1
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Adolf F, Du J, Goodall EA, Walsh RM, Rawson S, von Gronau S, Harper JW, Hanna J, Schulman BA. Visualizing chaperone-mediated multistep assembly of the human 20S proteasome. Nat Struct Mol Biol 2024; 31:1176-1188. [PMID: 38600324 PMCID: PMC11327110 DOI: 10.1038/s41594-024-01268-9] [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: 11/05/2023] [Accepted: 03/06/2024] [Indexed: 04/12/2024]
Abstract
Dedicated assembly factors orchestrate the stepwise production of many molecular machines, including the 28-subunit proteasome core particle (CP) that mediates protein degradation. Here we report cryo-electron microscopy reconstructions of seven recombinant human subcomplexes that visualize all five chaperones and the three active site propeptides across a wide swath of the assembly pathway. Comparison of these chaperone-bound intermediates and a matching mature CP reveals molecular mechanisms determining the order of successive subunit additions, as well as how proteasome subcomplexes and assembly factors structurally adapt upon progressive subunit incorporation to stabilize intermediates, facilitate the formation of subsequent intermediates and ultimately rearrange to coordinate proteolytic activation with gated access to active sites. This work establishes a methodologic approach for structural analysis of multiprotein complex assembly intermediates, illuminates specific functions of assembly factors and reveals conceptual principles underlying human proteasome biogenesis, thus providing an explanation for many previous biochemical and genetic observations.
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Affiliation(s)
- Frank Adolf
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
| | - Jiale Du
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Ellen A Goodall
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Richard M Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Wade Harper
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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2
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Loy CA, Trader DJ. Primed for Interactions: Investigating the Primed Substrate Channel of the Proteasome for Improved Molecular Engagement. Molecules 2024; 29:3356. [PMID: 39064934 PMCID: PMC11279888 DOI: 10.3390/molecules29143356] [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: 05/30/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Protein homeostasis is a tightly conserved process that is regulated through the ubiquitin proteasome system (UPS) in a ubiquitin-independent or ubiquitin-dependent manner. Over the past two decades, the proteasome has become an excellent therapeutic target through inhibition of the catalytic core particle, inhibition of subunits responsible for recognizing and binding ubiquitinated proteins, and more recently, through targeted protein degradation using proteolysis targeting chimeras (PROTACs). The majority of the developed inhibitors of the proteasome's core particle rely on gaining selectivity through binding interactions within the unprimed substrate channel. Although this has allowed for selective inhibitors and chemical probes to be generated for the different proteasome isoforms, much remains unknown about the interactions that could be harnessed within the primed substrate channel to increase potency or selectivity. Herein, we discuss small molecules that interact with the primed substrate pocket and how their differences may give rise to altered activity. Taking advantage of additional interactions with the primed substrate pocket of the proteasome could allow for the generation of improved chemical tools for perturbing or monitoring proteasome activity.
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Affiliation(s)
| | - Darci J. Trader
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92617, USA;
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3
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Tatsumi K, Kitahata S, Komatani Y, Katsuyama A, Yakushiji F, Ichikawa S. Modulation of proteasome subunit selectivity of syringolins. Bioorg Med Chem 2024; 106:117733. [PMID: 38704960 DOI: 10.1016/j.bmc.2024.117733] [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: 03/26/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024]
Abstract
Development of selective or dual proteasome subunit inhibitors based on syringolin B as a scaffold is described. We focused our efforts on a structure-activity relationship study of inhibitors with various substituents at the 3-position of the macrolactam moiety of syringolin B analogue to evaluate whether this would be sufficient to confer subunit selectivity by using sets of analogues with hydrophobic, basic and acidic substituents, which were designed to target Met45, Glu53 and Arg45 embedded in the S1 subsite, respectively. The structure-activity relationship study using systematic analogues provided insight into the origin of the subunit-selective inhibitory activity. This strategy would be sufficient to confer subunit selectivity regarding β5 and β2 subunits.
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Affiliation(s)
- Kengo Tatsumi
- Faculty of Pharmaceutical Science, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Shun Kitahata
- Faculty of Pharmaceutical Science, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Yuya Komatani
- Faculty of Pharmaceutical Science, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Akira Katsuyama
- Faculty of Pharmaceutical Science, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Fumika Yakushiji
- Faculty of Pharmaceutical Science, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Science, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Center for Research and Education on Drug Discovery, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan; Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
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4
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Adolf F, Du J, Goodall EA, Walsh RM, Rawson S, von Gronau S, Harper JW, Hanna J, Schulman BA. Visualizing chaperone-mediated multistep assembly of the human 20S proteasome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.27.577538. [PMID: 38328185 PMCID: PMC10849659 DOI: 10.1101/2024.01.27.577538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Dedicated assembly factors orchestrate stepwise production of many molecular machines, including the 28-subunit proteasome core particle (CP) that mediates protein degradation. Here, we report cryo-EM reconstructions of seven recombinant human subcomplexes that visualize all five chaperones and the three active site propeptides across a wide swath of the assembly pathway. Comparison of these chaperone-bound intermediates and a matching mature CP reveals molecular mechanisms determining the order of successive subunit additions, and how proteasome subcomplexes and assembly factors structurally adapt upon progressive subunit incorporation to stabilize intermediates, facilitate the formation of subsequent intermediates, and ultimately rearrange to coordinate proteolytic activation with gated access to active sites. The structural findings reported here explain many previous biochemical and genetic observations. This work establishes a methodologic approach for structural analysis of multiprotein complex assembly intermediates, illuminates specific functions of assembly factors, and reveals conceptual principles underlying human proteasome biogenesis.
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Affiliation(s)
- Frank Adolf
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Jiale Du
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Ellen A. Goodall
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Richard M. Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J. Wade Harper
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Brenda A. Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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5
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Fernandes PMP, Guedes RA, Victor BL, Salvador JAR, Guedes RC. Decoding the secrets: how conformational and structural regulators inhibit the human 20S proteasome. Front Chem 2024; 11:1322628. [PMID: 38260042 PMCID: PMC10801056 DOI: 10.3389/fchem.2023.1322628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Acquired resistance to drugs that modulate specific protein functions, such as the human proteasome, presents a significant challenge in targeted therapies. This underscores the importance of devising new methodologies to predict drug binding and potential resistance due to specific protein mutations. In this work, we conducted an extensive computational analysis to ascertain the effects of selected mutations (Ala49Thr, Ala50Val, and Cys52Phe) within the active site of the human proteasome. Specifically, we sought to understand how these mutations might disrupt protein function either by altering protein stability or by impeding interactions with a clinical administered drug. Leveraging molecular dynamics simulations and molecular docking calculations, we assessed the effect of these mutations on protein stability and ligand affinity. Notably, our results indicate that the Cys52Phe mutation critically impacts protein-ligand binding, providing valuable insights into potential proteasome inhibitor resistance.
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Affiliation(s)
- Pedro M. P. Fernandes
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Romina A. Guedes
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Bruno L. Victor
- BioISI─Biosystems & Integrative Sciences Institute, Faculty of Sciences, Universidade de Lisboa, Lisboa, Portugal
| | - Jorge A. R. Salvador
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
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6
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Zhu Y, Shigeyoshi K, Hayakawa Y, Fujiwara S, Kishida M, Ohki H, Horibe T, Shionyu M, Mizukami T, Hasegawa M. Acceleration of Protein Degradation by 20S Proteasome-Binding Peptides Generated by In Vitro Artificial Evolution. Int J Mol Sci 2023; 24:17486. [PMID: 38139315 PMCID: PMC10743564 DOI: 10.3390/ijms242417486] [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: 10/27/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Although the 20S core particle (CP) of the proteasome is an important component of the 26S holoenzyme, the stand-alone 20S CP acts directly on intrinsically disordered and oxidized/damaged proteins to degrade them in a ubiquitin-independent manner. It has been postulated that some structural features of substrate proteins are recognized by the 20S CP to promote substrate uptake, but the mechanism of substrate recognition has not been fully elucidated. In this study, we screened peptides that bind to the 20S CP from a random eight-residue pool of amino acid sequences using complementary DNA display an in vitro molecular evolution technique. The identified 20S CP-binding amino acid sequence was chemically synthesized and its effects on the 20S CP were investigated. The 20S CP-binding peptide stimulated the proteolytic activity of the inactive form of 20S CP. The peptide bound directly to one of the α-subunits, opening a gate for substrate entry on the α-ring. Furthermore, the attachment of this peptide sequence to α-synuclein enhanced its degradation by the 20S CP in vitro. In addition to these results, docking simulations indicated that this peptide binds to the top surface of the α-ring. These peptides could function as a key to control the opening of the α-ring gate.
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Affiliation(s)
- Yunhao Zhu
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
| | - Kaishin Shigeyoshi
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
| | - Yumiko Hayakawa
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
| | - Sae Fujiwara
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
| | - Masamichi Kishida
- Modality Research Laboratories, Biologics Division, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Hitoshi Ohki
- Modality Research Laboratories, Biologics Division, Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Tomohisa Horibe
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
| | - Masafumi Shionyu
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
| | - Tamio Mizukami
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
- Frontier Pharma Inc., 1281-8 Tamura, Nagahama 526-0829, Japan
| | - Makoto Hasegawa
- Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama 526-0829, Japan
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7
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Kaur A, Surnilla A, Zaitouna AJ, Mumphrey MB, Basrur V, Grigorova I, Cieslik M, Carrington M, Nesvizhskii AI, Raghavan M. Mass Spectrometric Profiling of HLA-B44 Peptidomes Provides Evidence for Tapasin-Mediated Tryptophan Editing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1298-1307. [PMID: 37737643 PMCID: PMC10592002 DOI: 10.4049/jimmunol.2300232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/29/2023] [Indexed: 09/23/2023]
Abstract
The extreme polymorphisms of HLA class I proteins result in structural variations in their peptide binding sites to achieve diversity in Ag presentation. External factors could independently constrict or alter HLA class I peptide repertoires. Such effects of the assembly factor tapasin were assessed for HLA-B*44:05 (Y116) and a close variant, HLA-B*44:02 (D116), which have low and high tapasin dependence, respectively, for their cell surface expression. Analyses of the HLA-B*44:05 peptidomes in the presence and absence of tapasin reveal that peptides with C-terminal tryptophans and higher predicted affinities are preferentially selected by tapasin, coincident with reduced frequencies of peptides with other C-terminal amino acids, including leucine. Comparisons of the HLA-B*44:05 and HLA-B*44:02 peptidomes indicate the expected structure-based alterations near the peptide C termini, but also C-terminal amino acid frequency and predicted affinity changes among the unique and shared peptide groups for B*44:02 and B*44:05. Overall, these findings indicate that the presence of tapasin and the tapasin dependence of assembly alter HLA class I peptide-binding preferences at the peptide C terminus. The particular C-terminal amino acid preferences that are altered by tapasin are expected to be determined by the intrinsic peptide-binding specificities of HLA class I allotypes. Additionally, the findings suggest that tapasin deficiency and reduced tapasin dependence expand the permissive affinities of HLA class I-bound peptides, consistent with prior findings that HLA class I allotypes with low tapasin dependence have increased breadth of CD8+ T cell epitope presentation and are more protective in HIV infections.
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Affiliation(s)
- Amanpreet Kaur
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Avrokin Surnilla
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anita J. Zaitouna
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael B. Mumphrey
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Irina Grigorova
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Alexey I. Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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8
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Guedes RA, Grilo JH, Carvalho AN, Fernandes PMP, Ressurreição AS, Brito V, Santos AO, Silvestre S, Gallerani E, Gama MJ, Gavioli R, Salvador JAR, Guedes RC. New Scaffolds of Proteasome Inhibitors: Boosting Anticancer Potential by Exploiting the Synergy of In Silico and In Vitro Methodologies. Pharmaceuticals (Basel) 2023; 16:1096. [PMID: 37631011 PMCID: PMC10458307 DOI: 10.3390/ph16081096] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Cancer is a complex multifactorial disease whose pathophysiology involves multiple metabolic pathways, including the ubiquitin-proteasome system, for which several proteasome inhibitors have already been approved for clinical use. However, the resistance to existing therapies and the occurrence of severe adverse effects is still a concern. The purpose of this study was the discovery of novel scaffolds of proteasome inhibitors with anticancer activity, aiming to overcome the limitations of the existing proteasome inhibitors. Thus, a structure-based virtual screening protocol was developed using the structure of the human 20S proteasome, and 246 compounds from virtual databases were selected for in vitro evaluation, namely proteasome inhibition assays and cell viability assays. Compound 4 (JHG58) was shortlisted as the best hit compound based on its potential in terms of proteasome inhibitory activity and its ability to induce cell death (both with IC50 values in the low micromolar range). Molecular docking studies revealed that compound 4 interacts with key residues, namely with the catalytic Thr1, Ala20, Thr21, Lys33, and Asp125 at the chymotrypsin-like catalytic active site. The hit compound is a good candidate for additional optimization through a hit-to-lead campaign.
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Affiliation(s)
- Romina A. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Jorge H. Grilo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Andreia N. Carvalho
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Pedro M. P. Fernandes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Ana S. Ressurreição
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Vanessa Brito
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal; (V.B.); (A.O.S.); (S.S.)
| | - Adriana O. Santos
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal; (V.B.); (A.O.S.); (S.S.)
| | - Samuel Silvestre
- Health Sciences Research Centre (CICS-UBI), University of Beira Interior, 6200-506 Covilhã, Portugal; (V.B.); (A.O.S.); (S.S.)
| | - Eleonora Gallerani
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Maria João Gama
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
| | - Riccardo Gavioli
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Jorge A. R. Salvador
- Center for Innovative Biomedicine and Biotechnology (CIBB), Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, 1649-003 Lisboa, Portugal or (R.A.G.); (J.H.G.); (A.N.C.); (P.M.P.F.); (A.S.R.); (M.J.G.)
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9
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Ielo L, Patamia V, Citarella A, Schirmeister T, Stagno C, Rescifina A, Micale N, Pace V. Selective noncovalent proteasome inhibiting activity of trifluoromethyl-containing gem-quaternary aziridines. Arch Pharm (Weinheim) 2023:e2300174. [PMID: 37119396 DOI: 10.1002/ardp.202300174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/01/2023]
Abstract
The ubiquitin-proteasome pathway (UPP) represents the principal proteolytic apparatus in the cytosol and nucleus of all eukaryotic cells. Nowadays, proteasome inhibitors (PIs) are well-known as anticancer agents. However, although three of them have been approved by the US Food and Drug Administration (FDA) for treating multiple myeloma and mantel cell lymphoma, they present several side effects and develop resistance. For these reasons, the development of new PIs with better pharmacological characteristics is needed. Recently, noncovalent inhibitors have gained much attention since they are less toxic as compared with covalent ones, providing an alternative mechanism for solid tumors. Herein, we describe a new class of bis-homologated chloromethyl(trifluoromethyl)aziridines as selective noncovalent PIs. In silico and in vitro studies were conducted to elucidate the mechanism of action of such compounds. Human gastrointestinal absorption (HIA) and blood-brain barrier (BBB) penetration were also considered together with absorption, distribution, metabolism, and excretion (ADMET) predictions.
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Affiliation(s)
- Laura Ielo
- Department of Chemistry, University of Turin, Torino, Italy
| | - Vincenzo Patamia
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | | | - Tanja Schirmeister
- Department of Medicinal Chemistry, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Claudio Stagno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Antonio Rescifina
- Department of Drug and Health Sciences, University of Catania, Catania, Italy
| | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Messina, Italy
| | - Vittorio Pace
- Department of Chemistry, University of Turin, Torino, Italy
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
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10
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A Role for the Proteasome Alpha2 Subunit N-Tail in Substrate Processing. Biomolecules 2023; 13:biom13030480. [PMID: 36979414 PMCID: PMC10046698 DOI: 10.3390/biom13030480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
The proteolytic active sites of the 26S proteasome are sequestered within the catalytic chamber of its 20S core particle (CP). Access to this chamber is through a narrow channel defined by the seven outer α subunits. In the resting state, the N-termini of neighboring α subunits form a gate blocking access to the channel. The attachment of the activators or regulatory particles rearranges the blocking α subunit N-termini facilitating the entry of substrates. By truncating or mutating each of the participating α N-termini, we report that whereas only a few N-termini are important for maintaining the closed gate, all seven N-termini participate in the open gate. Specifically, the open state is stabilized by a hydrogen bond between an invariant tyrosine (Y) in each subunit with a conserved aspartate (D) in its counterclockwise neighbor. The lone exception is the α1–α2 pair leaving a gap in the ring circumference. The third residue (X) of this YD(X) motif aligns with the open channel. Phenylalanine at this position in the α2 subunit comes in direct contact with the translocating substrate. Consequently, deletion of the α2 N-terminal tail attenuates proteolysis despite the appearance of an open gate state. In summary, the interlacing N-terminal YD(X) motifs regulate both the gating and translocation of the substrate.
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11
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Targeting immunoproteasome in neurodegeneration: A glance to the future. Pharmacol Ther 2023; 241:108329. [PMID: 36526014 DOI: 10.1016/j.pharmthera.2022.108329] [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: 10/03/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
The immunoproteasome is a specialized form of proteasome equipped with modified catalytic subunits that was initially discovered to play a pivotal role in MHC class I antigen processing and immune system modulation. However, over the last years, this proteolytic complex has been uncovered to serve additional functions unrelated to antigen presentation. Accordingly, it has been proposed that immunoproteasome synergizes with canonical proteasome in different cell types of the nervous system, regulating neurotransmission, metabolic pathways and adaptation of the cells to redox or inflammatory insults. Hence, studying the alterations of immunoproteasome expression and activity is gaining research interest to define the dynamics of neuroinflammation as well as the early and late molecular events that are likely involved in the pathogenesis of a variety of neurological disorders. Furthermore, these novel functions foster the perspective of immunoproteasome as a potential therapeutic target for neurodegeneration. In this review, we provide a brain and retina-wide overview, trying to correlate present knowledge on structure-function relationships of immunoproteasome with the variety of observed neuro-modulatory functions.
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12
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Structure of the reduced microsporidian proteasome bound by PI31-like peptides in dormant spores. Nat Commun 2022; 13:6962. [PMID: 36379934 PMCID: PMC9666519 DOI: 10.1038/s41467-022-34691-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 11/02/2022] [Indexed: 11/17/2022] Open
Abstract
Proteasomes play an essential role in the life cycle of intracellular pathogens with extracellular stages by ensuring proteostasis in environments with limited resources. In microsporidia, divergent parasites with extraordinarily streamlined genomes, the proteasome complexity and structure are unknown, which limits our understanding of how these unique pathogens adapt and compact essential eukaryotic complexes. We present cryo-electron microscopy structures of the microsporidian 20S and 26S proteasome isolated from dormant or germinated Vairimorpha necatrix spores. The discovery of PI31-like peptides, known to inhibit proteasome activity, bound simultaneously to all six active sites within the central cavity of the dormant spore proteasome, suggests reduced activity in the environmental stage. In contrast, the absence of the PI31-like peptides and the existence of 26S particles post-germination in the presence of ATP indicates that proteasomes are reactivated in nutrient-rich conditions. Structural and phylogenetic analyses reveal that microsporidian proteasomes have undergone extensive reductive evolution, lost at least two regulatory proteins, and compacted nearly every subunit. The highly derived structure of the microsporidian proteasome, and the minimized version of PI31 presented here, reinforce the feasibility of the development of specific inhibitors and provide insight into the unique evolution and biology of these medically and economically important pathogens.
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13
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Novel Class of Proteasome Inhibitors: In Silico and In Vitro Evaluation of Diverse Chloro(trifluoromethyl)aziridines. Int J Mol Sci 2022; 23:ijms232012363. [PMID: 36293216 PMCID: PMC9603864 DOI: 10.3390/ijms232012363] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 01/24/2023] Open
Abstract
The ubiquitin-proteasome pathway (UPP) is the major proteolytic system in the cytosol and nucleus of all eukaryotic cells. The role of proteasome inhibitors (PIs) as critical agents for regulating cancer cell death has been established. Aziridine derivatives are well-known alkylating agents employed against cancer. However, to the best of our knowledge, aziridine derivatives showing inhibitory activity towards proteasome have never been described before. Herein we report a new class of selective and nonPIs bearing an aziridine ring as a core structure. In vitro cell-based assays (two leukemia cell lines) also displayed anti-proliferative activity for some compounds. In silico studies indicated non-covalent binding mode and drug-likeness for these derivatives. Taken together, these results are promising for developing more potent PIs.
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14
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T-Type Calcium Channels: A Mixed Blessing. Int J Mol Sci 2022; 23:ijms23179894. [PMID: 36077291 PMCID: PMC9456242 DOI: 10.3390/ijms23179894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
The role of T-type calcium channels is well established in excitable cells, where they preside over action potential generation, automaticity, and firing. They also contribute to intracellular calcium signaling, cell cycle progression, and cell fate; and, in this sense, they emerge as key regulators also in non-excitable cells. In particular, their expression may be considered a prognostic factor in cancer. Almost all cancer cells express T-type calcium channels to the point that it has been considered a pharmacological target; but, as the drugs used to reduce their expression are not completely selective, several complications develop, especially within the heart. T-type calcium channels are also involved in a specific side effect of several anticancer agents, that act on microtubule transport, increase the expression of the channel, and, thus, the excitability of sensory neurons, and make the patient more sensitive to pain. This review puts into context the relevance of T-type calcium channels in cancer and in chemotherapy side effects, considering also the cardiotoxicity induced by new classes of antineoplastic molecules.
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15
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Fernando LM, Quesada-Candela C, Murray M, Ugoaru C, Yanowitz JL, Allen AK. Proteasomal subunit depletions differentially affect germline integrity in C. elegans. Front Cell Dev Biol 2022; 10:901320. [PMID: 36060813 PMCID: PMC9428126 DOI: 10.3389/fcell.2022.901320] [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: 03/21/2022] [Accepted: 07/08/2022] [Indexed: 11/25/2022] Open
Abstract
The 26S proteasome is a multi-subunit protein complex that is canonically known for its ability to degrade proteins in cells and maintain protein homeostasis. Non-canonical or non-proteolytic roles of proteasomal subunits exist but remain less well studied. We provide characterization of germline-specific functions of different 19S proteasome regulatory particle (RP) subunits in C. elegans using RNAi specifically from the L4 stage and through generation of endogenously tagged 19S RP lid subunit strains. We show functions for the 19S RP in regulation of proliferation and maintenance of integrity of mitotic zone nuclei, in polymerization of the synaptonemal complex (SC) onto meiotic chromosomes and in the timing of SC subunit redistribution to the short arm of the bivalent, and in turnover of XND-1 proteins at late pachytene. Furthermore, we report that certain 19S RP subunits are required for proper germ line localization of WEE-1.3, a major meiotic kinase. Additionally, endogenous fluorescent labeling revealed that the two isoforms of the essential 19S RP proteasome subunit RPN-6.1 are expressed in a tissue-specific manner in the hermaphrodite. Also, we demonstrate that the 19S RP subunits RPN-6.1 and RPN-7 are crucial for the nuclear localization of the lid subunits RPN-8 and RPN-9 in oocytes, further supporting the ability to utilize the C. elegans germ line as a model to study proteasome assembly real-time. Collectively, our data support the premise that certain 19S RP proteasome subunits are playing tissue-specific roles, especially in the germ line. We propose C. elegans as a versatile multicellular model to study the diverse proteolytic and non-proteolytic roles that proteasome subunits play in vivo.
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Affiliation(s)
| | - Cristina Quesada-Candela
- Magee-Womens Research Institute and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Makaelah Murray
- Department of Biology, Howard University, Washington, DC, United States
| | - Caroline Ugoaru
- Department of Biology, Howard University, Washington, DC, United States
| | - Judith L. Yanowitz
- Magee-Womens Research Institute and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Departments of Developmental Biology, Microbiology, and Molecular Genetics, The Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- *Correspondence: Judith L. Yanowitz, ; Anna K. Allen,
| | - Anna K. Allen
- Department of Biology, Howard University, Washington, DC, United States
- *Correspondence: Judith L. Yanowitz, ; Anna K. Allen,
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16
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Structural insights into the human PA28-20S proteasome enabled by efficient tagging and purification of endogenous proteins. Proc Natl Acad Sci U S A 2022; 119:e2207200119. [PMID: 35858375 PMCID: PMC9388094 DOI: 10.1073/pnas.2207200119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The ability to produce folded and functional proteins is a necessity for structural biology and many other biological sciences. This task is particularly challenging for numerous biomedically important targets in human cells, including membrane proteins and large macromolecular assemblies, hampering mechanistic studies and drug development efforts. Here we describe a method combining CRISPR-Cas gene editing and fluorescence-activated cell sorting to rapidly tag and purify endogenous proteins in HEK cells for structural characterization. We applied this approach to study the human proteasome from HEK cells and rapidly determined cryogenic electron microscopy structures of major proteasomal complexes, including a high-resolution structure of intact human PA28αβ-20S. Our structures reveal that PA28 with a subunit stoichiometry of 3α/4β engages tightly with the 20S proteasome. Addition of a hydrophilic peptide shows that polypeptides entering through PA28 are held in the antechamber of 20S prior to degradation in the proteolytic chamber. This study provides critical insights into an important proteasome complex and demonstrates key methodologies for the tagging of proteins from endogenous sources.
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17
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Thomas TA, Smith DM. Proteasome activator 28γ (PA28γ) allosterically activates trypsin-like proteolysis by binding to the α-ring of the 20S proteasome. J Biol Chem 2022; 298:102140. [PMID: 35714770 PMCID: PMC9287138 DOI: 10.1016/j.jbc.2022.102140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/21/2022] Open
Abstract
Proteasome activator 28γ (PA28γ/REGγ) is a member of the 11S family of proteasomal regulators that is constitutively expressed in the nucleus and implicated in various diseases, including certain cancers and systemic lupus erythematosus. Despite years of investigation, how PA28γ functions to stimulate proteasomal protein degradation remains unclear. Alternative hypotheses have been proposed for the molecular mechanism of PA28γ, including the following: (1) substrate selection, (2) allosteric upregulation of the trypsin-like (T-L) site, (3) allosteric inhibition of the chymotrypsin-like (CT-L) and caspase-like (C-L) sites, (4) conversion of the CT-L or C-L sites to new T-L sites, and (5) gate opening alone or in combination with a previous hypothesis. Here, by mechanistically decoupling gating effects from active site effects, we unambiguously demonstrate that WT PA28γ allosterically activates the T-L site. We show PA28γ binding increases the Kcat/Km by 13-fold for T-L peptide substrates while having little-to-no effect on hydrolysis kinetics for CT-L or C-L substrates. Furthermore, mutagenesis and domain swaps of PA28γ reveal that it does not select for T-L peptide substrates through either the substrate entry pore or the distal intrinsically disordered region. We also show that a previously reported point mutation can functionally switch PA28γ from a T-L activating to a gate-opening activator in a mutually exclusive fashion. Finally, using cryogenic electron microscopy, we visualized the PA28γ-proteasome complex at 4.3 Å and confirmed its expected quaternary structure. The results of this study provide unambiguous evidence that PA28γ can function by binding the 20S proteasome to allosterically activate the T-L proteolytic site.
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Affiliation(s)
- Taylor A Thomas
- Department of Biochemistry, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, USA
| | - David M Smith
- Department of Biochemistry, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, USA; Department of Neuroscience, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, USA; WVU Rockefeller Neuroscience Institute, Morgantown, West Virginia, USA; WVU Cancer Institute, Morgantown, West Virginia, USA.
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18
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Ferrari V, Stroobant V, Abi Habib J, Naulaerts S, Van den Eynde BJ, Vigneron N. New Insights into the Mechanisms of Proteasome-Mediated Peptide Splicing Learned from Comparing Splicing Efficiency by Different Proteasome Subtypes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2817-2828. [PMID: 35688464 DOI: 10.4049/jimmunol.2101198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/03/2022] [Indexed: 06/15/2023]
Abstract
By tying peptide fragments originally distant in parental proteins, the proteasome can generate spliced peptides that are recognized by CTL. This occurs by transpeptidation involving a peptide-acyl-enzyme intermediate and another peptide fragment present in the catalytic chamber. Four main subtypes of proteasomes exist: the standard proteasome (SP), the immunoproteasome, and intermediate proteasomes β1-β2-β5i (single intermediate proteasome) and β1i-β2-β5i (double intermediate proteasome). In this study, we use a tandem mass tag-quantification approach to study the production of six spliced human antigenic peptides by the four proteasome subtypes. Peptides fibroblast growth factor-5172-176/217-220, tyrosinase368-373/336-340, and gp10040-42/47-52 are better produced by the SP than the other proteasome subtypes. The peptides SP110296-301/286-289, gp100195-202/191or192, and gp10047-52/40-42 are better produced by the immunoproteasome and double intermediate proteasome. The current model of proteasome-catalyzed peptide splicing suggests that the production of a spliced peptide depends on the abundance of the peptide splicing partners. Surprisingly, we found that despite the fact that reciprocal peptides RTK_QLYPEW (gp10040-42/47-52) and QLYPEW_RTK (gp10047-52/40-42) are composed of identical splicing partners, their production varies differently according to the proteasome subtype. These differences were maintained after in vitro digestions involving identical amounts of the splicing fragments. Our results indicate that the amount of splicing partner is not the only factor driving peptide splicing and suggest that peptide splicing efficiency also relies on other factors, such as the affinity of the C-terminal splice reactant for the primed binding site of the catalytic subunit.
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Affiliation(s)
- Violette Ferrari
- Ludwig Institute for Cancer Research, Brussels, Belgium
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Lifesciences and Biotechnology, Brussels, Belgium; and
| | - Vincent Stroobant
- Ludwig Institute for Cancer Research, Brussels, Belgium
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Lifesciences and Biotechnology, Brussels, Belgium; and
| | - Joanna Abi Habib
- Ludwig Institute for Cancer Research, Brussels, Belgium
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Lifesciences and Biotechnology, Brussels, Belgium; and
| | - Stefan Naulaerts
- Ludwig Institute for Cancer Research, Brussels, Belgium
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Lifesciences and Biotechnology, Brussels, Belgium; and
| | - Benoit J Van den Eynde
- Ludwig Institute for Cancer Research, Brussels, Belgium;
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Lifesciences and Biotechnology, Brussels, Belgium; and
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Nathalie Vigneron
- Ludwig Institute for Cancer Research, Brussels, Belgium;
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
- Walloon Excellence in Lifesciences and Biotechnology, Brussels, Belgium; and
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19
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Sellin M, Berg S, Hagen P, Zhang J. The molecular mechanism and challenge of targeting XPO1 in treatment of relapsed and refractory myeloma. Transl Oncol 2022; 22:101448. [PMID: 35660848 PMCID: PMC9166471 DOI: 10.1016/j.tranon.2022.101448] [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: 11/22/2021] [Revised: 04/14/2022] [Accepted: 05/06/2022] [Indexed: 11/29/2022] Open
Abstract
Significant progress has been made on the treatment of MM during past two decades. Acquired drug-resistance continues to drive early relapse in primary refractory MM. XPO1 over-expression and cargo mislocalization are associated with drug-resistance. XPO1 inhibitor selinexor restores drug sensitivity to subsets of RR-MM cells.
Multiple myeloma (MM) treatment regimens have vastly improved since the introduction of immunomodulators, proteasome inhibitors, and anti-CD38 monoclonal antibodies; however, MM is considered an incurable disease due to inevitable relapse and acquired drug resistance. Understanding the molecular mechanism by which drug resistance is acquired will help create novel strategies to prevent relapse and help develop novel therapeutics to treat relapsed/refractory (RR)-MM patients. Currently, only homozygous deletion/mutation of TP53 gene due to “double-hits” on Chromosome 17p region is consistently associated with a poor prognosis. The exciting discovery of XPO1 overexpression and mislocalization of its cargos in the RR-MM cells has led to a novel treatment options. Clinical studies have demonstrated that the XPO1 inhibitor selinexor can restore sensitivity of RR-MM to PIs and dexamethasone. We will elaborate on the problems of MM treatment strategies and discuss the mechanism and challenges of using XPO1 inhibitors in RR-MM therapies while deliberating potential solutions.
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Affiliation(s)
- Mark Sellin
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Loyola University Chicago, USA
| | - Stephanie Berg
- Loyola University Chicago, Department of Cancer Biology and Internal Medicine, Cardinal Bernardin Cancer Center, Stritch School of Medicine, Maywood, IL, USA.
| | - Patrick Hagen
- Department of Medicine, Division of Hematology/Oncology, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, USA
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20
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Linhorst A, Lübke T. The Human Ntn-Hydrolase Superfamily: Structure, Functions and Perspectives. Cells 2022; 11:cells11101592. [PMID: 35626629 PMCID: PMC9140057 DOI: 10.3390/cells11101592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 01/27/2023] Open
Abstract
N-terminal nucleophile (Ntn)-hydrolases catalyze the cleavage of amide bonds in a variety of macromolecules, including the peptide bond in proteins, the amide bond in N-linked protein glycosylation, and the amide bond linking a fatty acid to sphingosine in complex sphingolipids. Ntn-hydrolases are all sharing two common hallmarks: Firstly, the enzymes are synthesized as inactive precursors that undergo auto-proteolytic self-activation, which, as a consequence, reveals the active site nucleophile at the newly formed N-terminus. Secondly, all Ntn-hydrolases share a structural consistent αββα-fold, notwithstanding the total lack of amino acid sequence homology. In humans, five subclasses of the Ntn-superfamily have been identified so far, comprising relevant members such as the catalytic active subunits of the proteasome or a number of lysosomal hydrolases, which are often associated with lysosomal storage diseases. This review gives an updated overview on the structural, functional, and (patho-)physiological characteristics of human Ntn-hydrolases, in particular.
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21
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van der Wal L, Bezstarosti K, Demmers JAA. A ubiquitinome analysis to study the functional roles of the proteasome associated deubiquitinating enzymes USP14 and UCH37. J Proteomics 2022; 262:104592. [PMID: 35489684 DOI: 10.1016/j.jprot.2022.104592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 04/05/2022] [Accepted: 04/17/2022] [Indexed: 12/12/2022]
Abstract
The removal of (poly)ubiquitin chains at the proteasome is a key step in the protein degradation pathway that determines which proteins are degraded and ultimately decides cell fate. Three different deubiquitinating enzymes (DUBs) are associated to the human proteasome, PSMD14 (RPN11), USP14 and UCH37 (UCHL5). However, the functional roles and specificities of these proteasomal DUBs remain elusive. To reveal the specificities of proteasome associated DUBs, we used SILAC based quantitative ubiquitinomics to study the effects of CRISPR-Cas9 based knockout of each of these DUBs on the dynamic cellular ubiquitinome. We observed distinct effects on the global ubiquitinome upon removal of either USP14 or UCH37, while the simultaneous removal of both DUBs suggested less functional redundancy than previously anticipated. We also investigated whether the small molecule inhibitor b-AP15 has the potential to specifically target USP14 and UCH37 by comparing treatment of wild-type versus USP14/UCH37 double-knockout cells with this drug. Strikingly, broad and severe off-target effects were observed, questioning the alleged specificity of this inhibitor. In conclusion, this work presents novel insights into the function of proteasome associated DUBs and illustrates the power of in-depth ubiquitinomics for screening the activity of DUBs and of DUB modulating compounds. SIGNIFICANCE Introduction: The removal of (poly)ubiquitin chains at the proteasome is a key step in the protein degradation pathway that determines which proteins are degraded and ultimately decides cell fate. Three different deubiquitinating enzymes (DUBs) are associated to the human proteasome, PSMD14/RPN11, USP14 and UCH37/UCHL5. However, the functional roles and specificities of these proteasomal DUBs remains elusive. MATERIALS & METHODS We have applied a SILAC based quantitative ubiquitinomics to study the effects of CRISPR-Cas9 based knockout of each of these DUBs on the dynamic cellular ubiquitinome. Also, we have studied the function of the small molecule inhibitor b-AP15, which has the potential to specifically target USP14 and UCH37. RESULTS We report distinct effects on the ubiquitinome and the ability of the proteasome to clear proteins upon removal of either USP14 or UCH37, while the simultaneous removal of both DUBs suggests less redundancy than previously anticipated. In addition, broad and severe off-target effects were observed for b-AP15, questioning the alleged specificity of this inhibitor. CONCLUSIONS This work presents novel insights into the function of proteasome associated DUBs and illustrates the power of in-depth ubiquitinomics for screening the activity of DUBs and of DUB modulating compounds.
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Affiliation(s)
- Lennart van der Wal
- Proteomics Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, the Netherlands.
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22
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Li YC, Wang Y, Zou W. Exploration on the Mechanism of Ubiquitin Proteasome System in Cerebral Stroke. Front Aging Neurosci 2022; 14:814463. [PMID: 35462700 PMCID: PMC9022456 DOI: 10.3389/fnagi.2022.814463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/14/2022] [Indexed: 12/23/2022] Open
Abstract
Stroke’s secondary damage, such as inflammation, oxidative stress, and mitochondrial dysfunction, are thought to be crucial factors in the disease’s progression. Despite the fact that there are numerous treatments for secondary damage following stroke, such as antiplatelet therapy, anticoagulant therapy, surgery, and so on, the results are disappointing and the side effects are numerous. It is critical to develop novel and effective strategies for improving patient prognosis. The ubiquitin proteasome system (UPS) is the hub for the processing and metabolism of a wide range of functional regulatory proteins in cells. It is critical for the maintenance of cell homeostasis. With the advancement of UPS research in recent years, it has been discovered that UPS is engaged in a variety of physiological and pathological processes in the human body. UPS is expected to play a role in the onset and progression of stroke via multiple targets and pathways. This paper explores the method by which UPS participates in the linked pathogenic process following stroke, in order to give a theoretical foundation for further research into UPS and stroke treatment.
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Affiliation(s)
- Yu-Chao Li
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yan Wang
- School of Traditional Chinese Medicine, Ningxia Medical University, Yinchuan, China
| | - Wei Zou
- Heilongjiang University of Chinese Medicine, Harbin, China
- First Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, China
- *Correspondence: Wei Zou,
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23
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Functional Differences between Proteasome Subtypes. Cells 2022; 11:cells11030421. [PMID: 35159231 PMCID: PMC8834425 DOI: 10.3390/cells11030421] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 12/30/2022] Open
Abstract
Four proteasome subtypes are commonly present in mammalian tissues: standard proteasomes, which contain the standard catalytic subunits β1, β2 and β5; immunoproteasomes containing the immuno-subunits β1i, β2i and β5i; and two intermediate proteasomes, containing a mix of standard and immuno-subunits. Recent studies revealed the expression of two tissue-specific proteasome subtypes in cortical thymic epithelial cells and in testes: thymoproteasomes and spermatoproteasomes. In this review, we describe the mechanisms that enable the ATP- and ubiquitin-dependent as well as the ATP- and ubiquitin-independent degradation of proteins by the proteasome. We focus on understanding the role of the different proteasome subtypes in maintaining protein homeostasis in normal physiological conditions through the ATP- and ubiquitin-dependent degradation of proteins. Additionally, we discuss the role of each proteasome subtype in the ATP- and ubiquitin-independent degradation of disordered proteins. We also discuss the role of the proteasome in the generation of peptides presented by MHC class I molecules and the implication of having different proteasome subtypes for the peptide repertoire presented at the cell surface. Finally, we discuss the role of the immunoproteasome in immune cells and its modulation as a potential therapy for autoimmune diseases.
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24
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Rahdar A, Reza Hajinezhad M, Sargazi S, Barani M, Karimi P, Velasco B, Taboada P, Pandey S, Bameri Z, Zarei S. Pluronic F127/carfilzomib-based nanomicelles as promising nanocarriers: synthesis, characterization, biological, and in silico evaluations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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25
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Tripathi SC, Vedpathak D, Ostrin EJ. The Functional and Mechanistic Roles of Immunoproteasome Subunits in Cancer. Cells 2021; 10:cells10123587. [PMID: 34944095 PMCID: PMC8700164 DOI: 10.3390/cells10123587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022] Open
Abstract
Cell-mediated immunity is driven by antigenic peptide presentation on major histocompatibility complex (MHC) molecules. Specialized proteasome complexes called immunoproteasomes process viral, bacterial, and tumor antigens for presentation on MHC class I molecules, which can induce CD8 T cells to mount effective immune responses. Immunoproteasomes are distinguished by three subunits that alter the catalytic activity of the proteasome and are inducible by inflammatory stimuli such as interferon-γ (IFN-γ). This inducible activity places them in central roles in cancer, autoimmunity, and inflammation. While accelerated proteasomal degradation is an important tumorigenic mechanism deployed by several cancers, there is some ambiguity regarding the role of immunoproteasome induction in neoplastic transformation. Understanding the mechanistic and functional relevance of the immunoproteasome provides essential insights into developing targeted therapies, including overcoming resistance to standard proteasome inhibition and immunomodulation of the tumor microenvironment. In this review, we discuss the roles of the immunoproteasome in different cancers.
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Affiliation(s)
- Satyendra Chandra Tripathi
- Department of Biochemistry, All India Institute of Medical Sciences Nagpur, Nagpur 441108, MH, India;
- Correspondence: (S.C.T.); (E.J.O.)
| | - Disha Vedpathak
- Department of Biochemistry, All India Institute of Medical Sciences Nagpur, Nagpur 441108, MH, India;
| | - Edwin Justin Ostrin
- Department of General Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Correspondence: (S.C.T.); (E.J.O.)
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Gene-Expression Programming-Based Model for Estimating the Compressive Strength of Cement-Fly Ash Stabilized Soil and Parametric Study. INFRASTRUCTURES 2021. [DOI: 10.3390/infrastructures6120181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The study aims to develop a reliable model using gene-expression programming (GEP) technique for estimating the unconfined compressive strength (UCS) of soil stabilization by cement and fly ash. The model considered the effects of several parameters, including the fly ash characteristics such as calcium oxide (CaO) content, CaO/SiO2 ratio, and loss of ignition. The research results show that the proposed model demonstrates superior performance with a high correlation coefficient (R > 0.955) and low errors. Therefore, the model could be confidently applied in practice for a variety of fly ash qualities. Besides, the parametric study was conducted to examine the effect of fly ash characteristics on the strength of soil stabilization. The study indicates that if the fly ash contains a high amount of calcium oxide, the strength of fly ash stabilized soil is significant. In addition, fly ash could be used in combination with cement to increase the strength of the mixture. A fly ash replacement ratio is suggested from 0.19 to 0.35, corresponding to the total binder used from 10% to 30%. The research findings could help engineers in optimizing the fly ash proportion and estimating the UCS of soil stabilization by cement and fly ash.
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Mihalovits LM, Ferenczy GG, Keserű GM. Mechanistic and thermodynamic characterization of oxathiazolones as potent and selective covalent immunoproteasome inhibitors. Comput Struct Biotechnol J 2021; 19:4486-4496. [PMID: 34471494 PMCID: PMC8379283 DOI: 10.1016/j.csbj.2021.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 01/20/2023] Open
Abstract
The ubiquitin–proteasome system is responsible for the degradation of proteins and plays a critical role in key cellular processes. While the constitutive proteasome (cPS) is expressed in all eukaryotic cells, the immunoproteasome (iPS) is primarily induced during disease processes, and its inhibition is beneficial in the treatment of cancer, autoimmune disorders and neurodegenerative diseases. Oxathiazolones were reported to selectively inhibit iPS over cPS, and the inhibitory activity of several oxathiazolones against iPS was experimentally determined. However, the detailed mechanism of the chemical reaction leading to irreversible iPS inhibition and the key selectivity drivers are unknown, and separate characterization of the noncovalent and covalent inhibition steps is not available for several compounds. Here, we investigate the chemical reaction between oxathiazolones and the Thr1 residue of iPS by quantum mechanics/molecular mechanics (QM/MM) simulations to establish a plausible reaction mechanism and to determine the rate-determining step of covalent complex formation. The modelled binding mode and reaction mechanism are in line with the selective inhibition of iPS versus cPS by oxathiazolones. The kinact value of several ligands was estimated by constructing the potential of mean force of the rate-determining step by QM/MM simulations coupled with umbrella sampling. The equilibrium constant Ki of the noncovalent complex formation was evaluated by classical force field-based thermodynamic integration. The calculated Ki and kinact values made it possible to analyse the contribution of the noncovalent and covalent steps to the overall inhibitory activity. Compounds with similar intrinsic reactivities exhibit varying selectivities for iPS versus cPS owing to subtle differences in the binding modes that slightly affect Ki, the noncovalent affinity, and importantly alter kinact, the covalent reactivity of the bound compounds. A detailed understanding of the inhibitory mechanism of oxathiazolones is useful in designing iPS selective inhibitors with improved drug-like properties.
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Affiliation(s)
- Levente M Mihalovits
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest 1117, Hungary
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Bastien J, Menon S, Messa M, Nyfeler B. Molecular targets and approaches to restore autophagy and lysosomal capacity in neurodegenerative disorders. Mol Aspects Med 2021; 82:101018. [PMID: 34489092 DOI: 10.1016/j.mam.2021.101018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 01/18/2023]
Abstract
Autophagy is a catabolic process that promotes cellular fitness by clearing aggregated protein species, pathogens and damaged organelles through lysosomal degradation. The autophagic process is particularly important in the nervous system where post-mitotic neurons rely heavily on protein and organelle quality control in order to maintain cellular health throughout the lifetime of the organism. Alterations of autophagy and lysosomal function are hallmarks of various neurodegenerative disorders. In this review, we conceptualize some of the mechanistic and genetic evidence pointing towards autophagy and lysosomal dysfunction as a causal driver of neurodegeneration. Furthermore, we discuss rate-limiting pathway nodes and potential approaches to restore pathway activity, from autophagy initiation, cargo sequestration to lysosomal capacity.
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Affiliation(s)
- Julie Bastien
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Suchithra Menon
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Mirko Messa
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Beat Nyfeler
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
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Reboud-Ravaux M. [The proteasome - structural aspects and inhibitors: a second life for a validated drug target]. Biol Aujourdhui 2021; 215:1-23. [PMID: 34397372 DOI: 10.1051/jbio/2021005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 02/06/2023]
Abstract
The proteasome is the central component of the adaptable ubiquitin proteasome system (UPS) discovered in the 1980's. It sustains protein homeostasis (proteostasis) under a large variety of physiological and pathological conditions. Its dysregulation has been often associated to various human diseases. Its potential regulation by modulators has emerged as promising avenue to develop treatments of various pathologies. The FDA approval in 2003 of the proteasome inhibitor bortezomib to treat multiple myeloma, then mantle lymphoma in 2006, has considerably increased the clinical interest of proteasome inhibition. Second-generation proteasome inhibitors (carfilzomib and ixazomib) have been approved to overcome bortezomib resistance and improved toxicity profile and route of administration. Selective inhibition of immunoproteasome is a promising approach towards the development of immunomodulatory drugs. The design of these drugs relies greatly on the elucidation of high-resolution structures of the targeted proteasomes. The ATPase-dependent 26S proteasome (2.4 MDa) consists of a 20S proteolytic core and one or two 19S regulatory particles. The 20S core contains three types of catalytic sites. In recent years, due to technical advances especially in atomic cryo-electron microscopy, significant progress has been made in the understanding of 26S proteasome structure and its dynamics. Stepwise conformational changes of the 19S particle induced by ATP hydrolysis lead to substrate translocation, 20S pore opening and processive protein degradation by the 20S proteolytic subunits (2β1, 2β2 and 2β5). A large variety of structurally different inhibitors, both natural products or synthetic compounds targeting immuno- and constitutive proteasomes, has been discovered. The latest advances in this drug discovery are presented. Knowledge about structures, inhibition mechanism and detailed biological regulations of proteasomes can guide strategies for the development of next-generation inhibitors to treat human diseases, especially cancers, immune disorders and pathogen infections. Proteasome activators are also potentially applicable to the reduction of proteotoxic stresses in neurodegeneration and aging.
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Affiliation(s)
- Michèle Reboud-Ravaux
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, 7 quai Saint Bernard, 75252 Paris Cedex 05, France
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A Nut for Every Bolt: Subunit-Selective Inhibitors of the Immunoproteasome and Their Therapeutic Potential. Cells 2021; 10:cells10081929. [PMID: 34440698 PMCID: PMC8394499 DOI: 10.3390/cells10081929] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
At the heart of the ubiquitin-proteasome system, the 20S proteasome core particle (CP) breaks down the majority of intracellular proteins tagged for destruction. Thereby, the CP controls many cellular processes including cell cycle progression and cell signalling. Inhibitors of the CP can suppress these essential biological pathways, resulting in cytotoxicity, an effect that is beneficial for the treatment of certain blood cancer patients. During the last decade, several preclinical studies demonstrated that selective inhibition of the immunoproteasome (iCP), one of several CP variants in mammals, suppresses autoimmune diseases without inducing toxic side effects. These promising findings led to the identification of natural and synthetic iCP inhibitors with distinct chemical structures, varying potency and subunit selectivity. This review presents the most prominent iCP inhibitors with respect to possible scientific and medicinal applications, and discloses recent trends towards pan-immunoproteasome reactive inhibitors that cumulated in phase II clinical trials of the lead compound KZR-616 for chronic inflammations.
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Klein M, Busch M, Friese-Hamim M, Crosignani S, Fuchss T, Musil D, Rohdich F, Sanderson MP, Seenisamy J, Walter-Bausch G, Zanelli U, Hewitt P, Esdar C, Schadt O. Structure-Based Optimization and Discovery of M3258, a Specific Inhibitor of the Immunoproteasome Subunit LMP7 (β5i). J Med Chem 2021; 64:10230-10245. [PMID: 34228444 DOI: 10.1021/acs.jmedchem.1c00604] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteasomes are broadly expressed key components of the ubiquitin-dependent protein degradation pathway containing catalytically active subunits (β1, β2, and β5). LMP7 (β5i) is a subunit of the immunoproteasome, an inducible isoform that is predominantly expressed in hematopoietic cells. Clinically effective pan-proteasome inhibitors for the treatment of multiple myeloma (MM) nonselectively target LMP7 and other subunits of the constitutive proteasome and immunoproteasome with comparable potency, which can limit the therapeutic applicability of these drugs. Here, we describe the discovery and structure-based hit optimization of novel amido boronic acids, which selectively inhibit LMP7 while sparing all other subunits. The exploitation of structural differences between the proteasome subunits culminated in the identification of the highly potent, exquisitely selective, and orally available LMP7 inhibitor 50 (M3258). Based on the strong antitumor activity observed with M3258 in MM models and a favorable preclinical data package, a phase I clinical trial was initiated in relapsed/refractory MM patients.
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Affiliation(s)
- Markus Klein
- Merck KGaA, Frankfurter Str. 250, Darmstadt 64293, Germany
| | - Michael Busch
- Merck KGaA, Frankfurter Str. 250, Darmstadt 64293, Germany
| | | | | | - Thomas Fuchss
- Merck KGaA, Frankfurter Str. 250, Darmstadt 64293, Germany
| | - Djordje Musil
- Merck KGaA, Frankfurter Str. 250, Darmstadt 64293, Germany
| | - Felix Rohdich
- Merck KGaA, Frankfurter Str. 250, Darmstadt 64293, Germany
| | | | | | | | - Ugo Zanelli
- Merck KGaA, Frankfurter Str. 250, Darmstadt 64293, Germany
| | - Philip Hewitt
- Merck KGaA, Frankfurter Str. 250, Darmstadt 64293, Germany
| | | | - Oliver Schadt
- Merck KGaA, Frankfurter Str. 250, Darmstadt 64293, Germany
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Song C, Satoh T, Sekiguchi T, Kato K, Murata K. Structural Fluctuations of the Human Proteasome α7 Homo-Tetradecamer Double Ring Imply the Proteasomal α-Ring Assembly Mechanism. Int J Mol Sci 2021; 22:ijms22094519. [PMID: 33926037 PMCID: PMC8123668 DOI: 10.3390/ijms22094519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/17/2021] [Accepted: 04/23/2021] [Indexed: 11/16/2022] Open
Abstract
The 20S proteasome, which is composed of layered α and β heptameric rings, is the core complex of the eukaryotic proteasome involved in proteolysis. The α7 subunit is a component of the α ring, and it self-assembles into a homo-tetradecamer consisting of two layers of α7 heptameric rings. However, the structure of the α7 double ring in solution has not been fully elucidated. We applied cryo-electron microscopy to delineate the structure of the α7 double ring in solution, revealing a structure different from the previously reported crystallographic model. The D7-symmetrical double ring was stacked with a 15° clockwise twist and a separation of 3 Å between the two rings. Two more conformations, dislocated and fully open, were also identified. Our observations suggest that the α7 double-ring structure fluctuates considerably in solution, allowing for the insertion of homologous α subunits, finally converting to the hetero-heptameric α rings in the 20S proteasome.
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Affiliation(s)
- Chihong Song
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; (C.S.); (T.S.)
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
- School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan;
| | - Taichiro Sekiguchi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; (C.S.); (T.S.)
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan;
- School of Physical Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; (C.S.); (T.S.)
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan;
- School of Physical Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
- Correspondence: (K.K.); (K.M.)
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; (C.S.); (T.S.)
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
- School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi 444-8787, Japan
- Correspondence: (K.K.); (K.M.)
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Uranga J, Hasecke L, Proppe J, Fingerhut J, Mata RA. Theoretical Studies of the Acid-Base Equilibria in a Model Active Site of the Human 20S Proteasome. J Chem Inf Model 2021; 61:1942-1953. [PMID: 33719420 DOI: 10.1021/acs.jcim.0c01459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The 20S proteasome is a macromolecule responsible for the chemical step in the ubiquitin-proteasome system of degrading unnecessary and unused proteins of the cell. It plays a central role both in the rapid growth of cancer cells and in viral infection cycles. Herein, we present a computational study of the acid-base equilibria in an active site of the human proteasome (caspase-like), an aspect which is often neglected despite the crucial role protons play in the catalysis. As example substrates, we take the inhibition by epoxy- and boronic acid-containing warheads. We have combined cluster quantum mechanical calculations, replica exchange molecular dynamics, and Bayesian optimization of nonbonded potential terms in the inhibitors. In relation to the latter, we propose an easily scalable approach for the reevaluation of nonbonded potentials making use of the hybrid quantum mechanics molecular mechanics dynamics information. Our results show that coupled acid-base equilibria need to be considered when modeling the inhibition mechanism. The coupling between a neighboring lysine and the reacting threonine is not affected by the presence of the studied inhibitors.
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Affiliation(s)
- Jon Uranga
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Lukas Hasecke
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Jonny Proppe
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Jan Fingerhut
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
| | - Ricardo A Mata
- Institute of Physical Chemistry, University of Göttingen, Tammannstrasse 6, 37077 Göttingen, Germany
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34
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Erokhov PA, Kulikov AM, Karpova YD, Rodoman GV, Sumedi IR, Goncharov AL, Razbirin DV, Gorelova VS, Sharova NP, Astakhova TM. Proteasomes in Patient Rectal Cancer and Different Intestine Locations: Where Does Proteasome Pool Change? Cancers (Basel) 2021; 13:1108. [PMID: 33807574 PMCID: PMC7961961 DOI: 10.3390/cancers13051108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/01/2021] [Indexed: 01/12/2023] Open
Abstract
A special problem in the surgery of rectal cancer is connected with a need for appropriate removal of intestine parts, along with the tumor, including the fragment close to the sphincter. To determine the length of fragments to remove, it is necessary to reveal areas without changes in molecule functioning, specific for tumor. The purpose of the present study was to investigate functioning the proteasomes, the main actors in protein hydrolysis, in patient rectal adenocarcinoma and different intestine locations. Chymotrypsin-like and caspase-like activities, open to complex influence of different factors, were analyzed in 43-54 samples by Suc-LLVY-AMC- and Z-LLE-AMC-hydrolysis correspondingly. Both activities may be arranged by the decrease in the location row: cancer→adjacent tissue→proximal (8-20 cm from tumor) and distal (2 and 4 cm from tumor) sides. These activities did not differ noticeably in proximal and distal locations. Similar patterns were detected for the activities and expression of immune subunits LMP2 and LMP7 and expression of 19S and PA28αβ activators. The largest changes in tumor were related to proteasome subtype containing LMP2 and PA28αβ that was demonstrated by native electrophoresis. Thus, the results indicate a significance of subtype LMP2-PA28αβ for tumor and absence of changes in proteasome pool in distal fragments of 2-4 cm from tumor.
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Affiliation(s)
- Pavel A. Erokhov
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; (P.A.E.); (A.M.K.); (Y.D.K.); (V.S.G.); (T.M.A.)
| | - Alexey M. Kulikov
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; (P.A.E.); (A.M.K.); (Y.D.K.); (V.S.G.); (T.M.A.)
| | - Yaroslava D. Karpova
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; (P.A.E.); (A.M.K.); (Y.D.K.); (V.S.G.); (T.M.A.)
| | - Grigory V. Rodoman
- Pirogov Russian National Research Medical University of Ministry of Health of Russian Federation, 1 Ostrovityanov Street, 117997 Moscow, Russia; (G.V.R.); (I.R.S.); (A.L.G.); (D.V.R.)
| | - Ilia R. Sumedi
- Pirogov Russian National Research Medical University of Ministry of Health of Russian Federation, 1 Ostrovityanov Street, 117997 Moscow, Russia; (G.V.R.); (I.R.S.); (A.L.G.); (D.V.R.)
| | - Artem L. Goncharov
- Pirogov Russian National Research Medical University of Ministry of Health of Russian Federation, 1 Ostrovityanov Street, 117997 Moscow, Russia; (G.V.R.); (I.R.S.); (A.L.G.); (D.V.R.)
| | - Dmitry V. Razbirin
- Pirogov Russian National Research Medical University of Ministry of Health of Russian Federation, 1 Ostrovityanov Street, 117997 Moscow, Russia; (G.V.R.); (I.R.S.); (A.L.G.); (D.V.R.)
| | - Vera S. Gorelova
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; (P.A.E.); (A.M.K.); (Y.D.K.); (V.S.G.); (T.M.A.)
| | - Natalia P. Sharova
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; (P.A.E.); (A.M.K.); (Y.D.K.); (V.S.G.); (T.M.A.)
| | - Tatiana M. Astakhova
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; (P.A.E.); (A.M.K.); (Y.D.K.); (V.S.G.); (T.M.A.)
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35
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Ware CA, Buhimschi CS, Zhao G, El Helou Y, Buhimschi IA. Amniotic Fluid Proteasome and Immunoproteasome in the Setting of Intra-Amniotic Infection, Inflammation, and Preterm Birth. Reprod Sci 2021; 28:2562-2573. [PMID: 33665784 DOI: 10.1007/s43032-021-00512-7] [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: 11/10/2020] [Accepted: 02/21/2021] [Indexed: 11/30/2022]
Abstract
Preterm birth is an important determinant of neonatal morbidity and mortality and intra-amniotic infection (IAI) and inflammation play a causative role. The constitutive proteasome and immunoproteasome are key players in maintenance of proteostasis and their alteration outside pregnancy has been linked to pathogenesis of numerous inflammatory diseases. Our goal was to evaluate the levels, activities, and potential origin of amniotic fluid (AF) proteasome in women with preterm birth induced by infection and/or inflammation. Total proteasome and immunoproteasome concentrations were measured in AF retrieved by trans-abdominal amniocentesis from 155 pregnant women. Proteasome activities were measured with fluorogenic substrates targeting caspase-like (CAS-L), trypsin-like (TRY-L), or chymotrypsin-like (CHE-L) lytic activities. We found that IAI significantly upregulated AF concentrations of total proteasome and of the immunoproteasome (P<0.001 for both) with no differences based on gestational age. Based on substrate preference and profile of pharmacologic inhibition, we identified the CHE-L activity of the immunoproteasome as the primary lytic activity upregulated in AF of pregnancies complicated by IAI. When compared with matched maternal blood and cord blood, proteasome activity was by far the highest in AF and this was further elevated in IAI. Western blot confirmed β5 (PSMB5) and β5i (PSMB8) subunits of the constitutive proteasome and immunoproteasome are present in AF and IHC staining of fetal membranes pointed to chorio-decidua as a potential source. In conclusion, IAI is associated with increased AF immunoproteasome activity that by analogy with other inflammatory diseases may generate antigenic oligopeptides and may play a role in triggering preterm birth.
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Affiliation(s)
- Courtney A Ware
- Department of Obstetrics and Gynecology, The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Catalin S Buhimschi
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - Guomao Zhao
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, IL, 60612, USA.,Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH, 43215, USA
| | - Yara El Helou
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, IL, 60612, USA
| | - Irina A Buhimschi
- Department of Obstetrics and Gynecology, University of Illinois College of Medicine, Chicago, IL, 60612, USA. .,Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH, 43215, USA.
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Tang M, Xu C, Cao H, Shi Y, Chen J, Chai Y, Li Z. Tomato calmodulin-like protein SlCML37 is a calcium (Ca 2+) sensor that interacts with proteasome maturation factor SlUMP1 and plays a role in tomato fruit chilling stress tolerance. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153373. [PMID: 33652171 DOI: 10.1016/j.jplph.2021.153373] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 05/25/2023]
Abstract
Calmodulin-like proteins (CMLs), as well as their targets, play significant roles in various key developmental and stress responses in the plant. In tomato (Solanum lycopersicum), there are at least 52 CML genes in its genome. However, most of their functions are not well known, especially in response to cold stress. Here, we investigated SlCML37 biochemical and structural characteristics, including a typical α-helical secondary structure and exposing its hydrophobic regions after binding to Ca2+. Then we certificated that SlCML37 protein could physically interact with SlUMP1 by using yeast two-hybrid, bimolecular florescence complementation (BiFC) and GST pull-down assays. Further analysis showed that SlCML37-transgenic tomato fruit conferred significantly improved tolerance to chilling stress. This study indicates a possible role of calmodulin-like protein-mediated proteasome assemble in the regulation of plant cold response.
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Affiliation(s)
- Mingfeng Tang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China; Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China; Institute of Agricultural Quality Standard and Testing Technology, Chongqing Academy of Agricultural Sciences, 401329, Chongqing, China
| | - Chan Xu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China; Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China
| | - Haohao Cao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China; Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China
| | - Yuan Shi
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China; Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China
| | - Jing Chen
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China; Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China
| | - Yong Chai
- Institute of Agricultural Quality Standard and Testing Technology, Chongqing Academy of Agricultural Sciences, 401329, Chongqing, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331, Chongqing, China; Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, 401331, Chongqing, China.
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The Prognostic Value of Whole-Blood PSMB5, CXCR4, POMP, and RPL5 mRNA Expression in Patients with Multiple Myeloma Treated with Bortezomib. Cancers (Basel) 2021; 13:cancers13050951. [PMID: 33668794 PMCID: PMC7956525 DOI: 10.3390/cancers13050951] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/08/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The mRNA expression of nine previously described genes that may affect resistance to multiple myeloma (MM), viz., ABCB1, CXCR4, MAF, MARCKS, POMP, PSMB5, RPL5, TXN, and XBP1, was compared between bortezomib-refractory and bortezomib-sensitive patients. RPL5 was the only gene to be significantly down-regulated in MM patients compared with non-MM individuals, while POMP was significantly up-regulated in the bortezomib-refractory patients. Multivariate analysis found the best independent predictors of progression-free survival to be high PSMB5 and CXCR expression and autologous stem cell transplantation, and that high expression of POMP and RPL5 were associated with shorter survival. Abstract Proteasome inhibitors, like bortezomib, play a key role in the treatment of multiple myeloma (MM); however, most patients eventually relapse and eventually show multiple drug resistance, and the molecular mechanisms of this resistance remain unclear. The aim of our study is to assess the expression of previously described genes that may influence the resistance to bortezomib treatment at the mRNA level (ABCB1, CXCR4, MAF, MARCKS, POMP, PSMB5, RPL5, TXN, and XBP1) and prognosis of MM patients. mRNA expression was determined in 73 MM patients treated with bortezomib-based regimens (30 bortzomib-sensitive and 43 bortezomib-refractory patients) and 11 healthy controls. RPL5 was significantly down-regulated in multiple myeloma patients as compared with healthy controls. Moreover, POMP was significantly up-regulated in MM patients refractory to bortezomib-based treatment. In multivariate analysis, high expression of PSMB5 and CXCR and autologous stem cell transplantation were independent predictors of progression-free survival, and high expression of POMP and RPL5 was associated with shorter overall survival.
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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Cryo-EM of mammalian PA28αβ-iCP immunoproteasome reveals a distinct mechanism of proteasome activation by PA28αβ. Nat Commun 2021; 12:739. [PMID: 33531497 PMCID: PMC7854634 DOI: 10.1038/s41467-021-21028-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
The proteasome activator PA28αβ affects MHC class I antigen presentation by associating with immunoproteasome core particles (iCPs). However, due to the lack of a mammalian PA28αβ-iCP structure, how PA28αβ regulates proteasome remains elusive. Here we present the complete architectures of the mammalian PA28αβ-iCP immunoproteasome and free iCP at near atomic-resolution by cryo-EM, and determine the spatial arrangement between PA28αβ and iCP through XL-MS. Our structures reveal a slight leaning of PA28αβ towards the α3-α4 side of iCP, disturbing the allosteric network of the gatekeeper α2/3/4 subunits, resulting in a partial open iCP gate. We find that the binding and activation mechanism of iCP by PA28αβ is distinct from those of constitutive CP by the homoheptameric TbPA26 or PfPA28. Our study sheds lights on the mechanism of enzymatic activity stimulation of immunoproteasome and suggests that PA28αβ-iCP has experienced profound remodeling during evolution to achieve its current level of function in immune response. The proteasome activator PA28αβ affects MHC class I antigen presentation by associating with immunoproteasome core particles (iCPs). Cryo-EM structures of the mammalian PA28αβ -iCP immunoproteasome and free iCP, combined with cross-linking data, reveal the complex architecture and suggest a distinct immunoproteasome activation mechanism.
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Dwivedi V, Yaniv K, Sharon M. Beyond cells: The extracellular circulating 20S proteasomes. Biochim Biophys Acta Mol Basis Dis 2020; 1867:166041. [PMID: 33338594 DOI: 10.1016/j.bbadis.2020.166041] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 01/08/2023]
Abstract
Accumulating evidence arising from numerous clinical studies indicate that assembled and functional 20S proteasome complexes circulate freely in plasma. Elevated levels of this core proteolytic complex have been found in the plasma of patients suffering from blood, skin and solid cancers, autoimmune disorders, trauma and sepsis. Moreover, in various diseases, there is a positive correlation between circulating 20S proteasome (c20S) levels and treatment efficacy and survival rates, suggesting the involvement of this under-studied c20S complex in pathophysiology. However, many aspects of this system remain enigmatic, as we still do not know the origin, biological role or mechanisms of extracellular transport and regulation of c20S proteasomes. In this review, we provide an overview of the current understanding of the c20S proteasome system and discuss the remaining gaps in knowledge.
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Affiliation(s)
- Vandita Dwivedi
- Departments of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Karina Yaniv
- Departments of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Sharon
- Departments of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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Molecular and cellular dynamics of the 26S proteasome. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140583. [PMID: 33321258 DOI: 10.1016/j.bbapap.2020.140583] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 01/16/2023]
Abstract
In eukaryotic cells, the ubiquitin-proteasome system serves to remove proteins that are either dysfunctional or no longer needed. The 26S proteasome is a 2.5 MDa multisubunit complex comprising the 20S core particle, where degradation is executed, and one or two regulatory particles which prepare substrates for degradation. Whereas the 20S core particles of several species had been studied extensively by X-ray crystallography, the 26S holocomplex structure had remained elusive for a long time. Recent advances in single-particle cryo-electron microscopy have changed the situation and provided atomic resolution models of this intriguing molecular machine and its dynamics. Besides, cryo-electron tomography enables structural studies in situ, providing molecular resolution images of macromolecules inside pristinely preserved cellular environments. This has greatly contributed to our understanding of proteasome dynamics in the context of cells.
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Hubbell GE, Tepe JJ. Natural product scaffolds as inspiration for the design and synthesis of 20S human proteasome inhibitors. RSC Chem Biol 2020; 1:305-332. [PMID: 33791679 PMCID: PMC8009326 DOI: 10.1039/d0cb00111b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/01/2020] [Indexed: 12/13/2022] Open
Abstract
The 20S proteasome is a valuable target for the treatment of a number of diseases including cancer, neurodegenerative disease, and parasitic infection. In an effort to discover novel inhibitors of the 20S proteasome, many reseaarchers have looked to natural products as potential leads for drug discovery. The following review discusses the efforts made in the field to isolate and identify natural products as inhibitors of the proteasome. In addition, we describe some of the modifications made to natural products in order to discover more potent and selective inhibitors for potential disease treatment.
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Affiliation(s)
- Grace E. Hubbell
- Department of Chemistry, Michigan State UniversityEast LansingMI 48823USA
| | - Jetze J. Tepe
- Department of Chemistry, Michigan State UniversityEast LansingMI 48823USA
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Bhattacharya K, Weidenauer L, Luengo TM, Pieters EC, Echeverría PC, Bernasconi L, Wider D, Sadian Y, Koopman MB, Villemin M, Bauer C, Rüdiger SGD, Quadroni M, Picard D. The Hsp70-Hsp90 co-chaperone Hop/Stip1 shifts the proteostatic balance from folding towards degradation. Nat Commun 2020; 11:5975. [PMID: 33239621 PMCID: PMC7688965 DOI: 10.1038/s41467-020-19783-w] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
Hop/Stip1/Sti1 is thought to be essential as a co-chaperone to facilitate substrate transfer between the Hsp70 and Hsp90 molecular chaperones. Despite this proposed key function for protein folding and maturation, it is not essential in a number of eukaryotes and bacteria lack an ortholog. We set out to identify and to characterize its eukaryote-specific function. Human cell lines and the budding yeast with deletions of the Hop/Sti1 gene display reduced proteasome activity due to inefficient capping of the core particle with regulatory particles. Unexpectedly, knock-out cells are more proficient at preventing protein aggregation and at promoting protein refolding. Without the restraint by Hop, a more efficient folding activity of the prokaryote-like Hsp70-Hsp90 complex, which can also be demonstrated in vitro, compensates for the proteasomal defect and ensures the proteostatic equilibrium. Thus, cells may act on the level and/or activity of Hop to shift the proteostatic balance between folding and degradation. Hop, also known as Stip1 or Sti1, facilitates substrate transfer between the Hsp70 and Hsp90 molecular chaperones. Characterization of proteostasis-related pathways in STIP1 knock-out cell lines reveals that in eukaryotes Stip1 modulates the balance between protein folding and degradation.
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Affiliation(s)
- Kaushik Bhattacharya
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland
| | - Lorenz Weidenauer
- Protein Analysis Facility, Center for Integrative Genomics, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Tania Morán Luengo
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands.,Science for Life, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Ellis C Pieters
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands.,Science for Life, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Pablo C Echeverría
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland.,European Association for the Study of the Liver, 1203, Genève, Switzerland
| | - Lilia Bernasconi
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland
| | - Diana Wider
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland
| | - Yashar Sadian
- Bioimaging Center, Université de Genève, Sciences II, 1211, Genève 4, Switzerland
| | - Margreet B Koopman
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands.,Science for Life, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Matthieu Villemin
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland
| | - Christoph Bauer
- Bioimaging Center, Université de Genève, Sciences II, 1211, Genève 4, Switzerland
| | - Stefan G D Rüdiger
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands.,Science for Life, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Manfredo Quadroni
- Protein Analysis Facility, Center for Integrative Genomics, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Didier Picard
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 1211, Genève 4, Switzerland.
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Uysal S, Soyer Z, Saylam M, Tarikogullari AH, Yilmaz S, Kirmizibayrak PB. Design, synthesis and biological evaluation of novel naphthoquinone-4-aminobenzensulfonamide/carboxamide derivatives as proteasome inhibitors. Eur J Med Chem 2020; 209:112890. [PMID: 33039723 DOI: 10.1016/j.ejmech.2020.112890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 10/23/2022]
Abstract
A series of novel 4-aminobenzensulfonamide/carboxamide derivatives bearing naphthoquinone pharmacophore were designed, sythesized and evaluated for their proteasome inhibitory and antiproliferative activities against human breast cancer cell line (MCF-7). The structures of the synthesized compounds were confirmed by spectral and elemental analyses. The proteasome inhibitory activity studies were carried out using cell-based assay. The antiproteasomal activity results revealed that most of the compounds exhibited inhibitory activity with different percentages against the caspase-like (C-L, β1 subunit), trypsin-like (T-L, β2 subunit) and chymotrypsin-like (ChT-L, β5 subunit) activities of proteasome. Among the tested compounds, compound 14 bearing 5-chloro-2-pyridyl ring on the nitrogen atom of sulfonamide group is the most active compound in the series and displayed higher inhibition with IC50 values of 9.90 ± 0.61, 44.83 ± 4.23 and 22.27 ± 0.15 μM against ChT-L, C-L and T-L activities of proteasome compared to the lead compound PI-083 (IC50 = 12.47 ± 0.21, 53.12 ± 2.56 and 26.37 ± 0.5 μM), respectively. The antiproliferative activity was also determined by MTT (3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide) assay in vitro. According to the antiproliferative activity results, all of the compounds exhibited cell growth inhibitory activity in a range of IC50 = 1.72 ± 0.14-20.8 ± 0.5 μM and compounds 13 and 28 were found to be the most active compounds with IC50 values of 1.79 ± 0.21 and 1.72 ± 0.14 μM, respectively. Furthermore, molecular modeling studies were carried out for the compounds 13, 14 and 28 to investigate the ligand-enzyme binding interactions.
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Affiliation(s)
- Sirin Uysal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, İzmir, Turkey
| | - Zeynep Soyer
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, İzmir, Turkey.
| | - Merve Saylam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, İzmir Katip Celebi University, İzmir, Turkey
| | - Ayse H Tarikogullari
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, İzmir, Turkey
| | - Sinem Yilmaz
- Department of Biotechnology, Institute of Science, Ege University, İzmir, Turkey; Department of Bioengineering, Faculty of Engineering, University of Alaaddin Keykubat, Antalya, Turkey
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Tundo GR, Sbardella D, Santoro AM, Coletta A, Oddone F, Grasso G, Milardi D, Lacal PM, Marini S, Purrello R, Graziani G, Coletta M. The proteasome as a druggable target with multiple therapeutic potentialities: Cutting and non-cutting edges. Pharmacol Ther 2020; 213:107579. [PMID: 32442437 PMCID: PMC7236745 DOI: 10.1016/j.pharmthera.2020.107579] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 01/10/2023]
Abstract
Ubiquitin Proteasome System (UPS) is an adaptable and finely tuned system that sustains proteostasis network under a large variety of physiopathological conditions. Its dysregulation is often associated with the onset and progression of human diseases; hence, UPS modulation has emerged as a promising new avenue for the development of treatments of several relevant pathologies, such as cancer and neurodegeneration. The clinical interest in proteasome inhibition has considerably increased after the FDA approval in 2003 of bortezomib for relapsed/refractory multiple myeloma, which is now used in the front-line setting. Thereafter, two other proteasome inhibitors (carfilzomib and ixazomib), designed to overcome resistance to bortezomib, have been approved for treatment-experienced patients, and a variety of novel inhibitors are currently under preclinical and clinical investigation not only for haematological malignancies but also for solid tumours. However, since UPS collapse leads to toxic misfolded proteins accumulation, proteasome is attracting even more interest as a target for the care of neurodegenerative diseases, which are sustained by UPS impairment. Thus, conceptually, proteasome activation represents an innovative and largely unexplored target for drug development. According to a multidisciplinary approach, spanning from chemistry, biochemistry, molecular biology to pharmacology, this review will summarize the most recent available literature regarding different aspects of proteasome biology, focusing on structure, function and regulation of proteasome in physiological and pathological processes, mostly cancer and neurodegenerative diseases, connecting biochemical features and clinical studies of proteasome targeting drugs.
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Affiliation(s)
- G R Tundo
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy.
| | | | - A M Santoro
- CNR, Institute of Crystallography, Catania, Italy
| | - A Coletta
- Department of Chemistry, University of Aarhus, Aarhus, Denmark
| | - F Oddone
- IRCCS-Fondazione Bietti, Rome, Italy
| | - G Grasso
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - D Milardi
- CNR, Institute of Crystallography, Catania, Italy
| | - P M Lacal
- Laboratory of Molecular Oncology, IDI-IRCCS, Rome, Italy
| | - S Marini
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
| | - R Purrello
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - G Graziani
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - M Coletta
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy.
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Allmeroth K, Horn M, Kroef V, Miethe S, Müller RU, Denzel MS. Bortezomib resistance mutations in PSMB5 determine response to second-generation proteasome inhibitors in multiple myeloma. Leukemia 2020; 35:887-892. [PMID: 32690882 PMCID: PMC7932915 DOI: 10.1038/s41375-020-0989-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 01/20/2023]
Affiliation(s)
- Kira Allmeroth
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931, Cologne, Germany
| | - Moritz Horn
- Acus Laboratories GmbH c/o Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931, Cologne, Germany
| | - Virginia Kroef
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931, Cologne, Germany
| | - Stephan Miethe
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931, Cologne, Germany
| | - Roman-Ulrich Müller
- CECAD-Cluster of Excellence, University of Cologne, Joseph-Stelzmann-Str. 26, D-50931, Cologne, Germany.,Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Kerpener Str. 62, D-50937, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, D-50931, Cologne, Germany
| | - Martin S Denzel
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, D-50931, Cologne, Germany. .,CECAD-Cluster of Excellence, University of Cologne, Joseph-Stelzmann-Str. 26, D-50931, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, D-50931, Cologne, Germany.
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Sengupta A, Mukherjee S, Ghosh S, Keswani T, Sarkar S, Majumdar G, Das M, Bhattacharyya A. Partial impairment of late-stage autophagic flux in murine splenocytes leads to sqstm1/p62 mediated nrf2-keap1 antioxidant pathway activation and induced proteasome-mediated degradation in malaria. Microb Pathog 2020; 147:104289. [PMID: 32693118 DOI: 10.1016/j.micpath.2020.104289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 04/29/2020] [Accepted: 05/26/2020] [Indexed: 01/15/2023]
Abstract
Splenomegaly, a major symptom in Plasmodium infection, is extensively studied for its immunopathological role in mice malaria model infected with Plasmodium berghei ANKA. The status of autophagic regulation in hosts in malaria pathogenesis remains unreported till date. This study demonstrated the autophagy, proteasomal degradation and NRF2-KEAP1 antioxidant pathway status in the host during Plasmodium infection taking murine spleen as our organ of interest. Initial staining and autophagic gene expression indicate a possibility of autophagic pathway activation. Although the conversion of LC3A to LC3B and lysosome-autophagosome fusion increases, the final degradation step remains incomplete. Resultant upregulation of p62 and its altered phosphorylated status enhances its binding to keap1 causing NRF2 translocation to the nucleus. NRF2 act as transcription factor upregulating p62 level itself leading to an autoinduction loop of p62 expression. Interestingly, enhancement of P62 interaction with proteasome subunit RPT1 indicates a possible role in transporting ubiquitinated cargo to proteasome complex. Ubiquitination level increased with subsequent upregulation of all three modes of proteasomal degradation i.e trypsin-like, caspase-like and especially chymotrypsin-like. Sqstm1/p62 plays a critical central role in regulating autophagy, proteasomal degradation, and NRF2-KEAP1 pathway. The incomplete autophagic flux in the final step may be a key therapeutic target, as autophagic degradation and subsequent pathogenic peptide presentation is of utmost necessity for downstream immune response.
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Affiliation(s)
- Anirban Sengupta
- Immunology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
| | - Saikat Mukherjee
- Immunology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
| | - Soubhik Ghosh
- Immunology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
| | - Tarun Keswani
- Department of Medicine and Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Samrat Sarkar
- Immunology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
| | - Gargi Majumdar
- Immunology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
| | - Madhusudan Das
- Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
| | - Arindam Bhattacharyya
- Immunology Laboratory, Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
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48
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Guzmán-Téllez P, Martínez-Valencia D, Silva-Olivares A, Del Ángel RM, Serrano-Luna J, Shibayama M. Naegleria fowleri and Naegleria gruberi 20S proteasome: identification and characterization. Eur J Cell Biol 2020; 99:151085. [PMID: 32646643 DOI: 10.1016/j.ejcb.2020.151085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/17/2020] [Accepted: 05/07/2020] [Indexed: 11/26/2022] Open
Abstract
The Naegleria are ubiquitous free-living amoebae and are characterized by the presence of three phases in their biological cycle: trophozoite, cyst and flagellate. Of this genus, only Naegleria fowleri has been reported as pathogenic to humans. The proteasome is a multi-catalytic complex and is considered to be the most important structure responsible for the degradation of intracellular proteins. This structure is related to the maintenance of cellular homeostasis and, in pathogenic microorganisms, to the modulation of their virulence. Until now, the proteasome and its function have not been described for the Naegleria genus. In the current study, using bioinformatic analysis, protein sequences homologous to those reported for the subunits of the 20S proteasome in other organisms were found, and virtual modelling was used to determine their three-dimensional structure. The presence of structural and catalytic subunits of the 20S proteasome was detected by Western and dot blot assays. Its localization was observed by immunofluorescence microscopy to be mainly in the cytoplasm, and a leading role of the chymotrypsin-like catalytic activity was determined using fluorogenic peptidase assays and specific proteasome inhibitors. Finally, the role of the 20S proteasome in the proliferation and differentiation of Naegleria genus trophozoites was demonstrated.
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Affiliation(s)
- Paula Guzmán-Téllez
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, 07360 Mexico City, Mexico
| | - Diana Martínez-Valencia
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, 07360 Mexico City, Mexico
| | - Angélica Silva-Olivares
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, 07360 Mexico City, Mexico
| | - Rosa M Del Ángel
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, 07360 Mexico City, Mexico
| | - Jesús Serrano-Luna
- Department of Cell Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, 07360 Mexico City, Mexico.
| | - Mineko Shibayama
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, 07360 Mexico City, Mexico.
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49
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Vimer S, Ben-Nissan G, Morgenstern D, Kumar-Deshmukh F, Polkinghorn C, Quintyn RS, Vasil’ev YV, Beckman JS, Elad N, Wysocki VH, Sharon M. Comparative Structural Analysis of 20S Proteasome Ortholog Protein Complexes by Native Mass Spectrometry. ACS CENTRAL SCIENCE 2020; 6:573-588. [PMID: 32342007 PMCID: PMC7181328 DOI: 10.1021/acscentsci.0c00080] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Indexed: 05/06/2023]
Abstract
Ortholog protein complexes are responsible for equivalent functions in different organisms. However, during evolution, each organism adapts to meet its physiological needs and the environmental challenges imposed by its niche. This selection pressure leads to structural diversity in protein complexes, which are often difficult to specify, especially in the absence of high-resolution structures. Here, we describe a multilevel experimental approach based on native mass spectrometry (MS) tools for elucidating the structural preservation and variations among highly related protein complexes. The 20S proteasome, an essential protein degradation machinery, served as our model system, wherein we examined five complexes isolated from different organisms. We show that throughout evolution, from the Thermoplasma acidophilum archaeal prokaryotic complex to the eukaryotic 20S proteasomes in yeast (Saccharomyces cerevisiae) and mammals (rat - Rattus norvegicus, rabbit - Oryctolagus cuniculus and human - HEK293 cells), the proteasome increased both in size and stability. Native MS structural signatures of the rat and rabbit 20S proteasomes, which heretofore lacked high-resolution, three-dimensional structures, highly resembled that of the human complex. Using cryoelectron microscopy single-particle analysis, we were able to obtain a high-resolution structure of the rat 20S proteasome, allowing us to validate the MS-based results. Our study also revealed that the yeast complex, and not those in mammals, was the largest in size and displayed the greatest degree of kinetic stability. Moreover, we also identified a new proteoform of the PSMA7 subunit that resides within the rat and rabbit complexes, which to our knowledge have not been previously described. Altogether, our strategy enables elucidation of the unique structural properties of protein complexes that are highly similar to one another, a framework that is valid not only to ortholog protein complexes, but also for other highly related protein assemblies.
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Affiliation(s)
- Shay Vimer
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
| | - David Morgenstern
- Israel
Structural Proteomics Center, Weizmann Institute
of Science, Rehovot, Israel
| | | | - Caley Polkinghorn
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
| | - Royston S. Quintyn
- Department
of Chemistry and Biochemistry and Resource for Native Mass Spectrometry
Guided Structural Biology, Ohio State University, Columbus, Ohio 43210, United States
| | - Yury V. Vasil’ev
- e-MSion
Inc., 2121 NE Jack London
Drive, Corvallis, Oregon 97330, United States
| | - Joseph S. Beckman
- e-MSion
Inc., 2121 NE Jack London
Drive, Corvallis, Oregon 97330, United States
- Linus
Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Nadav Elad
- Department
of Chemical Research Support, Weizmann Institute
of Science, Rehovot, Israel
| | - Vicki H. Wysocki
- Department
of Chemistry and Biochemistry and Resource for Native Mass Spectrometry
Guided Structural Biology, Ohio State University, Columbus, Ohio 43210, United States
| | - Michal Sharon
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
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50
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Kondakova IV, Shashova EE, Sidenko EA, Astakhova TM, Zakharova LA, Sharova NP. Estrogen Receptors and Ubiquitin Proteasome System: Mutual Regulation. Biomolecules 2020; 10:biom10040500. [PMID: 32224970 PMCID: PMC7226411 DOI: 10.3390/biom10040500] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/21/2020] [Accepted: 03/25/2020] [Indexed: 12/11/2022] Open
Abstract
This review provides information on the structure of estrogen receptors (ERs), their localization and functions in mammalian cells. Additionally, the structure of proteasomes and mechanisms of protein ubiquitination and cleavage are described. According to the modern concept, the ubiquitin proteasome system (UPS) is involved in the regulation of the activity of ERs in several ways. First, UPS performs the ubiquitination of ERs with a change in their functional activity. Second, UPS degrades ERs and their transcriptional regulators. Third, UPS affects the expression of ER genes. In addition, the opportunity of the regulation of proteasome functioning by ERs—in particular, the expression of immune proteasomes—is discussed. Understanding the complex mechanisms underlying the regulation of ERs and proteasomes has great prospects for the development of new therapeutic agents that can make a significant contribution to the treatment of diseases associated with the impaired function of these biomolecules.
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Affiliation(s)
- Irina V. Kondakova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 5 Kooperativny Street, 634009 Tomsk, Russia; (I.V.K.); (E.E.S.); (E.A.S.)
| | - Elena E. Shashova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 5 Kooperativny Street, 634009 Tomsk, Russia; (I.V.K.); (E.E.S.); (E.A.S.)
| | - Evgenia A. Sidenko
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 5 Kooperativny Street, 634009 Tomsk, Russia; (I.V.K.); (E.E.S.); (E.A.S.)
| | - Tatiana M. Astakhova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; (T.M.A.); (L.A.Z.)
| | - Liudmila A. Zakharova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; (T.M.A.); (L.A.Z.)
| | - Natalia P. Sharova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; (T.M.A.); (L.A.Z.)
- Correspondence: ; Tel.: +7-499-135-7674; Fax: +7-499-135-3322
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