteins, due to challenges in elucidating the mechanism of BAX activation and identifying druggable surfaces of BAX. Here, we discuss recent studies that have provided structure-function insights and identified regulatory surfaces that control BAX activation. Moreover, we emphasize the development of small molecule orthosteric, allosteric, and oligomerization modulators that provide novel opportunities for biological investigation and progress towards drugging BAX.
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21
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Dai H, Meng XW, Ye K, Jia J, Kaufmann SH. Therapeutics targeting BCL2 family proteins. MECHANISMS OF CELL DEATH AND OPPORTUNITIES FOR THERAPEUTIC DEVELOPMENT 2022:197-260. [DOI: 10.1016/b978-0-12-814208-0.00007-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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22
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Martens MD, Karch J, Gordon JW. The molecular mosaic of regulated cell death in the cardiovascular system. Biochim Biophys Acta Mol Basis Dis 2021; 1868:166297. [PMID: 34718119 DOI: 10.1016/j.bbadis.2021.166297] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 10/07/2021] [Accepted: 10/22/2021] [Indexed: 12/11/2022]
Abstract
Cell death is now understood to be a highly regulated process that contributes to normal development and tissue homeostasis, alongside its role in the etiology of various pathological conditions. Through detailed molecular analysis, we have come to know that all cells do not always die in the same way, and that there are at least 7 processes involved, including: apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, and autophagy-mediated cell death. These processes act as pieces in the mosaic of cardiomyocyte cell death, which come together depending on context and stimulus. This review details each individual process, as well as highlights how they come together to produce various cardiac pathologies. By knowing how the pieces go together we can aim towards the development of efficacious therapeutics, which will enable us to prevent cardiomyocyte loss in the face of stress, both reducing mortality and improving quality of life.
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Affiliation(s)
- Matthew D Martens
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Manitoba, Canada; The Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba, Canada
| | - Jason Karch
- Department of Molecular Physiology and Biophysics, Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, United States
| | - Joseph W Gordon
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Manitoba, Canada; College of Nursing, Rady Faculty of Health Science, University of Manitoba, Winnipeg, Manitoba, Canada; The Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Theme of the Children's Hospital Research Institute of Manitoba, Canada.
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23
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Hassan SSU, Muhammad I, Abbas SQ, Hassan M, Majid M, Jin HZ, Bungau S. Stress Driven Discovery of Natural Products From Actinobacteria with Anti-Oxidant and Cytotoxic Activities Including Docking and ADMET Properties. Int J Mol Sci 2021; 22:ijms222111432. [PMID: 34768863 PMCID: PMC8584265 DOI: 10.3390/ijms222111432] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022] Open
Abstract
Elicitation through abiotic stress, including chemical elicitors like heavy metals, is a new technique for drug discovery. In this research, the effect of heavy metals on actinobacteria Streptomyces sp. SH-1312 for secondary metabolite production, with strong pharmacological activity, along with pharmacokinetics profile, was firstly investigated. The optimum metal stress conditions consisted of actinobacteria strain Streptomyces sp. SH-1312 with addition of mix metals (Co2+ + Zn2+) ions at 0.5 mM in Gause’s medium. Under these conditions, the stress metabolite anhydromevalonolactone (MVL) was produced, which was absent in the normal culture of strain and other metals combinations. Furthermore, the stress metabolite was also evaluated for its anti-oxidant and cytotoxic activities. The compound exhibited remarkable anti-oxidant activities, recording the IC50 value of 19.65 ± 5.7 µg/mL in DPPH, IC50 of 15.49 ± 4.8 against NO free radicals, the IC50 value of 19.65 ± 5.22 µg/mL against scavenging ability, and IC50 value of 19.38 ± 7.11 µg/mL for iron chelation capacity and the cytotoxic activities against PC3 cell lines were recorded with IC50 values of 35.81 ± 4.2 µg/mL after 24 h, 23.29 ± 3.8 µg/mL at 48 h, and 16.25 ± 6.5 µg/mL after 72 h. Further mechanistic studies have revealed that the compound MVL has shown its pharmacological efficacy by upregulation of P53 and BAX while downregulation of BCL-2 expression, indicating that MVL is following apoptosis in varying degrees. To better understand the pharmacological properties of MVL, in this work, the absorption, distribution, metabolism, excretion, and toxicity (ADMET) were also evaluated. During ADMET predictions, MVL has displayed a safer profile in case of hepatotoxicity, cytochrome inhibition and also displayed as non-cardiotoxic. The compound MVL showed good binding energy in the molecular docking studies, and the results revealed that MVL bind in the active region of the target protein of P53 and BAX. This work triumphantly announced a prodigious effect of heavy metals on actinobacteria with fringe benefits as a key tool of MVL production with a strong pharmacological and pharmacokinetic profile.
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Affiliation(s)
- Syed Shams ul Hassan
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (S.S.u.H.); (I.M.)
- Department of Natural Product Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ishaq Muhammad
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (S.S.u.H.); (I.M.)
- Department of Natural Product Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Syed Qamar Abbas
- Department of Pharmacy, Sarhad University of Science and Technology, Peshawar 25000, Pakistan;
| | - Mubashir Hassan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan;
| | - Muhammad Majid
- Department of Pharmacy, Capital University of Science and Technology, Islamabad 44000, Pakistan
- Correspondence: (M.M.); (H.-Z.J.); Tel./Fax: +86-021-34205989 (H.-Z.J.)
| | - Hui-Zi Jin
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (S.S.u.H.); (I.M.)
- Department of Natural Product Chemistry, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence: (M.M.); (H.-Z.J.); Tel./Fax: +86-021-34205989 (H.-Z.J.)
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, 410028 Oradea, Romania;
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24
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Zheng S, Chen Y, Ma M, Li M. Mechanism of quercetin on the improvement of ovulation disorder and regulation of ovarian CNP/NPR2 in PCOS model rats. J Formos Med Assoc 2021; 121:1081-1092. [PMID: 34538551 DOI: 10.1016/j.jfma.2021.08.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 05/26/2021] [Accepted: 08/12/2021] [Indexed: 01/09/2023] Open
Abstract
PURPOSE To investigate the effects of quercetin on ovulation disorder and expression of androgen receptor (AR) and C-type natriuretic peptide (CNP) / Natriuretic Peptide Receptor 2 (NPR2) in dehydroepiandrosterone (DHEA)-induced polycystic ovary syndrome (PCOS) rat model. METHODS DHEA was used to construct the PCOS rat model. After intervention with quercetin, metformin, and AR, the estrous cycle, ovarian and uterine weight of rats were measured. The morphological changes of ovarian and uterine were detected by hematoxylin-eosin staining (HE staining). Luteinizing hormone (LH) and follicle-stimulating hormone (FSH) were measured by Enzyme linked immunosorbent assay (ELISA). Immunohistochemical detection of interleukin-6 (IL-6), interleukin-1β (IL-1β), tumor necrosis factor-alpha (TNF-α), B-cell lymphoma-2 (BCL-2), BCL2-Associated X (Bax) and AR expression in ovarian. Determination of the expression of CNP and NPR2 mRNA by qRT-PCR. Chromatin immunocoprecipitation (ChIP) was used to detect the ability of AR to bind to CNP or NPR2 promoter. RESULTS The results showed that quercetin could significantly reduce the expression of Testosterone (T) , Estradiol (E2) , LH, Bax, IL-1β, IL-6 and TNF-α, increase the expression of FSH and Bcl-2, inhibit the expression of AR, regulate the expression of CNP / NPR2 gene and protein by affecting the combination of AR with the specific sequence of CNP and NPR2 gene promoters, restore the maturation of oocyte and ovulation. CONCLUSION The results suggest that quercetin can alleviate the hormone, metabolic and ovulatory aberrations caused by PCOS, and provide experimental basis for the clinical application of quercetin in PCOS.
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Affiliation(s)
- Shaoyan Zheng
- Pharmacy Department, Foshan Women And Children Hospital Affiliated to Southern Medical University, China.
| | - Yanxia Chen
- Pharmacy Department, The First Hospital of Guangzhou University of Traditional Chinese Medicine, China
| | - Mingying Ma
- Pharmacy Department, Nanfang Hospital Affiliated to Southern Medical University, China
| | - Miaoxia Li
- Comprehensive Laboratory, Guangdong Huiqun Chinese Traditional Medicine CO., Ltd, China
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25
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Lipids modulate the BH3-independent membrane targeting and activation of BAX and Bcl-xL. Proc Natl Acad Sci U S A 2021; 118:2025834118. [PMID: 34493661 DOI: 10.1073/pnas.2025834118] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 07/21/2021] [Indexed: 12/13/2022] Open
Abstract
Regulation of apoptosis is tightly linked with the targeting of numerous Bcl-2 proteins to the mitochondrial outer membrane (MOM), where their activation or inhibition dictates cell death or survival. According to the traditional view of apoptotic regulation, BH3-effector proteins are indispensable for the cytosol-to-MOM targeting and activation of proapoptotic and antiapoptotic members of the Bcl-2 protein family. This view is challenged by recent studies showing that these processes can occur in cells lacking BH3 effectors by as yet to be determined mechanism(s). Here, we exploit a model membrane system that recapitulates key features of MOM to demonstrate that the proapoptotic Bcl-2 protein BAX and antiapoptotic Bcl-xL have an inherent ability to interact with membranes in the absence of BH3 effectors, but only in the presence of cellular concentrations of Mg2+/Ca2+ Under these conditions, BAX and Bcl-xL are selectively targeted to membranes, refolded, and activated in the presence of anionic lipids especially the mitochondrial-specific lipid cardiolipin. These results provide a mechanistic explanation for the mitochondrial targeting and activation of Bcl-2 proteins in cells lacking BH3 effectors. At cytosolic Mg2+ levels, the BH3-independent activation of BAX could provide localized amplification of apoptotic signaling at regions enriched in cardiolipin (e.g., contact sites between MOM and mitochondrial inner membrane). Increases in MOM cardiolipin, as well as cytosolic [Ca2+] during apoptosis could further contribute to its MOM targeting and activity. Meanwhile, the BH3-independent targeting and activation of Bcl-xL to the MOM is expected to counter the action of proapoptotic BAX, thereby preventing premature commitment to apoptosis.
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26
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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27
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Bloch NB, Wales TE, Prew MS, Levy HR, Engen JR, Walensky LD. The conformational stability of pro-apoptotic BAX is dictated by discrete residues of the protein core. Nat Commun 2021; 12:4932. [PMID: 34389733 PMCID: PMC8363748 DOI: 10.1038/s41467-021-25200-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/28/2021] [Indexed: 11/09/2022] Open
Abstract
BAX is a pro-apoptotic member of the BCL-2 family, which regulates the balance between cellular life and death. During homeostasis, BAX predominantly resides in the cytosol as a latent monomer but, in response to stress, transforms into an oligomeric protein that permeabilizes the mitochondria, leading to apoptosis. Because renegade BAX activation poses a grave risk to the cell, the architecture of BAX must ensure monomeric stability yet enable conformational change upon stress signaling. The specific structural features that afford both stability and dynamic flexibility remain ill-defined and represent a critical control point of BAX regulation. We identify a nexus of interactions involving four residues of the BAX core α5 helix that are individually essential to maintaining the structure and latency of monomeric BAX and are collectively required for dimeric assembly. The dual yet distinct roles of these residues reveals the intricacy of BAX conformational regulation and opportunities for therapeutic modulation.
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Affiliation(s)
- Noah B Bloch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Michelle S Prew
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hannah R Levy
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
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28
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Feng G, Zhang X, Li Y, Wang R. Analysis of the Binding Sites on BAX and the Mechanism of BAX Activators through Extensive Molecular Dynamics Simulations. J Chem Inf Model 2021; 62:5208-5222. [PMID: 34047559 DOI: 10.1021/acs.jcim.0c01420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The BAX protein is a pro-apoptotic member of the Bcl-2 family, which triggers apoptosis by causing permeabilization of the mitochondrial outer membrane. However, the activation mechanism of BAX is far from being understood. Although a few small-molecule BAX activators have been reported in the literature, their crystal structures in complex with BAX have not been resolved. So far, their binding modes were modeled at most by simple molecular docking efforts. Lack of an in-depth understanding of the activation mechanism of BAX hinders the development of more effective BAX activators. In this work, we employed cosolvent molecular dynamics simulation to detect the potential binding sites on the surface of BAX and performed a long-time molecular dynamics simulation (50 μs in total) to derive the possible binding modes of three BAX activators (i.e., BAM7, BTC-8, and BTSA1) reported in the literature. Our results indicate that the trigger, S184, and vMIA sites are the three major binding sites on the full-length BAX structure. Moreover, the canonical hydrophobic groove is clearly detected on the α9-truncated BAX structure, which is consistent with the outcomes of relevant experimental studies. Interestingly, it is observed that solvent probes bind to the trigger bottom pocket more stably than the PPI trigger site. Each activator was subjected to unbiased molecular dynamics simulations started at the three major binding sites in five parallel jobs. Our MD results indicate that all three activators tend to stay at the trigger site with favorable MM-GB/SA binding energies. BAM7 and BTSA1 can enter the trigger bottom pocket and thereby enhance the movement of the α1-α2 loop, which may be a key factor at the early stage of BAX activation. Our molecular modeling results may provide useful guidance for designing smart biological experiments to further explore BAX activation and directing structure-based efforts toward discovering more effective BAX activators.
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Affiliation(s)
- Guoqin Feng
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China.,State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
| | - Xiangying Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
| | - Yan Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
| | - Renxiao Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China.,State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China.,Shanxi Key Laboratory of Innovative Drugs for the Treatment of Serious Diseases Based on Chronic Inflammation, College of Traditional Chinese Medicines, Shanxi University of Chinese Medicine, Taiyuan, Shanxi 030619, People's Republic of China
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29
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Li K, van Delft MF, Dewson G. Too much death can kill you: inhibiting intrinsic apoptosis to treat disease. EMBO J 2021; 40:e107341. [PMID: 34037273 DOI: 10.15252/embj.2020107341] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/11/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023] Open
Abstract
Apoptotic cell death is implicated in both physiological and pathological processes. Since many types of cancerous cells intrinsically evade apoptotic elimination, induction of apoptosis has become an attractive and often necessary cancer therapeutic approach. Conversely, some cells are extremely sensitive to apoptotic stimuli leading to neurodegenerative disease and immune pathologies. However, due to several challenges, pharmacological inhibition of apoptosis is still only a recently emerging strategy to combat pathological cell loss. Here, we describe several key steps in the intrinsic (mitochondrial) apoptosis pathway that represent potential targets for inhibitors in disease contexts. We also discuss the mechanisms of action, advantages and limitations of small-molecule and peptide-based inhibitors that have been developed to date. These inhibitors serve as important research tools to dissect apoptotic signalling and may foster new treatments to reduce unwanted cell loss.
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Affiliation(s)
- Kaiming Li
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Royal Parade, Melbourne, VIC, Australia
| | - Mark F van Delft
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Royal Parade, Melbourne, VIC, Australia
| | - Grant Dewson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Royal Parade, Melbourne, VIC, Australia
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30
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Pogmore JP, Uehling D, Andrews DW. Pharmacological Targeting of Executioner Proteins: Controlling Life and Death. J Med Chem 2021; 64:5276-5290. [PMID: 33939407 DOI: 10.1021/acs.jmedchem.0c02200] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Small-molecule mediated modulation of protein interactions of Bcl-2 (B-cell lymphoma-2) family proteins was clinically validated in 2015 when Venetoclax, a selective inhibitor of the antiapoptotic protein BCL-2, achieved breakthrough status designation by the FDA for treatment of lymphoid malignancies. Since then, substantial progress has been made in identifying inhibitors of other interactions of antiapoptosis proteins. However, targeting their pro-apoptotic counterparts, the "executioners" BAX, BAK, and BOK that both initiate and commit the cell to dying, has lagged behind. However, recent publications demonstrate that these proteins can be positively or negatively regulated using small molecule tool compounds. The results obtained with these molecules suggest that pharmaceutical regulation of apoptosis will have broad implications that extend beyond activating cell death in cancer. We review recent advances in identifying compounds and their utility in the exogenous control of life and death by regulating executioner proteins, with emphasis on the prototype BAX.
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Affiliation(s)
- Justin P Pogmore
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1J7, Canada.,Biological Sciences, Sunnybrook Research Institute, University of Toronto, Toronto, Ontario M4N 3M5, Canada
| | - David Uehling
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 1M1, Canada
| | - David W Andrews
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1J7, Canada.,Biological Sciences, Sunnybrook Research Institute, University of Toronto, Toronto, Ontario M4N 3M5, Canada
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31
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Callens M, Kraskovskaya N, Derevtsova K, Annaert W, Bultynck G, Bezprozvanny I, Vervliet T. The role of Bcl-2 proteins in modulating neuronal Ca 2+ signaling in health and in Alzheimer's disease. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118997. [PMID: 33711363 PMCID: PMC8041352 DOI: 10.1016/j.bbamcr.2021.118997] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/11/2022]
Abstract
The family of B-cell lymphoma-2 (Bcl-2) proteins exerts key functions in cellular health. Bcl-2 primarily acts in mitochondria where it controls the initiation of apoptosis. However, during the last decades, it has become clear that this family of proteins is also involved in controlling intracellular Ca2+ signaling, a critical process for the function of most cell types, including neurons. Several anti- and pro-apoptotic Bcl-2 family members are expressed in neurons and impact neuronal function. Importantly, expression levels of neuronal Bcl-2 proteins are affected by age. In this review, we focus on the emerging roles of Bcl-2 proteins in neuronal cells. Specifically, we discuss how their dysregulation contributes to the onset, development, and progression of neurodegeneration in the context of Alzheimer's disease (AD). Aberrant Ca2+ signaling plays an important role in the pathogenesis of AD, and we propose that dysregulation of the Bcl-2-Ca2+ signaling axis may contribute to the progression of AD and that herein, Bcl-2 may constitute a potential therapeutic target for the treatment of AD.
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Affiliation(s)
- Manon Callens
- KU Leuven, Laboratory of Molecular & Cellular Signaling, Department of Cellular & Molecular Medicine, Campus Gasthuisberg O/N-I bus 802, Herestraat 49, BE-3000 Leuven, Belgium
| | - Nina Kraskovskaya
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg State Polytechnic University, Saint Petersburg, Russia
| | - Kristina Derevtsova
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg State Polytechnic University, Saint Petersburg, Russia
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB Center for Brain and Disease Research & KU Leuven, Department of Neurosciences, Gasthuisberg, O&N5, Rm 7.357, B-3000 Leuven, Belgium
| | - Geert Bultynck
- KU Leuven, Laboratory of Molecular & Cellular Signaling, Department of Cellular & Molecular Medicine, Campus Gasthuisberg O/N-I bus 802, Herestraat 49, BE-3000 Leuven, Belgium.
| | - Ilya Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Peter the Great St. Petersburg State Polytechnic University, Saint Petersburg, Russia; Department of Physiology, UT Southwestern Medical Center at Dallas, Dallas, TX, United States.
| | - Tim Vervliet
- KU Leuven, Laboratory of Molecular & Cellular Signaling, Department of Cellular & Molecular Medicine, Campus Gasthuisberg O/N-I bus 802, Herestraat 49, BE-3000 Leuven, Belgium
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32
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LIU XM, XU M, ZHANG H, AI K, DENG SF, YU YH. Effects of electroacupuncture on urodynamics, intramedullary apoptosis and bidirectional regulation of neurotrophic factors in neurogenic bladder rats after supersacral spinal cord injury. WORLD JOURNAL OF ACUPUNCTURE-MOXIBUSTION 2021. [DOI: 10.1016/j.wjam.2021.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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33
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Cohen DT, Wales TE, McHenry MW, Engen JR, Walensky LD. Site-Dependent Cysteine Lipidation Potentiates the Activation of Proapoptotic BAX. Cell Rep 2021; 30:3229-3239.e6. [PMID: 32160532 PMCID: PMC7343539 DOI: 10.1016/j.celrep.2020.02.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 12/23/2019] [Accepted: 02/11/2020] [Indexed: 11/19/2022] Open
Abstract
BCL-2 family proteins converge at the mitochondrial outer membrane to regulate apoptosis and maintain the critical balance between cellular life and death. This physiologic process is essential to organism homeostasis and relies on protein-protein and protein-lipid interactions among BCL-2 family proteins in the mitochondrial lipid environment. Here, we find that trans-2-hexadecenal (t-2-hex), previously implicated in regulating BAX-mediated apoptosis, does so by direct covalent reaction with C126, which is located on the surface of BAX at the junction of its α5/α6 core hydrophobic hairpin. The application of nuclear magnetic resonance spectroscopy, hydrogen-deuterium exchange mass spectrometry, specialized t-2-hex-containing liposomes, and BAX mutational studies in mitochondria and cells reveals structure-function insights into the mechanism by which covalent lipidation at the mitochondria sensitizes direct BAX activation. The functional role of BAX lipidation as a control point of mitochondrial apoptosis could provide a therapeutic strategy for BAX modulation by chemical modification of C126. Cohen et al. show that trans-2-hexadecenal (t-2-hex) potentiates BAX-mediated apoptosis by non-enzymatic covalent lipidation of BAX C126. t-2-hex derivatization induces BAX-activating conformational changes and enhances BH3-triggered BAX poration of liposomal and mitochondrial membranes in a C126-dependent manner. This mechanism informs a therapeutic strategy for modulating BAX-mediated apoptosis by targeting C126.
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Affiliation(s)
- Daniel T Cohen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Matthew W McHenry
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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34
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Veena VK, Choudhury AR, Harikrishnan A. In vitro and in silico anti-leukemic activity of 2-amino-6-nitro-4-(4-oxo-2-thioxothiazolidin-5-yl)-4H-chromene-3-carbonitrile (ANC) through inhibition of anti-apoptotic Bcl-2 proteins. J Biomol Struct Dyn 2021; 40:7018-7026. [PMID: 33682616 DOI: 10.1080/07391102.2021.1893223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An array of 4H-chromene derivatives have been reported for anticancer properties but their selectivity and mode of anticancer activity are unexplored. In this context, we have investigated a biologically active synthetically designed 4H-Chromene carbonitrile derivative, 2-amino-6-nitro-4-(4-oxo-2-thioxothiazolidin-5-yl)-4H-chromene-3-carbonitrile (ANC) that is strongly and selectively inhibited Bcl-2 over expressing human leukemic (HL-60 and K562) cells for its interaction and elucidated the mode of action. The interaction of ANC was investigated against the antiapoptotic proteins such as Bcl-2, Bax, Bcl-xL and Bcl-w that were overexpressed in leukemic cells using in silico and fluorescent spectroscopic studies. Fluorescent spectroscopic based interaction studies showed that the derivative had strong interaction with Bcl-xL followed by Bcl-2/Bax and least interaction with Bcl-w. Based on the results, the ANC had strong interactions with antiapoptotic Bcl-2 and Bax proteins than the Bcl-xL and Bcl-w proteins. The in vitro biological validation of ANC treated leukemic cells showed downregulation of Bcl-xL than Bcl-2 but least effect on Bcl-w proteins. Furthermore, the ANC had possible four isomers as RR, RS, SR and SS isomers. Among them, RS isomer of ANC had shown more active that correlated with biological interactions and gene expression studies of ACN with oncoproteins. These results confirmed the induction of apoptosis by RS-ACN isomer through inhibition of antiapoptotic machineries of leukemic cells confirming the antiapoptotic Bcl-2 inhibitory activities.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vijay Kumar Veena
- Department of Biotechnology, School of Applied Sciences, REVA University, Bangalore, Karnataka, India
| | - Ahana Roy Choudhury
- Centre for Bioinformatics, School of Life Science, Pondicherry University, Kalapet, Puducherry, India
| | - Adhikesavan Harikrishnan
- Department of Chemistry, School of Arts and Sciences, Vinayaka Mission Research Foundation-Aarupadai Veedu (VMRF-AV) campus, Chennai, Tamil Nadu, India
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35
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Spitz AZ, Zacharioudakis E, Reyna DE, Garner TP, Gavathiotis E. Eltrombopag directly inhibits BAX and prevents cell death. Nat Commun 2021; 12:1134. [PMID: 33602934 PMCID: PMC7892824 DOI: 10.1038/s41467-021-21224-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/14/2021] [Indexed: 01/08/2023] Open
Abstract
The BCL-2 family protein BAX has essential activity in mitochondrial regulation of cell death. While BAX activity ensures tissue homeostasis, when dysregulated it contributes to aberrant cell death in several diseases. During cellular stress BAX is transformed from an inactive cytosolic conformation to a toxic mitochondrial oligomer. Although the BAX transformation process is not well understood, drugs that interfere with this process are useful research tools and potential therapeutics. Here, we show that Eltrombopag, an FDA-approved drug, is a direct inhibitor of BAX. Eltrombopag binds the BAX trigger site distinctly from BAX activators, preventing them from triggering BAX conformational transformation and simultaneously promoting stabilization of the inactive BAX structure. Accordingly, Eltrombopag is capable of inhibiting BAX-mediated apoptosis induced by cytotoxic stimuli. Our data demonstrate structure-function insights into a mechanism of BAX inhibition and reveal a mechanism for Eltrombopag that may expand its use in diseases of uncontrolled cell death.
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Affiliation(s)
- Adam Z Spitz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Emmanouil Zacharioudakis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Denis E Reyna
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Thomas P Garner
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Evripidis Gavathiotis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
- Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA.
- Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY, USA.
- Institute of Aging Research, Albert Einstein College of Medicine, Bronx, NY, USA.
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36
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Cancer cell death strategies by targeting Bcl-2's BH4 domain. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:118983. [PMID: 33549704 DOI: 10.1016/j.bbamcr.2021.118983] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
The Bcl-2-family proteins have long been known for their role as key regulators of apoptosis. Overexpression of various members of the family is associated with oncogenesis. Its founding member, anti-apoptotic Bcl-2 regulates cell death at different levels, whereby Bcl-2 emerged as a major drug target to eradicate cancers through cell death. This resulted in the development of venetoclax, a Bcl-2 antagonist that acts as a BH3 mimetic. Venetoclax already entered the clinic to treat relapse chronic lymphocytic leukemia patients. Here, we discuss the role of Bcl-2 as a decision-maker in cell death with focus on the recent advances in anti-cancer therapeutics that target the BH4 domain of Bcl-2, thereby interfering with non-canonical functions of Bcl-2 in Ca2+-signaling modulation. In particular, we critically discuss previously developed tools, including the peptide BIRD-2 (Bcl-2/IP3R-disrupter-2) and the small molecule BDA-366. In addition, we present a preliminary analysis of two recently identified molecules that emerged from a molecular modeling approach to target Bcl-2's BH4 domain, which however failed to induce cell death in two Bcl-2-dependent diffuse large B-cell lymphoma cell models. Overall, antagonizing the non-canonical functions of Bcl-2 by interfering with its BH4-domain biology holds promise to elicit cell death in cancer, though improved tools and on-target antagonizing small molecules remain necessary and ought to be designed.
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Fukuda Y, Pazyra-Murphy MF, Silagi ES, Tasdemir-Yilmaz OE, Li Y, Rose L, Yeoh ZC, Vangos NE, Geffken EA, Seo HS, Adelmant G, Bird GH, Walensky LD, Marto JA, Dhe-Paganon S, Segal RA. Binding and transport of SFPQ-RNA granules by KIF5A/KLC1 motors promotes axon survival. J Cell Biol 2021; 220:e202005051. [PMID: 33284322 PMCID: PMC7721913 DOI: 10.1083/jcb.202005051] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 10/15/2020] [Accepted: 11/06/2020] [Indexed: 01/03/2023] Open
Abstract
Complex neural circuitry requires stable connections formed by lengthy axons. To maintain these functional circuits, fast transport delivers RNAs to distal axons where they undergo local translation. However, the mechanism that enables long-distance transport of RNA granules is not yet understood. Here, we demonstrate that a complex containing RNA and the RNA-binding protein (RBP) SFPQ interacts selectively with a tetrameric kinesin containing the adaptor KLC1 and the motor KIF5A. We show that the binding of SFPQ to the KIF5A/KLC1 motor complex is required for axon survival and is impacted by KIF5A mutations that cause Charcot-Marie Tooth (CMT) disease. Moreover, therapeutic approaches that bypass the need for local translation of SFPQ-bound proteins prevent axon degeneration in CMT models. Collectively, these observations indicate that KIF5A-mediated SFPQ-RNA granule transport may be a key function disrupted in KIF5A-linked neurologic diseases and that replacing axonally translated proteins serves as a therapeutic approach to axonal degenerative disorders.
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Affiliation(s)
- Yusuke Fukuda
- Department of Neurobiology, Harvard Medical School, Boston, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Maria F. Pazyra-Murphy
- Department of Neurobiology, Harvard Medical School, Boston, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Elizabeth S. Silagi
- Department of Neurobiology, Harvard Medical School, Boston, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Ozge E. Tasdemir-Yilmaz
- Department of Neurobiology, Harvard Medical School, Boston, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Yihang Li
- Department of Neurobiology, Harvard Medical School, Boston, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Lillian Rose
- Department of Neurobiology, Harvard Medical School, Boston, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Zoe C. Yeoh
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Guillaume Adelmant
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Gregory H. Bird
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Loren D. Walensky
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jarrod A. Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Rosalind A. Segal
- Department of Neurobiology, Harvard Medical School, Boston, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
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The Mysteries around the BCL-2 Family Member BOK. Biomolecules 2020; 10:biom10121638. [PMID: 33291826 PMCID: PMC7762061 DOI: 10.3390/biom10121638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022] Open
Abstract
BOK is an evolutionarily conserved BCL-2 family member that resembles the apoptotic effectors BAK and BAX in sequence and structure. Based on these similarities, BOK has traditionally been classified as a BAX-like pro-apoptotic protein. However, the mechanism of action and cellular functions of BOK remains controversial. While some studies propose that BOK could replace BAK and BAX to elicit apoptosis, others attribute to this protein an indirect way of apoptosis regulation. Adding to the debate, BOK has been associated with a plethora of non-apoptotic functions that makes this protein unpredictable when dictating cell fate. Here, we compile the current knowledge and open questions about this paradoxical protein with a special focus on its structural features as the key aspect to understand BOK biological functions.
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Dobbs JM, Jenkins ML, Burke JE. Escherichia coli and Sf9 Contaminant Databases to Increase Efficiency of Tandem Mass Spectrometry Peptide Identification in Structural Mass Spectrometry Experiments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2202-2209. [PMID: 32869988 DOI: 10.1021/jasms.0c00283] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Filtering of nonspecifically binding contaminant proteins from affinity purification mass spectrometry (AP-MS) data is a well-established strategy to improve statistical confidence in identified proteins. The CRAPome (contaminant repository for affinity purification) describes the contaminating background content present in many purification strategies. However, full contaminant lists for nickel-nitrilotriacetic acid (NiNTA) and glutathione S-transferase (GST) affinity matrices are lacking. Similarly, no Spodoptera frugiperda (Sf9) contaminants are available, and only the FLAG-purified contaminants are described for Escherichia coli. For MS experiments that use recombinant protein, such as structural mass spectrometry experiments (hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking, and radical foot-printing), failing to include these contaminants in the search database during the initial tandem MS (MS/MS) identification stage can result in complications in peptide identification. We have created contaminant FASTA databases for Sf9 and E. coli NiNTA or GST purification strategies and show that the use of these databases can effectively improve HDX-MS protein coverage, fragment count, and confidence in peptide identification. This approach provides a robust strategy toward the design of contaminant databases for any purification approach that will expand the complexity of systems able to be interrogated by HDX-MS.
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Affiliation(s)
- Joseph M Dobbs
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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40
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Targeting a helix-in-groove interaction between E1 and E2 blocks ubiquitin transfer. Nat Chem Biol 2020; 16:1218-1226. [PMID: 32807965 PMCID: PMC7904387 DOI: 10.1038/s41589-020-0625-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 06/20/2020] [Accepted: 07/12/2020] [Indexed: 01/04/2023]
Abstract
The ubiquitin-proteasome system (UPS) is a highly regulated protein disposal process critical to cell survival. Inhibiting the pathway induces proteotoxic stress and can be an effective cancer treatment. The therapeutic window observed upon proteasomal blockade has motivated multiple UPS-targeting strategies, including preventing ubiquitination altogether. E1 initiates the cascade by transferring ubiquitin to E2 enzymes. A small molecule that engages the E1 ATP-binding site and derivatizes ubiquitin disrupts enzymatic activity and kills cancer cells. However, binding-site mutations cause resistance, motivating alternative approaches to block this promising target. We identified an interaction between the E2 N-terminal alpha-1 helix and a pocket within the E1 ubiquitin-fold domain as a potentially druggable site. Stapled peptides modeled after the E2 alpha-1 helix bound to the E1 groove, induced a consequential conformational change and inhibited E1 ubiquitin thiotransfer, disrupting E2 ubiquitin charging and ubiquitination of cellular proteins. Thus, we provide a blueprint for a distinct E1-targeting strategy to treat cancer.
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41
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A redox switch regulates the structure and function of anti-apoptotic BFL-1. Nat Struct Mol Biol 2020; 27:781-789. [PMID: 32661419 PMCID: PMC7544158 DOI: 10.1038/s41594-020-0458-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 06/03/2020] [Indexed: 01/27/2023]
Abstract
Apoptosis is regulated by BCL-2 family proteins. Anti-apoptotic members suppress cell death by deploying a surface groove to capture the critical BH3 α-helix of pro-apoptotic members. Cancer cells hijack this mechanism by overexpressing anti-apoptotic BCL-2 family proteins to enforce cellular immortality. We previously identified and harnessed a unique cysteine (C55) in the groove of anti-apoptotic BFL-1 to selectively neutralize its oncogenic activity using a covalent stapled-peptide inhibitor. Here, we find that disulfide bonding between a native cysteine pair at the groove (C55) and C-terminal α9 helix (C175) of BFL-1 operates as a redox switch to control the accessibility of the anti-apoptotic pocket. Reducing the C55-C175 disulfide triggers α9 release, which promotes mitochondrial translocation, groove exposure for BH3 interaction and inhibition of mitochondrial permeabilization by pro-apoptotic BAX. C55-C175 disulfide formation in an oxidative cellular environment abrogates the ability of BFL-1 to bind BH3 domains. Thus, we identify a mechanism of conformational control of BFL-1 by an intramolecular redox switch.
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42
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Hauseman ZJ, Harvey EP, Newman CE, Wales TE, Bucci JC, Mintseris J, Schweppe DK, David L, Fan L, Cohen DT, Herce HD, Mourtada R, Ben-Nun Y, Bloch NB, Hansen SB, Wu H, Gygi SP, Engen JR, Walensky LD. Homogeneous Oligomers of Pro-apoptotic BAX Reveal Structural Determinants of Mitochondrial Membrane Permeabilization. Mol Cell 2020; 79:68-83.e7. [PMID: 32533918 PMCID: PMC7472837 DOI: 10.1016/j.molcel.2020.05.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/13/2020] [Accepted: 05/20/2020] [Indexed: 10/24/2022]
Abstract
BAX is a pro-apoptotic protein that transforms from a cytosolic monomer into a toxic oligomer that permeabilizes the mitochondrial outer membrane. How BAX monomers assemble into a higher-order conformation, and the structural determinants essential to membrane permeabilization, remain a mechanistic mystery. A key hurdle has been the inability to generate a homogeneous BAX oligomer (BAXO) for analysis. Here, we report the production and characterization of a full-length BAXO that recapitulates physiologic BAX activation. Multidisciplinary studies revealed striking conformational consequences of oligomerization and insight into the macromolecular structure of oligomeric BAX. Importantly, BAXO enabled the assignment of specific roles to particular residues and α helices that mediate individual steps of the BAX activation pathway, including unexpected functionalities of BAX α6 and α9 in driving membrane disruption. Our results provide the first glimpse of a full-length and functional BAXO, revealing structural requirements for the elusive execution phase of mitochondrial apoptosis.
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Affiliation(s)
- Zachary J Hauseman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Edward P Harvey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Catherine E Newman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Joel C Bucci
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Julian Mintseris
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Devin K Schweppe
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Liron David
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lixin Fan
- Small Angle X-ray Scattering Core, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Daniel T Cohen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Henry D Herce
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Rida Mourtada
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Yael Ben-Nun
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Noah B Bloch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Scott B Hansen
- The Scripps Research Institute-Florida, Jupiter, FL 33458, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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Bird GH, Fu A, Escudero S, Godes M, Opoku-Nsiah K, Wales TE, Cameron MD, Engen JR, Danial NN, Walensky LD. Hydrocarbon-Stitched Peptide Agonists of Glucagon-Like Peptide-1 Receptor. ACS Chem Biol 2020; 15:1340-1348. [PMID: 32348108 DOI: 10.1021/acschembio.0c00308] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Glucagon-like peptide 1 (GLP-1) is a natural peptide agonist of the GLP-1 receptor (GLP-1R) found on pancreatic β-cells. Engagement of the receptor stimulates insulin release in a glucose-dependent fashion and increases β-cell mass, two ideal features for pharmacologic management of type 2 diabetes. Thus, intensive efforts have focused on developing GLP-1-based peptide agonists of GLP-1R for therapeutic application. A primary challenge has been the naturally short half-life of GLP-1 due to its rapid proteolytic degradation in vivo. Whereas mutagenesis and lipidation strategies have yielded clinical agents, we developed an alternative approach to preserving the structure and function of GLP-1 by all-hydrocarbon i, i + 7 stitching. This particular "stitch" is especially well-suited for reinforcing and protecting the structural fidelity of GLP-1. Lead constructs demonstrate striking proteolytic stability and potent biological activity in vivo. Thus, we report a facile approach to generating alternative GLP-1R agonists for glycemic control.
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Affiliation(s)
- Gregory H. Bird
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Accalia Fu
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston Massachusetts 02215, United States
- Department of Cell Biology, Harvard Medical School, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Silvia Escudero
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Marina Godes
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Kwadwo Opoku-Nsiah
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Michael D. Cameron
- DMPK Core, Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Nika N. Danial
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston Massachusetts 02215, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Department of Medicine, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Loren D. Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
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Harvey EP, Hauseman ZJ, Cohen DT, Rettenmaier TJ, Lee S, Huhn AJ, Wales TE, Seo HS, Luccarelli J, Newman CE, Guerra RM, Bird GH, Dhe-Paganon S, Engen JR, Wells JA, Walensky LD. Identification of a Covalent Molecular Inhibitor of Anti-apoptotic BFL-1 by Disulfide Tethering. Cell Chem Biol 2020; 27:647-656.e6. [PMID: 32413285 DOI: 10.1016/j.chembiol.2020.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/13/2020] [Accepted: 04/03/2020] [Indexed: 02/06/2023]
Abstract
The BCL-2 family is composed of anti- and pro-apoptotic members that respectively protect or disrupt mitochondrial integrity. Anti-apoptotic overexpression can promote oncogenesis by trapping the BCL-2 homology 3 (BH3) "killer domains" of pro-apoptotic proteins in a surface groove, blocking apoptosis. Groove inhibitors, such as the relatively large BCL-2 drug venetoclax (868 Da), have emerged as cancer therapies. BFL-1 remains an undrugged oncogenic protein and can cause venetoclax resistance. Having identified a unique C55 residue in the BFL-1 groove, we performed a disulfide tethering screen to determine if C55 reactivity could enable smaller molecules to block BFL-1's BH3-binding functionality. We found that a disulfide-bearing N-acetyltryptophan analog (304 Da adduct) effectively targeted BFL-1 C55 and reversed BFL-1-mediated suppression of mitochondrial apoptosis. Structural analyses implicated the conserved leucine-binding pocket of BFL-1 as the interaction site, resulting in conformational remodeling. Thus, therapeutic targeting of BFL-1 may be achievable through the design of small, cysteine-reactive drugs.
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Affiliation(s)
- Edward P Harvey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Zachary J Hauseman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Daniel T Cohen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - T Justin Rettenmaier
- Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology, University of California, 1700 Fourth Street, San Francisco, CA 94143, USA
| | - Susan Lee
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Annissa J Huhn
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, 412 The Fenway, Boston, MA 02115, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - James Luccarelli
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Catherine E Newman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Rachel M Guerra
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Gregory H Bird
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, 412 The Fenway, Boston, MA 02115, USA
| | - James A Wells
- Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology, University of California, 1700 Fourth Street, San Francisco, CA 94143, USA
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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Separase-triggered apoptosis enforces minimal length of mitosis. Nature 2020; 580:542-547. [PMID: 32322059 DOI: 10.1038/s41586-020-2187-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 02/10/2020] [Indexed: 01/13/2023]
Abstract
Prolonged mitosis often results in apoptosis1. Shortened mitosis causes tumorigenic aneuploidy, but it is unclear whether it also activates the apoptotic machinery2. Separase, a cysteine protease and trigger of all eukaryotic anaphases, has a caspase-like catalytic domain but has not previously been associated with cell death3,4. Here we show that human cells that enter mitosis with already active separase rapidly undergo death in mitosis owing to direct cleavage of anti-apoptotic MCL1 and BCL-XL by separase. Cleavage not only prevents MCL1 and BCL-XL from sequestering pro-apoptotic BAK, but also converts them into active promoters of death in mitosis. Our data strongly suggest that the deadliest cleavage fragment, the C-terminal half of MCL1, forms BAK/BAX-like pores in the mitochondrial outer membrane. MCL1 and BCL-XL are turned into separase substrates only upon phosphorylation by NEK2A. Early mitotic degradation of this kinase is therefore crucial for preventing apoptosis upon scheduled activation of separase in metaphase. Speeding up mitosis by abrogation of the spindle assembly checkpoint results in a temporal overlap of the enzymatic activities of NEK2A and separase and consequently in cell death. We propose that NEK2A and separase jointly check on spindle assembly checkpoint integrity and eliminate cells that are prone to chromosome missegregation owing to accelerated progression through early mitosis.
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Ivanova H, Vervliet T, Monaco G, Terry LE, Rosa N, Baker MR, Parys JB, Serysheva II, Yule DI, Bultynck G. Bcl-2-Protein Family as Modulators of IP 3 Receptors and Other Organellar Ca 2+ Channels. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035089. [PMID: 31501195 DOI: 10.1101/cshperspect.a035089] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The pro- and antiapoptotic proteins belonging to the B-cell lymphoma-2 (Bcl-2) family exert a critical control over cell-death processes by enabling or counteracting mitochondrial outer membrane permeabilization. Beyond this mitochondrial function, several Bcl-2 family members have emerged as critical modulators of intracellular Ca2+ homeostasis and dynamics, showing proapoptotic and antiapoptotic functions. Bcl-2 family proteins specifically target several intracellular Ca2+-transport systems, including organellar Ca2+ channels: inositol 1,4,5-trisphosphate receptors (IP3Rs) and ryanodine receptors (RyRs), Ca2+-release channels mediating Ca2+ flux from the endoplasmic reticulum, as well as voltage-dependent anion channels (VDACs), which mediate Ca2+ flux across the mitochondrial outer membrane into the mitochondria. Although the formation of protein complexes between Bcl-2 proteins and these channels has been extensively studied, a major advance during recent years has been elucidating the complex interaction of Bcl-2 proteins with IP3Rs. Distinct interaction sites for different Bcl-2 family members were identified in the primary structure of IP3Rs. The unique molecular profiles of these Bcl-2 proteins may account for their distinct functional outcomes when bound to IP3Rs. Furthermore, Bcl-2 inhibitors used in cancer therapy may affect IP3R function as part of their proapoptotic effect and/or as an adverse effect in healthy cells.
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Affiliation(s)
- Hristina Ivanova
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Tim Vervliet
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Giovanni Monaco
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Lara E Terry
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642
| | - Nicolas Rosa
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Mariah R Baker
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Structural Biology Imaging Center, Houston, Texas 77030
| | - Jan B Parys
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Structural Biology Imaging Center, Houston, Texas 77030
| | - David I Yule
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642
| | - Geert Bultynck
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
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Moldoveanu T, Czabotar PE. BAX, BAK, and BOK: A Coming of Age for the BCL-2 Family Effector Proteins. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a036319. [PMID: 31570337 DOI: 10.1101/cshperspect.a036319] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The BCL-2 family of proteins control a key checkpoint in apoptosis, that of mitochondrial outer membrane permeabilization or, simply, mitochondrial poration. The family consists of three subgroups: BH3-only initiators that respond to apoptotic stimuli; antiapoptotic guardians that protect against cell death; and the membrane permeabilizing effectors BAX, BAK, and BOK. On activation, effector proteins are converted from inert monomers into membrane permeabilizing oligomers. For many years, this process has been poorly understood at the molecular level, but a number of recent advances have provided important insights. We review the regulation of these effectors, their activation, subsequent conformational changes, and the ensuing oligomerization events that enable mitochondrial poration, which initiates apoptosis through release of key signaling factors such as cytochrome c We highlight the mysteries that remain in understanding these important proteins in an endeavor to provide a comprehensive picture of where the field currently sits and where it is moving toward.
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Affiliation(s)
- Tudor Moldoveanu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.,Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis Tennessee 38105, USA
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, University of Melbourne, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
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Conformational Switching in Bcl-xL: Enabling Non-Canonic Inhibition of Apoptosis Involves Multiple Intermediates and Lipid Interactions. Cells 2020; 9:cells9030539. [PMID: 32111007 PMCID: PMC7140517 DOI: 10.3390/cells9030539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/13/2020] [Accepted: 02/17/2020] [Indexed: 12/21/2022] Open
Abstract
The inhibition of mitochondrial permeabilization by the anti-apoptotic protein Bcl-xL is crucial for cell survival and homeostasis. Its inhibitory role requires the partitioning of Bcl-xL to the mitochondrial outer membrane from an inactive state in the cytosol, leading to its extensive refolding. The molecular mechanisms behind these events and the resulting conformations in the bilayer are unclear, and different models have been proposed to explain them. In the most recently proposed non-canonical model, the active form of Bcl-xL employs its N-terminal BH4 helix to bind and block its pro-apoptotic target. Here, we used a combination of various spectroscopic techniques to study the release of the BH4 helix (α1) during the membrane insertion of Bcl-xL. This refolding was characterized by a gradual increase in helicity due to the lipid-dependent partitioning-coupled folding and formation of new helix αX (presumably in the originally disordered loop between helices α1 and α2). Notably, a comparison of various fluorescence and circular dichroism measurements suggested the presence of multiple Bcl-xL conformations in the bilayer. This conclusion was explicitly confirmed by single-molecule measurements of Förster Resonance Energy Transfer from Alexa-Fluor-488-labeled Bcl-xL D189C to a mCherry fluorescent protein attached at the N-terminus. These measurements clearly indicated that the refolding of Bcl-xL in the bilayer is not a two-state transition and involves multiple membranous intermediates of variable compactness.
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Makarov AA, Pirrone GF, Shchurik V, Regalado EL, Mangion I. Liposome Artificial Membrane Permeability Assay by MALDI-hydrogen-deuterium exchange mass spectrometry for peptides and small proteins. Anal Chim Acta 2020; 1099:111-118. [PMID: 31986267 DOI: 10.1016/j.aca.2019.09.063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/30/2019] [Accepted: 09/23/2019] [Indexed: 02/07/2023]
Abstract
The pharmaceutical industry's focus has expanded to include peptide and protein-based therapeutics; however, some analytical challenges have arisen along the way, including the urgent need for fast and robust measurement of the membrane permeability of peptides and small proteins. In this study, a simple and efficient approach that utilizes MALDI-TOF-MS to study peptide and protein permeability through an artificial liposome membrane in conjunction with a differential hydrogen-deuterium exchange (HDX) methodology is described. A non-aqueous (aprotic) matrix was evaluated for use with MALDI sample preparation in order to eliminate undesirable hydrogen-deuterium back-exchange. Peptides and proteins were incubated with liposomes and their penetration into the liposome membrane over time was measured by MALDI-MS. A differential HDX approach was used to distinguish the peptides outside of the liposome from those inside. In this regard, the peptides on the outside of the liposomes were labeled using short exposure to deuterium oxide, while the peptides inside of the liposomes were protected from labeling. Subsequently, the unlabeled versus labeled peak area ratios for peptide and protein samples were compared using MALDI-TOF-MS. In this proof-of-concept study, we developed the Liposome Artificial Membrane Permeability Assay (LAMPA) workflow to study three well-known membrane-active model peptides (melittin, alamethicin, and gramicidin) and two model proteins (aprotinin and ubiquitin). The permeability results obtained from this were corroborated by previously reported data for studied peptides and proteins. The proposed LAMPA by MALDI-HDX-MS can be applied in an ultra-high-throughput manner for studying and rank-ordering membrane permeability of peptides and small proteins.
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Affiliation(s)
- Alexey A Makarov
- Merck & Co., Inc., MRL, Analytical Research & Development /Process Research & Development, 126 E. Lincoln Ave., Rahway, NJ, 07065, USA.
| | - Gregory F Pirrone
- Merck & Co., Inc., MRL, Analytical Research & Development /Process Research & Development, 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Vladimir Shchurik
- Merck & Co., Inc., MRL, Analytical Research & Development /Process Research & Development, 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Erik L Regalado
- Merck & Co., Inc., MRL, Analytical Research & Development /Process Research & Development, 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
| | - Ian Mangion
- Merck & Co., Inc., MRL, Analytical Research & Development /Process Research & Development, 126 E. Lincoln Ave., Rahway, NJ, 07065, USA
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50
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PEGylation-based strategy to identify pathways involved in the activation of apoptotic BAX protein. Biochim Biophys Acta Gen Subj 2020; 1864:129541. [PMID: 31987956 DOI: 10.1016/j.bbagen.2020.129541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 10/25/2022]
Abstract
BACKGROUND BAX activation is a crucial step for commitment to apoptosis. Several activators, such as BimBH3-based therapeutic peptides and cleaved Bid (cBid) protein, can trigger BAX-mediated apoptosis, but it is unclear whether they proceed through the same pathway. METHODS Here we utilize PEGylation-based approach, which is shown to efficiently shield individual binding grooves in BAX from activators, to investigate and reveal that the activators take different routes to induce BAX-mediated apoptosis. Various spectroscopic/biochemical tools, including electron spin resonance, circular dichroism, fluorescence recovery after photobleaching, and label-transfer assay, were employed to reveal details in the processes. RESULTS We observe a key mutant BAX 164-PEG that acts differently in response to cBid and BimBH3 stimuli. While BimBH3 directly interacts with the trigger groove (TG) to induce the conformational changes in BAX that includes the release of α9 from the canonical groove (CG) and oligomerization, cBid engages with CG and works with mitochondrial lipids to fully activate BAX. CONCLUSION PEGylation-based approach is proven useful to shield individual binding grooves of BAX from apoptotic stimuli. Groove engagement in CG of BAX is required for a full cBid-induced BAX activation. This study has identified differences in the pathways involved during the initiation of BAX activation by full-length cBid protein versus synthetic BimBH3-based peptides. GENERAL SIGNIFICANCE Our finding is potentially valuable for therapeutic application as the pore-forming activity of 164-PEG is independent from the cBid-mediated apoptotic pathways, but can be administrated by the synthetic short peptides.
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