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Hagen JT, Montgomery MM, Aruleba RT, Chrest BR, Green TD, Kassai M, Zeczycki TN, Schmidt CA, Bhowmick D, Tan SF, Feith DJ, Chalfant CE, Loughran TP, Liles D, Minden MD, Schimmer AD, Cabot MC, Mclung JM, Fisher-Wellman KH. Mitochondria inside acute myeloid leukemia cells hydrolyze ATP to resist chemotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589110. [PMID: 38659944 PMCID: PMC11042215 DOI: 10.1101/2024.04.12.589110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Despite early optimism, therapeutics targeting oxidative phosphorylation (OxPhos) have faced clinical setbacks, stemming from their inability to distinguish healthy from cancerous mitochondria. Herein, we describe an actionable bioenergetic mechanism unique to cancerous mitochondria inside acute myeloid leukemia (AML) cells. Unlike healthy cells which couple respiration to the synthesis of ATP, AML mitochondria were discovered to support inner membrane polarization by consuming ATP. Because matrix ATP consumption allows cells to survive bioenergetic stress, we hypothesized that AML cells may resist cell death induced by OxPhos damaging chemotherapy by reversing the ATP synthase reaction. In support of this, targeted inhibition of BCL-2 with venetoclax abolished OxPhos flux without impacting mitochondrial membrane potential. In surviving AML cells, sustained polarization of the mitochondrial inner membrane was dependent on matrix ATP consumption. Mitochondrial ATP consumption was further enhanced in AML cells made refractory to venetoclax, consequential to downregulations in both the proton-pumping respiratory complexes, as well as the endogenous F1-ATPase inhibitor ATP5IF1. In treatment-naive AML, ATP5IF1 knockdown was sufficient to drive venetoclax resistance, while ATP5IF1 overexpression impaired F1-ATPase activity and heightened sensitivity to venetoclax. Collectively, our data identify matrix ATP consumption as a cancer-cell intrinsic bioenergetic vulnerability actionable in the context of mitochondrial damaging chemotherapy.
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Affiliation(s)
- James T Hagen
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Mclane M Montgomery
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Raphael T Aruleba
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Brett R Chrest
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Thomas D Green
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
| | - Miki Kassai
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC
| | - Cameron A Schmidt
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
- Department of Biology, East Carolina University, Greenville, NC
| | - Debajit Bhowmick
- Flow Cytometry Core Facility, Brody School of Medicine at East Carolina University, Greenville, NC
| | - Su-Fern Tan
- Department of Medicine, Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
| | - David J Feith
- Department of Medicine, Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
| | - Charles E Chalfant
- Department of Medicine, Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
- Department of Cell Biology, University of Virginia, Charlottesville, VA
- Research Service, Richmond Veterans Administration Medical Center, Richmond, VA
| | - Thomas P Loughran
- Department of Medicine, Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA
- University of Virginia Cancer Center, Charlottesville, VA
| | - Darla Liles
- Department of Internal Medicine, Brody School of Medicine, East Carolina University, Greenville, NC
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Myles C Cabot
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC
| | - Joseph M Mclung
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
- Department of Cardiovascular Sciences, Brody School of Medicine, East Carolina University, Greenville, NC
| | - Kelsey H Fisher-Wellman
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, NC
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
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2
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Hurrish KH, Su Y, Patel S, Ramage CL, Zhao J, Temby BR, Carter JL, Edwards H, Buck SA, Wiley SE, Hüttemann M, Polin L, Kushner J, Dzinic SH, White K, Bao X, Li J, Yang J, Boerner J, Hou Z, Al-Atrash G, Konoplev SN, Busquets J, Tiziani S, Matherly LH, Taub JW, Konopleva M, Ge Y, Baran N. Enhancing anti-AML activity of venetoclax by isoflavone ME-344 through suppression of OXPHOS and/or purine biosynthesis in vitro. Biochem Pharmacol 2024; 220:115981. [PMID: 38081370 DOI: 10.1016/j.bcp.2023.115981] [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: 09/29/2023] [Revised: 11/16/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Venetoclax (VEN), in combination with low dose cytarabine (AraC) or a hypomethylating agent, is FDA approved to treat acute myeloid leukemia (AML) in patients who are over the age of 75 or cannot tolerate standard chemotherapy. Despite high response rates to these therapies, most patients succumb to the disease due to relapse and/or drug resistance, providing an unmet clinical need for novel therapies to improve AML patient survival. ME-344 is a potent isoflavone with demonstrated inhibitory activity toward oxidative phosphorylation (OXPHOS) and clinical activity in solid tumors. Given that OXPHOS inhibition enhances VEN antileukemic activity against AML, we hypothesized that ME-344 could enhance the anti-AML activity of VEN. Here we report that ME-344 enhanced VEN to target AML cell lines and primary patient samples while sparing normal hematopoietic cells. Cooperative suppression of OXPHOS was detected in a subset of AML cell lines and primary patient samples. Metabolomics analysis revealed a significant reduction of purine biosynthesis metabolites by ME-344. Further, lometrexol, a purine biosynthesis inhibitor, synergistically enhanced VEN-induced apoptosis in AML cell lines. Interestingly, AML cells with acquired AraC resistance showed significantly increased purine biosynthesis metabolites and sensitivities to ME-344. Furthermore, synergy between ME-344 and VEN was preserved in these AraC-resistant AML cells. In vivo studies revealed significantly prolonged survival upon combination therapy of ME-344 and VEN in NSGS mice bearing parental or AraC-resistant MV4-11 leukemia compared to the vehicle control. This study demonstrates that ME-344 enhances VEN antileukemic activity against preclinical models of AML by suppressing OXPHOS and/or purine biosynthesis.
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Affiliation(s)
- Katie H Hurrish
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yongwei Su
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Shraddha Patel
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cassandra L Ramage
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianlei Zhao
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Brianna R Temby
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jenna L Carter
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI, USA; MD/PhD Program, Wayne State University School of Medicine, Detroit, MI, USA
| | - Holly Edwards
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Steven A Buck
- Division of Pediatric Hematology/Oncology, Children's Hospital of Michigan, Detroit, MI, USA
| | | | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Lisa Polin
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Juiwanna Kushner
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sijana H Dzinic
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Kathryn White
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Xun Bao
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jing Li
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jay Yang
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Julie Boerner
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Zhanjun Hou
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Gheath Al-Atrash
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sergej N Konoplev
- Department of Leukemia, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
| | - Jonathan Busquets
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Stefano Tiziani
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Larry H Matherly
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI, USA; Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jeffrey W Taub
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA; Division of Pediatric Hematology/Oncology, Children's Hospital of Michigan, Detroit, MI, USA; Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Marina Konopleva
- Department of Leukemia, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA.
| | - Yubin Ge
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI, USA; Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
| | - Natalia Baran
- Department of Leukemia, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA.
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Kamath ND, Matreyek KA. Multiplex Functional Characterization of Protein Variant Libraries in Mammalian Cells with Single-Copy Genomic Integration and High-Throughput DNA Sequencing. Methods Mol Biol 2024; 2774:135-152. [PMID: 38441763 DOI: 10.1007/978-1-0716-3718-0_10] [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] [Indexed: 03/07/2024]
Abstract
Sequencing-based, massively parallel genetic assays have enabled simultaneous characterization of the genotype-phenotype relationships for libraries encoding thousands of unique protein variants. Since plasmid transfection and lentiviral transduction have characteristics that limit multiplexing with pooled libraries, we developed a mammalian synthetic biology platform that harnesses the Bxb1 bacteriophage DNA recombinase to insert single promoterless plasmids encoding a transgene of interest into a pre-engineered "landing pad" site within the cell genome. The transgene is expressed behind a genomically integrated promoter, ensuring only one transgene is expressed per cell, preserving a strict genotype-phenotype link. Upon selecting cells based on a desired phenotype, the transgene can be sequenced to ascribe each variant a phenotypic score. We describe how to create and utilize landing pad cells for large-scale, library-based genetic experiments. Using the provided examples, the experimental template can be adapted to explore protein variants in diverse biological problems within mammalian cells.
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Affiliation(s)
- Nisha D Kamath
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kenneth A Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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4
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Maes S, Deploey N, Peelman F, Eyckerman S. Deep mutational scanning of proteins in mammalian cells. CELL REPORTS METHODS 2023; 3:100641. [PMID: 37963462 PMCID: PMC10694495 DOI: 10.1016/j.crmeth.2023.100641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/06/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023]
Abstract
Protein mutagenesis is essential for unveiling the molecular mechanisms underlying protein function in health, disease, and evolution. In the past decade, deep mutational scanning methods have evolved to support the functional analysis of nearly all possible single-amino acid changes in a protein of interest. While historically these methods were developed in lower organisms such as E. coli and yeast, recent technological advancements have resulted in the increased use of mammalian cells, particularly for studying proteins involved in human disease. These advancements will aid significantly in the classification and interpretation of variants of unknown significance, which are being discovered at large scale due to the current surge in the use of whole-genome sequencing in clinical contexts. Here, we explore the experimental aspects of deep mutational scanning studies in mammalian cells and report the different methods used in each step of the workflow, ultimately providing a useful guide toward the design of such studies.
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Affiliation(s)
- Stefanie Maes
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Nick Deploey
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Frank Peelman
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.
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5
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Roelle S, Kamath ND, Matreyek KA. Mammalian Genomic Manipulation with Orthogonal Bxb1 DNA Recombinase Sites for the Functional Characterization of Protein Variants. ACS Synth Biol 2023; 12:3352-3365. [PMID: 37922210 PMCID: PMC10661055 DOI: 10.1021/acssynbio.3c00355] [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: 06/10/2023] [Revised: 09/22/2023] [Accepted: 10/19/2023] [Indexed: 11/05/2023]
Abstract
The Bxb1 bacteriophage serine DNA recombinase is an efficient tool for engineering recombinant DNA into the genomes of cultured cells. Generally, a single engineered "landing pad" site is introduced into the cell genome, permitting the integration of transgenic circuits or libraries of transgene variants. While sufficient for many studies, the extent of genetic manipulation possible with a single recombinase site is limiting and insufficient for more complex cell-based assays. Here, we harnessed two orthogonal Bxb1 recombinase sites to enable alternative avenues for using mammalian synthetic biology to characterize transgenic protein variants. By designing plasmids flanked by a second pair of auxiliary recombination sites, we demonstrate that we can avoid the genomic integration of undesirable bacterial DNA elements using the same starting cells engineered for whole-plasmid integration. We also created "double landing pad" cells simultaneously harboring two orthogonal Bxb1 recombinase sites at separate genomic loci, allowing complex cell-based genetic assays. Integration of a genetically encoded calcium indicator allowed for the real-time monitoring of intracellular calcium signaling dynamics, including kinetic perturbations that occur upon overexpression of the wild-type or variant version of the calcium signaling relay protein STIM1. A panel of missense mutants of the HIV-1 accessory protein Vif was paired with various paralogs within the human Apobec3 innate immune protein family to identify combinations capable or incapable of interacting within cells. These cells allow transgenic protein variant libraries to be readily paired with assay-specific protein partners or biosensors, enabling new functional readouts for large-scale genetic assays for protein function.
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Affiliation(s)
- Sarah
M. Roelle
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Nisha D. Kamath
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Kenneth A. Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
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Althaher AR, Alwahsh M. An overview of ATP synthase, inhibitors, and their toxicity. Heliyon 2023; 9:e22459. [PMID: 38106656 PMCID: PMC10722325 DOI: 10.1016/j.heliyon.2023.e22459] [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: 08/15/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Mitochondrial complex V (ATP synthase) is a remarkable molecular motor crucial in generating ATP and sustaining mitochondrial function. Its importance in cellular metabolism cannot be overstated, as malfunction of ATP synthase has been linked to various pathological conditions. Both natural and synthetic ATP synthase inhibitors have been extensively studied, revealing their inhibitory sites and modes of action. These findings have opened exciting avenues for developing new therapeutics and discovering new pesticides and herbicides to safeguard global food supplies. However, it is essential to remember that these compounds can also adversely affect human and animal health, impacting vital organs such as the nervous system, heart, and kidneys. This review aims to provide a comprehensive overview of mitochondrial ATP synthase, its structural and functional features, and the most common inhibitors and their potential toxicities.
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Affiliation(s)
- Arwa R. Althaher
- Department of Pharmacy, Al-Zaytoonah University of Jordan, Amman 11733, Jordan
| | - Mohammad Alwahsh
- Department of Pharmacy, Al-Zaytoonah University of Jordan, Amman 11733, Jordan
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7
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Boykov IN, Montgomery MM, Hagen JT, Aruleba RT, McLaughlin KL, Coalson HS, Nelson MA, Pereyra AS, Ellis JM, Zeczycki TN, Vohra NA, Tan SF, Cabot MC, Fisher-Wellman KH. Pan-tissue mitochondrial phenotyping reveals lower OXPHOS expression and function across cancer types. Sci Rep 2023; 13:16742. [PMID: 37798427 PMCID: PMC10556099 DOI: 10.1038/s41598-023-43963-5] [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: 07/03/2023] [Accepted: 09/30/2023] [Indexed: 10/07/2023] Open
Abstract
Targeting mitochondrial oxidative phosphorylation (OXPHOS) to treat cancer has been hampered due to serious side-effects potentially arising from the inability to discriminate between non-cancerous and cancerous mitochondria. Herein, comprehensive mitochondrial phenotyping was leveraged to define both the composition and function of OXPHOS across various murine cancers and compared to both matched normal tissues and other organs. When compared to both matched normal tissues, as well as high OXPHOS reliant organs like heart, intrinsic expression of the OXPHOS complexes, as well as OXPHOS flux were discovered to be consistently lower across distinct cancer types. Assuming intrinsic OXPHOS expression/function predicts OXPHOS reliance in vivo, these data suggest that pharmacologic blockade of mitochondrial OXPHOS likely compromises bioenergetic homeostasis in healthy oxidative organs prior to impacting tumor mitochondrial flux in a clinically meaningful way. Although these data caution against the use of indiscriminate mitochondrial inhibitors for cancer treatment, considerable heterogeneity was observed across cancer types with respect to both mitochondrial proteome composition and substrate-specific flux, highlighting the possibility for targeting discrete mitochondrial proteins or pathways unique to a given cancer type.
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Affiliation(s)
- Ilya N Boykov
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - McLane M Montgomery
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - James T Hagen
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Raphael T Aruleba
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Kelsey L McLaughlin
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Hannah S Coalson
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Margaret A Nelson
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Andrea S Pereyra
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Jessica M Ellis
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Nasreen A Vohra
- Department of Surgery, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Su-Fern Tan
- Department of Medicine, Division of Hematology/Oncology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Myles C Cabot
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Kelsey H Fisher-Wellman
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, NC, USA.
- East Carolina Diabetes and Obesity Institute, East Carolina University, 115 Heart Drive, Greenville, NC, 27834, USA.
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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8
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Qureshi A, Connolly JB. Bioinformatic and literature assessment of toxicity and allergenicity of a CRISPR-Cas9 engineered gene drive to control Anopheles gambiae the mosquito vector of human malaria. Malar J 2023; 22:234. [PMID: 37580703 PMCID: PMC10426224 DOI: 10.1186/s12936-023-04665-5] [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: 12/02/2022] [Accepted: 08/07/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Population suppression gene drive is currently being evaluated, including via environmental risk assessment (ERA), for malaria vector control. One such gene drive involves the dsxFCRISPRh transgene encoding (i) hCas9 endonuclease, (ii) T1 guide RNA (gRNA) targeting the doublesex locus, and (iii) DsRed fluorescent marker protein, in genetically-modified mosquitoes (GMMs). Problem formulation, the first stage of ERA, for environmental releases of dsxFCRISPRh previously identified nine potential harms to the environment or health that could occur, should expressed products of the transgene cause allergenicity or toxicity. METHODS Amino acid sequences of hCas9 and DsRed were interrogated against those of toxins or allergens from NCBI, UniProt, COMPARE and AllergenOnline bioinformatic databases and the gRNA was compared with microRNAs from the miRBase database for potential impacts on gene expression associated with toxicity or allergenicity. PubMed was also searched for any evidence of toxicity or allergenicity of Cas9 or DsRed, or of the donor organisms from which these products were originally derived. RESULTS While Cas9 nuclease activity can be toxic to some cell types in vitro and hCas9 was found to share homology with the prokaryotic toxin VapC, there was no evidence from previous studies of a risk of toxicity to humans and other animals from hCas9. Although hCas9 did contain an 8-mer epitope found in the latex allergen Hev b 9, the full amino acid sequence of hCas9 was not homologous to any known allergens. Combined with a lack of evidence in the literature of Cas9 allergenicity, this indicated negligible risk to humans of allergenicity from hCas9. No matches were found between the gRNA and microRNAs from either Anopheles or humans. Moreover, potential exposure to dsxFCRISPRh transgenic proteins from environmental releases was assessed as negligible. CONCLUSIONS Bioinformatic and literature assessments found no convincing evidence to suggest that transgenic products expressed from dsxFCRISPRh were allergens or toxins, indicating that environmental releases of this population suppression gene drive for malaria vector control should not result in any increased allergenicity or toxicity in humans or animals. These results should also inform evaluations of other GMMs being developed for vector control and in vivo clinical applications of CRISPR-Cas9.
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Affiliation(s)
- Alima Qureshi
- Department of Life Sciences, Imperial College London, Silwood Park, Sunninghill, Ascot, UK
| | - John B Connolly
- Department of Life Sciences, Imperial College London, Silwood Park, Sunninghill, Ascot, UK.
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9
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Jones NH, Kapoor TM. Achieving the promise and avoiding the peril of chemical probes using genetics. Curr Opin Struct Biol 2023; 81:102628. [PMID: 37364429 PMCID: PMC10561518 DOI: 10.1016/j.sbi.2023.102628] [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: 01/26/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Abstract
Chemical probes can be valuable tools for studying protein targets, but addressing concerns about a probe's cellular target or its specificity can be challenging. A reliable strategy is to use a mutation that does not alter a target's function but confers resistance (or sensitizes) to the inhibitor in both cellular and biochemical assays. However, challenges remain in finding such mutations. Here, we discuss structure- and cell-based approaches to identify resistance- and sensitivity-conferring mutations. Further, we describe how resistance-conferring mutations can help with compound design, and the use of saturation mutagenesis to characterize a compound binding site. We highlight how genetic approaches can ensure the proper use of chemical inhibitors to pursue mechanistic studies and test therapeutic hypotheses.
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Affiliation(s)
- Natalie H Jones
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.
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10
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Lai Y, Zhang Y, Zhou S, Xu J, Du Z, Feng Z, Yu L, Zhao Z, Wang W, Tang Y, Yang X, Guddat LW, Liu F, Gao Y, Rao Z, Gong H. Structure of the human ATP synthase. Mol Cell 2023:S1097-2765(23)00324-6. [PMID: 37244256 DOI: 10.1016/j.molcel.2023.04.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/06/2023] [Accepted: 04/28/2023] [Indexed: 05/29/2023]
Abstract
Biological energy currency ATP is produced by F1Fo-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main rotational states and one substate of human ATP synthase using cryoelectron microscopy. These structures reveal that the release of ADP occurs when the β subunit of F1Fo-ATP synthase is in the open conformation, showing how ADP binding is coordinated during synthesis. The accommodation of the symmetry mismatch between F1 and Fo motors is resolved by the torsional flexing of the entire complex, especially the γ subunit, and the rotational substep of the c subunit. Water molecules are identified in the inlet and outlet half-channels, suggesting that the proton transfer in these two half-channels proceed via a Grotthus mechanism. Clinically relevant mutations are mapped to the structure, showing that they are mainly located at the subunit-subunit interfaces, thus causing instability of the complex.
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Affiliation(s)
- Yuezheng Lai
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yuying Zhang
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shan Zhou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Jinxu Xu
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhanqiang Du
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ziyan Feng
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Long Yu
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ziqing Zhao
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Weiwei Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yanting Tang
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Fengjiang Liu
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China.
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300350, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, China; Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China.
| | - Hongri Gong
- State Key Laboratory of Medicinal Chemical Biology and Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China; Institute for Immunology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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11
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Sung DB, Lee JS. Natural-product-based fluorescent probes: recent advances and applications. RSC Med Chem 2023; 14:412-432. [PMID: 36970151 PMCID: PMC10034199 DOI: 10.1039/d2md00376g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Fluorescent probes are attractive tools for biology, drug discovery, disease diagnosis, and environmental analysis. In bioimaging, these easy-to-operate and inexpensive probes can be used to detect biological substances, obtain detailed cell images, track in vivo biochemical reactions, and monitor disease biomarkers without damaging biological samples. Over the last few decades, natural products have attracted extensive research interest owing to their great potential as recognition units for state-of-the-art fluorescent probes. This review describes representative natural-product-based fluorescent probes and recent discoveries, with a particular focus on fluorescent bioimaging and biochemical studies.
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Affiliation(s)
- Dan-Bi Sung
- Marine Natural Products Chemistry Laboratory, Korea Institute of Ocean Science and Technology Busan Republic of Korea
| | - Jong Seok Lee
- Marine Natural Products Chemistry Laboratory, Korea Institute of Ocean Science and Technology Busan Republic of Korea
- Department of Marine Biotechnology, Korea University of Science and Technology Daejeon Republic of Korea
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12
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Tong X, Zhou F. Integrated bioinformatic analysis of mitochondrial metabolism-related genes in acute myeloid leukemia. Front Immunol 2023; 14:1120670. [PMID: 37138869 PMCID: PMC10149950 DOI: 10.3389/fimmu.2023.1120670] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/30/2023] [Indexed: 05/05/2023] Open
Abstract
Background Acute myeloid leukemia (AML) is a common hematologic malignancy characterized by poor prognoses and high recurrence rates. Mitochondrial metabolism has been increasingly recognized to be crucial in tumor progression and treatment resistance. The purpose of this study was to examined the role of mitochondrial metabolism in the immune regulation and prognosis of AML. Methods In this study, mutation status of 31 mitochondrial metabolism-related genes (MMRGs) in AML were analyzed. Based on the expression of 31 MMRGs, mitochondrial metabolism scores (MMs) were calculated by single sample gene set enrichment analysis. Differential analysis and weighted co-expression network analysis were performed to identify module MMRGs. Next, univariate Cox regression and the least absolute and selection operator regression were used to select prognosis-associated MMRGs. A prognosis model was then constructed using multivariate Cox regression to calculate risk score. We validated the expression of key MMRGs in clinical specimens using immunohistochemistry (IHC). Then differential analysis was performed to identify differentially expressed genes (DEGs) between high- and low-risk groups. Functional enrichment, interaction networks, drug sensitivity, immune microenvironment, and immunotherapy analyses were also performed to explore the characteristic of DEGs. Results Given the association of MMs with prognosis of AML patients, a prognosis model was constructed based on 5 MMRGs, which could accurately distinguish high-risk patients from low-risk patients in both training and validation datasets. IHC results showed that MMRGs were highly expressed in AML samples compared to normal samples. Additionally, the 38 DEGs were mainly related to mitochondrial metabolism, immune signaling, and multiple drug resistance pathways. In addition, high-risk patients with more immune-cell infiltration had higher Tumor Immune Dysfunction and Exclusion scores, indicating poor immunotherapy response. mRNA-drug interactions and drug sensitivity analyses were performed to explore potential druggable hub genes. Furthermore, we combined risk score with age and gender to construct a prognosis model, which could predict the prognosis of AML patients. Conclusion Our study provided a prognostic predictor for AML patients and revealed that mitochondrial metabolism is associated with immune regulation and drug resistant in AML, providing vital clues for immunotherapies.
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13
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West AV, Woo CM. Photoaffinity Labeling Chemistries Used to Map Biomolecular Interactions. Isr J Chem 2022. [DOI: 10.1002/ijch.202200081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Alexander V. West
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford St Cambridge MA USA
| | - Christina M. Woo
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford St Cambridge MA USA
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14
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West AV, Amako Y, Woo CM. Design and Evaluation of a Cyclobutane Diazirine Alkyne Tag for Photoaffinity Labeling in Cells. J Am Chem Soc 2022; 144:21174-21183. [DOI: 10.1021/jacs.2c08257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alexander V. West
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yuka Amako
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M. Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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15
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Cofas-Vargas LF, Mendoza-Espinosa P, Avila-Barrientos LP, Prada-Gracia D, Riveros-Rosas H, García-Hernández E. Exploring the druggability of the binding site of aurovertin, an exogenous allosteric inhibitor of FOF1-ATP synthase. Front Pharmacol 2022; 13:1012008. [PMID: 36313289 PMCID: PMC9615146 DOI: 10.3389/fphar.2022.1012008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
In addition to playing a central role in the mitochondria as the main producer of ATP, FOF1-ATP synthase performs diverse key regulatory functions in the cell membrane. Its malfunction has been linked to a growing number of human diseases, including hypertension, atherosclerosis, cancer, and some neurodegenerative, autoimmune, and aging diseases. Furthermore, inhibition of this enzyme jeopardizes the survival of several bacterial pathogens of public health concern. Therefore, FOF1-ATP synthase has emerged as a novel drug target both to treat human diseases and to combat antibiotic resistance. In this work, we carried out a computational characterization of the binding sites of the fungal antibiotic aurovertin in the bovine F1 subcomplex, which shares a large identity with the human enzyme. Molecular dynamics simulations showed that although the binding sites can be described as preformed, the inhibitor hinders inter-subunit communications and exerts long-range effects on the dynamics of the catalytic site residues. End-point binding free energy calculations revealed hot spot residues for aurovertin recognition. These residues were also relevant to stabilize solvent sites determined from mixed-solvent molecular dynamics, which mimic the interaction between aurovertin and the enzyme, and could be used as pharmacophore constraints in virtual screening campaigns. To explore the possibility of finding species-specific inhibitors targeting the aurovertin binding site, we performed free energy calculations for two bacterial enzymes with experimentally solved 3D structures. Finally, an analysis of bacterial sequences was carried out to determine conservation of the aurovertin binding site. Taken together, our results constitute a first step in paving the way for structure-based development of new allosteric drugs targeting FOF1-ATP synthase sites of exogenous inhibitors.
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Affiliation(s)
- Luis Fernando Cofas-Vargas
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Mexico City, Mexico
| | - Paola Mendoza-Espinosa
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Mexico City, Mexico
- Tecnologico de Monterrey, The Institute for Obesity Research, Monterrey, Mexico
| | | | - Diego Prada-Gracia
- Unidad de Investigación en Biología Computacional y Diseño de Fármacos, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Héctor Riveros-Rosas
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Cd. Universitaria, Mexico City, Mexico
| | - Enrique García-Hernández
- Universidad Nacional Autónoma de México, Instituto de Química, Ciudad Universitaria, Mexico City, Mexico
- *Correspondence: Enrique García-Hernández,
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16
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Yang W, Frickenstein AN, Sheth V, Holden A, Mettenbrink EM, Wang L, Woodward AA, Joo BS, Butterfield SK, Donahue ND, Green DE, Thomas AG, Harcourt T, Young H, Tang M, Malik ZA, Harrison RG, Mukherjee P, DeAngelis PL, Wilhelm S. Controlling Nanoparticle Uptake in Innate Immune Cells with Heparosan Polysaccharides. NANO LETTERS 2022; 22:7119-7128. [PMID: 36048773 PMCID: PMC9486251 DOI: 10.1021/acs.nanolett.2c02226] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We used heparosan (HEP) polysaccharides for controlling nanoparticle delivery to innate immune cells. Our results show that HEP-coated nanoparticles were endocytosed in a time-dependent manner by innate immune cells via both clathrin-mediated and macropinocytosis pathways. Upon endocytosis, we observed HEP-coated nanoparticles in intracellular vesicles and the cytoplasm, demonstrating the potential for nanoparticle escape from intracellular vesicles. Competition with other glycosaminoglycan types inhibited the endocytosis of HEP-coated nanoparticles only partially. We further found that nanoparticle uptake into innate immune cells can be controlled by more than 3 orders of magnitude via systematically varying the HEP surface density. Our results suggest a substantial potential for HEP-coated nanoparticles to target innate immune cells for efficient intracellular delivery, including into the cytoplasm. This HEP nanoparticle surface engineering technology may be broadly used to develop efficient nanoscale devices for drug and gene delivery as well as possibly for gene editing and immuno-engineering applications.
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Affiliation(s)
- Wen Yang
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Alex N. Frickenstein
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Vinit Sheth
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Alyssa Holden
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Evan M. Mettenbrink
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Lin Wang
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Alexis A. Woodward
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Bryan S. Joo
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Sarah K. Butterfield
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Nathan D. Donahue
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Dixy E. Green
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
| | - Abigail G. Thomas
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Tekena Harcourt
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Hamilton Young
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Mulan Tang
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Zain A. Malik
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Roger G. Harrison
- School of Chemical, Biological and Materials Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Priyabrata Mukherjee
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
| | - Paul L. DeAngelis
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
| | - Stefan Wilhelm
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
- Institute for Biomedical Engineering, Science, and Technology (IBEST), University of Oklahoma, Norman, Oklahoma, 73019, USA
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Mattos DR, Wan X, Serrill JD, Nguyen MH, Humphreys IR, Viollet B, Smith AB, McPhail KL, Ishmael JE. The Marine-Derived Macrolactone Mandelalide A Is an Indirect Activator of AMPK. Mar Drugs 2022; 20:md20070418. [PMID: 35877711 PMCID: PMC9320534 DOI: 10.3390/md20070418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 02/06/2023] Open
Abstract
The mandelalides are complex macrolactone natural products with distinct macrocycle motifs and a bioactivity profile that is heavily influenced by compound glycosylation. Mandelalides A and B are direct inhibitors of mitochondrial ATP synthase (complex V) and therefore more toxic to mammalian cells with an oxidative metabolic phenotype. To provide further insight into the pharmacology of the mandelalides, we studied the AMP-activated protein kinase (AMPK) energy stress pathway and report that mandelalide A is an indirect activator of AMPK. Wild-type mouse embryonic fibroblasts (MEFs) and representative human non-small cell lung cancer (NSCLC) cells showed statistically significant increases in phospho-AMPK (Thr172) and phospho-ACC (Ser79) in response to mandelalide A. Mandelalide L, which also harbors an A-type macrocycle, induced similar increases in phospho-AMPK (Thr172) and phospho-ACC (Ser79) in U87-MG glioblastoma cells. In contrast, MEFs co-treated with an AMPK inhibitor (dorsomorphin), AMPKα-null MEFs, or NSCLC cells lacking liver kinase B1 (LKB1) lacked this activity. Mandelalide A was significantly more cytotoxic to AMPKα-null MEFs than wild-type cells, suggesting that AMPK activation serves as a protective response to mandelalide-induced depletion of cellular ATP. However, LKB1 status alone was not predictive of the antiproliferative effects of mandelalide A against NSCLC cells. When EGFR status was considered, erlotinib and mandelalide A showed strong cytotoxic synergy in combination against erlotinib-resistant 11-18 NSCLC cells but not against erlotinib-sensitive PC-9 cells. Finally, prolonged exposures rendered mandelalide A, a potent and efficacious cytotoxin, against a panel of human glioblastoma cell types regardless of the underlying metabolic phenotype of the cell. These results add biological relevance to the mandelalide series and provide the basis for their further pre-clinical evaluation as ATP synthase inhibitors and secondary activators of AMPK.
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Affiliation(s)
- Daphne R. Mattos
- Department of Pharmaceutical Sciences, College of Pharmacy, Corvallis, OR 97331, USA; (D.R.M.); (X.W.); (J.D.S.); (I.R.H.); (K.L.M.)
| | - Xuemei Wan
- Department of Pharmaceutical Sciences, College of Pharmacy, Corvallis, OR 97331, USA; (D.R.M.); (X.W.); (J.D.S.); (I.R.H.); (K.L.M.)
| | - Jeffrey D. Serrill
- Department of Pharmaceutical Sciences, College of Pharmacy, Corvallis, OR 97331, USA; (D.R.M.); (X.W.); (J.D.S.); (I.R.H.); (K.L.M.)
| | - Minh H. Nguyen
- Department of Chemistry, Laboratory for Research on the Structure of Matter, and Monell Chemical Senses Center, University of Pennsylvania, Philadelphia, PA 19104, USA; (M.H.N.); (A.B.S.III)
| | - Ian R. Humphreys
- Department of Pharmaceutical Sciences, College of Pharmacy, Corvallis, OR 97331, USA; (D.R.M.); (X.W.); (J.D.S.); (I.R.H.); (K.L.M.)
| | - Benoit Viollet
- CNRS, INSERM, Institut Cochin, Université Paris Cité, F-75014 Paris, France;
| | - Amos B. Smith
- Department of Chemistry, Laboratory for Research on the Structure of Matter, and Monell Chemical Senses Center, University of Pennsylvania, Philadelphia, PA 19104, USA; (M.H.N.); (A.B.S.III)
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Corvallis, OR 97331, USA; (D.R.M.); (X.W.); (J.D.S.); (I.R.H.); (K.L.M.)
| | - Jane E. Ishmael
- Department of Pharmaceutical Sciences, College of Pharmacy, Corvallis, OR 97331, USA; (D.R.M.); (X.W.); (J.D.S.); (I.R.H.); (K.L.M.)
- Correspondence:
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18
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Courbon GM, Rubinstein JL. CryoEM Reveals the Complexity and Diversity of ATP Synthases. Front Microbiol 2022; 13:864006. [PMID: 35783400 PMCID: PMC9244403 DOI: 10.3389/fmicb.2022.864006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/30/2022] [Indexed: 11/14/2022] Open
Abstract
During respiration, adenosine triphosphate (ATP) synthases harness the electrochemical proton motive force (PMF) generated by the electron transport chain (ETC) to synthesize ATP. These macromolecular machines operate by a remarkable rotary catalytic mechanism that couples transmembrane proton translocation to rotation of a rotor subcomplex, and rotation to ATP synthesis. Initially, x-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cross-linking were the only ways to gain insights into the three-dimensional (3D) structures of ATP synthases and, in particular, provided ground-breaking insights into the soluble parts of the complex that explained the catalytic mechanism by which rotation is coupled to ATP synthesis. In contrast, early electron microscopy was limited to studying the overall shape of the assembly. However, advances in electron cryomicroscopy (cryoEM) have allowed determination of high-resolution structures, including the membrane regions of ATP synthases. These studies revealed the high-resolution structures of the remaining ATP synthase subunits and showed how these subunits work together in the intact macromolecular machine. CryoEM continues to uncover the diversity of ATP synthase structures across species and has begun to show how ATP synthases can be targeted by therapies to treat human diseases.
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Affiliation(s)
- Gautier M. Courbon
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON, Canada
| | - John L. Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON, Canada
- *Correspondence: John L. Rubinstein
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Computational Design of Inhibitors Targeting the Catalytic β Subunit of Escherichia coli FOF1-ATP Synthase. Antibiotics (Basel) 2022; 11:antibiotics11050557. [PMID: 35625201 PMCID: PMC9138118 DOI: 10.3390/antibiotics11050557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 01/27/2023] Open
Abstract
With the uncontrolled growth of multidrug-resistant bacteria, there is an urgent need to search for new therapeutic targets, to develop drugs with novel modes of bactericidal action. FoF1-ATP synthase plays a crucial role in bacterial bioenergetic processes, and it has emerged as an attractive antimicrobial target, validated by the pharmaceutical approval of an inhibitor to treat multidrug-resistant tuberculosis. In this work, we aimed to design, through two types of in silico strategies, new allosteric inhibitors of the ATP synthase, by targeting the catalytic β subunit, a centerpiece in communication between rotor subunits and catalytic sites, to drive the rotary mechanism. As a model system, we used the F1 sector of Escherichia coli, a bacterium included in the priority list of multidrug-resistant pathogens. Drug-like molecules and an IF1-derived peptide, designed through molecular dynamics simulations and sequence mining approaches, respectively, exhibited in vitro micromolar inhibitor potency against F1. An analysis of bacterial and Mammalia sequences of the key structural helix-turn-turn motif of the C-terminal domain of the β subunit revealed highly and moderately conserved positions that could be exploited for the development of new species-specific allosteric inhibitors. To our knowledge, these inhibitors are the first binders computationally designed against the catalytic subunit of FOF1-ATP synthase.
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Affiliation(s)
- Patrick M M Shelton
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.
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