1
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Santoro AM, Persico M, D’Urso A, Cunsolo A, Tkachuk O, Milardi D, Purrello R, Tundo GR, Sbardella D, Osmulski PA, Gaczynska M, Coletta M, Fattorusso C. Tetra-anionic porphyrin mimics protein-protein interactions between regulatory particles and the catalytic core, allosterically activating human 20S proteasome. J Enzyme Inhib Med Chem 2025; 40:2482892. [PMID: 40192126 PMCID: PMC11980194 DOI: 10.1080/14756366.2025.2482892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 03/03/2025] [Accepted: 03/11/2025] [Indexed: 04/11/2025] Open
Abstract
Decreased proteasome activity is a hallmark of brain and retinal neurodegenerative diseases (Alzheimer's, Parkinson's diseases, glaucoma) boosting the search for molecules acting as proteasome activators. Based on the hypothesis of an electrostatic key code driving catalytic core particle (20S) activation by regulatory particles (RPs), we identified the tetra-anionic meso-Tetrakis(4-sulphonatophenyl)-porphyrin (H2TPPS) as a new activator of human proteasome. By means of an integrated approach, including bioinformatics, enzymatic kinetic analysis, atomic force microscopy, and dynamic docking simulations, we show how binding of H2TPPS affects the closed/open conformational equilibrium of human 20S to ultimately promote substrate gate opening and proteolytic activity. These outcomes support our hypothesis and pave the way to the rational discovery of new proteasome allosteric modulators able to reproduce the key structural elements of regulatory particles responsible for catalytic activation.
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Affiliation(s)
- A. M. Santoro
- National Research Council, Institute of Crystallography, Sede Secondaria di Catania, Catania, Italy
| | - M. Persico
- Department of Pharmacy, University of Naples “Federico II”, Napoli, Italy
| | - A. D’Urso
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - A. Cunsolo
- Department of Chemical Sciences, University of Catania, Catania, Italy
- Epic Sciences, San Diego, California, USA
| | - O. Tkachuk
- Department of Pharmacy, University of Naples “Federico II”, Napoli, Italy
| | - D. Milardi
- National Research Council, Institute of Crystallography, Sede Secondaria di Catania, Catania, Italy
| | - R. Purrello
- Department of Chemical Sciences, University of Catania, Catania, Italy
| | - G. R. Tundo
- Department of Clinical Sciences and Translational Medicine, University of Roma Tor Vergata, Roma, Italy
| | | | - P. A. Osmulski
- Department of Molecular Medicine, University of Texas Health at San Antonio, San Antonio, Texas, USA
| | - M. Gaczynska
- Department of Molecular Medicine, University of Texas Health at San Antonio, San Antonio, Texas, USA
| | | | - C. Fattorusso
- Department of Pharmacy, University of Naples “Federico II”, Napoli, Italy
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2
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Silva EB, Jiang Z, Liu C, Fajtová P, Teixeira TR, de Castro Fiorini Maia G, Liu LJ, El‐Sakkary N, Skinner DE, Syed A, Wang SC, Caffrey CR, O'Donoghue AJ. Enhancing schistosomiasis drug discovery approaches with optimized proteasome substrates. Protein Sci 2025; 34:e70180. [PMID: 40411405 PMCID: PMC12102734 DOI: 10.1002/pro.70180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Revised: 03/30/2025] [Accepted: 05/09/2025] [Indexed: 05/26/2025]
Abstract
Schistosomiasis, a neglected tropical disease infecting over 200 million people globally, has limited therapeutic options. The 20S proteasome is a validated drug target for many parasitic infections, including those caused by Plasmodium and Leishmania, and we have previously demonstrated antischistosomal activity with inhibitors targeting Schistosoma mansoni 20S proteasome (Sm20S). Here, we developed optimized subunit-specific substrates for Sm20S based on data generated by Multiplex Substrate Profiling by Mass Spectrometry (MSP-MS). These substrates exhibit 9-fold or more improved activity compared to traditional human constitutive 20S proteasome (c20S) substrates. The optimized substrates also eliminated the need for extensive Sm20S purification, as robust enzyme activity could be detected in parasite extracts following an ammonium sulfate precipitation step. Finally, we show that the substrate and inhibition profiles for the 20S proteasome from the three medically important schistosome species are similar. This suggests that Sm20S-focused inhibitor development can be efficiently extrapolated to the other schistosome species, leading to significant time and resource savings.
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Affiliation(s)
- Elany B. Silva
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Biochemistry & ImmunologyFederal University of Minas GeraisBelo HorizonteBrazil
| | - Zhenze Jiang
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Chenxi Liu
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Pavla Fajtová
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Thaiz R. Teixeira
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | | | - Lawrence J. Liu
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Nelly El‐Sakkary
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Danielle E. Skinner
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Ali Syed
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Steven C Wang
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Anthony J. O'Donoghue
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaCaliforniaUSA
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3
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Shen S, Zhang Q, Wang Y, Chen H, Gong S, Liu Y, Gai C, Chen H, Zhu E, Yang B, Liu L, Cao S, Zhao M, Ren W, Li M, Peng Z, Zhang L, Zhang S, Shen J, Zhang B, Lee PK, Li K, Li L, Yang H. Targeting ubiquitin-independent proteasome with small molecule increases susceptibility in pan-KRAS-mutant cancer models. J Clin Invest 2025; 135:e185278. [PMID: 40091835 PMCID: PMC11910216 DOI: 10.1172/jci185278] [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: 07/25/2024] [Accepted: 01/16/2025] [Indexed: 03/19/2025] Open
Abstract
Despite advances in the development of direct KRAS inhibitors, KRAS-mutant cancers continue to exhibit resistance to the currently available therapies. Here, we identified REGγ as a mutant KRAS-associated factor that enhanced REGγ transcription through the KRAS intermediate NRF2, suggesting that the REGγ-proteasome is a potential target for pan-KRAS inhibitor development. We elucidated a mechanism involving the KRAS/NRF2/REGγ regulatory axis, which links activated KRAS to the ATP- and ubiquitin-independent proteasome. We subsequently developed RLY01, a REGγ-proteasome inhibitor that effectively suppressed tumor growth in KRAS-mutant cancer models and lung cancer organoids. Notably, the combination of RLY01 and the KRASG12C inhibitor AMG510 exhibited enhanced antitumor efficacy in KRASG12C cancer cells. Collectively, our data support the hypothesis that KRAS mutations enhance the capacity of the REGγ-proteasome by increasing REGγ expression, highlighting the potential of ubiquitin-independent proteasome inhibition as a therapeutic approach for pan-KRAS-mutant cancers.
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Affiliation(s)
- Shihui Shen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
- Joint Center for Translational Medicine, Shanghai Fifth People's Hospital, Fudan University and School of Life Science, East China Normal University, Shanghai, China
| | - Qiansen Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yuhan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Hui Chen
- Joint Center for Translational Medicine, Shanghai Fifth People's Hospital, Fudan University and School of Life Science, East China Normal University, Shanghai, China
| | - Shuangming Gong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yun Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Conghao Gai
- Organic Chemistry Group, College of Pharmacy, Naval Medical University, Shanghai, China
| | - Hansen Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Enhao Zhu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Bo Yang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Lin Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Siyuan Cao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Mengting Zhao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Wenjie Ren
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Mengjuan Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhuoya Peng
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Lu Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Shaoying Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Juwen Shen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Bianhong Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Patrick Kh Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Kun Li
- Health Science Center, East China Normal University, Shanghai, China
| | - Lei Li
- Joint Center for Translational Medicine, Shanghai Fifth People's Hospital, Fudan University and School of Life Science, East China Normal University, Shanghai, China
| | - Huaiyu Yang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
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4
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Zeng G, Xu G, Gao L, Zheng X, Chi X, Shen Z, Cao Y, Xi J, Che J, Dong X, Shi Y, Ma J, Zhang C, Zeng L, Zhu H, Shao J, Zhou Y, Li J, Zhang J. Development of novel epoxyketone macrocyclic peptidyl proteasome inhibitors through OPA-mediated one-step cyclization of unprotected peptides. Bioorg Chem 2025; 156:108180. [PMID: 39855110 DOI: 10.1016/j.bioorg.2025.108180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2024] [Revised: 01/14/2025] [Accepted: 01/16/2025] [Indexed: 01/27/2025]
Abstract
Cyclization is a pivotal strategy for enhancing the drug-like characteristics of polypeptides. To develop potent and metabolically stable proteasome inhibitors, we generated a macrocyclic peptide skeleton using a straightforward and efficient cyclization strategy. Subsequent stability assessments confirmed the practicality of this approach. Leveraging this skeleton, we designed and synthesized a series of epoxyketone macrocyclic peptidyl proteasome inhibitors. Approximately half of these compounds showcased robust inhibitory potency, with IC50 values below 200 nM against chymotrypsin-like (ChT-L, β5) activity. Notably, compounds 6f, 6g, and 6m demonstrated pronounced anti-proliferative activities at low nanomolar concentrations against three hematoma cell lines (RPMI-8226, RS4;11, and MV-4-11) as well as the NCI-H1299 cell line. These findings highlight the potential of these cyclic peptides to bolster the stability of proteasome inhibitors, thereby providing valuable insights for the advancement of innovative proteasome inhibitor therapies.
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Affiliation(s)
- Gongruixue Zeng
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province School of Medicine Hangzhou City University China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 Zhejiang Province, China
| | - Gaoya Xu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203 China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lixin Gao
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203 China; The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiaoli Zheng
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province School of Medicine Hangzhou City University China
| | - Xinglong Chi
- Center of Safety Evaluation and Research, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Zheyuan Shen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 Zhejiang Province, China
| | - Yu Cao
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou 310023 Zhejiang Province, China
| | - Jianjun Xi
- Department of Pharmaceutical Preparation, Hangzhou Xixi Hospital, Hangzhou 310023 Zhejiang Province, China
| | - Jinxin Che
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 Zhejiang Province, China
| | - Xiaowu Dong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 Zhejiang Province, China
| | - Yaoli Shi
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province School of Medicine Hangzhou City University China
| | - Jiayi Ma
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province School of Medicine Hangzhou City University China
| | - Chong Zhang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province School of Medicine Hangzhou City University China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 Zhejiang Province, China
| | - Linghui Zeng
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province School of Medicine Hangzhou City University China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 Zhejiang Province, China
| | - Huajian Zhu
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province School of Medicine Hangzhou City University China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 Zhejiang Province, China
| | - Jiaan Shao
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province School of Medicine Hangzhou City University China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 Zhejiang Province, China
| | - Yubo Zhou
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jia Li
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203 China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Jiankang Zhang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province School of Medicine Hangzhou City University China; College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058 Zhejiang Province, China.
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5
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Tang T, Luo J, Zhang D, Lu Y, Liao W, Zhang J. Innovative design and potential applications of covalent strategy in drug discovery. Eur J Med Chem 2025; 284:117202. [PMID: 39756145 DOI: 10.1016/j.ejmech.2024.117202] [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: 08/29/2024] [Revised: 12/19/2024] [Accepted: 12/21/2024] [Indexed: 01/07/2025]
Abstract
Covalent inhibitors provide persistent inhibition while maintaining excellent selectivity and efficacy by creating stable covalent connections with specific amino acids in target proteins. This technique enables the precise inhibition of previously undruggable targets, lowering the frequency of administration and potentially bypassing drug resistance. Because of these advantages, covalent inhibitors have tremendous potential in treating cancer, inflammation, and infectious illnesses, making them extremely important in modern pharmacological research. Covalent inhibitors targeting EGFR, BTK, and KRAS (G12X), which overcome drug resistance and off-target, non-"medicinal" difficulties, as well as covalent inhibitors targeting SARS-CoV-2 Mpro, have paved the way for the development of new antiviral medicines. Furthermore, the use of covalent methods in drug discovery procedures, such as covalent PROTACs, covalent molecular gels, covalent probes, CoLDR, and Dual-targeted covalent inhibitors, preserves these tactics' inherent features while incorporating the advantages of covalent inhibitors. This synthesis opens up new therapeutic opportunities. This review comprehensively examines the use of covalent techniques in drug discovery, emphasizing their transformational potential for future drug development.
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Affiliation(s)
- Tianyong Tang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jiaxiang Luo
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Dan Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yang Lu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250355, Shandong, China
| | - Wen Liao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases & Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Jifa Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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6
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Arseni L, Sigismondo G, Yazdanparast H, Hermansen JU, Mack N, Ohl S, Kalter V, Iskar M, Kalxdorf M, Friedel D, Rettel M, Paul Y, Ringshausen I, Eldering E, Dubois J, Kater AP, Zapatka M, Roessner PM, Tausch E, Stilgenbauer S, Dietrich S, Savitski MM, Skånland SS, Krijgsveld J, Lichter P, Seiffert M. Longitudinal omics data and preclinical treatment suggest the proteasome inhibitor carfilzomib as therapy for ibrutinib-resistant CLL. Nat Commun 2025; 16:1041. [PMID: 39863584 PMCID: PMC11762753 DOI: 10.1038/s41467-025-56318-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 01/15/2025] [Indexed: 01/27/2025] Open
Abstract
Chronic lymphocytic leukemia is a malignant lymphoproliferative disorder for which primary or acquired drug resistance represents a major challenge. To investigate the underlying molecular mechanisms, we generate a mouse model of ibrutinib resistance, in which, after initial treatment response, relapse under therapy occurrs with an aggressive outgrowth of malignant cells, resembling observations in patients. A comparative analysis of exome, transcriptome and proteome of sorted leukemic murine cells during treatment and after relapse suggests alterations in the proteasome activity as a driver of ibrutinib resistance. Preclinical treatment with the irreversible proteasome inhibitor carfilzomib administered upon ibrutinib resistance prolongs survival of mice. Longitudinal proteomic analysis of ibrutinib-resistant patients identifies deregulation in protein post-translational modifications. Additionally, cells from ibrutinib-resistant patients effectively respond to several proteasome inhibitors in co-culture assays. Altogether, our results from orthogonal omics approaches identify proteasome inhibition as potentially attractive treatment for chronic lymphocytic leukemia patients resistant or refractory to ibrutinib.
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MESH Headings
- Piperidines
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Adenine/analogs & derivatives
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Animals
- Humans
- Oligopeptides/pharmacology
- Oligopeptides/therapeutic use
- Mice
- Pyrimidines/pharmacology
- Pyrimidines/therapeutic use
- Pyrazoles/pharmacology
- Pyrazoles/therapeutic use
- Proteasome Inhibitors/pharmacology
- Proteasome Inhibitors/therapeutic use
- Proteomics
- Proteasome Endopeptidase Complex/metabolism
- Cell Line, Tumor
- Female
- Disease Models, Animal
- Transcriptome
- Male
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Affiliation(s)
- Lavinia Arseni
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Haniyeh Yazdanparast
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johanne U Hermansen
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K. G. Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Norman Mack
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sibylle Ohl
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Verena Kalter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Murat Iskar
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Dennis Friedel
- Division of Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mandy Rettel
- EMBL, Proteomics Core Facility, Heidelberg, Germany
| | - Yashna Paul
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ingo Ringshausen
- Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Eric Eldering
- Department of Experimental Immunology, Cancer Center Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Julie Dubois
- Department of Hematology, Cancer Center Amsterdam, Amsterdam Institute for Infection and Immunity, Lymphoma and Myeloma Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Arnon P Kater
- Department of Hematology, Cancer Center Amsterdam, Amsterdam Institute for Infection and Immunity, Lymphoma and Myeloma Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp M Roessner
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eugen Tausch
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Stephan Stilgenbauer
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Sascha Dietrich
- Heidelberg University, Department of Hematology, Heidelberg, Germany
- Düsseldorf University, Department of Hematology, Düsseldorf, Germany
| | - Mikhail M Savitski
- EMBL, Proteomics Core Facility, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Sigrid S Skånland
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K. G. Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Seiffert
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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7
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Eadsforth TC, Torrie LS, Rowland P, Edgar EV, MacLean LM, Paterson C, Robinson DA, Shepherd SM, Thomas J, Thomas MG, Gray DW, Postis VLG, De Rycker M. Pharmacological and structural understanding of the Trypanosoma cruzi proteasome provides key insights for developing site-specific inhibitors. J Biol Chem 2025; 301:108049. [PMID: 39638245 PMCID: PMC11748689 DOI: 10.1016/j.jbc.2024.108049] [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: 05/22/2024] [Revised: 11/15/2024] [Accepted: 11/26/2024] [Indexed: 12/07/2024] Open
Abstract
The proteasome is considered an excellent drug target for many infectious diseases as well as cancer. Challenges with robust and safe supply of proteasomes from infectious agents, lack of structural information, and complex pharmacology due to multiple active sites have hampered progress in the infectious disease space. We recombinantly expressed the proteasome of the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease, and demonstrate pharmacological equivalence to the native T. cruzi proteasome. Active-site mutant recombinant proteasomes reveal substrate promiscuity for WT proteasomes, with important implications for assessing pharmacological responses of active-site selective inhibitors. Using these mutant proteasomes, we show that some selective parasite proteasome inhibitors only partially inhibit the chymotrypsin-like activity, including a newly developed 5-(phenoxymethyl)furan-2-carboxamide-based proteasome inhibitor. In spite of partial inhibition, these compounds remain potent inhibitors of intracellular T. cruzi growth. Drug-resistant mutants provide further insights in drug mode-of-inhibition. We also present the high-resolution CryoEM structures of both native and recombinantly-expressed T. cruzi proteasomes which reveal pharmacologically relevant differences in the ligand-binding site compared to the related Leishmania proteasome. Furthermore, we show that the trypanosomatid β4/β5 selectivity pocket is not present in the proteasome structures of other protozoan parasites. This work highlights the need, and provides approaches, to precisely assess proteasome substrate selectivity and pharmacology. It enables structure-guided drug discovery for this promising Chagas disease drug target, provides a new chemical starting point for drug discovery, and paves the road for development of robust proteasome drug discovery programmes for other eukaryotic infectious diseases.
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Affiliation(s)
- Thomas C Eadsforth
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Leah S Torrie
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | | | | | - Lorna M MacLean
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Christy Paterson
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - David A Robinson
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Sharon M Shepherd
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - John Thomas
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Michael G Thomas
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - David W Gray
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Vincent L G Postis
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK
| | - Manu De Rycker
- Wellcome Centre for Anti-Infectives Research, University of Dundee, Dundee, UK.
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8
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Uthumange SS, Liew AJH, Chee XW, Yeong KY. Ringing medicinal chemistry: The importance of 3-membered rings in drug discovery. Bioorg Med Chem 2024; 116:117980. [PMID: 39536361 DOI: 10.1016/j.bmc.2024.117980] [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: 08/23/2024] [Revised: 10/16/2024] [Accepted: 10/28/2024] [Indexed: 11/16/2024]
Abstract
Scaffold-based drug design has become increasingly prominent in the pharmaceutical field due to the systematic and effective approach through which it facilitates the development of novel drugs. The identification of key scaffolds provides medicinal chemists with a fundamental framework for subsequent research. With mounting evidence suggesting that increased aromaticity could impede the chances of developmental success for oral drug candidates, there is an imperative need for a more thorough exploration of alternative ring systems to mitigate attrition risks. The unique characteristics exhibited by three-membered rings have led to their application in medicinal chemistry. This review explores the use of cyclopropane-, aziridine-, thiirane-, and epoxide-containing compounds in drug discovery, focusing on their roles in approved medicines and drug candidates. Specifically, the importance of the three-membered ring systems in rending biological activity for each drug molecule was highlighted. The undeniable therapeutic value and intriguing features presented by these compounds suggest significant pharmacological potential, providing justification for their incorporation into the design of novel drug candidates.
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Affiliation(s)
- Sahani Sandalima Uthumange
- School of Science, Monash University (Malaysia Campus), Jalan Lagoon Selatan, Bandar Sunway, 47500 Selangor, Malaysia
| | - Angie Jun Hui Liew
- School of Science, Monash University (Malaysia Campus), Jalan Lagoon Selatan, Bandar Sunway, 47500 Selangor, Malaysia
| | - Xavier Wezen Chee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Keng Yoon Yeong
- School of Science, Monash University (Malaysia Campus), Jalan Lagoon Selatan, Bandar Sunway, 47500 Selangor, Malaysia.
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9
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Nangia AK. Molecular tweaking by generative cheminformatics and ligand-protein structures for rational drug discovery. Bioorg Chem 2024; 153:107920. [PMID: 39489080 DOI: 10.1016/j.bioorg.2024.107920] [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: 08/19/2024] [Accepted: 10/23/2024] [Indexed: 11/05/2024]
Abstract
The purpose of this review is two-fold: (1) to summarize artificial intelligence and machine learning approaches and document the role of ligand-protein structures in directing drug discovery; (2) to present examples of drugs from the recent literature (past decade) of case studies where such strategies have been applied to accelerate the discovery pipeline. Compared to 50 years ago when drug discovery was largely a synthetic chemist driven research exercise, today a holistic approach needs to be adopted with seamless integration between synthetic and medicinal chemistry, supramolecular complexes, computations, artificial intelligence, machine learning, structural biology, chemical biology, diffraction analytical tools, drugs databases, and pharmacology. The urgency for an integrated and collaborative platform to accelerate drug discovery in an academic setting is emphasized.
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Affiliation(s)
- Ashwini K Nangia
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India.
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10
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Tyrna P, Procyk G, Szeleszczuk Ł, Młynarczuk-Biały I. Different Strategies to Overcome Resistance to Proteasome Inhibitors-A Summary 20 Years after Their Introduction. Int J Mol Sci 2024; 25:8949. [PMID: 39201634 PMCID: PMC11354503 DOI: 10.3390/ijms25168949] [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: 07/02/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 09/02/2024] Open
Abstract
Proteasome inhibitors (PIs), bortezomib, carfilzomib, and ixazomib, are the first-line treatment for multiple myeloma (MM). They inhibit cytosolic protein degradation in cells, which leads to the accumulation of misfolded and malfunctioned proteins in the cytosol and endoplasmic reticulum, resulting in cell death. Despite being a breakthrough in MM therapy, malignant cells develop resistance to PIs via different mechanisms. Understanding these mechanisms drives research toward new anticancer agents to overcome PI resistance. In this review, we summarize the mechanism of action of PIs and how MM cells adapt to these drugs to develop resistance. Finally, we explore these mechanisms to present strategies to interfere with PI resistance. The strategies include new inhibitors of the ubiquitin-proteasome system, drug efflux inhibitors, autophagy disruption, targeting stress response mechanisms, affecting survival and cell cycle regulators, bone marrow microenvironment modulation, and immunotherapy. We list potential pharmacological targets examined in in vitro, in vivo, and clinical studies. Some of these strategies have already provided clinicians with new anti-MM medications, such as panobinostat and selinexor. We hope that further exploration of the subject will broaden the range of therapeutic options and improve patient outcomes.
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Affiliation(s)
- Paweł Tyrna
- Histology and Embryology Students’ Science Association, Department of Histology and Embryology, Faculty of Medicine, Warsaw Medical University, Chalubinskiego 5, 02-004 Warsaw, Poland;
| | - Grzegorz Procyk
- 1st Chair and Department of Cardiology, Medical University of Warsaw, Banacha 1A, 02-097 Warsaw, Poland;
| | - Łukasz Szeleszczuk
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., 02-093 Warsaw, Poland;
| | - Izabela Młynarczuk-Biały
- Department of Histology and Embryology, Faculty of Medicine, Warsaw Medical University, Chalubinskiego 5, 02-004 Warsaw, Poland
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11
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Klett T, Schwer M, Ernst LN, Engelhardt MU, Jaag SJ, Masberg B, Knappe C, Lämmerhofer M, Gehringer M, Boeckler FM. Evaluation of a Covalent Library of Diverse Warheads (CovLib) Binding to JNK3, USP7, or p53. Drug Des Devel Ther 2024; 18:2653-2679. [PMID: 38974119 PMCID: PMC11226190 DOI: 10.2147/dddt.s466829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024] Open
Abstract
Purpose Over the last few years, covalent fragment-based drug discovery has gained significant importance. Thus, striving for more warhead diversity, we conceived a library consisting of 20 covalently reacting compounds. Our covalent fragment library (CovLib) contains four different warhead classes, including five α-cyanoacacrylamides/acrylates (CA), three epoxides (EO), four vinyl sulfones (VS), and eight electron-deficient heteroarenes with a leaving group (SNAr/SN). Methods After predicting the theoretical solubility of the fragments by LogP and LogS during the selection process, we determined their experimental solubility using a turbidimetric solubility assay. The reactivities of the different compounds were measured in a high-throughput 5,5'-dithiobis-(2-nitrobenzoic acid) DTNB assay, followed by a (glutathione) GSH stability assay. We employed the CovLib in a (differential scanning fluorimetry) DSF-based screening against different targets: c-Jun N-terminal kinase 3 (JNK3), ubiquitin-specific protease 7 (USP7), and the tumor suppressor p53. Finally, the covalent binding was confirmed by intact protein mass spectrometry (MS). Results In general, the purchased fragments turned out to be sufficiently soluble. Additionally, they covered a broad spectrum of reactivity. All investigated α-cyanoacrylamides/acrylates and all structurally confirmed epoxides turned out to be less reactive compounds, possibly due to steric hindrance and reversibility (for α-cyanoacrylamides/acrylates). The SNAr and vinyl sulfone fragments are either highly reactive or stable. DSF measurements with the different targets JNK3, USP7, and p53 identified reactive fragment hits causing a shift in the melting temperatures of the proteins. MS confirmed the covalent binding mode of all these fragments to USP7 and p53, while additionally identifying the SNAr-type electrophile SN002 as a mildly reactive covalent hit for p53. Conclusion The screening and target evaluation of the CovLib revealed first interesting hits. The highly cysteine-reactive fragments VS004, SN001, SN006, and SN007 covalently modify several target proteins and showed distinct shifts in the melting temperatures up to +5.1 °C and -9.1 °C.
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Affiliation(s)
- Theresa Klett
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Martin Schwer
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Larissa N Ernst
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Marc U Engelhardt
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Simon J Jaag
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Benedikt Masberg
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Cornelius Knappe
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Michael Lämmerhofer
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Matthias Gehringer
- Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Medicinal Chemistry, Institute for Biomedical Engineering, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Frank M Boeckler
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
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12
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Forooghi K, Amiri Rudbari H, Stagno C, Iraci N, Cuevas-Vicario JV, Kordestani N, Schirmeister T, Efferth T, Omer EA, Moini N, Aryaeifar M, Blacque O, Azadbakht R, Micale N. Structural features and antiproliferative activity of Pd(II) complexes with halogenated ligands: a comparative study between Schiff base and reduced Schiff base complexes. Dalton Trans 2024; 53:10571-10591. [PMID: 38855858 DOI: 10.1039/d4dt00132j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
In order to investigate the structural features and antiproliferative activity of Pd(II) complexes containing halogenated ligands with different flexibility, several Schiff base and reduced Schiff base Pd(II) complexes, namely X1X2PicPd, X1X2PyPd, X1X2Pic(R)Pd, and X1X2Py(R)Pd (where X1 = X2 = Cl, Br and I; Pic: 2-picolylamine; Py = 2-(2-pyridyl)ethylamine), were synthesized and characterized by spectroscopic methods and, in the case of Br2PyPd, Cl2Py(R)Pd and ClBrPy(R)Pd, also by X-ray crystallography. The results of the X-ray crystallography showed that in both series of complexes the Pd(II) ion has a distorted square-planar geometry, although the coordination modes of the two ligands are different. In the Schiff base-type complexes the ligand acts as a tridentate chelate with NN'O donor atoms, whereas in the reduced Schiff base-type complexes the ligand acts as a bidentate chelate with NN' donor atoms. In both series of complexes, the chloride ions occupy the residual coordination sites of the Pd(II) ion. TD-DFT calculations were performed for a better understanding of the UV-Vis spectra. From these calculations it was found that the signal appearing at ∼400 nm in the complexes with reduced Schiff base ligands (X1X2Pic(R)Pd and X1X2Py(R)Pd) is mainly due to a HOMO → LUMO transition, while for the Schiff base complex ClBrPyPd the signal is due to a HOMO → LUMO+1 transition. For the complex I2PicPd, combinations of HOMO-4 → LUMO and HOMO-2 → LUMO transitions were found to be responsible for that signal. In regard to the biological activity profile, all complexes were first investigated as proteasome inhibitors by fluorometric methods. From these enzymatic assays, it emerged that they are good inhibitors with IC50 values in the low-micromolar range and that their inhibitory activity is strictly related to the presence of the metal ion. Subsequently they were also subjected to cell-based assays (the resazurin method) to assess their antiproliferative properties by using two leukemic cell lines, namely the drug-sensitive CCRF-CEM cell line and its multidrug-resistant sub-cell line CEM/ADR5000. In this test they displayed IC50 values in the sub-micromolar and low-micromolar range determined for a selected metal complex (Br2Pic(R)Pd) and ligand (Cl2Pic(R)), respectively. Moreover, docking studies were performed on the two expected molecular targets, i.e. proteasome and DNA, to shed light on the mechanisms of action of these types of Pd(II) complexes.
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Affiliation(s)
- Kimia Forooghi
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
| | - Hadi Amiri Rudbari
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
| | - Claudio Stagno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, I-98166 Messina, Italy.
| | - Nunzio Iraci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, I-98166 Messina, Italy.
| | - José V Cuevas-Vicario
- Departamento de Química, Facultad de Ciencias, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001, Burgos, Spain
| | - Nazanin Kordestani
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
- CNRS, Univ. Bordeaux, Bordeaux INP, ICMCB, UMR 5026, F-33600 Pessac, France
| | - Tanja Schirmeister
- Department of Medicinal Chemistry, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, staudinger Weg 5, 55128 Mainz, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, staudinger Weg 5, 55128 Mainz, Germany
| | - Ejlal A Omer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, staudinger Weg 5, 55128 Mainz, Germany
| | - Nakisa Moini
- Department of Inorganic Chemistry, Faculty of Chemistry, Alzahra University, Tehran, Iran
| | - Mahnaz Aryaeifar
- Department of Chemistry, University of Isfahan, Isfahan 81746-73441, Iran.
| | - Olivier Blacque
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Reza Azadbakht
- Department of Inorganic Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan, Iran
| | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, I-98166 Messina, Italy.
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13
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Götz MG, Godwin K, Price R, Dorn R, Merrill-Steskal G, Klemmer W, Hansen H, Produturi G, Rocha M, Palmer M, Molacek L, Strater Z, Groll M. Macrocyclic Oxindole Peptide Epoxyketones-A Comparative Study of Macrocyclic Inhibitors of the 20S Proteasome. ACS Med Chem Lett 2024; 15:533-539. [PMID: 38628795 PMCID: PMC11017298 DOI: 10.1021/acsmedchemlett.4c00017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/22/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
Peptide macrocycles have recently gained attention as protease inhibitors due to their metabolic stability and specificity. However, the development of peptide macrocycles with improved binding potency has so far been challenging. Here we present macrocyclic peptides derived from the clinically applied proteasome inhibitor carfilzomib with an oxindole group that mimics the natural product TMC-95A. Fluorescence kinetic activity assays reveal a high potency of the oxindole group (IC50 = 0.19 μM) compared with agents lacking this motif. X-ray structures of the ligands with the β5-subunit of the yeast 20S proteasome illustrate that the installed macrocycle forces strong hydrogen bonding of the oxindole group with β5-Gly23NH. Thus, the binding of our designed oxindole epoxyketones is entropically and enthalpically favored in contrast to more flexible proteasome inhibitors such as carfilzomib.
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Affiliation(s)
- Marion G. Götz
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Kacey Godwin
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Rachel Price
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Robert Dorn
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | | | - William Klemmer
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Hunter Hansen
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Gautam Produturi
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Megan Rocha
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Mathias Palmer
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Lea Molacek
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Zack Strater
- Department
of Chemistry, Whitman College, Walla Walla, Washington 99362, United States
| | - Michael Groll
- Technical
University of Munich, TUM School of Natural
Sciences, Department of Bioscience, Center for Protein Assemblies
(CPA), Ernst-Otto-Fischer
Strasse 8, 85748 Garching, Germany
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14
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Morstein J, Amatuni A, Shuster A, Kuttenlochner W, Ko T, Abegg D, Groll M, Adibekian A, Renata H, Trauner DH. Optical Control of Proteasomal Protein Degradation with a Photoswitchable Lipopeptide. Angew Chem Int Ed Engl 2024; 63:e202314791. [PMID: 38109686 PMCID: PMC12079555 DOI: 10.1002/anie.202314791] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023]
Abstract
Photolipids have emerged as attractive tools for the optical control of lipid functions. They often contain an azobenzene photoswitch that imparts a cis double-bond upon irradiation. Herein, we present the application of photoswitching to a lipidated natural product, the potent proteasome inhibitor cepafungin I. Several azobenzene-containing lipids were attached to the cyclopeptide core, yielding photoswitchable derivatives. Most notably, PhotoCep4 exhibited a 10-fold higher cellular potency in its light-induced cis-form, matching the potency of natural cepafungin I. The length of the photolipid tail and distal positioning of the azobenzene photoswitch with respect to the macrocycle is critical for this activity. In a proteome-wide experiment, light-triggered PhotoCep4 modulation showed high overlap with constitutively active cepafungin I. The mode of action was studied using crystallography and revealed an identical binding of the cyclopeptide in comparison to cepafungin I, suggesting that differences in their cellular activity originate from switching the tail structure. The photopharmacological approach described herein could be applicable to many other natural products as lipid conjugation is common and often necessary for potent activity. Such lipids are often introduced late in synthetic routes, enabling facile chemical modifications.
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Affiliation(s)
- Johannes Morstein
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Alexander Amatuni
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, USA
| | - Anton Shuster
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, USA
| | - Wolfgang Kuttenlochner
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Tongil Ko
- Department of Chemistry, New York University, New York, New York 10003, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Daniel Abegg
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Michael Groll
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Alexander Adibekian
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Hans Renata
- Department of Chemistry, BioScience Research Collaborative, Rice University, Houston, Texas 77005, USA
| | - Dirk H. Trauner
- Department of Chemistry, New York University, New York, New York 10003, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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15
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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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16
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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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17
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Sultana S, Abdullah M, Li J, Hochstrasser M, Kachroo AH. Species-specific protein-protein interactions govern the humanization of the 20S proteasome in yeast. Genetics 2023; 225:iyad117. [PMID: 37364278 PMCID: PMC10471208 DOI: 10.1093/genetics/iyad117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Yeast and humans share thousands of genes despite a billion years of evolutionary divergence. While many human genes can functionally replace their yeast counterparts, nearly half of the tested shared genes cannot. For example, most yeast proteasome subunits are "humanizable," except subunits comprising the β-ring core, including β2c (HsPSMB7, a constitutive proteasome subunit). We developed a high-throughput pipeline to humanize yeast proteasomes by generating a large library of Hsβ2c mutants and screening them for complementation of a yeast β2 (ScPup1) knockout. Variants capable of replacing ScPup1 included (1) those impacting local protein-protein interactions (PPIs), with most affecting interactions between the β2c C-terminal tail and the adjacent β3 subunit, and (2) those affecting β2c proteolytic activity. Exchanging the full-length tail of human β2c with that of ScPup1 enabled complementation. Moreover, wild-type human β2c could replace yeast β2 if human β3 was also provided. Unexpectedly, yeast proteasomes bearing a catalytically inactive HsPSMB7-T44A variant that blocked precursor autoprocessing were viable, suggesting an intact propeptide stabilizes late assembly intermediates. In contrast, similar modifications in human β2i (HsPSMB10), an immunoproteasome subunit and the co-ortholog of yeast β2, do not enable complementation in yeast, suggesting distinct interactions are involved in human immunoproteasome core assembly. Broadly, our data reveal roles for specific PPIs governing functional replaceability across vast evolutionary distances.
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Affiliation(s)
- Sarmin Sultana
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC H3G 1M8, Canada
| | - Mudabir Abdullah
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC H3G 1M8, Canada
| | - Jianhui Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Aashiq H Kachroo
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC H3G 1M8, Canada
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18
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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: 1.0] [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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19
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Burkhart JG, Wu G, Song X, Raimondi F, McWeeney S, Wong MH, Deng Y. Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease. PATTERNS (NEW YORK, N.Y.) 2023; 4:100758. [PMID: 37521042 PMCID: PMC10382942 DOI: 10.1016/j.patter.2023.100758] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/20/2022] [Accepted: 05/01/2023] [Indexed: 08/01/2023]
Abstract
Functional heterogeneity of healthy human tissues complicates interpretation of molecular studies, impeding precision therapeutic target identification and treatment. Considering this, we generated a graph neural network with Reactome-based architecture and trained it using 9,115 samples from Genotype-Tissue Expression (GTEx). Our graph neural network (GNN) achieves adjusted Rand index (ARI) = 0.7909, while a Resnet18 control model achieves ARI = 0.7781, on 370 held-out healthy human tissue samples from The Cancer Genome Atlas (TCGA), despite the Resnet18 using over 600 times the parameters. Our GNN also succeeds in separating 83 healthy skin samples from 95 lesional psoriasis samples, revealing that upregulation of 26S- and NUB1-mediated degradation of NEDD8, UBD, and their conjugates is central to the largest perturbed reaction network component in psoriasis. We show that our results are not discoverable using traditional differential expression and hypergeometric pathway enrichment analyses yet are supported by separate human multi-omics and small-molecule mouse studies, suggesting future molecular disease studies may benefit from similar GNN analytical approaches.
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Affiliation(s)
- Joshua G. Burkhart
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI 96813, USA
| | - Guanming Wu
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Xubo Song
- Department of Computer Science and Electrical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | | | - Shannon McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Melissa H. Wong
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97201, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI 96813, USA
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20
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Deshmukh FK, Ben-Nissan G, Olshina MA, Füzesi-Levi MG, Polkinghorn C, Arkind G, Leushkin Y, Fainer I, Fleishman SJ, Tawfik D, Sharon M. Allosteric regulation of the 20S proteasome by the Catalytic Core Regulators (CCRs) family. Nat Commun 2023; 14:3126. [PMID: 37253751 DOI: 10.1038/s41467-023-38404-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/26/2023] [Indexed: 06/01/2023] Open
Abstract
Controlled degradation of proteins is necessary for ensuring their abundance and sustaining a healthy and accurately functioning proteome. One of the degradation routes involves the uncapped 20S proteasome, which cleaves proteins with a partially unfolded region, including those that are damaged or contain intrinsically disordered regions. This degradation route is tightly controlled by a recently discovered family of proteins named Catalytic Core Regulators (CCRs). Here, we show that CCRs function through an allosteric mechanism, coupling the physical binding of the PSMB4 β-subunit with attenuation of the complex's three proteolytic activities. In addition, by dissecting the structural properties that are required for CCR-like function, we could recapitulate this activity using a designed protein that is half the size of natural CCRs. These data uncover an allosteric path that does not involve the proteasome's enzymatic subunits but rather propagates through the non-catalytic subunit PSMB4. This way of 20S proteasome-specific attenuation opens avenues for decoupling the 20S and 26S proteasome degradation pathways as well as for developing selective 20S proteasome inhibitors.
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Affiliation(s)
- Fanindra Kumar Deshmukh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maya A Olshina
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Maria G Füzesi-Levi
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Caley Polkinghorn
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Galina Arkind
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yegor Leushkin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Irit Fainer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Dan Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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21
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Türker F, Bharadwaj RA, Kleinman JE, Weinberger DR, Hyde TM, White CJ, Williams DW, Margolis SS. Orthogonal approaches required to measure proteasome composition and activity in mammalian brain tissue. J Biol Chem 2023:104811. [PMID: 37172721 DOI: 10.1016/j.jbc.2023.104811] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/20/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Proteasomes are large macromolecular complexes with multiple distinct catalytic activities that are each vital to human brain health and disease. Despite their importance, standardized approaches to investigate proteasomes have not been universally adapted. Here, we describe pitfalls and define straightforward orthogonal biochemical approaches essential to measure and understand changes in proteasome composition and activity in the mammalian central nervous system. Through our experimentation in the mammalian brain, we determined an abundance of catalytically active proteasomes exist with and without a 19S cap(s), the regulatory particle essential for ubiquitin-dependent degradation. Moreover, we learned that in-cell measurements using activity-based probes (ABPs) are more sensitive in determining the available activity of the 20S proteasome without the 19S cap and in measuring individual catalytic subunit activities of each β subunit within all neuronal proteasomes. Subsequently, applying these tools to human brain samples, we were surprised to find that post-mortem tissue retained little to no 19S-capped proteasome, regardless of age, sex, or disease state. Comparing brain tissues (parahippocampal gyrus) from human Alzheimer's disease (AD) patients and unaffected subjects, available 20S proteasome activity was significantly elevated in severe cases of AD, an observation not previously noted. Taken together, our study establishes standardized approaches for comprehensive investigation of proteasomes in mammalian brain tissue, and we reveal new insight into brain proteasome biology.
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Affiliation(s)
- Fulya Türker
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rahul A Bharadwaj
- The Lieber Institute for Brain Development, Baltimore, MD 21205, USA
| | - Joel E Kleinman
- The Lieber Institute for Brain Development, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel R Weinberger
- The Lieber Institute for Brain Development, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas M Hyde
- The Lieber Institute for Brain Development, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Cory J White
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dionna W Williams
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA; Department of Molecular Microbiology & Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland 21205, USA; Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Seth S Margolis
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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22
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Chari A, Stark H. Prospects and Limitations of High-Resolution Single-Particle Cryo-Electron Microscopy. Annu Rev Biophys 2023; 52:391-411. [PMID: 37159297 DOI: 10.1146/annurev-biophys-111622-091300] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Single particle cryo-electron microscopy (cryo-EM) has matured into a robust method for the determination of biological macromolecule structures in the past decade, complementing X-ray crystallography and nuclear magnetic resonance. Constant methodological improvements in both cryo-EM hardware and image processing software continue to contribute to an exponential growth in the number of structures solved annually. In this review, we provide a historical view of the many steps that were required to make cryo-EM a successful method for the determination of high-resolution protein complex structures. We further discuss aspects of cryo-EM methodology that are the greatest pitfalls challenging successful structure determination to date. Lastly, we highlight and propose potential future developments that would improve the method even further in the near future.
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Affiliation(s)
- Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany;
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23
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Mons E, Kim RQ, Mulder MPC. Technologies for Direct Detection of Covalent Protein-Drug Adducts. Pharmaceuticals (Basel) 2023; 16:547. [PMID: 37111304 PMCID: PMC10146396 DOI: 10.3390/ph16040547] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
In the past two decades, drug candidates with a covalent binding mode have gained the interest of medicinal chemists, as several covalent anticancer drugs have successfully reached the clinic. As a covalent binding mode changes the relevant parameters to rank inhibitor potency and investigate structure-activity relationship (SAR), it is important to gather experimental evidence on the existence of a covalent protein-drug adduct. In this work, we review established methods and technologies for the direct detection of a covalent protein-drug adduct, illustrated with examples from (recent) drug development endeavors. These technologies include subjecting covalent drug candidates to mass spectrometric (MS) analysis, protein crystallography, or monitoring intrinsic spectroscopic properties of the ligand upon covalent adduct formation. Alternatively, chemical modification of the covalent ligand is required to detect covalent adducts by NMR analysis or activity-based protein profiling (ABPP). Some techniques are more informative than others and can also elucidate the modified amino acid residue or bond layout. We will discuss the compatibility of these techniques with reversible covalent binding modes and the possibilities to evaluate reversibility or obtain kinetic parameters. Finally, we expand upon current challenges and future applications. Overall, these analytical techniques present an integral part of covalent drug development in this exciting new era of drug discovery.
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Affiliation(s)
- Elma Mons
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (E.M.)
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Robbert Q. Kim
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (E.M.)
| | - Monique P. C. Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (E.M.)
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24
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Atta H, Alzahaby N, Hamdy NM, Emam SH, Sonousi A, Ziko L. New trends in synthetic drugs and natural products targeting 20S proteasomes in cancers. Bioorg Chem 2023; 133:106427. [PMID: 36841046 DOI: 10.1016/j.bioorg.2023.106427] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/15/2023] [Accepted: 02/12/2023] [Indexed: 02/19/2023]
Abstract
Cancer is a global health challenge that remains to be a field of extensive research aiming to find new anticancer therapeutics. The 20S proteasome complex is one of the targets of anticancerdrugs, as it is correlated with several cancer types. Herein, we aim to discuss the 20S proteasome subunits and investigatethe currently studied proteasome inhibitors targeting the catalytically active proteasome subunits. In this review, we summarize the proteindegradation mechanism of the 20S proteasome complex and compareit with the 26S proteasome complex. Afterwards, the localization of the 20S proteasome is summarized as well as its use as a diagnosticandprognostic marker. The FDA-approved proteasome inhibitors (PIs) under clinical trials are summarized and their current limited use in solid tumors is also reviewed in addition to the expression of theβ5 subunit in differentcell lines. The review discusses in-silico analysis of the active subunit of the 20S proteasome complex. For development of new proteasome inhibitor drugs, the natural products inhibiting the 20S proteasome are summarized, as well as novel methodologies and challenges for the natural product discovery and current information about the biosynthetic gene clusters encoding them. We herein briefly summarize some resistancemechanismsto the proteasomeinhibitors. Additionally, we focus on the three main classes of proteasome inhibitors: 1] boronic acid, 2] beta-lactone and 3] epoxide inhibitor classes, as well as other PI classes, and their IC50 values and their structure-activity relationship (SAR). Lastly,we summarize several future prospects of developing new proteasome inhibitors towards the treatment of tumors, especially solid tumors.
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Affiliation(s)
- Hind Atta
- School of Life and Medical Sciences, University of Hertfordshire Hosted By Global Academic Foundation, Egypt
| | - Nouran Alzahaby
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia 11566, Cairo, Egypt
| | - Nadia M Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia 11566, Cairo, Egypt
| | - Soha H Emam
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Amr Sonousi
- School of Life and Medical Sciences, University of Hertfordshire Hosted By Global Academic Foundation, Egypt; Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Laila Ziko
- School of Life and Medical Sciences, University of Hertfordshire Hosted By Global Academic Foundation, Egypt; Biology Department, School of Sciences and Engineering, American University in Cairo, Egypt.
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25
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Allardyce D, Adu Mantey P, Szalecka M, Nkwo R, Loizidou EZ. Identification of a new class of proteasome inhibitors based on a naphthyl-azotricyclic-urea-phenyl scaffold. RSC Med Chem 2023; 14:573-582. [PMID: 36970145 PMCID: PMC10034219 DOI: 10.1039/d2md00404f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/06/2023] [Indexed: 02/09/2023] Open
Abstract
Proteasomes play an important role in protein degradation and regulation of many cellular pathways by maintaining protein balance. Inhibitors of proteasomes disrupt this balance affecting proteins that are key in malignancies and as such have found applications in the treatment of multiple myeloma and mantle cell lymphoma. However, resistance mechanisms have been reported for these proteasome inhibitors including mutations at the β5 site which necessitates the constant development of new inhibitors. In this work, we report the identification of a new class of proteasome inhibitors, polycyclic molecules bearing a naphthyl-azotricyclic-urea-phenyl scaffold, from screening of the ZINC library of natural products. The most potent of these compounds showed evidence of dose dependency through proteasome assays with IC50 values in the low micromolar range, and kinetic analysis revealed competitive binding at the β5c site with an estimated inhibition constant, K i, of 1.15 μM. Inhibition was also shown for the β5i site of the immunoproteasome at levels similar to those of the constitutive proteasome. Structure-activity relationship studies identified the naphthyl substituent to be crucial for activity and this was attributed to enhanced hydrophobic interactions within β5c. Further to this, halogen substitution within the naphthyl ring enhanced the activity and allowed for π-π interactions with Y169 in β5c and Y130 and F124 in β5i. The combined data highlight the importance of hydrophobic and halogen interactions in β5 binding and assist in the design of next generation inhibitors of proteasomes.
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Affiliation(s)
- Duncan Allardyce
- Faculty of Science and Technology, Department of Natural Sciences, Middlesex University The Burroughs London NW4 4BT UK
| | - Priscilla Adu Mantey
- Faculty of Science and Technology, Department of Natural Sciences, Middlesex University The Burroughs London NW4 4BT UK
| | - Monika Szalecka
- Faculty of Science and Technology, Department of Natural Sciences, Middlesex University The Burroughs London NW4 4BT UK
| | - Robert Nkwo
- Faculty of Science and Technology, Department of Natural Sciences, Middlesex University The Burroughs London NW4 4BT UK
| | - Eriketi Z Loizidou
- Faculty of Science and Technology, Department of Natural Sciences, Middlesex University The Burroughs London NW4 4BT UK
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26
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Wang X, Zhang H, Wang Y, Bramasole L, Guo K, Mourtada F, Meul T, Hu Q, Viteri V, Kammerl I, Konigshoff M, Lehmann M, Magg T, Hauck F, Fernandez IE, Meiners S. DNA sensing via the cGAS/STING pathway activates the immunoproteasome and adaptive T-cell immunity. EMBO J 2023; 42:e110597. [PMID: 36912165 PMCID: PMC10106989 DOI: 10.15252/embj.2022110597] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/09/2023] [Accepted: 02/20/2023] [Indexed: 03/14/2023] Open
Abstract
The immunoproteasome is a specialized type of proteasome involved in MHC class I antigen presentation, antiviral adaptive immunity, autoimmunity, and is also part of a broader response to stress. Whether the immunoproteasome is regulated by DNA stress, however, is not known. We here demonstrate that mitochondrial DNA stress upregulates the immunoproteasome and MHC class I antigen presentation pathway via cGAS/STING/type I interferon signaling resulting in cell autonomous activation of CD8+ T cells. The cGAS/STING-induced adaptive immune response is also observed in response to genomic DNA and is conserved in epithelial and mesenchymal cells of mice and men. In patients with idiopathic pulmonary fibrosis, chronic activation of the cGAS/STING-induced adaptive immune response in aberrant lung epithelial cells concurs with CD8+ T-cell activation in diseased lungs. Genetic depletion of the immunoproteasome and specific immunoproteasome inhibitors counteract DNA stress induced cytotoxic CD8+ T-cell activation. Our data thus unravel cytoplasmic DNA sensing via the cGAS/STING pathway as an activator of the immunoproteasome and CD8+ T cells. This represents a novel potential pathomechanism for pulmonary fibrosis that opens new therapeutic perspectives.
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Affiliation(s)
- Xinyuan Wang
- Comprehensive Pneumology Center (CPC), Member of the German Center for Lung Research (DZL), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Munich, Germany.,State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Huabin Zhang
- Neurosurgical Research, Department of Neurosurgery, University Hospital and Walter-Brendel-Centre of Experimental Medicine, Faculty of Medicine, Ludwig-Maximilians-University, Munich, Germany.,The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuqin Wang
- Research Center Borstel/Leibniz Lung Center, Borstel, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany.,Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Laylan Bramasole
- Research Center Borstel/Leibniz Lung Center, Borstel, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany.,Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Kai Guo
- Research Center Borstel/Leibniz Lung Center, Borstel, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany.,Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Fatima Mourtada
- Research Center Borstel/Leibniz Lung Center, Borstel, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany.,Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Thomas Meul
- Comprehensive Pneumology Center (CPC), Member of the German Center for Lung Research (DZL), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Munich, Germany
| | - Qianjiang Hu
- Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), University Hospital Grosshadern, Ludwig-Maximilians-University, Munich, Germany
| | - Valeria Viteri
- Comprehensive Pneumology Center (CPC), Member of the German Center for Lung Research (DZL), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Munich, Germany
| | - Ilona Kammerl
- Comprehensive Pneumology Center (CPC), Member of the German Center for Lung Research (DZL), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Munich, Germany
| | - Melanie Konigshoff
- Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), University Hospital Grosshadern, Ludwig-Maximilians-University, Munich, Germany.,Division of Pulmonary, Allergy and Critical Care Medicine, School of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mareike Lehmann
- Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), University Hospital Grosshadern, Ludwig-Maximilians-University, Munich, Germany
| | - Thomas Magg
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian Hauck
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Isis E Fernandez
- Comprehensive Pneumology Center (CPC), Member of the German Center for Lung Research (DZL), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Munich, Germany.,Department of Medicine V, University Hospital, LMU Munich, Munich, Germany
| | - Silke Meiners
- Comprehensive Pneumology Center (CPC), Member of the German Center for Lung Research (DZL), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum München, Munich, Germany.,Research Center Borstel/Leibniz Lung Center, Borstel, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany.,Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
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27
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Zeng G, Yu Q, Zhuang R, Zhu H, Shao J, Xi J, Zhang J. Recent Advances and Future Perspectives of Noncompetitive Proteasome Inhibitors. Bioorg Chem 2023; 135:106507. [PMID: 37030106 DOI: 10.1016/j.bioorg.2023.106507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/17/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
The proteasome regulates intracellular processes, maintains biological homeostasis, and has shown great significance in the study of various diseases, such as neurodegenerative diseases, immune-related diseases, and cancer, especially in hematologic malignancies such as multiple myeloma (MM) and mantle cell lymphoma (MCL). All clinically used proteasome inhibitors bind to the active site of the proteasome and thus exhibit a competitive mechanism. The development of resistance and intolerance during treatment drives the search for inhibitors with different mechanisms of action. In this review, we provide an overview of noncompetitive proteasome inhibitors, including their mechanisms of action, function, possible applications, and their advantages and disadvantages compared with competitive inhibitors.
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28
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Miltner N, Kalló G, Csősz É, Miczi M, Nagy T, Mahdi M, Mótyán JA, Tőzsér J. Identification of SARS-CoV-2 Main Protease (Mpro) Cleavage Sites Using Two-Dimensional Electrophoresis and In Silico Cleavage Site Prediction. Int J Mol Sci 2023; 24:ijms24043236. [PMID: 36834648 PMCID: PMC9965337 DOI: 10.3390/ijms24043236] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/03/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a crucial role in its life cycle. The Mpro-mediated limited proteolysis of the viral polyproteins is necessary for the replication of the virus, and cleavage of the host proteins of the infected cells may also contribute to viral pathogenesis, such as evading the immune responses or triggering cell toxicity. Therefore, the identification of host substrates of the viral protease is of special interest. To identify cleavage sites in cellular substrates of SARS-CoV-2 Mpro, we determined changes in the HEK293T cellular proteome upon expression of the Mpro using two-dimensional gel electrophoresis. The candidate cellular substrates of Mpro were identified by mass spectrometry, and then potential cleavage sites were predicted in silico using NetCorona 1.0 and 3CLP web servers. The existence of the predicted cleavage sites was investigated by in vitro cleavage reactions using recombinant protein substrates containing the candidate target sequences, followed by the determination of cleavage positions using mass spectrometry. Unknown and previously described SARS-CoV-2 Mpro cleavage sites and cellular substrates were also identified. Identification of target sequences is important to understand the specificity of the enzyme, as well as aiding the improvement and development of computational methods for cleavage site prediction.
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Affiliation(s)
- Noémi Miltner
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Gergő Kalló
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Éva Csősz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Márió Miczi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Tibor Nagy
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Mohamed Mahdi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (J.A.M.); (J.T.); Tel.: +36-52-512-900 (J.A.M. & J.T.)
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (J.A.M.); (J.T.); Tel.: +36-52-512-900 (J.A.M. & J.T.)
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29
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Zhan W, Li D, Saha P, Wang R, Zhang H, Ajay AK, Deban C, Sukenick G, Azzi J, Lin G. Discovery of Highly Selective Inhibitors of the Human Constitutive Proteasome β5c Chymotryptic Subunit. J Med Chem 2023; 66:1172-1185. [PMID: 36608337 PMCID: PMC10157300 DOI: 10.1021/acs.jmedchem.2c00733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We describe our discovery and development of potent and highly selective inhibitors of human constitutive proteasome chymotryptic activity (β5c). Structure-activity relationship studies of the novel class of inhibitors focused on optimization of N-cap, C-cap, and side chain of the chemophore asparagine. Compound 32 is the most potent and selective β5c inhibitor in this study. A docking study provides a structure rationale for potency and selectivity. Kinetic studies show a reversible and noncompetitive inhibition mechanism. It enters the cells to engage the proteasome target, potently and selectively kills multiple myeloma cells, and does so by synergizing with a β5i-selective inhibitor.
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Affiliation(s)
- Wenhu Zhan
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, United States
| | - Daqiang Li
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, United States
| | - Priya Saha
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, United States
| | - Rong Wang
- NMR Analytical Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Hao Zhang
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, United States
| | - Amrendra K. Ajay
- Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Christa Deban
- Transplantation Research Center, Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - George Sukenick
- NMR Analytical Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, United States
| | - Jamil Azzi
- Renal Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gang Lin
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065, United States
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30
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High-Throughput Screening of FDA-Approved Drug Library Reveals Ixazomib Is a Broad-Spectrum Antiviral Agent against Arboviruses. Viruses 2022; 14:v14071381. [PMID: 35891362 PMCID: PMC9322861 DOI: 10.3390/v14071381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
The emergence of significant arboviruses and their spillover transmission to humans represent a major threat to global public health. No approved drugs are available for the treatment of significant arboviruses in circulation today. The repurposing of clinically approved drugs is one of the most rapid and promising strategies in the identification of effective treatments for diseases caused by arboviruses. Here, we screened small-molecule compounds with anti-tick-borne encephalitis virus, West Nile virus, yellow fever virus and chikungunya virus activity from 2580 FDA-approved drugs. In total, 60 compounds showed antiviral efficacy against all four of the arboviruses in Huh7 cells. Among these compounds, ixazomib and ixazomib citrate (inhibitors of 20S proteasome β5) exerted antiviral effects at a low-micromolar concentration. The time-of-drug-addition assay suggested that ixazomib and ixazomib citrate disturbed multiple processes in viruses’ life cycles. Furthermore, ixazomib and ixazomib citrate potently inhibited chikungunya virus replication and relieved virus-induced footpad swelling in a mouse model. These results offer critical information which supports the role of ixazomib as a broad-spectrum agent against arboviruses.
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31
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Exploring the Anticancer Effects of Brominated Plastoquinone Analogs with Promising Cytotoxic Activity in MCF-7 Breast Cancer Cells via Cell Cycle Arrest and Oxidative Stress Induction. Pharmaceuticals (Basel) 2022; 15:ph15070777. [PMID: 35890076 PMCID: PMC9318129 DOI: 10.3390/ph15070777] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 02/04/2023] Open
Abstract
Plastoquinone analogs are privileged structures among the known antiproliferative natural product-based compound families. Exploiting one of these analogs as a lead structure, we report the investigation of the brominated PQ analogs (BrPQ) in collaboration with the National Cancer Institute of Bethesda within the Developmental Therapeutics Program (DTP). These analogs exhibited growth inhibition in the micromolar range across leukemia, non-small cell lung cancer (EKVX, HOP-92, and NCI-H522), colon cancer (HCT-116, HOP-92), melanoma (LOX IMVI), and ovarian cancer (OVCAR-4) cell lines. One brominated PQ analog (BrPQ5) was selected for a full panel five-dose in vitro assay by the NCI’s Development Therapeutic Program (DTP) division to determine GI50, TGI, and LC50 parameters. The brominated PQ analog (BrPQ5) displayed remarkable activity against most tested cell lines, with GI50 values ranging from 1.55 to 4.41 µM. The designed molecules (BrPQ analogs) obeyed drug-likeness rules, displayed a favorable predictive Absorption, Distribution, Metabolism, and Excretion (ADME) profile, and an in silico simulation predicted a possible BrPQ5 interaction with proteasome catalytic subunits. Furthermore, the in vitro cytotoxic activity of BrPQ5 was assessed, and IC50 values for U-251 glioma, MCF-7 and MDA-MB-231 breast cancers, DU145 prostate cancer, HCT-116 colon cancer, and VHF93 fibroblast cell lines were evaluated using an MTT assay. MCF-7 was the most affected cell line, and the effects of BrPQ5 on cell proliferation, cell cycle, oxidative stress, apoptosis/necrosis induction, and proteasome activity were further investigated in MCF-7 cells. The in vitro assay results showed that BrPQ5 caused cytotoxicity in MCF-7 breast cancer cells via cell cycle arrest and oxidative stress induction. However, BrPQ5 did not inhibit the catalytic activity of the proteasome. These results provide valuable insights for further discovery of novel antiproliferative agents.
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32
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Alves C, Silva J, Afonso MB, Guedes RA, Guedes RC, Alvariño R, Pinteus S, Gaspar H, Goettert MI, Alfonso A, Rodrigues CMP, Alpoím MC, Botana L, Pedrosa R. Disclosing the antitumour potential of the marine bromoditerpene sphaerococcenol A on distinct cancer cellular models. Biomed Pharmacother 2022; 149:112886. [PMID: 35378501 DOI: 10.1016/j.biopha.2022.112886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 11/30/2022] Open
Abstract
Nature has revealed to be a key source of innovative anticancer drugs. This study evaluated the antitumour potential of the marine bromoditerpene sphaerococcenol A on different cancer cellular models. Dose-response analyses (0.1-100 µM; 24 h) were accomplished in eight different tumour cell lines (A549, CACO-2, HCT-15, MCF-7, NCI-H226, PC-3, SH-SY5Y, SK-MEL-28). Deeper studies were conducted on MFC-7 cells, namely, determination of hydrogen peroxide (H2O2) levels and evaluation of apoptosis biomarkers (phosphatidylserine membrane translocation, mitochondrial dysfunction, Caspase-9 activity, and DNA changes). The ability of the compound to induce genotoxicity was verified in L929 fibroblasts. Sphaerococcenol A capacity to impact colorectal-cancer stem cells (CSCs) tumourspheres (HT29, HCT116, SW620) was evaluated by determining tumourspheres viability, number, and area, as well as the proteasome inhibitory activity. Sphaerococcenol A hepatoxicity was studied in AML12 hepatocytes. The compound exhibited cytotoxicity in all malignant cell lines (IC50 ranging from 4.5 to 16.6 µM). MCF-7 cells viability loss was accompanied by H2O2 generation, mitochondrial dysfunction, Caspase-9 activation and DNA nuclear morphology changes. Furthermore, the compound displayed the lowest IC50 on HT29-derived tumourspheres (0.70 µM), followed by HCT116 (1.77 µM) and SW620 (2.74 µM), impacting the HT29 tumoursphere formation by reducing their number and area. Finally, the compound displayed low cytotoxicity on AML12 hepatocytes without genotoxicity. Overall, sphaerococcenol A exhibits broad cytotoxic effects on different tumour cells, increasing H2O2 production and apoptosis. It also affects colorectal CSCs-enriched tumoursphere development. These data highlight the relevance to include sphaerococcenol A in further pharmacological studies aiming cancer treatments.
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Affiliation(s)
- Celso Alves
- MARE-Marine and Environmental Sciences Centre, Politécnico de Leiria, 2520-630 Peniche, Portugal.
| | - Joana Silva
- MARE-Marine and Environmental Sciences Centre, Politécnico de Leiria, 2520-630 Peniche, Portugal
| | - Marta B Afonso
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Romina A Guedes
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Rita C Guedes
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Rebeca Alvariño
- Department of Pharmacology, Faculty of Veterinary, University of Santiago de Compostela, 27002 Lugo, Spain
| | - Susete Pinteus
- MARE-Marine and Environmental Sciences Centre, Politécnico de Leiria, 2520-630 Peniche, Portugal
| | - Helena Gaspar
- MARE-Marine and Environmental Sciences Centre, Politécnico de Leiria, 2520-630 Peniche, Portugal; BioISI - Biosystems and Integrative Sciences Institute Faculty of Science, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Márcia I Goettert
- Cell Culture Laboratory, Postgraduate Programme in Biotechnology, University of Vale do Taquari - Univates, Lajeado, RS 95914-014, Brazil
| | - Amparo Alfonso
- Department of Pharmacology, Faculty of Veterinary, University of Santiago de Compostela, 27002 Lugo, Spain
| | - Cecília M P Rodrigues
- Research Institute for Medicines (iMed.ULisboa) Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Maria C Alpoím
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-517 Coimbra, Portugal
| | - Luis Botana
- Department of Pharmacology, Faculty of Veterinary, University of Santiago de Compostela, 27002 Lugo, Spain
| | - Rui Pedrosa
- MARE-Marine and Environmental Sciences Centre, ESTM, Politécnico de Leiria, 2520-614 Peniche, Portugal.
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33
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Mercier R, LaPointe P. The role of cellular proteostasis in anti-tumor immunity. J Biol Chem 2022; 298:101930. [PMID: 35421375 PMCID: PMC9108985 DOI: 10.1016/j.jbc.2022.101930] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/21/2022] [Accepted: 03/31/2022] [Indexed: 12/25/2022] Open
Abstract
Immune checkpoint blockade therapy is perhaps the most important development in cancer treatment in recent memory. It is based on decades of investigation into the biology of immune cells and the role of the immune system in controlling cancer growth. While the molecular circuitry that governs the immune system in general - and anti-tumor immunity in particular - is intensely studied, far less attention has been paid to the role of cellular stress in this process. Proteostasis, intimately linked to cell stress responses, refers to the dynamic regulation of the cellular proteome and is maintained through a complex network of systems that govern the synthesis, folding, and degradation of proteins in the cell. Disruption of these systems can result in the loss of protein function, altered protein function, the formation of toxic aggregates, or pathologies associated with cell stress. However, the importance of proteostasis extends beyond its role in maintaining proper protein function; proteostasis governs how tolerant cells may be to mutations in protein coding genes and the overall half-life of proteins. Such gene expression changes may be associated with human diseases including neurodegenerative diseases, metabolic disease, and cancer and manifest at the protein level against the backdrop of the proteostasis network in any given cellular environment. In this review, we focus on the role of proteostasis in regulating immune responses against cancer as well the role of proteostasis in determining immunogenicity of cancer cells.
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Affiliation(s)
- Rebecca Mercier
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Paul LaPointe
- Department of Cell Biology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada.
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34
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Revisiting Proteasome Inhibitors: Molecular Underpinnings of Their Development, Mechanisms of Resistance and Strategies to Overcome Anti-Cancer Drug Resistance. Molecules 2022; 27:molecules27072201. [PMID: 35408601 PMCID: PMC9000344 DOI: 10.3390/molecules27072201] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
Proteasome inhibitors have shown relevant clinical activity in several hematological malignancies, namely in multiple myeloma and mantle cell lymphoma, improving patient outcomes such as survival and quality of life, when compared with other therapies. However, initial response to the therapy is a challenge as most patients show an innate resistance to proteasome inhibitors, and those that respond to the therapy usually develop late relapses suggesting the development of acquired resistance. The mechanisms of resistance to proteasome inhibition are still controversial and scarce in the literature. In this review, we discuss the development of proteasome inhibitors and the mechanisms of innate and acquired resistance to their activity—a major challenge in preclinical and clinical therapeutics. An improved understanding of these mechanisms is crucial to guiding the design of new and more effective drugs to tackle these devastating diseases. In addition, we provide a comprehensive overview of proteasome inhibitors used in combination with other chemotherapeutic agents, as this is a key strategy to combat resistance.
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35
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Dai Z, An LY, Chen XY, Yang F, Zhao N, Li CC, Ren R, Li BY, Tao WY, Li P, Jiang C, Yan F, Jiang ZY, You QD, Di B, Xu LL. Target Fishing Reveals a Novel Mechanism of 1,2,4-Oxadiazole Derivatives Targeting Rpn6, a Subunit of 26S Proteasome. J Med Chem 2022; 65:5029-5043. [PMID: 35253427 DOI: 10.1021/acs.jmedchem.1c02210] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1,2,4-Oxadiazole derivatives, a class of Nrf2-ARE activators, exert an extensive therapeutic effect on inflammation, cancer, neurodegeneration, and microbial infection. Among these analogues, DDO-7263 is the most potent Nrf2 activator and used as the core structure for bioactive probes to explore the precise mechanism. In this work, we obtained compound 7, a mimic of DDO-7263, and biotin-labeled and fluorescein-based probes, which exhibited homologous biological activities to DDO-7263, including activating Nrf2 and its downstream target genes, anti-oxidative stress, and anti-inflammatory effects. Affinity chromatography and mass analysis techniques revealed Rpn6 as the potential target protein regulating the Nrf2 signaling pathway. In vitro affinity experiments further confirmed that DDO-7263 upregulated Nrf2 through binding to Rpn6 to block the assembly of 26S proteasome and the subsequent degradation of ubiquitinated Nrf2. These results indicated that Rpn6 is a promising candidate target to activate the Nrf2 pathway for protecting cells and tissues from oxidative, electrophilic, and exogenous microbial stimulation.
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Affiliation(s)
- Zhen Dai
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Lu-Yan An
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Yi Chen
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Fan Yang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Ni Zhao
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Cui-Cui Li
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Ren Ren
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Bing-Yan Li
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Wei-Yan Tao
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Pei Li
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Cheng Jiang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Fang Yan
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Zheng-Yu Jiang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Qi-Dong You
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Bin Di
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Li-Li Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
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36
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The YΦ motif defines the structure-activity relationships of human 20S proteasome activators. Nat Commun 2022; 13:1226. [PMID: 35264557 PMCID: PMC8907193 DOI: 10.1038/s41467-022-28864-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 02/11/2022] [Indexed: 11/08/2022] Open
Abstract
The 20S proteasome (20S) facilitates turnover of most eukaryotic proteins. Substrate entry into the 20S first requires opening of gating loops through binding of HbYX motifs that are present at the C-termini of certain proteasome activators (PAs). The HbYX motif has been predominantly characterized in the archaeal 20S, whereas little is known about the sequence preferences of the human 20S (h20S). Here, we synthesize and screen ~120 HbYX-like peptides, revealing unexpected differences from the archaeal system and defining the h20S recognition sequence as the Y-F/Y (YФ) motif. To gain further insight, we create a functional chimera of the optimized sequence, NLSYYT, fused to the model activator, PA26E102A. A cryo-EM structure of PA26E102A-h20S is used to identify key interactions, including non-canonical contacts and gate-opening mechanisms. Finally, we demonstrate that the YФ sequence preferences are tuned by valency, allowing multivalent PAs to sample greater sequence space. These results expand the model for termini-mediated gating and provide a template for the design of h20S activators. The proteasome complexes, composed of 20S core particles and one or two regulatory particles (proteasome activators), degrade most eukaryotic proteins. Here, the authors identify a sequence motif and resolve its interactions mediating the activation of the human 20S proteasome.
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37
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Liu H, Du X, Zhang J, Li J, Chen S, Duanmu H, Li H. Quantitative redox proteomics revealed molecular mechanisms of salt tolerance in the roots of sugar beet monomeric addition line M14. BOTANICAL STUDIES 2022; 63:5. [PMID: 35247135 PMCID: PMC8898211 DOI: 10.1186/s40529-022-00337-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 02/23/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND Salt stress is often associated with excessive production of reactive oxygen species (ROS). Oxidative stress caused by the accumulation of ROS is a major factor that negatively affects crop growth and yield. Root is the primary organ that senses and transmits the salt stress signal to the whole plant. How oxidative stress affect redox sensitive proteins in the roots is not known. RESULTS In this study, the redox proteome of sugar beet M14 roots under salt stress was investigated. Using iTRAQ reporters, we determined that salt stress caused significant changes in the abundance of many proteins (2305 at 20 min salt stress and 2663 at 10 min salt stress). Using iodoTMT reporters, a total of 95 redox proteins were determined to be responsive to salt stress after normalizing again total protein level changes. Notably, most of the differential redox proteins were involved in metabolism, ROS homeostasis, and stress and defense, while a small number play a role in transport, biosynthesis, signal transduction, transcription and photosynthesis. Transcription levels of 14 genes encoding the identified redox proteins were analyzed using qRT-PCR. All the genes were induced by salt stress at the transcriptional level. CONCLUSIONS Based on the redox proteomics results, we construct a map of the regulatory network of M14 root redox proteins in response to salt stress. This study further refines the molecular mechanism of salt resistance at the level of protein redox regulation.
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Affiliation(s)
- He Liu
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin, 150080, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150080, China
| | - Xiaoxue Du
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin, 150080, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150080, China
| | - Jialin Zhang
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin, 150080, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150080, China
| | - Jinna Li
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin, 150080, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150080, China
| | - Sixue Chen
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA
- Department of Biology, Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA
| | - Huizi Duanmu
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin, 150080, China.
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, 150080, China.
| | - Haiying Li
- Key Laboratory of Molecular Biology of Heilongjiang Province, College of Life Sciences, Heilongjiang University, Harbin, 150080, China.
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150080, China.
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38
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Tyagi R, Srivastava M, Jain P, Pandey RP, Asthana S, Kumar D, Raj VS. Development of potential proteasome inhibitors against Mycobacterium tuberculosis. J Biomol Struct Dyn 2022; 40:2189-2203. [PMID: 33074049 DOI: 10.1080/07391102.2020.1835722] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 10/08/2020] [Indexed: 10/23/2022]
Abstract
Tuberculosis (TB) has been recently declared as a health emergency because of sporadic increase in Multidrug-resistant Tuberculosis (MDR-TB) problem throughout the world. TB causing bacteria, Mycobacterium tuberculosis has become resistant to the first line of treatment along with second line of treatment and drugs, which are accessible to us. Thus, there is an urgent need of identification of key targets and development of potential therapeutic approach(s), which can overcome the Mycobacterium tuberculosis complications. In the present study, Mycobacterium tuberculosis proteasome has been taken as a potential target as it is one of the key regulatory proteins in Mycobacterium tuberculosis propagation. Further, a library of 400 compounds (small molecule) from Medicines for Malaria Venture (MMV) were screened against the target (proteasome) using molecular docking and simulation approach, and selected lead compounds were validated in in vitro model. In this study, we have identified two potent small molecules from the MMV Pathogen Box library, MMV019838 and MMV687146 with -9.8 kcal/mol and -8.7 kcal/mol binding energy respectively, which actively interact with the catalytic domain/active domain of Mycobacterium tuberculosis proteasome and inhibit the Mycobacterium tuberculosis growth in in vitro culture. Furthermore, the molecular docking and simulation study of MMV019838 and MMV687146 with proteasome show strong and stable interaction with Mycobacterium tuberculosis compared to human proteasome and show no cytotoxicity effect. A better understanding of proteasome inhibition in Mycobacterium tuberculosis in in vitro and in vivo model would eventually allow us to understand the molecular mechanism(s) and discover a novel and potent therapeutic agent against Tuberculosis. Active efflux of drugs mediated by efflux pumps that confer drug resistance is one of the mechanisms developed by bacteria to counter the adverse effects of antibiotics and chemicals. Efflux pump activity was tested for a specific compound MMV019838 which was showing good in silico results than MIC values.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rashmi Tyagi
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi, Haryana, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Preeti Jain
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi, Haryana, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Dhruv Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida, India
| | - V Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi, Haryana, India
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39
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Insulin-Degrading Enzyme Is a Non Proteasomal Target of Carfilzomib and Affects the 20S Proteasome Inhibition by the Drug. Biomolecules 2022; 12:biom12020315. [PMID: 35204815 PMCID: PMC8869475 DOI: 10.3390/biom12020315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/12/2022] [Accepted: 01/27/2022] [Indexed: 02/07/2023] Open
Abstract
Carfilzomib is a last generation proteasome inhibitor (PI) with proven clinical efficacy in the treatment of relapsed/refractory multiple myeloma. This drug is considered to be extremely specific in inhibiting the chymotrypsin-like activity of the 20S proteasome, encoded by the β5 subunit, overcoming some bortezomib limitations, the first PI approved for multiple myeloma therapy which is however burdened by a significant toxicity profile, due also to its off-target effects. Here, molecular approaches coupled with molecular docking studies have been used to unveil that the Insulin-Degrading Enzyme, a ubiquitous and highly conserved Zn2+ peptidase, often found to associate with proteasome in cell-based models, is targeted by carfilzomib in vitro. The drug behaves as a modulator of IDE activity, displaying an inhibitory effect over 10-fold lower than for the 20S. Notably, the interaction of IDE with the 20S enhances in vitro the inhibitory power of carfilzomib on proteasome, so that the IDE-20S complex is an even better target of carfilzomib than the 20S alone. Furthermore, IDE gene silencing after delivery of antisense oligonucleotides (siRNA) significantly reduced carfilzomib cytotoxicity in rMC1 cells, a validated model of Muller glia, suggesting that, in cells, the inhibitory activity of this drug on cell proliferation is somewhat linked to IDE and, possibly, also to its interaction with proteasome.
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40
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Chan CW, Yong CY, Chang HM, Ng PY, Davamani F, Chitra E, Lee VS, Tan KW, Maah MJ, Ng CH. Anticancer chiral and racemic ternary copper(II) complexes: Multiple mechanisms and epigenetic histone methyltransferase enzymes as novel targets. Polyhedron 2022. [DOI: 10.1016/j.poly.2021.115617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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41
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The Central Role of the Ubiquitin-Proteasome System in EBV-Mediated Oncogenesis. Cancers (Basel) 2022; 14:cancers14030611. [PMID: 35158879 PMCID: PMC8833352 DOI: 10.3390/cancers14030611] [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: 12/08/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Epstein–Barr virus (EBV) is the first discovered human tumor virus, which contributes to the oncogenesis of many human cancers. The ubiquitin–proteasome system is a key player during EBV-mediated oncogenesis and has been developed as a crucial therapeutic target for treatment. In this review, we briefly describe how EBV antigens can modulate the ubiquitin–proteasome system for targeted protein degradation and how they are regulated in the EBV life cycle to mediate oncogenesis. Additionally, the developed proteasome inhibitors are discussed for the treatment of EBV-associated cancers. Abstract Deregulation of the ubiquitin–proteasome system (UPS) plays a critical role in the development of numerous human cancers. Epstein–Barr virus (EBV), the first known human tumor virus, has evolved distinct molecular mechanisms to manipulate the ubiquitin–proteasome system, facilitate its successful infection, and drive opportunistic cancers. The interactions of EBV antigens with the ubiquitin–proteasome system can lead to oncogenesis through the targeting of cellular factors involved in proliferation. Recent studies highlight the central role of the ubiquitin–proteasome system in EBV infection. This review will summarize the versatile strategies in EBV-mediated oncogenesis that contribute to the development of specific therapeutic approaches to treat EBV-associated malignancies.
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42
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Wang J, Fang Y, Fan RA, Kirk CJ. Proteasome Inhibitors and Their Pharmacokinetics, Pharmacodynamics, and Metabolism. Int J Mol Sci 2021; 22:ijms222111595. [PMID: 34769030 PMCID: PMC8583966 DOI: 10.3390/ijms222111595] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022] Open
Abstract
The proteasome is responsible for mediating intracellular protein degradation and regulating cellular function with impact on tumor and immune effector cell biology. The proteasome is found predominantly in two forms, the constitutive proteasome and the immunoproteasome. It has been validated as a therapeutic drug target through regulatory approval with 2 distinct chemical classes of small molecular inhibitors (boronic acid derivatives and peptide epoxyketones), including 3 compounds, bortezomib (VELCADE), carfilzomib (KYPROLIS), and ixazomib (NINLARO), for use in the treatment of the plasma cell neoplasm, multiple myeloma. Additionally, a selective inhibitor of immunoproteasome (KZR-616) is being developed for the treatment of autoimmune diseases. Here, we compare and contrast the pharmacokinetics (PK), pharmacodynamics (PD), and metabolism of these 2 classes of compounds in preclinical models and clinical studies. The distinct metabolism of peptide epoxyketones, which is primarily mediated by microsomal epoxide hydrolase, is highlighted and postulated as a favorable property for the development of this class of compound in chronic conditions.
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Fang Y, Johnson H, Anderl JL, Muchamuel T, McMinn D, Morisseau C, Hammock BD, Kirk C, Wang J. Role of Epoxide Hydrolases and Cytochrome P450s on Metabolism of KZR-616, a First-in-Class Selective Inhibitor of the Immunoproteasome. Drug Metab Dispos 2021; 49:810-821. [PMID: 34234005 DOI: 10.1124/dmd.120.000307] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 06/24/2021] [Indexed: 11/22/2022] Open
Abstract
KZR-616 is an irreversible tripeptide epoxyketone-based selective inhibitor of the human immunoproteasome. Inhibition of the immunoproteasome results in anti-inflammatory activity in vitro and based on promising therapeutic activity in animal models of rheumatoid arthritis and systemic lupus erythematosus KZR-616 is being developed for potential treatment of multiple autoimmune and inflammatory diseases. The presence of a ketoepoxide pharmacophore presents unique challenges in the study of drug metabolism during lead optimization and clinical candidate profiling. This study presents a thorough and systematic in vitro and cell-based enzymatic metabolism and kinetic investigation to identify the major enzymes involved in the metabolism and elimination of KZR-616. Upon exposure to liver microsomes in the absence of NADPH, KZR-616 and its analogs were converted to their inactive diol derivatives with varying degrees of stability. Diol formation was also shown to be the major metabolite in pharmacokinetic studies in monkeys and correlated with in vitro stability results for individual compounds. Further study in intact hepatocytes revealed that KZR-616 metabolism was sensitive to an inhibitor of microsomal epoxide hydrolase (mEH) but not inhibitors of cytochrome P450 (P450) or soluble epoxide hydrolase (sEH). Primary human hepatocytes were determined to be the most robust source of mEH activity for study in vitro. These findings also suggest that the exposure of KZR-616 in vivo is unlikely to be affected by coadministration of inhibitors or inducers of P450 and sEH. SIGNIFICANCE STATEMENT: This work presents a thorough and systematic investigation of metabolism and kinetics of KZR-616 and related analogs in in vitro and cell-based enzymatic systems. Information gained could be useful in assessing novel covalent proteasome inhibitors during lead compound optimization. These studies also demonstrate a robust source in vitro test system that correlated with in vivo pharmacokinetics for KZR-616 and two additional tripeptide epoxyketones.
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Affiliation(s)
- Ying Fang
- Kezar Life Sciences, South San Francisco, California
| | - Henry Johnson
- Kezar Life Sciences, South San Francisco, California
| | | | | | - Dustin McMinn
- Kezar Life Sciences, South San Francisco, California
| | | | | | | | - Jinhai Wang
- Kezar Life Sciences, South San Francisco, California
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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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45
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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: 2.5] [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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46
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The proteasome and its role in the nervous system. Cell Chem Biol 2021; 28:903-917. [PMID: 33905676 DOI: 10.1016/j.chembiol.2021.04.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/04/2021] [Accepted: 04/05/2021] [Indexed: 12/14/2022]
Abstract
Proteasomes are multisubunit complexes that catalyze the majority of protein degradation in mammalian cells to maintain protein homeostasis and influence the regulation of most cellular processes. The proteasome, a multicatalytic protease complex, is a ring-like structure with a narrow pore that exhibits regulated gating, enabling the selective degradation of target proteins into peptide fragments. This process of removing proteins is essential for eliminating proteins that are no longer wanted, such as unfolded or aggregated proteins. This is important for preserving cellular function relevant to brain health and disease. Recently, in the nervous system, specialized proteasomes have been shown to generate peptides with important cellular functions. These discoveries challenge the prevailing notion that proteasomes primarily operate to eliminate proteins and identify signaling-competent proteasomes. This review focuses on the structure, function, and regulation of proteasomes and sheds light on emerging areas of investigation regarding the role of proteasomes in the nervous system.
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47
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Mendes ML, Dittmar G. Analysis of the Dynamic Proteasome Structure by Cross-Linking Mass Spectrometry. Biomolecules 2021; 11:biom11040505. [PMID: 33801594 PMCID: PMC8067131 DOI: 10.3390/biom11040505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
The 26S proteasome is a macromolecular complex that degrades proteins maintaining cell homeostasis; thus, determining its structure is a priority to understand its function. Although the 20S proteasome's structure has been known for some years, the highly dynamic nature of the 19S regulatory particle has presented a challenge to structural biologists. Advances in cryo-electron microscopy (cryo-EM) made it possible to determine the structure of the 19S regulatory particle and showed at least seven different conformational states of the proteasome. However, there are still many questions to be answered. Cross-linking mass spectrometry (CLMS) is now routinely used in integrative structural biology studies, and it promises to take integrative structural biology to the next level, answering some of these questions.
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48
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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: 0.5] [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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Song R, Qiao W, He J, Huang J, Luo Y, Yang T. Proteases and Their Modulators in Cancer Therapy: Challenges and Opportunities. J Med Chem 2021; 64:2851-2877. [PMID: 33656892 DOI: 10.1021/acs.jmedchem.0c01640] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteostasis is the process of regulating intracellular proteins to maintain the balance of the cell proteome, which is crucial for cancer cell survival. Several proteases located in the cytoplasm, mitochondria, lysosome, and extracellular environment have been identified as potential antitumor targets because of their involvement in proteostasis. Although the discovery of small-molecule inhibitors targeting proteases faces particular challenges, rapid advances in chemical biology and structural biology, and the new technology of drug discovery have facilitated the development of promising protease modulators. In this review, the protein structure and function of important tumor-related proteases and their inhibitors are presented. We also provide a prospective on advances and the outlook of new drug strategies that target these proteases.
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Affiliation(s)
- Rao Song
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wenliang Qiao
- Lung Cancer Center, Laboratory of Lung Cancer, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Jun He
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jiasheng Huang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.,Laboratory of Human Disease and Immunotherapies, West China Hospital, Sichuan University, Chengdu 610041, China
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50
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Lee MS, Lim SH, Yu AR, Hwang CY, Kang I, Yeo EJ. Carfilzomib in Combination with Bortezomib Enhances Apoptotic Cell Death in B16-F1 Melanoma Cells. BIOLOGY 2021; 10:biology10020153. [PMID: 33671902 PMCID: PMC7918982 DOI: 10.3390/biology10020153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
Simple Summary The incidence rate of metastatic melanoma has been rapidly increasing worldwide and its 5-year survival rate is very low. Due to partial responses, various side effects, and resistance to any known cancer therapeutics, more potent and safer therapeutics are needed to increase the survival rate of patients with melanoma. Since proteasome inhibitors, such as bortezomib and carfilzomib, have been suggested as treatments for various cancers, we investigated their potential for the treatment of melanoma by studying their molecular mechanisms of action in B16-F1 melanoma cells. In this study, we found that both bortezomib and carfilzomib lead to apoptosis via ER stress as well as ROS accumulation and MMP loss in melanoma cells. Bortezomib and carfilzomib synergistically reduced B16-F1 tumor growth in vitro and in a C57BL/6 xenograft mouse model. Therefore, a combination therapy with carfilzomib and bortezomib at submaximal concentrations may reduce their side effects and be beneficial for melanoma treatment. Abstract Proteasome inhibitors, such as bortezomib (BZ) and carfilzomib (CFZ), have been suggested as treatments for various cancers. To utilize BZ and/or CFZ as effective therapeutics for treating melanoma, we studied their molecular mechanisms using B16-F1 melanoma cells. Flow cytometry of Annexin V-fluorescein isothiocyanate-labeled cells indicated apoptosis induction by treatment with BZ and CFZ. Apoptosis was evidenced by the activation of various caspases, including caspase 3, 8, 9, and 12. Treatment with BZ and CFZ induced endoplasmic reticulum (ER) stress, as indicated by an increase in eIF2α phosphorylation and the expression of ER stress-associated proteins, including GRP78, ATF6α, ATF4, XBP1, and CCAAT/enhancer-binding protein homologous protein. The effects of CFZ on ER stress and apoptosis were lower than that of BZ. Nevertheless, CFZ and BZ synergistically induced ER stress and apoptosis in B16-F1 cells. Furthermore, the combinational pharmacological interactions of BZ and CFZ against the growth of B16-F1 melanoma cells were assessed by calculating the combination index and dose-reduction index with the CompuSyn software. We found that the combination of CFZ and BZ at submaximal concentrations could obtain dose reduction by exerting synergistic inhibitory effects on cell growth. Moreover, this drug combination reduced tumor growth in C57BL/6 syngeneic mice. Taken together, these results suggest that CFZ in combination with BZ may be a beneficial and potential strategy for melanoma treatment.
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Affiliation(s)
- Min Seung Lee
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Korea; (M.S.L.); (S.H.L.)
| | - So Hyun Lim
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Korea; (M.S.L.); (S.H.L.)
| | - Ah-Ran Yu
- Department of Biomedical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Korea; (A.-R.Y.); (C.Y.H.)
| | - Chi Yeon Hwang
- Department of Biomedical Sciences, Graduate School, Kyung Hee University, Seoul 02447, Korea; (A.-R.Y.); (C.Y.H.)
| | - Insug Kang
- Department of Biochemistry and Molecular Biology, School of Medicine, Biomedical Science Institute, Kyung Hee University, Seoul 02447, Korea
- Correspondence: (I.K.); (E.-J.Y.); Tel.: +82-29-610-922 (I.K.); +82-32-899-6050 (E.-J.Y.); Fax: +82-29-656-349 (I.K.); +82-32-899-6039 (E.-J.Y.)
| | - Eui-Ju Yeo
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Korea; (M.S.L.); (S.H.L.)
- Correspondence: (I.K.); (E.-J.Y.); Tel.: +82-29-610-922 (I.K.); +82-32-899-6050 (E.-J.Y.); Fax: +82-29-656-349 (I.K.); +82-32-899-6039 (E.-J.Y.)
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