1
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Tassone G, Pozzi C, Mangani S. Metal Ion Binding to Human Glutaminyl Cyclase: A Structural Perspective. Int J Mol Sci 2024; 25:8279. [PMID: 39125848 PMCID: PMC11312887 DOI: 10.3390/ijms25158279] [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: 07/24/2024] [Accepted: 07/28/2024] [Indexed: 08/12/2024] Open
Abstract
Glutaminyl-peptide cyclotransferases (QCs) convert the N-terminal glutamine or glutamate residues of protein and peptide substrates into pyroglutamate (pE) by releasing ammonia or a water molecule. The N-terminal pE modification protects peptides/proteins against proteolytic degradation by amino- or exopeptidases, increasing their stability. Mammalian QC is abundant in the brain and a large amount of evidence indicates that pE peptides are involved in the onset of neural human pathologies such as Alzheimer's and Huntington's disease and synucleinopathies. Hence, human QC (hQC) has become an intensively studied target for drug development against these diseases. Soon after its characterization, hQC was identified as a Zn-dependent enzyme, but a partial restoration of the enzyme activity in the presence of the Co(II) ion was also reported, suggesting a possible role of this metal ion in catalysis. The present work aims to investigate the structure of demetallated hQC and of the reconstituted enzyme with Zn(II) and Co(II) and their behavior in the presence of known inhibitors. Furthermore, our structural determinations provide a possible explanation for the presence of the mononuclear metal binding site of hQC, despite the presence of the same conserved metal binding motifs present in distantly related dinuclear aminopeptidase enzymes.
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Affiliation(s)
- Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018–2022, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy;
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018–2022, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy;
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via Luigi Sacconi 6, I-50019 Sesto Fiorentino, Italy
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018–2022, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy;
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2
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Wei C, Zhang H, Niu L, Zhong Q, Yan H, Wang J. 4D-QSAR, ADMET properties, and molecular dynamics simulations for designing N-substituted urea/thioureas as human glutaminyl cyclase inhibitors. Comput Biol Chem 2024; 112:108131. [PMID: 38968781 DOI: 10.1016/j.compbiolchem.2024.108131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 07/07/2024]
Abstract
Human glutaminyl cyclase (hQC) inhibitors have great potential to be used as anti- Alzheimer's disease (AD) agents by reducing the toxic pyroform of β-amyloid in the brains of AD patients. The four-dimensional quantitative structure activity relationship (4D-QSAR) model of N-substituted urea/thioureas was established with satisfying predictive ability and statistical reliability (Q2 = 0.521, R2 = 0.933, R2prep = 0.619). By utilizing the developed 4D-QSAR model, a set of new N-substituted urea/thioureas was designed and evaluated for their Absorption Distribution Metabolism Excretion and Toxicity (ADMET) properties. The results of molecular dynamics (MD) simulations, Principal component analysis (PCA), free energy landscape (FEL), dynamic cross-correlation matrix (DCCM) and molecular mechanics generalized Born Poisson-Boltzmann surface area (MM-PBSA) free energy calculations, revealed that the designed compounds were remained stable in protein binding pocket and compounds b ∼ f (-35.1 to -44.55 kcal/mol) showed higher binding free energy than that of compound 14 (-33.51 kcal/mol). The findings of this work will be a theoretical foundation for further research and experimental validation of urea/thiourea derivatives as hQC inhibitors.
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Affiliation(s)
- Chaochun Wei
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, PR China
| | - Haolin Zhang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, PR China
| | - Lexuan Niu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, PR China
| | - Qidi Zhong
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, PR China
| | - Hong Yan
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, PR China.
| | - Juan Wang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, PR China.
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3
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Mou J, Ning XL, Wang XY, Hou SY, Meng FB, Zhou C, Wu JW, Li C, Jia T, Wu X, Wu Y, Chen Y, Li GB. X-ray Structure-Guided Discovery of a Potent Benzimidazole Glutaminyl Cyclase Inhibitor That Shows Activity in a Parkinson's Disease Mouse Model. J Med Chem 2024; 67:8730-8756. [PMID: 38817193 DOI: 10.1021/acs.jmedchem.4c00049] [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: 06/01/2024]
Abstract
The secretory glutaminyl cyclase (sQC) and Golgi-resident glutaminyl cyclase (gQC) are responsible for N-terminal protein pyroglutamation and associated with various human diseases. Although several sQC/gQC inhibitors have been reported, only one inhibitor, PQ912, is currently undergoing clinic trials for the treatment of Alzheimer's disease. We report an X-ray crystal structure of sQC complexed with PQ912, revealing that the benzimidazole makes "anchor" interactions with the active site zinc ion and catalytic triad. Structure-guided design and optimization led to a series of new benzimidazole derivatives exhibiting nanomolar inhibition for both sQC and gQC. In a MPTP-induced Parkinson's disease (PD) mouse model, BI-43 manifested efficacy in mitigating locomotor deficits through reversing dopaminergic neuronal loss, reducing microglia, and decreasing levels of the sQC/gQC substrates, α-synuclein, and CCL2. This study not only offers structural basis and new leads for drug discovery targeting sQC/gQC but also provides evidence supporting sQC/gQC as potential targets for PD treatment.
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Affiliation(s)
- Jun Mou
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xiang-Li Ning
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xin-Yue Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Shu-Yan Hou
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Fan-Bo Meng
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Cong Zhou
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Jing-Wei Wu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Chunyan Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Tao Jia
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Xiaoai Wu
- Department of Nuclear Medicine, Laboratory of Clinical Nuclear Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Wu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Yongping Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Guo-Bo Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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4
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Zhou Q, Cai J, Qin F, Liu J, Li C, Xiong W, Wang Y, Xu C, Wu H. Discovery of potential scaffolds for glutaminyl cyclase inhibitors: Virtual screening, synthesis, and evaluation. Bioorg Med Chem 2024; 97:117542. [PMID: 38104495 DOI: 10.1016/j.bmc.2023.117542] [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: 08/29/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Glutaminyl cyclase (QC) plays a crucial role in the early stages of Alzheimer's disease (AD), thus inhibition of QC may be a promising strategy for the treatment of early AD. Therefore, QC inhibitors with novel chemical scaffolds may contribute to the development of additional anti-AD agents. We conducted a virtual screening of 3 million compounds from the Chemdiv and Enamine databases, to discover potential scaffolds for QC inhibitors. Three scaffolds, 120974, 147706, and 141449, were selected from this structure-based virtual screening through a combination of pharmacophore modeling, a receptor-ligand pharmacophore model, and the GALAHAD model, and furtherly filtered by chelation with zinc ion and docking properties. Consequently, three compounds, 1, 2, and 3, were designed and synthesized based on these three scaffolds, respectively. The IC50 of compounds 1 and 3 against QC were 14.19 ± 4.21 and 4.34 ± 0.35 μM, respectively. Our results indicate that the new scaffolds selected using a virtual screening process exhibit potential as novel QC inhibitors.
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Affiliation(s)
- Qingqing Zhou
- School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518055, China
| | - Jiaxin Cai
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Feixia Qin
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Jiao Liu
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Chenyang Li
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Wei Xiong
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yinan Wang
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Chenshu Xu
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China.
| | - Haiqiang Wu
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China.
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5
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Coimbra JRM, Moreira PI, Santos AE, Salvador JAR. Therapeutic potential of glutaminyl cyclases: Current status and emerging trends. Drug Discov Today 2023; 28:103644. [PMID: 37244566 DOI: 10.1016/j.drudis.2023.103644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/11/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Glutaminyl cyclase (QC) activity has been identified as a key effector in distinct biological processes. Human glutaminyl-peptide cyclotransferase (QPCT) and glutaminyl-peptide cyclotransferase-like (QPCTL) are considered attractive therapeutic targets in many human disorders, such as neurodegenerative diseases, and a range of inflammatory conditions, as well as for cancer immunotherapy, because of their capacity to modulate cancer immune checkpoint proteins. In this review, we explore the biological functions and structures of QPCT/L enzymes and highlight their therapeutic relevance. We also summarize recent developments in the discovery of small-molecule inhibitors targeting these enzymes, including an overview of preclinical and clinical studies.
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Affiliation(s)
- Judite R M Coimbra
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal; Center for Neuroscience and Cell Biology (CNC), Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Paula I Moreira
- Center for Neuroscience and Cell Biology (CNC), Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal; Laboratory of Physiology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Armanda E Santos
- Center for Neuroscience and Cell Biology (CNC), Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal; Laboratory of Biochemistry and Biology, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal.
| | - Jorge A R Salvador
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal; Center for Neuroscience and Cell Biology (CNC), Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal.
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6
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Chen D, Chen Q, Qin X, Tong P, Peng L, Zhang T, Xia C. Development and evolution of human glutaminyl cyclase inhibitors (QCIs): an alternative promising approach for disease-modifying treatment of Alzheimer's disease. Front Aging Neurosci 2023; 15:1209863. [PMID: 37600512 PMCID: PMC10435661 DOI: 10.3389/fnagi.2023.1209863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Human glutaminyl cyclase (hQC) is drawing considerable attention and emerging as a potential druggable target for Alzheimer's disease (AD) due to its close involvement in the pathology of AD via the post-translational pyroglutamate modification of amyloid-β. A recent phase 2a study has shown promising early evidence of efficacy for AD with a competitive benzimidazole-based QC inhibitor, PQ912, which also demonstrated favorable safety profiles. This finding has sparked new hope for the treatment of AD. In this review, we briefly summarize the discovery and evolution of hQC inhibitors, with a particular interest in classic Zinc binding group (ZBG)-containing chemicals reported in recent years. Additionally, we highlight several high-potency inhibitors and discuss new trends and challenges in the development of QC inhibitors as an alternative and promising disease-modifying therapy for AD.
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Affiliation(s)
- Daoyuan Chen
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Qingxiu Chen
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Xiaofei Qin
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Peipei Tong
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Liping Peng
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
| | - Tao Zhang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, School of Basic Medical Sciences, Institute of Basic Medicine, Fujian Medical University, Fuzhou, China
| | - Chunli Xia
- School of Bioengineering, Zunyi Medical University, Zhuhai, China
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7
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Tsai KC, Zhang YX, Kao HY, Fung KM, Tseng TS. Pharmacophore-driven identification of human glutaminyl cyclase inhibitors from foods, plants and herbs unveils the bioactive property and potential of Azaleatin in the treatment of Alzheimer's disease. Food Funct 2022; 13:12632-12647. [PMID: 36416361 DOI: 10.1039/d2fo02507h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Alzheimer's disease (AD) is the leading cause of disabilities in old age and a rapidly growing condition in the elderly population. AD brings significant burden and has a devastating impact on public health, society and the global economy. Thus, developing new therapeutics to combat AD is imperative. Human glutaminyl cyclase (hQC), which catalyzes the formation of neurotoxic pyroglutamate (pE)-modified β-amyloid (Aβ) peptides, is linked to the amyloidogenic process that leads to the initiation of AD. Hence, hQC is an essential target for developing anti-AD therapeutics. Here, we systematically screened and identified hQC inhibitors from natural products by pharmacophore-driven inhibitor screening coupled with biochemical and biophysical examinations. We employed receptor-ligand pharmacophore generation to build pharmacophore models and Phar-MERGE and Phar-SEN for inhibitor screening through ligand-pharmacophore mapping. About 11 and 24 hits identified from the Natural Product and Traditional Chinese Medicine databases, respectively, showed diverse hQC inhibitory abilities. Importantly, the inhibitors TCM1 (Azaleatin; IC50 = 1.1 μM) and TCM2 (Quercetin; IC50 = 4.3 μM) found in foods and plants exhibited strong inhibitory potency against hQC. Furthermore, the binding affinity and molecular interactions were analyzed by surface plasmon resonance (SPR) and molecular modeling/simulations to explore the possible modes of action of Azaleatin and Quercetin. Our study successfully screened and characterized the foundational biochemical and biophysical properties of Azaleatin and Quercetin toward targeting hQC, unveiling their bioactive potential in the treatment of AD.
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Affiliation(s)
- Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan. .,Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yi-Xuan Zhang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.
| | - Hsiang-Yun Kao
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.
| | - Kit-Man Fung
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan. .,Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tien-Sheng Tseng
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.
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8
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Endah E, Wulandari F, Putri Y, Jenie RI, Meiyanto E. Piperine Increases Pentagamavunon-1 Anti-cancer Activity on 4T1 Breast Cancer Through Mitotic Catastrophe Mechanism and Senescence with Sharing Targeting on Mitotic Regulatory Proteins. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2022; 21:e123820. [PMID: 35765510 PMCID: PMC9191230 DOI: 10.5812/ijpr.123820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/11/2021] [Accepted: 09/12/2021] [Indexed: 06/15/2023]
Abstract
Pentagamavunon-1 performs more potent anti-cancer effects than curcumin against various cancer cells, but it remains to be optimized. Piperine shows the activity as an enhancer of a therapeutic agent. This study expects to achieve higher effectiveness of PGV-1 on 4T1 breast cancer cells through co-treatment with piperine with exploring the effect of cytotoxicity, mitotic catastrophe, cellular senescence, and target proteins of PGV-1 and piperine on the regulation of mitosis in TNBC cells (4T1). The assays emphasize MTT assay, May Grünwald-Giemsa staining, SA-β-galactosidase assay, and bioinformatics analysis, respectively, to elicit the respected activities. The results revealed that PGV-1 performed a cytotoxic effect with an IC50 value of 9 µM while piperine showed a lower cytotoxic effect with an IC50 value of 800 µM on 4T1 cells 24 h treatment. However, the combination treatment of both showed a synergistic cytotoxic enhancement effect with an average CI value < 1. Furthermore, the combination of PGV-1 and piperine induced mitotic catastrophe and senescence better than the single treatment. Treatment of 1 µM of PGV-1 and 400 µM of piperine increased the percentage of senescent cells by 33%. Bioinformatics analysis revealed that PGV-1 and piperine target proteins play a role in mitotic regulation, namely CDK1, KIF11, AURKA, AURKB, and PLK1, to contribute to mitotic catastrophe. Therefore, piperine increases the effectiveness of PGV-1 to suppress 4T1 cells growth synergistically that may occur through mitotic catastrophe and senescence targeting on mitotic regulatory proteins.
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Affiliation(s)
- Endah Endah
- Department of Biotechnology, Graduate School, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Febri Wulandari
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Yurananda Putri
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Riris Istighfari Jenie
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Laboratory of Macromolecular Engineering, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edy Meiyanto
- Cancer Chemoprevention Research Center, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Laboratory of Macromolecular Engineering, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
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9
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Park E, Song KH, Kim D, Lee M, Van Manh N, Kim H, Hong KB, Lee J, Song JY, Kang S. 2-Amino-1,3,4-thiadiazoles as Glutaminyl Cyclases Inhibitors Increase Phagocytosis through Modification of CD47-SIRPα Checkpoint. ACS Med Chem Lett 2022; 13:1459-1467. [PMID: 36105338 PMCID: PMC9465712 DOI: 10.1021/acsmedchemlett.2c00256] [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: 05/27/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
Glutaminyl cyclases (QC, isoQC) convert N-terminal glutamine or glutamate into pyroglutamate (pGlu) on substrates. IsoQC has recently been demonstrated to promote pGlu formation on the N-terminus of CD47, the SIRPα binding site, contributing to the "don't eat me" cancer immune signaling of CD47-SIRPα. We developed new QC inhibitors by applying a structure-based optimization approach starting from fragments identified through library screening. Screening of metal binding fragments identified 5-(1H-benzimidazol-5-yl)-1,3,4-thiadiazol-2-amine (9) as a potent fragment, and further modification provided 5-(1-(3-methoxy-4-(3-(piperidin-1-yl)propoxy)benzyl)-1H-benzo[d]imidazol-5-yl)-1,3,4-thiadiazol-2-amine (22b) as a potent QC inhibitor. Treatment with 22b in A549 and H1975 lung cancer cells decreased the CD47/αhCD47-CC2C6 interaction, indicative of the CD47/SIRPα interaction, and enhanced the increased phagocytic activity of both THP-1 and U937 macrophages.
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Affiliation(s)
- Eunsun Park
- College
of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Kyung-Hee Song
- Division
of Radiation Biomedical Research, Korea
Institute of Radiological & Medical Sciences, Seoul 01812, Republic of Korea
| | - Darong Kim
- New
Drug Development Center, Daegu-Gyeongbuk
Medical Innovation Foundation, Daegu 41061, Republic
of Korea
| | - Minyoung Lee
- Medifron
DBT, 517ho, JEI-Platz,
186, Gasan digital 1-ro, Geumcheon-gu, Seoul 08502, Republic of Korea
| | - Nguyen Van Manh
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hee Kim
- Medifron
DBT, 517ho, JEI-Platz,
186, Gasan digital 1-ro, Geumcheon-gu, Seoul 08502, Republic of Korea
| | - Ki Bum Hong
- New
Drug Development Center, Daegu-Gyeongbuk
Medical Innovation Foundation, Daegu 41061, Republic
of Korea
| | - Jeewoo Lee
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jie-Young Song
- Division
of Radiation Biomedical Research, Korea
Institute of Radiological & Medical Sciences, Seoul 01812, Republic of Korea
| | - Soosung Kang
- College
of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea
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10
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Zhang Y, Wang Y, Zhao Z, Peng W, Wang P, Xu X, Zhao C. Glutaminyl cyclases, the potential targets of cancer and neurodegenerative diseases. Eur J Pharmacol 2022; 931:175178. [DOI: 10.1016/j.ejphar.2022.175178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/03/2022]
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11
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Functional Analysis of the GPI Transamidase Complex by Screening for Amino Acid Mutations in Each Subunit. Molecules 2021; 26:molecules26185462. [PMID: 34576938 PMCID: PMC8465894 DOI: 10.3390/molecules26185462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 12/20/2022] Open
Abstract
Glycosylphosphatidylinositol (GPI) anchor modification is a posttranslational modification of proteins that has been conserved in eukaryotes. The biosynthesis and transfer of GPI to proteins are carried out in the endoplasmic reticulum. Attachment of GPI to proteins is mediated by the GPI-transamidase (GPI-TA) complex, which recognizes and cleaves the C-terminal GPI attachment signal of precursor proteins. Then, GPI is transferred to the newly exposed C-terminus of the proteins. GPI-TA consists of five subunits: PIGK, GPAA1, PIGT, PIGS, and PIGU, and the absence of any subunit leads to the loss of activity. Here, we analyzed functionally important residues of the five subunits of GPI-TA by comparing conserved sequences among homologous proteins. In addition, we optimized the purification method for analyzing the structure of GPI-TA. Using purified GPI-TA, preliminary single particle images were obtained. Our results provide guidance for the structural and functional analysis of GPI-TA.
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12
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Van Manh N, Hoang VH, Ngo VTH, Ann J, Jang TH, Ha JH, Song JY, Ha HJ, Kim H, Kim YH, Lee J, Lee J. Discovery of highly potent human glutaminyl cyclase (QC) inhibitors as anti-Alzheimer's agents by the combination of pharmacophore-based and structure-based design. Eur J Med Chem 2021; 226:113819. [PMID: 34536669 DOI: 10.1016/j.ejmech.2021.113819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022]
Abstract
The inhibition of glutaminyl cyclase (QC) may provide a promising strategy for the treatment of early Alzheimer's disease (AD) by reducing the amount of the toxic pyroform of β-amyloid (AβΝ3pE) in the brains of AD patients. In this work, we identified potent QC inhibitors with subnanomolar IC50 values that were up to 290-fold higher than that of PQ912, which is currently being tested in Phase II clinical trials. Among the tested compounds, the cyclopentylmethyl derivative (214) exhibited the most potent in vitro activity (IC50 = 0.1 nM), while benzimidazole (227) showed the most promising in vivo efficacy, selectivity and druggable profile. 227 significantly reduced the concentration of pyroform Aβ and total Aβ in the brain of an AD animal model and improved the alternation behavior of mice during Y-maze tests. The crystal structure of human QC (hQC) in complex with 214 indicated tight binding at the active site, supporting that the specific inhibition of QC results in potent in vitro and in vivo activity. Considering the recent clinical success of donanemab, which targets AβΝ3pE, small molecule-based QC inhibitors may also provide potential therapeutic options for early-stage AD treatment.
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Affiliation(s)
- Nguyen Van Manh
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Van-Hai Hoang
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Van T H Ngo
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea; Graduate Department of Healthcare Science, Dainam University, Hanoi, Viet Nam
| | - Jihyae Ann
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Tae-Ho Jang
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea
| | - Jung-Hye Ha
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea
| | - Jae Young Song
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, Republic of Korea
| | - Hee-Jin Ha
- Medifron DBT, Seoul, 08502, Republic of Korea
| | - Hee Kim
- Medifron DBT, Seoul, 08502, Republic of Korea
| | | | - Jiyoun Lee
- Department of Global Medical Science, Sungshin University, Seoul, 01133, Republic of Korea
| | - Jeewoo Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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13
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Xu C, Zou H, Yu X, Xie Y, Cai J, Shang Q, Ouyang N, Wang Y, Xu P, He Z, Wu H. Repurposing FDA-Approved Compounds for the Discovery of Glutaminyl Cyclase Inhibitors as Drugs Against Alzheimer's Disease. ChemistryOpen 2021; 10:877-881. [PMID: 33377311 PMCID: PMC8409088 DOI: 10.1002/open.202000235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/07/2020] [Indexed: 12/01/2022] Open
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative causes of dementia, the pathology of which is still not much clear. It's challenging to discover the disease modifying agents for the prevention and treatment of AD over the years. Emerging evidence has been accumulated to reveal the crucial role of up-regulated glutaminyl cyclase (QC) in the initiation of AD. In the current study, the QC inhibitory potency of a library consisting of 1621 FDA-approved compounds was assessed. A total of 54 hits, 3.33 % of the pool, exhibited QC inhibitory activities. The Ki of the top 5 compounds with the highest QC inhibitory activities were measured. Among these selected hits, compounds affecting neuronal signaling pathways and other mechanisms were recognized. Moreover, several polyphenol derivatives with QC inhibitory activities were also identified. Frameworks and subsets contained in these hits were analyzed. Taken together, our results may contribute to the discovery and development of novel QC inhibitors as potential anti-AD agents.
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Affiliation(s)
- Chenshu Xu
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Haoman Zou
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Xi Yu
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Yazhou Xie
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Jiaxin Cai
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Qi Shang
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Na Ouyang
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Yinan Wang
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Pan Xu
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Zhendan He
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
| | - Haiqiang Wu
- School of Pharmaceutical Sciences Health Science CenterShenzhen University3688 Nanhai RoadShenzhen518055China
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14
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Chandran R, Dileep KV. Exploring the binding mode of PQ912 against secretory glutaminyl cyclase through systematic exploitation of conformational ensembles. Chem Biol Drug Des 2021; 98:850-856. [PMID: 34423556 DOI: 10.1111/cbdd.13940] [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: 05/10/2021] [Revised: 07/15/2021] [Accepted: 08/07/2021] [Indexed: 12/01/2022]
Abstract
Secretory glutaminyl cyclase (sQC) plays an important role in the formation of the pyroglutamate-amyloid beta (pGlu-Aβ) peptide, one of the most abundant variants of Aβ found in the Alzheimer's disease (AD) brain. This post-translationally modified pGlu-Aβ possesses high toxicity and rapid aggregation propensity when compared to the wild-type Aβ (WT-Aβ). Since pGlu-Aβ acts as seed for WT-Aβ, the inhibition of sQC limits the formation of pGlu-Aβ and reduces the overall load of Aβ plaques in the AD brain. PQ912 is a potent inhibitor of sQC and has been enrolled in phase 2b clinical trial of the AD drug development pipeline; however, the binding mode of PQ912 against sQC is not elucidated yet. Understanding the binding mode of PQ912 is important as it helps in the discovery against AD where sQC as a target. To explore the binding mode of PQ912, we employed ensemble docking towards 9 sQC structures that differ either in active site geometry or in the bound ligands. Further pose clustering and binding energy calculations yielded three possible binding modes for PQ912. Finally, all atom molecular dynamics simulations determined the most energetically favorable binding mode for PQ912, in the active site of sQC, which is similar to that of LSB-09, a recently reported sQC inhibitor containing benzimidazole-6-carboxamide moiety.
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Affiliation(s)
- Remya Chandran
- Department of Biotechnology and Microbiology, Kannur University, Thalassery, Kerala, India
| | - Kalarickal V Dileep
- Laboratory for Computational and Structural Biology, Jubilee Centre for Medical Research, Jubilee Mission Medical College and Research Institute, Thrissur, Kerala, India
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15
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Li Z, Gu X, Rao D, Lu M, Wen J, Chen X, Wang H, Cui X, Tang W, Xu S, Wang P, Yu L, Ge X. Luteolin promotes macrophage-mediated phagocytosis by inhibiting CD47 pyroglutamation. Transl Oncol 2021; 14:101129. [PMID: 34051623 PMCID: PMC8176368 DOI: 10.1016/j.tranon.2021.101129] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 01/06/2023] Open
Abstract
Interception of CD47-SIRPα signaling is an elusive yet intriguing goal for anti-tumor immunotherapy since unbiased CD47 blockade by its antibody cannot avoid erythrocyte destruction. We previously reported that isoQC, a Golgi-resident enzyme lacking in mature erythrocyte, disrupts the binding of CD47 to SIRPα by downregulating pGlu-CD47 and its interaction with SIRPα (Cell research 2019. 29:502–505). In this study, we explored the possibility of utilizing isoQC inhibition to address the challenge of CD47 antibody treatment induced anemia. We discovered a new lead compound of isoQC inhibitor, Luteolin, and revealed that posttranslational modification may work as an immunotherapeutic target by abolishing immune checkpoint signaling.
‘Don't eat me’ signal of CD47 is activated via its interaction with SIRPα protein on myeloid cells, especially phagocytic cells, and prevents malignant cells from anti-tumor immunity in which pyroglutamate modification of CD47 by glutaminyl-peptide cyclotransferase-like protein (isoQC) takes an important part evidenced by our previous report that isoQC is an essential regulator for CD47-SIRPα axis with a strong inhibition on macrophage-mediated phagoctyosis. Therefore, we screened for potential isoQC inhibitors by fluorescence-activated cell sorting assay and identified luteolin as a potent compound that blocked the pyroglutamation of CD47 by isoQC. We further demonstrated that luteolin directly bound to isoQC using pull-down assay and isothermal calorimetric (ITC) assay. In consistency, we showed that luteolin markedly abrogated the cell-surface interaction between CD47 and SIRPα in multiple myeloma H929 cells and consequently promoted the macrophage-mediated phagocytosis. Collectively, our study discovered a promising lead compound targeting isoQC, luteolin, which functions distinctly from current CD47 antibody-based drugs and therefore may potentially overcome the clinical side effects associated with CD47 antibody treatment-induced anemia.
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Affiliation(s)
- Zhiqiang Li
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Xuemei Gu
- Shanghai Clinical Medical College, Anhui Medical University, Hefei 230031, China
| | - Danni Rao
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Science, 19 Yuquan Road, Beijing 110039, China
| | - Meiling Lu
- Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jing Wen
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Xinyan Chen
- Putuo District People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hongbing Wang
- Putuo District People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xianghuan Cui
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Wenwen Tang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Shilin Xu
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Science, 19 Yuquan Road, Beijing 110039, China
| | - Ping Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China; Shanghai Clinical Medical College, Anhui Medical University, Hefei 230031, China.
| | - Lei Yu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China.
| | - Xin Ge
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200092, China.
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16
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Xu C, Wang YN, Wu H. Glutaminyl Cyclase, Diseases, and Development of Glutaminyl Cyclase Inhibitors. J Med Chem 2021; 64:6549-6565. [PMID: 34000808 DOI: 10.1021/acs.jmedchem.1c00325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyroglutamate (pE) modification, catalyzed mainly by glutaminyl cyclase (QC), is prevalent throughout nature and is particularly important in mammals including humans for the maturation of hormones, peptides, and proteins. In humans, the upregulation of QC is involved in multiple diseases and conditions including Alzheimer's disease, Huntington's disease, melanomas, thyroid carcinomas, accelerated atherosclerosis, septic arthritics, etc. This upregulation catalyzes the generation of modified mediators such as pE-amyloid beta (Aß) and pE-chemokine ligand 2 (CCL2) peptides. Not surprisingly, QC has emerged as a reasonable target for the development of therapeutics to combat these diseases and conditions. In this manuscript the deleterious effects of upregulated QC resulting in disease manifestation are reviewed, along with progress on the development of QC inhibitors.
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Affiliation(s)
- Chenshu Xu
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yi-Nan Wang
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Haiqiang Wu
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
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17
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A Unique Carboxylic-Acid Hydrogen-Bond Network (CAHBN) Confers Glutaminyl Cyclase Activity on M28 Family Enzymes. J Mol Biol 2021; 433:166960. [PMID: 33774034 DOI: 10.1016/j.jmb.2021.166960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/21/2021] [Accepted: 03/15/2021] [Indexed: 11/21/2022]
Abstract
Proteins with sequence or structure similar to those of di-Zn exopeptidases are usually classified as the M28-family enzymes, including the mammalian-type glutaminyl cyclases (QCs). QC catalyzes protein N-terminal pyroglutamate formation, a posttranslational modification important under many physiological and pathological conditions, and is a drug target for treating neurodegenerative diseases, cancers and inflammatory disorders. Without functional characterization, mammalian QCs and their orthologs remain indistinguishable at the sequence and structure levels from other M28-family proteins, leading to few reported QCs. Here, we show that a low-barrier carboxylic-acid hydrogen-bond network (CAHBN) is required for QC activity and discriminates QCs from M28-family peptidases. We demonstrate that the CAHBN-containing M28 peptidases deposited in the PDB are indeed QCs. Our analyses identify several thousands of QCs from the three domains of life, and we enzymatically and structurally characterize several. For the first time, the interplay between a CAHBN and the binuclear metal-binding center of mammalian QCs is made clear. We found that the presence or absence of CAHBN is a key discriminator for the formation of either the mono-Zn QCs or the di-Zn exopeptidases. Our study helps explain the possible roles of QCs in life.
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18
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Vijayan D, Chandra R. Amyloid Beta Hypothesis in Alzheimer's Disease: Major Culprits and Recent Therapeutic Strategies. Curr Drug Targets 2021; 21:148-166. [PMID: 31385768 DOI: 10.2174/1389450120666190806153206] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 07/13/2019] [Accepted: 07/26/2019] [Indexed: 01/18/2023]
Abstract
Alzheimer's disease (AD) is one of the most common forms of dementia and has been a global concern for several years. Due to the multi-factorial nature of the disease, AD has become irreversible, fatal and imposes a tremendous socio-economic burden. Even though experimental medicines suggested moderate benefits, AD still lacks an effective treatment strategy for the management of symptoms or cure. Among the various hypotheses that describe development and progression of AD, the amyloid hypothesis has been a long-term adherent to the AD due to the involvement of various forms of Amyloid beta (Aβ) peptides in the impairment of neuronal and cognitive functions. Hence, majority of the drug discovery approaches in the past have focused on the prevention of the accumulation of Aβ peptides. Currently, there are several agents in the phase III clinical trials that target Aβ or the various macromolecules triggering Aβ deposition. In this review, we present the state of the art knowledge on the functional aspects of the key players involved in the amyloid hypothesis. Furthermore, we also discuss anti-amyloid agents present in the Phase III clinical trials.
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Affiliation(s)
- Dileep Vijayan
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Remya Chandra
- Department of Biotechnology and Microbiology, Thalassery Campus, Kannur University, Kerala Pin 670 661, India
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19
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Dileep KV, Sakai N, Ihara K, Kato-Murayama M, Nakata A, Ito A, Sivaraman DM, Shin JW, Yoshida M, Shirouzu M, Zhang KYJ. Piperidine-4-carboxamide as a new scaffold for designing secretory glutaminyl cyclase inhibitors. Int J Biol Macromol 2020; 170:415-423. [PMID: 33373636 DOI: 10.1016/j.ijbiomac.2020.12.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 11/16/2022]
Abstract
Alzheimer's disease (AD), a common chronic neurodegenerative disease, has become a major public health concern. Despite years of research, therapeutics for AD are limited. Overexpression of secretory glutaminyl cyclase (sQC) in AD brain leads to the formation of a highly neurotoxic pyroglutamate variant of amyloid beta, pGlu-Aβ, which acts as a potential seed for the aggregation of full length Aβ. Preventing the formation of pGlu-Aβ through inhibition of sQC has become an attractive disease-modifying therapy in AD. In this current study, through a pharmacophore assisted high throughput virtual screening, we report a novel sQC inhibitor (Cpd-41) with a piperidine-4-carboxamide moiety (IC50 = 34 μM). Systematic molecular docking, MD simulations and X-ray crystallographic analysis provided atomistic details of the binding of Cpd-41 in the active site of sQC. The unique mode of binding and moderate toxicity of Cpd-41 make this molecule an attractive candidate for designing high affinity sQC inhibitors.
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Affiliation(s)
- K V Dileep
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Naoki Sakai
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kentaro Ihara
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Miyuki Kato-Murayama
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akiko Nakata
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akihiro Ito
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Laboratory of Cell Signaling, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - D M Sivaraman
- Laboratory for Advanced Genomics Circuit, Centre for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan; Department of Pathology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram 695 011, Kerala, India
| | - Jay W Shin
- Laboratory for Advanced Genomics Circuit, Centre for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Minoru Yoshida
- Seed Compounds Exploratory Unit for Drug Discovery Platform, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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20
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Su CTT, Sinha S, Eisenhaber B, Eisenhaber F. Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site. Biol Direct 2020; 15:14. [PMID: 32993792 PMCID: PMC7522609 DOI: 10.1186/s13062-020-00266-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/30/2020] [Indexed: 02/01/2023] Open
Abstract
Background The transamidase complex is a molecular machine in the endoplasmic reticulum of eukaryotes that attaches a glycosylphosphatidylinositol (GPI) lipid anchor to substrate proteins after cleaving a C-terminal propeptide with a defined sequence signal. Its five subunits are very hydrophobic; thus, solubility, heterologous expression and complex reconstruction are difficult. Therefore, theoretical approaches are currently the main source of insight into details of 3D structure and of the catalytic process. Results In this work, we generated model 3D structures of the lumenal domain of human GPAA1, the M28-type metallo-peptide-synthetase subunit of the transamidase, including zinc ion and model substrate positions. In comparative molecular dynamics (MD) simulations of M28-type structures and our GPAA1 models, we estimated the metal ion binding energies with evolutionary conserved amino acid residues in the catalytic cleft. We find that canonical zinc binding sites 2 and 3 are strongest binders for Zn1 and, where a second zinc is available, sites 2 and 4 for Zn2. Zinc interaction of site 5 with Zn1 enhances upon substrate binding in structures with only one zinc. Whereas a previously studied glutaminyl cyclase structure, the best known homologue to GPAA1, binds only one zinc ion at the catalytic site, GPAA1 can sterically accommodate two. The M28-type metallopeptidases segregate into two independent branches with regard to one/two zinc ion binding modality in a phylogenetic tree where the GPAA1 family is closer to the joint origin of both groups. For GPAA1 models, MD studies revealed two large loops (flaps) surrounding the active site being involved in an anti-correlated, breathing-like dynamics. Conclusions In the light of combined sequence-analytic and phylogenetic arguments as well as 3D structural modelling results, GPAA1 is most likely a single zinc ion metallopeptidase. Two large flaps environ the catalytic site restricting access to large substrates. Reviewers This article was reviewed by Thomas Dandekar (MD) and Michael Gromiha.
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Affiliation(s)
- Chinh Tran-To Su
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore
| | - Swati Sinha
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore.
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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21
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Kumar A, Bagri K, Nimbhal M, Kumar P. In silico exploration of the fingerprints triggering modulation of glutaminyl cyclase inhibition for the treatment of Alzheimer's disease using SMILES based attributes in Monte Carlo optimization. J Biomol Struct Dyn 2020; 39:7181-7193. [PMID: 32795153 DOI: 10.1080/07391102.2020.1806111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Alzheimer's disease is the most common neurodegenerative disorder and being a social burden Alzheimer's has become an economic liability on developing countries. With limited understanding regarding the cause of disease, it is commonly identified by extracellular deposit of amyloid β (Aβ) peptides as senile plaques. Pyroglutamated Aβ is identified from the brain of AD patients and constituted the majority of total Aβ present. The formation of Pyroglutamated Aβ could be hindered by the use of Glutaminyl cyclase inhibitors and could efficiently improve the symptoms of Alzheimer's. The literature revealed the competence of quantitative structure activity/property relationship studies in drug discovery. The present work explores the efficiency of Monte Carlo based QSAR modelling studies on a dataset of 125 Glutaminyl cyclase inhibitors with pKi taken as the endpoint for QSAR analysis. The dataset is divided into training, subtraining, calibration and validation sets resulting in the generation of five random splits. The validation is performed in accordance with the Organization of Economic Corporation and Development principles. The values of R2, Q2, index of ideality of correlation, concordance correlation coefficient, av. rm2 and delta rm2 of calibration set of the best split are found to be 0.9012, 0.8775, 0.9479, 0.9435, 0.8347 and 0.0847, respectively. The structural features responsible for increasing the inhibitory activity are identified. These structural features are added to a base compound from the dataset to design six novel molecules. These new molecules possess improved inhibitory activity as compare to the base compound. The results are further supported by docking studies.Communicated by Vsevolod Makeev.
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Affiliation(s)
- Ashwani Kumar
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar, India
| | - Kiran Bagri
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar, India
| | - Manisha Nimbhal
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar, India
| | - Parvin Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
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22
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Kupski O, Funk LM, Sautner V, Seifert F, Worbs B, Ramsbeck D, Meyer F, Diederichsen U, Buchholz M, Schilling S, Demuth HU, Tittmann K. Hydrazides Are Potent Transition-State Analogues for Glutaminyl Cyclase Implicated in the Pathogenesis of Alzheimer's Disease. Biochemistry 2020; 59:2585-2591. [PMID: 32551535 DOI: 10.1021/acs.biochem.0c00337] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Amyloidogenic plaques are hallmarks of Alzheimer's disease (AD) and typically consist of high percentages of modified Aβ peptides bearing N-terminally cyclized glutamate residues. The human zinc(II) enzyme glutaminyl cyclase (QC) was shown in vivo to catalyze the cyclization of N-terminal glutamates of Aβ peptides in a pathophysiological side reaction establishing QC as a druggable target for therapeutic treatment of AD. Here, we report crystallographic snapshots of human QC catalysis acting on the neurohormone neurotensin that delineate the stereochemical course of catalysis and suggest that hydrazides could mimic the transition state of peptide cyclization and deamidation. This hypothesis is validated by a sparse-matrix inhibitor screening campaign that identifies hydrazides as the most potent metal-binding group compared to classic Zn binders. The structural basis of hydrazide inhibition is illuminated by X-ray structure analysis of human QC in complex with a hydrazide-bearing peptide inhibitor and reveals a pentacoordinated Zn complex. Our findings inform novel strategies in the design of potent and highly selective QC inhibitors by employing hydrazides as the metal-binding warhead.
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Affiliation(s)
- Oliver Kupski
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lisa-Marie Funk
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Viktor Sautner
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Franziska Seifert
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany
| | - Brigitte Worbs
- Institute for Organic and Biomolecular Chemistry, Georg-August University Göttingen, Tammannstraß 2, 37077 Göttingen, Germany
| | - Daniel Ramsbeck
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Department of Drug Design and Target Validation, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Franc Meyer
- Institute for Inorganic Chemistry, Georg-August University Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry, Georg-August University Göttingen, Tammannstraß 2, 37077 Göttingen, Germany
| | - Mirko Buchholz
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Department of Drug Design and Target Validation, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Stephan Schilling
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Department of Drug Design and Target Validation, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Hans-Ulrich Demuth
- Fraunhofer Institute for Cell Therapy und Immunology IZI, Department of Drug Design and Target Validation, Weinbergweg 22, 06120 Halle/Saale, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, Georg-August University Göttingen, Julia-Lermontowa-Weg 3, 37077 Göttingen, Germany.,Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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23
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Xu A, He F, Yu C, Qu Y, Zhang Q, Lv J, Zhang X, Ran Y, Wei C, Wu J. The Development of Small Molecule Inhibitors of Glutaminyl Cyclase and Isoglutaminyl Cyclase for Alzheimer's Disease. ChemistrySelect 2019. [DOI: 10.1002/slct.201902852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ana Xu
- College of PharmacyShanDong University, 4 4 West WenHua Road JiNan 250012 China
| | - Feng He
- College of PharmacyShanDong University, 4 4 West WenHua Road JiNan 250012 China
| | - Chenggong Yu
- College of PharmacyShanDong University, 4 4 West WenHua Road JiNan 250012 China
| | - Ying Qu
- College of PharmacyShanDong University, 4 4 West WenHua Road JiNan 250012 China
| | - Qiuqiong Zhang
- College of PharmacyShanDong University, 4 4 West WenHua Road JiNan 250012 China
| | - Jiahui Lv
- College of PharmacyShanDong University, 4 4 West WenHua Road JiNan 250012 China
| | - Xiangna Zhang
- College of PharmacyShanDong University, 4 4 West WenHua Road JiNan 250012 China
| | - Yingying Ran
- College of PharmacyShanDong University, 4 4 West WenHua Road JiNan 250012 China
| | - Chao Wei
- College of PharmacyShanDong University, 4 4 West WenHua Road JiNan 250012 China
| | - Jingde Wu
- College of PharmacyShanDong University, 4 4 West WenHua Road JiNan 250012 China
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24
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Vijayan DK, Zhang KY. Human glutaminyl cyclase: Structure, function, inhibitors and involvement in Alzheimer’s disease. Pharmacol Res 2019; 147:104342. [DOI: 10.1016/j.phrs.2019.104342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/19/2019] [Accepted: 07/02/2019] [Indexed: 12/20/2022]
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25
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Hoang VH, Ngo VTH, Cui M, Manh NV, Tran PT, Ann J, Ha HJ, Kim H, Choi K, Kim YH, Chang H, Macalino SJY, Lee J, Choi S, Lee J. Discovery of Conformationally Restricted Human Glutaminyl Cyclase Inhibitors as Potent Anti-Alzheimer's Agents by Structure-Based Design. J Med Chem 2019; 62:8011-8027. [PMID: 31411468 DOI: 10.1021/acs.jmedchem.9b00751] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD) is an incurable, progressive neurodegenerative disease whose pathogenesis cannot be defined by one single element but consists of various factors; thus, there is a call for alternative approaches to tackle the multifaceted aspects of AD. Among the potential alternative targets, we aim to focus on glutaminyl cyclase (QC), which reduces the toxic pyroform of β-amyloid in the brains of AD patients. On the basis of a putative active conformation of the prototype inhibitor 1, a series of N-substituted thiourea, urea, and α-substituted amide derivatives were developed. The structure-activity relationship analyses indicated that conformationally restrained inhibitors demonstrated much improved QC inhibition in vitro compared to nonrestricted analogues, and several selected compounds demonstrated desirable therapeutic activity in an AD mouse model. The conformational analysis of a representative inhibitor indicated that the inhibitor appeared to maintain the Z-E conformation at the active site, as it is critical for its potent activity.
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Affiliation(s)
- Van-Hai Hoang
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Van T H Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Pharmacy , Ton Duc Thang University , Ho Chi Minh City 75307 , Vietnam
| | - Minghua Cui
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Nguyen Van Manh
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Phuong-Thao Tran
- Department of Pharmaceutical Chemistry , Hanoi University of Pharmacy , Hanoi 10000 , Vietnam
| | - Jihyae Ann
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Hee-Jin Ha
- Medifron DBT , Sandanro 349 , Danwon-Gu, Ansan-City , Gyeonggi-Do 15426 , Republic of Korea
| | - Hee Kim
- Medifron DBT , Sandanro 349 , Danwon-Gu, Ansan-City , Gyeonggi-Do 15426 , Republic of Korea
| | - Kwanghyun Choi
- Medifron DBT , Sandanro 349 , Danwon-Gu, Ansan-City , Gyeonggi-Do 15426 , Republic of Korea
| | - Young-Ho Kim
- Medifron DBT , Sandanro 349 , Danwon-Gu, Ansan-City , Gyeonggi-Do 15426 , Republic of Korea
| | - Hyerim Chang
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Stephani Joy Y Macalino
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Jiyoun Lee
- Department of Global Medical Science , Sungshin University , Seoul 01133 , Republic of Korea
| | - Sun Choi
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences , Ewha Womans University , Seoul 03760 , Republic of Korea
| | - Jeewoo Lee
- Laboratory of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
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26
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Tran PT, Hoang VH, Lee J, Hien TTT, Tung NT, Ngo ST. In vitroandin silicodetermination of glutaminyl cyclase inhibitors. RSC Adv 2019; 9:29619-29627. [PMID: 35531555 PMCID: PMC9071946 DOI: 10.1039/c9ra05763c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of neurodegenerative disease currently. It is widely accepted that AD is characterized by the self-assembly of amyloid beta (Aβ) peptides. The human glutaminyl cyclase (hQC) enzyme is characterized by association with Aβ peptide generation. The development of hQC inhibitors could prevent the self-aggregation of Aβ peptides, resulting in impeding AD. Utilizing structural knowledge of the hQC substrates and known hQC inhibitors, new heterocyclic and peptidomimetic derivatives were synthesized and were able to inhibit the hQC enzyme. The inhibiting abilities of these compounds were evaluated using a fluorometric assay. The binding mechanism at the atomic level was estimated using molecular docking, free energy perturbation, and quantum chemical calculation methods. The predicted log(BBB) and human intestinal absorption values indicated that these compounds are able to permeate the blood–brain barrier and be well-absorbed through the gastrointestinal tract. Overall, 5,6-dimethoxy-N-(3-(5-methyl-1H-imidazol-1-yl)propyl)-1H-benzo[d]imidazol-2-amine (1_2) was indicated as a potential drug for AD treatment. Rational design of new hQC inhibitors.![]()
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Affiliation(s)
- Phuong-Thao Tran
- Department of Pharmaceutical Chemistry
- Hanoi University of Pharmacy
- Hanoi
- Vietnam
| | - Van-Hai Hoang
- Institute of Research and Development
- Duy Tan University
- Da Nang 550000
- Vietnam
| | - Jeewoo Lee
- Laboratory of Medicinal Chemistry
- College of Pharmacy
- Seoul National University
- Seoul
- Korea
| | | | - Nguyen Thanh Tung
- Institute of Materials Science
- Vietnam Academy of Science and Technology
- Hanoi
- Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
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27
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Lin W, Zheng X, Fang D, Zhou S, Wu W, Zheng K. Identifying hQC Inhibitors of Alzheimer's Disease by Effective Customized Pharmacophore-Based Virtual Screening, Molecular Dynamic Simulation, and Binding Free Energy Analysis. Appl Biochem Biotechnol 2018; 187:1173-1192. [PMID: 30187344 DOI: 10.1007/s12010-018-2780-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/06/2018] [Indexed: 01/14/2023]
Abstract
Human glutaminyl cyclase (hQC) appeared as a promising new target with its inhibitors attracted much attention for the treatment of Alzheimer's disease (AD) in recent years. But so far, only a few compounds have been reported as hQC inhibitors. To find novel and potent hQC inhibitors, a high-specificity ZBG (zinc-binding groups)-based pharmacophore model comprising customized ZBG feature was first generated using HipHop algorithm in Discovery Studio software for screening out hQC inhibitors from the SPECS database. After purification by docking studies and drug-like ADMET properties filters, four potential hit compounds were retrieved. Subsequently, these hit compounds were subjected to 30-ns molecular dynamic (MD) simulations to explore their binding modes at the active side of hQC. MD simulations demonstrated that these hit compounds formed a chelating interaction with the zinc ion, which was consistent with the finding that the electrostatic interaction was the major driving force for binding to hQC confirmed with MMPBSA energy decomposition. Higher binding affinities of these compounds were also verified by the binding free energy calculations comparing with the references. Thus, these identified compounds might be potential hQC candidates and could be used for further investigation.
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Affiliation(s)
- Weicong Lin
- Department of Physical Chemistry, College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Xiaojie Zheng
- Department of Physical Chemistry, College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Danqing Fang
- Department of Cardiothoracic Surgery, Affiliated Second Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Shengfu Zhou
- Department of Physical Chemistry, College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Wenjuan Wu
- Department of Physical Chemistry, College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
| | - Kangcheng Zheng
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, 510275, China
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28
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The structure of the human glutaminyl cyclase–SEN177 complex indicates routes for developing new potent inhibitors as possible agents for the treatment of neurological disorders. J Biol Inorg Chem 2018; 23:1219-1226. [DOI: 10.1007/s00775-018-1605-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/16/2018] [Indexed: 12/17/2022]
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29
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Structure-activity relationship investigation of Phe-Arg mimetic region of human glutaminyl cyclase inhibitors. Bioorg Med Chem 2018; 26:3133-3144. [DOI: 10.1016/j.bmc.2018.04.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 11/20/2022]
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30
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Potent human glutaminyl cyclase inhibitors as potential anti-Alzheimer’s agents: Structure-activity relationship study of Arg-mimetic region. Bioorg Med Chem 2018; 26:1035-1049. [DOI: 10.1016/j.bmc.2018.01.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 01/17/2023]
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31
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Li M, Dong Y, Yu X, Li Y, Zou Y, Zheng Y, He Z, Liu Z, Quan J, Bu X, Wu H. Synthesis and Evaluation of Diphenyl Conjugated Imidazole Derivatives as Potential Glutaminyl Cyclase Inhibitors for Treatment of Alzheimer's Disease. J Med Chem 2017; 60:6664-6677. [PMID: 28700245 DOI: 10.1021/acs.jmedchem.7b00648] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
High expression of glutaminyl cyclase (QC) contributes to the initiation of Alzheimer's disease (AD) by catalyzing the generation of neurotoxic pyroglutamate (pE)-modified β-amyloid (Aβ) peptides. Preventing the generation of pE-Aβs by QC inhibition has been suggested as a novel approach to a disease-modifying therapy for AD. In this work, a series of diphenyl conjugated imidazole derivatives (DPCIs) was rationally designed and synthesized. Analogues with this scaffold exhibited potent inhibitory activity against human QC (hQC) and good in vitro blood-brain barrier (BBB) permeability. Further assessments corroborated that the selected hQC inhibitor 28 inhibits the activity of hQC, dramatically reduces the generation of pE-Aβs in cultured cells and in vivo, and improves the behavior of AD mice.
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Affiliation(s)
- Manman Li
- Department of Pharmacy, School of Medicine, Shenzhen University , Shenzhen 518060, China.,College of Life Sciences and Oceanography, Shenzhen University , Shenzhen 518060, China
| | - Yao Dong
- Department of Pharmacy, School of Medicine, Shenzhen University , Shenzhen 518060, China.,College of Life Sciences and Oceanography, Shenzhen University , Shenzhen 518060, China
| | - Xi Yu
- Department of Pharmacy, School of Medicine, Shenzhen University , Shenzhen 518060, China.,College of Life Sciences and Oceanography, Shenzhen University , Shenzhen 518060, China
| | - Yue Li
- Department of Pharmacy, School of Medicine, Shenzhen University , Shenzhen 518060, China
| | - Yongdong Zou
- College of Life Sciences and Oceanography, Shenzhen University , Shenzhen 518060, China
| | - Yizhi Zheng
- College of Life Sciences and Oceanography, Shenzhen University , Shenzhen 518060, China
| | - Zhendan He
- Department of Pharmacy, School of Medicine, Shenzhen University , Shenzhen 518060, China
| | - Zhigang Liu
- School of Medicine, Shenzhen University , Shenzhen 518060, China
| | - Junmin Quan
- Key Laboratory of Structural Biology, School of Chemical Biology & Biotechnology, Peking University, Shenzhen Graduate School , Shenzhen 518055, China
| | - Xianzhang Bu
- School of Pharmaceutical Science, Sun Yat-sen University , Guangzhou, 510006, China
| | - Haiqiang Wu
- Department of Pharmacy, School of Medicine, Shenzhen University , Shenzhen 518060, China.,College of Life Sciences and Oceanography, Shenzhen University , Shenzhen 518060, China.,Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, United States
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32
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Hoang VH, Tran PT, Cui M, Ngo VTH, Ann J, Park J, Lee J, Choi K, Cho H, Kim H, Ha HJ, Hong HS, Choi S, Kim YH, Lee J. Discovery of Potent Human Glutaminyl Cyclase Inhibitors as Anti-Alzheimer’s Agents Based on Rational Design. J Med Chem 2017; 60:2573-2590. [DOI: 10.1021/acs.jmedchem.7b00098] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Van-Hai Hoang
- Laboratory
of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences,
College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Phuong-Thao Tran
- Laboratory
of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences,
College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Department
of Pharmaceutical Chemistry, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Minghua Cui
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Van T. H. Ngo
- Laboratory
of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences,
College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jihyae Ann
- Laboratory
of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences,
College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongmi Park
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jiyoun Lee
- Department
of Global Medical Science, Sungshin University, Seoul 01133, Republic of Korea
| | - Kwanghyun Choi
- Medifron DBT, Sandanro 349, Danwon-Gu, Ansan-City, Gyeonggi-Do 15426, Republic of Korea
| | - Hanyang Cho
- Medifron DBT, Sandanro 349, Danwon-Gu, Ansan-City, Gyeonggi-Do 15426, Republic of Korea
| | - Hee Kim
- Medifron DBT, Sandanro 349, Danwon-Gu, Ansan-City, Gyeonggi-Do 15426, Republic of Korea
| | - Hee-Jin Ha
- Medifron DBT, Sandanro 349, Danwon-Gu, Ansan-City, Gyeonggi-Do 15426, Republic of Korea
| | - Hyun-Seok Hong
- Medifron DBT, Sandanro 349, Danwon-Gu, Ansan-City, Gyeonggi-Do 15426, Republic of Korea
| | - Sun Choi
- National Leading Research Laboratory of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Young-Ho Kim
- Medifron DBT, Sandanro 349, Danwon-Gu, Ansan-City, Gyeonggi-Do 15426, Republic of Korea
| | - Jeewoo Lee
- Laboratory
of Medicinal Chemistry, Research Institute of Pharmaceutical Sciences,
College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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33
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Liao JH, Chien CTH, Wu HY, Huang KF, Wang I, Ho MR, Tu IF, Lee IM, Li W, Shih YL, Wu CY, Lukyanov PA, Hsu STD, Wu SH. A Multivalent Marine Lectin from Crenomytilus grayanus Possesses Anti-cancer Activity through Recognizing Globotriose Gb3. J Am Chem Soc 2016; 138:4787-95. [PMID: 27010847 DOI: 10.1021/jacs.6b00111] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this study, we report the structure and function of a lectin from the sea mollusk Crenomytilus grayanus collected from the sublittoral zone of Peter the Great Bay of the Sea of Japan. The crystal structure of C. grayanus lectin (CGL) was solved to a resolution of 1.08 Å, revealing a β-trefoil fold that dimerizes into a dumbbell-shaped quaternary structure. Analysis of the crystal CGL structures bound to galactose, galactosamine, and globotriose Gb3 indicated that each CGL can bind three ligands through a carbohydrate-binding motif involving an extensive histidine- and water-mediated hydrogen bond network. CGL binding to Gb3 is further enhanced by additional side-chain-mediated hydrogen bonds in each of the three ligand-binding sites. NMR titrations revealed that the three binding sites have distinct microscopic affinities toward galactose and galactosamine. Cell viability assays showed that CGL recognizes Gb3 on the surface of breast cancer cells, leading to cell death. Our findings suggest the use of this lectin in cancer diagnosis and treatment.
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Affiliation(s)
- Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
| | - Chih-Ta Henry Chien
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University , Taipei 106, Taiwan
| | - Han-Ying Wu
- Institute of Biological Chemistry, Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University , Hsinchu 30043, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
| | - Iren Wang
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
| | - I-Fan Tu
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
| | - I-Ming Lee
- Institute of Biochemical Science, National Taiwan University , Taipei 106, Taiwan
| | - Wei Li
- Key Laboratory of Aquatic Products Processing and Utilization of Liaoning Province, Dalian Ocean University , Dalian 116023, P.R. China
| | - Yu-Ling Shih
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan
| | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica , Taipei 11529, Taiwan
| | - Pavel A Lukyanov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences , Vladivostok 690022, Russian Federation
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan.,Institute of Biological Chemistry, Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Science, National Taiwan University , Taipei 106, Taiwan
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan.,Department of Chemistry, National Taiwan University , Taipei 106, Taiwan.,Institute of Biological Chemistry, Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Science, National Taiwan University , Taipei 106, Taiwan
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34
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DiPisa F, Pozzi C, Benvenuti M, Andreini M, Marconi G, Mangani S. The soluble Y115E-Y117E variant of human glutaminyl cyclase is a valid target for X-ray and NMR screening of inhibitors against Alzheimer disease. Acta Crystallogr F Struct Biol Commun 2015; 71:986-92. [PMID: 26249687 PMCID: PMC4528929 DOI: 10.1107/s2053230x15010389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 05/30/2015] [Indexed: 11/10/2022] Open
Abstract
Recent developments in molecular pathology and genetics have allowed the identification of human glutaminyl cyclase (hQC) among the abnormal proteins involved in many neurodegenerative disorders. Difficulties in obtaining large quantities of pure protein may limit the use of crystallographic screening for drug development on this target. Site-directed mutagenesis experiments have led to the identification of some solvent-exposed residues that are absolutely critical to achieve increased solubility and to avoid precipitation of the enzyme in inclusion bodies when expressed in Escherichia coli. The designed variant Y115E-Y117E has been found to be able to provide large amounts of monodisperse, pure hQC from an E. coli expression system. To validate the use of the artificial construct as a target for large-scale X-ray and NMR screening campaigns in the search for new inhibitors of hQC, the X-ray crystal structures of the hQC Y115E-Y117E variant and of its adduct with the inhibitor PBD-150 were determined.
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Affiliation(s)
- Flavio DiPisa
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Cecilia Pozzi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Manuela Benvenuti
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Matteo Andreini
- Siena Biotech S.p.A., Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy
| | - Guido Marconi
- Siena Biotech S.p.A., Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy
| | - Stefano Mangani
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via Aldo Moro 2, 53100 Siena, Italy
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35
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Jimenez-Sanchez M, Lam W, Hannus M, Sönnichsen B, Imarisio S, Fleming A, Tarditi A, Menzies F, Dami TE, Xu C, Gonzalez-Couto E, Lazzeroni G, Heitz F, Diamanti D, Massai L, Satagopam VP, Marconi G, Caramelli C, Nencini A, Andreini M, Sardone GL, Caradonna NP, Porcari V, Scali C, Schneider R, Pollio G, O’Kane CJ, Caricasole A, Rubinsztein DC. siRNA screen identifies QPCT as a druggable target for Huntington's disease. Nat Chem Biol 2015; 11:347-354. [PMID: 25848931 PMCID: PMC4696152 DOI: 10.1038/nchembio.1790] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 03/05/2015] [Indexed: 11/09/2022]
Abstract
Huntington's disease (HD) is a currently incurable neurodegenerative condition caused by an abnormally expanded polyglutamine tract in huntingtin (HTT). We identified new modifiers of mutant HTT toxicity by performing a large-scale 'druggable genome' siRNA screen in human cultured cells, followed by hit validation in Drosophila. We focused on glutaminyl cyclase (QPCT), which had one of the strongest effects on mutant HTT-induced toxicity and aggregation in the cell-based siRNA screen and also rescued these phenotypes in Drosophila. We found that QPCT inhibition induced the levels of the molecular chaperone αB-crystallin and reduced the aggregation of diverse proteins. We generated new QPCT inhibitors using in silico methods followed by in vitro screening, which rescued the HD-related phenotypes in cell, Drosophila and zebrafish HD models. Our data reveal a new HD druggable target affecting mutant HTT aggregation and provide proof of principle for a discovery pipeline from druggable genome screen to drug development.
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Affiliation(s)
- Maria Jimenez-Sanchez
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0XY, UK
| | - Wun Lam
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0XY, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Michael Hannus
- Cenix BioScience GmbH, Tatzberg 47, 01307 Dresden, Germany
| | | | - Sara Imarisio
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0XY, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Angeleen Fleming
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0XY, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, UK, CB2 3EG
| | - Alessia Tarditi
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | - Fiona Menzies
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0XY, UK
| | - Teresa Ed Dami
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0XY, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, UK, CB2 3EG
- Department of Neuroscience, Psychology, Drug Research and Child Health, Division of Pharmacology and Toxicology, University of Florence, Florence, Italy
| | - Catherine Xu
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0XY, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, UK, CB2 3EG
| | | | - Giulia Lazzeroni
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | - Freddy Heitz
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | - Daniela Diamanti
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | - Luisa Massai
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | - Venkata P. Satagopam
- Structural and Computational Biology, EMBL, Meyerhofstr.1, 69117, Heidelberg, Germany
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, House of Biomedicine, 7 avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Guido Marconi
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | - Chiara Caramelli
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | - Arianna Nencini
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | - Matteo Andreini
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | - Gian Luca Sardone
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | | | - Valentina Porcari
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | - Carla Scali
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | - Reinhard Schneider
- Structural and Computational Biology, EMBL, Meyerhofstr.1, 69117, Heidelberg, Germany
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, House of Biomedicine, 7 avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Giuseppe Pollio
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | - Cahir J. O’Kane
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Andrea Caricasole
- Siena Biotech. Strada del Petriccio e Belriguardo, 35 53100 Siena, Italy
| | - David C. Rubinsztein
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0XY, UK
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36
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Wang YM, Huang KF, Tsai IH. Snake venom glutaminyl cyclases: Purification, cloning, kinetic study, recombinant expression, and comparison with the human enzyme. Toxicon 2014; 86:40-50. [DOI: 10.1016/j.toxicon.2014.04.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/18/2014] [Accepted: 04/29/2014] [Indexed: 11/17/2022]
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37
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Shih YP, Chou CC, Chen YL, Huang KF, Wang AHJ. Linked production of pyroglutamate-modified proteins via self-cleavage of fusion tags with TEV protease and autonomous N-terminal cyclization with glutaminyl cyclase in vivo. PLoS One 2014; 9:e94812. [PMID: 24733552 PMCID: PMC3986218 DOI: 10.1371/journal.pone.0094812] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 03/19/2014] [Indexed: 12/28/2022] Open
Abstract
Overproduction of N-terminal pyroglutamate (pGlu)-modified proteins utilizing Escherichia coli or eukaryotic cells is a challenging work owing to the fact that the recombinant proteins need to be recovered by proteolytic removal of fusion tags to expose the N-terminal glutaminyl or glutamyl residue, which is then converted into pGlu catalyzed by the enzyme glutaminyl cyclase. Herein we describe a new method for production of N-terminal pGlu-containing proteins in vivo via intracellular self-cleavage of fusion tags by tobacco etch virus (TEV) protease and then immediate N-terminal cyclization of passenger target proteins by a bacterial glutaminyl cyclase. To combine with the sticky-end PCR cloning strategy, this design allows the gene of target proteins to be efficiently inserted into the expression vector using two unique cloning sites (i.e., SnaB I and Xho I), and the soluble and N-terminal pGlu-containing proteins are then produced in vivo. Our method has been successfully applied to the production of pGlu-modified enhanced green fluorescence protein and monocyte chemoattractant proteins. This design will facilitate the production of protein drugs and drug target proteins that possess an N-terminal pGlu residue required for their physiological activities.
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Affiliation(s)
- Yan-Ping Shih
- Institute of Biological Chemistry and Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei, Taiwan
| | - Chi-Chi Chou
- Institute of Biological Chemistry and Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei, Taiwan
| | - Yi-Ling Chen
- Institute of Biological Chemistry and Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry and Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei, Taiwan
- * E-mail: (AHJW); (KFH)
| | - Andrew H.- J. Wang
- Institute of Biological Chemistry and Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei, Taiwan
- * E-mail: (AHJW); (KFH)
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38
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Huang KF, Hsu HL, Karim S, Wang AHJ. Structural and functional analyses of a glutaminyl cyclase from Ixodes scapularis reveal metal-independent catalysis and inhibitor binding. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:789-801. [PMID: 24598748 PMCID: PMC8494195 DOI: 10.1107/s1399004713033488] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/10/2013] [Indexed: 11/10/2022]
Abstract
Glutaminyl cyclases (QCs) from mammals and Drosophila are zinc-dependent enzymes that catalyze N-terminal pyroglutamate formation of numerous proteins and peptides. These enzymes have been found to be critical for the oviposition and embryogenesis of ticks, implying that they are possible physiological targets for tick control. Here, 1.10-1.15 Å resolution structures of a metal-independent QC from the black-legged tick Ixodes scapularis (Is-QC) are reported. The structures exhibit the typical scaffold of mammalian QCs but have two extra disulfide bridges that stabilize the central β-sheet, resulting in an increased thermal stability. Is-QC contains ~0.5 stoichiometric zinc ions, which could be removed by 1 mM EDTA. Compared with the Zn-bound form, apo-Is-QC has a nearly identical active-site structure and stability, but unexpectedly possesses significantly increased QC activities towards both synthetic and physiological substrates. Enzyme-kinetic analysis revealed that apo-Is-QC has a stronger substrate-binding affinity, suggesting that bound zinc interferes with substrate binding during catalysis. The structures of Is-QC bound to the inhibitor PBD150 revealed similar binding modes to both forms of Is-QC, with the exception of the inhibitor imidazole ring, which is consistent with the comparable inhibition activities of the inhibitor towards both forms of Is-QC. These findings have implications for the design of new QC inhibitors.
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Affiliation(s)
- Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 11529, Taiwan
| | - Hui-Ling Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 11529, Taiwan
| | - Shahid Karim
- Department of Biological Sciences, The University of Southern Mississippi, 18 College Drive #5018, Hattiesburg, MS 39406, USA
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 11529, Taiwan
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39
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Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. F1000Res 2013. [PMID: 25671081 DOI: 10.12688/f1000research.2-286.v1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The long term side effects of any newly introduced drug is a subject of intense research, and often raging controversies. One such example is the dipeptidyl peptidase-IV (DPP4) inhibitor used for treating type 2 diabetes, which is inconclusively implicated in increased susceptibility to acute pancreatitis. Previously, based on a computational analysis of the spatial and electrostatic properties of active site residues, we have demonstrated that phosphoinositide-specific phospholipase C (PI-PLC) from Bacillus cereus is a prolyl peptidase using in vivo experiments. In the current work, we first report the inhibition of the native activity of PI-PLC by two DPP4 inhibitors - vildagliptin (LAF-237) and K-579. While vildagliptin inhibited PI-PLC at micromolar concentrations, K-579 was a potent inhibitor even at nanomolar concentrations. Subsequently, we queried a comprehensive, non-redundant set of 5000 human proteins (50% similarity cutoff) with known structures using serine protease (SPASE) motifs derived from trypsin and DPP4. A pancreatic lipase and a gastric lipase are among the proteins that are identified as proteins having promiscuous SPASE scaffolds that could interact with DPP4 inhibitors. The presence of such scaffolds in human lipases is expected since they share the same catalytic mechanism with PI-PLC. However our methodology also detects other proteins, often with a completely different enzymatic mechanism, that have significantly congruent domains with the SPASE motifs. The reported elevated levels of serum lipase, although contested, could be rationalized by inhibition of lipases reported here. In an effort to further our understanding of the spatial and electrostatic basis of DPP4 inhibitors, we have also done a comprehensive analysis of all 76 known DPP4 structures liganded to inhibitors till date. Also, the methodology presented here can be easily adopted for other drugs, and provide the first line of filtering in the identification of pathways that might be inadvertently affected due to promiscuous scaffolds in proteins.
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Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India ; Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | | | - Bjarni Ásgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, IS-107 Reykjavik, Iceland
| | - Mouparna Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Anindya S Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Masataka Oda
- Division of Microbiology and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8514, Japan
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Abhaya M Dandekar
- Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | - Félix M Goñi
- Unidad de Bio, Universidad del Pais Vasco, Bilbao, Spain
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40
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Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. F1000Res 2013; 2:286. [PMID: 25671081 PMCID: PMC4309170 DOI: 10.12688/f1000research.2-286.v3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/29/2015] [Indexed: 12/25/2022] Open
Abstract
The long term side effects of any newly introduced drug is a subject of intense research, and often raging controversies. One such example is the dipeptidyl peptidase-IV (DPP4) inhibitor used for treating type 2 diabetes, which is inconclusively implicated in increased susceptibility to acute pancreatitis. Previously, based on a computational analysis of the spatial and electrostatic properties of active site residues, we have demonstrated that phosphoinositide-specific phospholipase C (PI-PLC) from
Bacillus cereus is a prolyl peptidase using
in vivo experiments. In the current work, we first report the inhibition of the native activity of PI-PLC by two DPP4 inhibitors - vildagliptin (LAF-237) and K-579. While vildagliptin inhibited PI-PLC at micromolar concentrations, K-579 was a potent inhibitor even at nanomolar concentrations. Subsequently, we queried a comprehensive, non-redundant set of 5000 human proteins (50% similarity cutoff) with known structures using serine protease (SPASE) motifs derived from trypsin and DPP4. A pancreatic lipase and a gastric lipase are among the proteins that are identified as proteins having promiscuous SPASE scaffolds that could interact with DPP4 inhibitors. The presence of such scaffolds in human lipases is expected since they share the same catalytic mechanism with PI-PLC. However our methodology also detects other proteins, often with a completely different enzymatic mechanism, that have significantly congruent domains with the SPASE motifs. The reported elevated levels of serum lipase, although contested, could be rationalized by inhibition of lipases reported here. In an effort to further our understanding of the spatial and electrostatic basis of DPP4 inhibitors, we have also done a comprehensive analysis of all 76 known DPP4 structures liganded to inhibitors till date. Also, the methodology presented here can be easily adopted for other drugs, and provide the first line of filtering in the identification of pathways that might be inadvertently affected due to promiscuous scaffolds in proteins.
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Affiliation(s)
- Sandeep Chakraborty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India ; Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | | | - Bjarni Ásgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, IS-107 Reykjavik, Iceland
| | - Mouparna Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Anindya S Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Masataka Oda
- Division of Microbiology and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Niigata, 951-8514, Japan
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Abhaya M Dandekar
- Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | - Félix M Goñi
- Unidad de Bio, Universidad del Pais Vasco, Bilbao, Spain
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41
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Abstract
Recombinant human Glutaminyl Cyclase expressed in E. coli is produced as inclusion bodies. Lack of glycosylation is the main origin of its accumulation in insoluble aggregates. Mutation of single isolated hydrophobic amino acids into negative amino acids was not able to circumvent inclusion bodies formation. On the contrary, substitution with carboxyl-terminal residues of two or three aromatic residues belonging to extended hydrophobic patches on the protein surface provided soluble but still active forms of the protein. These mutants could be expressed in isotopically enriched forms for NMR studies and the maximal attainable concentration was sufficient for the acquisition of 1H-15N HSQC spectra that represent the starting point for future drug development projects targeting Alzheimer’s disease.
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42
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Kolenko P, Koch B, Rahfeld JU, Schilling S, Demuth HU, Stubbs MT. Structure of glutaminyl cyclase from Drosophila melanogaster in space group I4. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:358-61. [PMID: 23545638 PMCID: PMC3614157 DOI: 10.1107/s1744309113005575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 02/26/2013] [Indexed: 05/06/2024]
Abstract
The structure of ligand-free glutaminyl cyclase (QC) from Drosophila melanogaster (DmQC) has been determined in a novel crystal form. The protein crystallized in space group I4, with unit-cell parameters a = b = 122.3, c = 72.7 Å. The crystal diffracted to a resolution of 2 Å at the home source. The structure was solved by molecular replacement and was refined to an R factor of 0.169. DmQC exhibits a typical α/β-hydrolase fold. The electron density of three monosaccharides could be localized. The accessibility of the active site will facilitate structural studies of novel inhibitor-binding modes.
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Affiliation(s)
- Petr Kolenko
- Department of Physical Biochemistry, Institute of Biochemistry and Biotechnology, MLU, Kurt-Mothes-Strasse 3, 06120 Halle, Germany.
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43
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Gramer MJ. Product Quality Considerations for Mammalian Cell Culture Process Development and Manufacturing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 139:123-66. [DOI: 10.1007/10_2013_214] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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44
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Koch B, Buchholz M, Wermann M, Heiser U, Schilling S, Demuth HU. Probing Secondary Glutaminyl Cyclase (QC) Inhibitor Interactions Applying an in silico-Modeling/Site-Directed Mutagenesis Approach: Implications for Drug Development. Chem Biol Drug Des 2012; 80:937-46. [DOI: 10.1111/cbdd.12046] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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45
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Koch B, Kolenko P, Buchholz M, Carrillo DR, Parthier C, Wermann M, Rahfeld JU, Reuter G, Schilling S, Stubbs MT, Demuth HU. Crystal structures of glutaminyl cyclases (QCs) from Drosophila melanogaster reveal active site conservation between insect and mammalian QCs. Biochemistry 2012; 51:7383-92. [PMID: 22897232 DOI: 10.1021/bi300687g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glutaminyl cyclases (QCs), which catalyze the formation of pyroglutamic acid (pGlu) at the N-terminus of a variety of peptides and proteins, have attracted particular attention for their potential role in Alzheimer's disease. In a transgenic Drosophila melanogaster (Dm) fruit fly model, oral application of the potent competitive QC inhibitor PBD150 was shown to reduce the burden of pGlu-modified Aβ. In contrast to mammals such as humans and rodents, there are at least three DmQC species, one of which (isoDromeQC) is localized to mitochondria, whereas DromeQC and an isoDromeQC splice variant possess signal peptides for secretion. Here we present the recombinant expression, characterization, and crystal structure determination of mature DromeQC and isoDromeQC, revealing an overall fold similar to that of mammalian QCs. In the case of isoDromeQC, the putative extended substrate binding site might be affected by the proximity of the N-terminal residues. PBD150 inhibition of DromeQC is roughly 1 order of magnitude weaker than that of the human and murine QCs. The inhibitor binds to isoDromeQC in a fashion similar to that observed for human QCs, whereas it adopts alternative binding modes in a DromeQC variant lacking the conserved cysteines near the active center and shows a disordered dimethoxyphenyl moiety in wild-type DromeQC, providing an explanation for the lower affinity. Our biophysical and structural data suggest that isoDromeQC and human QC are similar with regard to functional aspects. The two Dm enzymes represent a suitable model for further in-depth analysis of the catalytic mechanism of animal QCs, and isoDromeQC might serve as a model system for the structure-based design of potential AD therapeutics.
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Affiliation(s)
- Birgit Koch
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
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46
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Inhibition of glutaminyl cyclase attenuates cell migration modulated by monocyte chemoattractant proteins. Biochem J 2012; 442:403-12. [DOI: 10.1042/bj20110535] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
QC (glutaminyl cyclase) catalyses the formation of N-terminal pGlu (pyroglutamate) in peptides and proteins. pGlu formation in chemoattractants may participate in the regulation of macrophage activation and migration. However, a clear molecular mechanism for the regulation is lacking. The present study examines the role of QC-mediated pGlu formation on MCPs (monocyte chemoattractant proteins) in inflammation. We demonstrated in vitro the pGlu formation on MCPs by QC using MS. A potent QC inhibitor, PBD150, significantly reduced the N-terminal uncyclized-MCP-stimulated monocyte migration, whereas pGlu-containing MCP-induced cell migration was unaffected. QC small interfering RNA revealed a similar inhibitory effect. Lastly, we demonstrated that inhibiting QC can attenuate cell migration by lipopolysaccharide. These results strongly suggest that QC-catalysed N-terminal pGlu formation of MCPs is required for monocyte migration and provide new insights into the role of QC in the inflammation process. Our results also suggest that QC could be a drug target for some inflammatory disorders.
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47
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Ruiz-Carrillo D, Koch B, Parthier C, Wermann M, Dambe T, Buchholz M, Ludwig HH, Heiser U, Rahfeld JU, Stubbs MT, Schilling S, Demuth HU. Structures of Glycosylated Mammalian Glutaminyl Cyclases Reveal Conformational Variability near the Active Center. Biochemistry 2011; 50:6280-8. [DOI: 10.1021/bi200249h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- David Ruiz-Carrillo
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Birgit Koch
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Christoph Parthier
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Michael Wermann
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Tresfore Dambe
- PSF AG, Robert-Roessle-Strasse 10, D-13092 Berlin, Germany
| | - Mirko Buchholz
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | | | - Ulrich Heiser
- Probiodrug AG, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | | | - Milton T. Stubbs
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
- Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
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