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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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Zhu F, He S, Ni C, Wu Y, Wu H, Wen L. Study on the structure-activity relationship of rice immunopeptides based on molecular docking. Food Chem X 2024; 21:101158. [PMID: 38322762 PMCID: PMC10843992 DOI: 10.1016/j.fochx.2024.101158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 01/14/2024] [Accepted: 01/21/2024] [Indexed: 02/08/2024] Open
Abstract
Research on food-derived immunoregulatory peptides has attracted increasing attention of scientists worldwide. However, the structure-activity relationship of rice immunopeptides was not clearly. Herein, 114 rice immunopeptides were obtained by simulating the enzymatic hydrolysis of rice proteins and were further analyzed by NetMHCIipan-4.0. Subsequently, the molecular docking was used to simulate the binding of immunoreactive peptides to major histocompatibility complex class II (MHC-II) molecules. Results show that S, R, D, E, and T amino acid could easily form hydrogen bonds with MHC-II molecules, thus enhancing innate and adaptive immunity. Finally, glucose-modified rice immunopeptides were to investigate the binding of the peptides with MHC-II molecules after glycosylation modification; this provided a theoretical basis for the targeted modification of the generated immunopeptides. All in all, the present study provides a theoretical foundation to further utilize rice processing byproducts and other food products to enhance immunity.
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Affiliation(s)
- Fan Zhu
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha 410114, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Shuwen He
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Ce Ni
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Ying Wu
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Hao Wu
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Li Wen
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha 410114, China
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3
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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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4
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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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5
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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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6
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Deng H, Wang G, Zhao S, Tao Y, Zhang Z, Yang J, Lei Y. New hope for tumor immunotherapy: the macrophage-related "do not eat me" signaling pathway. Front Pharmacol 2023; 14:1228962. [PMID: 37484024 PMCID: PMC10358856 DOI: 10.3389/fphar.2023.1228962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023] Open
Abstract
The "do not eat me" signaling pathway is extremely active in tumor cells, providing a means for these cells to elude macrophage phagocytosis and escape immune surveillance. Representative markers of this pathway, such as CD47 and CD24, are highly expressed in numerous tumors. The interaction of SIRPα with CD47 reduces the accumulation of non-myosin ⅡA on the cell membrane. The combination of CD24 and Siglec10 ultimately leads to the recruitment of SHP-1 or SHP-2 to reduce signal transduction. Both of them weaken the ability of macrophages to engulf tumor cells. Blocking the mutual recognition between CD47-SIRPα or CD24-Siglec10 using large molecular proteins or small molecular drugs represents a promising avenue for tumor immunotherapy. Doing so can inhibit signal transduction and enhance macrophage clearance rates of cancer cells. In this paper, we summarize the characteristics of the drugs that affect the "do not eat me" signaling pathway via classical large molecular proteins and small molecule drugs, which target the CD47-SIRPα and CD24-Siglec10 signaling pathways, which target the CD47-SIRPα and CD24-Siglec10 signaling pathways. We expect it will offer insight into the development of new drugs centered on blocking the "do not eat me" signaling pathway.
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Affiliation(s)
- Han Deng
- General Practice Ward/International Medical Center, General Practice Medical Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Nursing, Sichuan University, Chengdu, Sichuan, China
| | - Guan Wang
- General Practice Ward/International Medical Center, General Practice Medical Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Nursing, Sichuan University, Chengdu, Sichuan, China
| | - Shengyan Zhao
- General Practice Ward/International Medical Center, General Practice Medical Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Nursing, Sichuan University, Chengdu, Sichuan, China
| | - Yiran Tao
- West China-California Research Center for Predictive Intervention Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhixiong Zhang
- General Practice Ward/International Medical Center, General Practice Medical Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Nursing, Sichuan University, Chengdu, Sichuan, China
| | - Jinliang Yang
- General Practice Ward/International Medical Center, General Practice Medical Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Nursing, Sichuan University, Chengdu, Sichuan, China
| | - Yi Lei
- General Practice Ward/International Medical Center, General Practice Medical Center, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China School of Nursing, Sichuan University, Chengdu, Sichuan, 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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Discovery of potent indazole-based human glutaminyl cyclase (QC) inhibitors as Anti-Alzheimer's disease agents. Eur J Med Chem 2022; 244:114837. [DOI: 10.1016/j.ejmech.2022.114837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/20/2022]
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9
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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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10
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Zeghouan O, Mahesha, Sellami S, Kashi I, Bouchameni C, Lokanath N. Analysis of structural conformation and supramolecular self-assembly of novel oxalate-bridged tetranuclear Cu(II) complex by combined crystallographic and computational studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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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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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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13
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Baumann N, Rösner T, Jansen JHM, Chan C, Marie Eichholz K, Klausz K, Winterberg D, Müller K, Humpe A, Burger R, Peipp M, Schewe DM, Kellner C, Leusen JHW, Valerius T. Enhancement of epidermal growth factor receptor antibody tumor immunotherapy by glutaminyl cyclase inhibition to interfere with CD47/signal regulatory protein alpha interactions. Cancer Sci 2021; 112:3029-3040. [PMID: 34058788 PMCID: PMC8353920 DOI: 10.1111/cas.14999] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/17/2021] [Accepted: 05/23/2021] [Indexed: 12/21/2022] Open
Abstract
Integrin associated protein (CD47) is an important target in immunotherapy, as it is expressed as a "don't eat me" signal on many tumor cells. Interference with its counter molecule signal regulatory protein alpha (SIRPα), expressed on myeloid cells, can be achieved with blocking Abs, but also by inhibiting the enzyme glutaminyl cyclase (QC) with small molecules. Glutaminyl cyclase inhibition reduces N-terminal pyro-glutamate formation of CD47 at the SIRPα binding site. Here, we investigated the impact of QC inhibition on myeloid effector cell-mediated tumor cell killing by epidermal growth factor receptor (EGFR) Abs and the influence of Ab isotypes. SEN177 is a QC inhibitor and did not interfere with EGFR Ab-mediated direct growth inhibition, complement-dependent cytotoxicity, or Ab-dependent cell-mediated cytotoxicity (ADCC) by mononuclear cells. However, binding of a human soluble SIRPα-Fc fusion protein to SEN177 treated cancer cells was significantly reduced in a dose-dependent manner, suggesting that pyro-glutamate formation of CD47 was affected. Glutaminyl cyclase inhibition in tumor cells translated into enhanced Ab-dependent cellular phagocytosis by macrophages and enhanced ADCC by polymorphonuclear neutrophilic granulocytes. Polymorphonuclear neutrophilic granulocyte-mediated ADCC was significantly more effective with EGFR Abs of human IgG2 or IgA2 isotypes than with IgG1 Abs, proposing that the selection of Ab isotypes could critically affect the efficacy of Ab therapy in the presence of QC inhibition. Importantly, QC inhibition also enhanced the therapeutic efficacy of EGFR Abs in vivo. Together, these results suggest a novel approach to specifically enhance myeloid effector cell-mediated efficacy of EGFR Abs by orally applicable small molecule QC inhibitors.
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Affiliation(s)
- Niklas Baumann
- Section for Stem Cell Transplantation and ImmunotherapyDepartment of Medicine IIChristian‐Albrechts‐University Kiel and University Medical Center Schleswig‐Holstein, Campus KielKielGermany
| | - Thies Rösner
- Section for Stem Cell Transplantation and ImmunotherapyDepartment of Medicine IIChristian‐Albrechts‐University Kiel and University Medical Center Schleswig‐Holstein, Campus KielKielGermany
| | - J. H. Marco Jansen
- Immunotherapy LaboratoryCenter for Translational ImmunologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Chilam Chan
- Immunotherapy LaboratoryCenter for Translational ImmunologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Klara Marie Eichholz
- Section for Stem Cell Transplantation and ImmunotherapyDepartment of Medicine IIChristian‐Albrechts‐University Kiel and University Medical Center Schleswig‐Holstein, Campus KielKielGermany
| | - Katja Klausz
- Section for Stem Cell Transplantation and ImmunotherapyDepartment of Medicine IIChristian‐Albrechts‐University Kiel and University Medical Center Schleswig‐Holstein, Campus KielKielGermany
| | - Dorothee Winterberg
- Pediatric Hematology/OncologyALL‐BFM Study GroupChristian‐Albrechts‐University Kiel and University Medical Center Schleswig‐Holstein, Campus KielKielGermany
| | - Kristina Müller
- Pediatric Hematology/OncologyALL‐BFM Study GroupChristian‐Albrechts‐University Kiel and University Medical Center Schleswig‐Holstein, Campus KielKielGermany
| | - Andreas Humpe
- Department of Transfusion Medicine, Cell Therapeutics and HemostaseologyUniversity HospitalLMU MunichMunichGermany
| | - Renate Burger
- Section for Stem Cell Transplantation and ImmunotherapyDepartment of Medicine IIChristian‐Albrechts‐University Kiel and University Medical Center Schleswig‐Holstein, Campus KielKielGermany
| | - Matthias Peipp
- Section for Stem Cell Transplantation and ImmunotherapyDepartment of Medicine IIChristian‐Albrechts‐University Kiel and University Medical Center Schleswig‐Holstein, Campus KielKielGermany
| | - Denis M. Schewe
- Pediatric Hematology/OncologyALL‐BFM Study GroupChristian‐Albrechts‐University Kiel and University Medical Center Schleswig‐Holstein, Campus KielKielGermany
| | - Christian Kellner
- Department of Transfusion Medicine, Cell Therapeutics and HemostaseologyUniversity HospitalLMU MunichMunichGermany
| | - Jeanette H. W. Leusen
- Immunotherapy LaboratoryCenter for Translational ImmunologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Thomas Valerius
- Section for Stem Cell Transplantation and ImmunotherapyDepartment of Medicine IIChristian‐Albrechts‐University Kiel and University Medical Center Schleswig‐Holstein, Campus KielKielGermany
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14
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Coimbra JRM, Salvador JAR. A patent review of glutaminyl cyclase inhibitors (2004-present). Expert Opin Ther Pat 2021; 31:809-836. [PMID: 33896339 DOI: 10.1080/13543776.2021.1917549] [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] [Indexed: 10/21/2022]
Abstract
Introduction: Glutaminyl cyclase (QC) enzymes catalyze the post-translational processing of several substrates with N-terminal glutamine or glutamate to form pyroglutamate (pE) residue. In addition to physiological functions, emerging evidence demonstrates that human QCs play a part in pathological processes in diverse diseases such as Alzheimer's disease (AD), inflammatory and cancer diseases.Areas covered: In recent years, efforts to effectively develop QC small-molecule inhibitors have been made and different chemical classes have been disclosed. This review summarizes the patents/applications regarding QC inhibitors released from 2004 (first patent) to now. The patents are mostly described in terms of chemical structures, biochemical/pharmacological activities, and potential clinical applications.Expert opinion: For more than 15 years of research, the knowledge on the QC activity domain has considerably increased and therapeutic potential of QC inhibitors has been explored. An important number of studies and patents have been published to expand the use of QC inhibitors. QC enzymes are pharmacologically interesting targets to be used as an AD-modifying therapy, or for other QC-associated disorder. Distinct classes of chemical scaffolds and potential clinical uses have been claimed by various organizations. For the coming years, there is much to experience in the QC field.
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Affiliation(s)
- Judite R M Coimbra
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.,Center for Neuroscience and Cell Biology (CNC), Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Jorge A R Salvador
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.,Center for Neuroscience and Cell Biology (CNC), Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
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15
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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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16
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Lamers S, Feng Q, Cheng Y, Yu S, Sun B, Lukman M, Jiang J, Ruiz-Carrillo D. Structural and kinetic characterization of Porphyromonas gingivalis glutaminyl cyclase. Biol Chem 2021; 402:759-768. [PMID: 33823093 DOI: 10.1515/hsz-2020-0298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/16/2021] [Indexed: 11/15/2022]
Abstract
Porphyromonas gingivalis is a bacterial species known to be involved in the pathogenesis of chronic periodontitis, that more recently has been as well associated with Alzheimer's disease. P. gingivalis expresses a glutaminyl cyclase (PgQC) whose human ortholog is known to participate in the beta amyloid peptide metabolism. We have elucidated the crystal structure of PgQC at 1.95 Å resolution in unbound and in inhibitor-complexed forms. The structural characterization of PgQC confirmed that PgQC displays a mammalian fold rather than a bacterial fold. Our biochemical characterization indicates that PgQC uses a mammalian-like catalytic mechanism enabled by the residues Asp149, Glu182, Asp183, Asp218, Asp267 and His299. In addition, we could observe that a non-conserved Trp193 may drive differences in the binding affinity of ligands which might be useful for drug development. With a screening of a small molecule library, we have identified a benzimidazole derivative rendering PgQC inhibition in the low micromolar range that might be amenable for further medicinal chemistry development.
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Affiliation(s)
- Sebastiaan Lamers
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Qiaoli Feng
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Yili Cheng
- Department of Health and Environmental Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Sihong Yu
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Bo Sun
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai201204, China
| | - Maxwell Lukman
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - Jie Jiang
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
| | - David Ruiz-Carrillo
- Department of Biological Sciences, School of Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu215123, China
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17
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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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18
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Burgess TL, Amason JD, Rubin JS, Duveau DY, Lamy L, Roberts DD, Farrell CL, Inglese J, Thomas CJ, Miller TW. A homogeneous SIRPα-CD47 cell-based, ligand-binding assay: Utility for small molecule drug development in immuno-oncology. PLoS One 2020; 15:e0226661. [PMID: 32240171 PMCID: PMC7117682 DOI: 10.1371/journal.pone.0226661] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/06/2020] [Indexed: 01/08/2023] Open
Abstract
CD47 is an immune checkpoint protein that downregulates both the innate and adaptive anti-tumor immune response via its counter receptor SIRPα. Biologics, including humanized CD47 monoclonal antibodies and decoy SIRPα receptors, that block the SIRPα-CD47 interaction, are currently being developed as cancer immunotherapy agents. However, adverse side effects and limited penetration of tumor tissue associated with their structure and large size may impede their clinical application. We recently developed a quantitative high throughput screening assay platform to identify small molecules that disrupt the binding of SIRPα and CD47 as an alternative approach to these protein-based therapeutics. Here, we report on the development and optimization of a cell-based binding assay to validate active small molecules from our biochemical screening effort. This assay has a low volume, high capacity homogenous format that relies on laser scanning cytometry (LSC) and associated techniques to enhance signal to noise measurement of cell surface binding. The LSC assay is specific, concentration dependent, and validated for the two major human SIRPα variants (V1 and V2), with results that parallel those of our biochemical data as well as published studies. We also utilized the LSC assay to confirm published studies showing that the inhibition of amino-terminal pyroglutamate formation on CD47 using the glutaminyl cyclase inhibitor SEN177 disrupts SIRPα binding. The SIRPα-CD47 interaction could be quantitatively measured in live and fixed tumor cells. Use of fixed cells reduces the burden of cell maintenance and provides stable cell standards to control for inter- and intra-assay variations. We also demonstrate the utility of the assay to characterize the activity of the first reported small molecule antagonists of the SIRPα-CD47 interaction. This assay will support the screening of thousands of compounds to identify or validate active small molecules as hits, develop structure activity relationships and assist in the optimization of hits to leads by a typical iterative medicinal chemistry campaign.
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Affiliation(s)
- Teresa L. Burgess
- Paradigm Shift Therapeutics LLC, Rockville, Maryland, United States of America
| | - Joshua D. Amason
- Paradigm Shift Therapeutics LLC, Rockville, Maryland, United States of America
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeffrey S. Rubin
- Paradigm Shift Therapeutics LLC, Rockville, Maryland, United States of America
| | - Damien Y. Duveau
- Division of Preclinical Innovation, National Center for Advancing Translational Studies, National Institutes of Health, Rockville, Maryland, United States of America
| | - Laurence Lamy
- Division of Preclinical Innovation, National Center for Advancing Translational Studies, National Institutes of Health, Rockville, Maryland, United States of America
| | - David D. Roberts
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - James Inglese
- Division of Preclinical Innovation, National Center for Advancing Translational Studies, National Institutes of Health, Rockville, Maryland, United States of America
| | - Craig J. Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Studies, National Institutes of Health, Rockville, Maryland, United States of America
| | - Thomas W. Miller
- Paradigm Shift Therapeutics LLC, Rockville, Maryland, United States of America
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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19
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Minh Hung H, Nguyen MT, Tran PT, Truong VK, Chapman J, Quynh Anh LH, Derreumaux P, Vu VV, Ngo ST. Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ 40 Peptide. J Chem Inf Model 2020; 60:1399-1408. [PMID: 32105466 DOI: 10.1021/acs.jcim.9b01074] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There is experimental evidence that the astaxanthin, betanin, and epigallocatechin-3-gallate (EGCG) compounds slow down the aggregation kinetics and the toxicity of the amyloid-β (Aβ) peptide. How these inhibitors affect the self-assembly at the atomic level remains elusive. To address this issue, we have performed for each ligand atomistic replica exchange molecular dynamic (REMD) simulations in an explicit solvent of the Aβ11-40 trimer from the U-shape conformation and MD simulations starting from Aβ1-40 dimer and tetramer structures characterized by different intra- and interpeptide conformations. We find that the three ligands have similar binding free energies on small Aβ40 oligomers but very distinct transient binding sites that will affect the aggregation of larger assemblies and fibril elongation of the Aβ40 peptide.
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Affiliation(s)
- Huynh Minh Hung
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
| | - Minh Tho Nguyen
- Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - Phuong-Thao Tran
- Department of Pharmaceutical Chemistry, Hanoi University of Pharmacy, Hanoi 100000, Vietnam
| | - Vi Khanh Truong
- School of Science, RMIT University, GPO Box 2476, Melbourne 3001, Australia
| | - James Chapman
- School of Science, RMIT University, GPO Box 2476, Melbourne 3001, Australia
| | - Le Huu Quynh Anh
- Department of Climate Change and Renewable Energy, Ho Chi Minh City University of Natural Resources and Environment, Ho Chi Minh City 700000, Vietnam
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam.,Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam.,Laboratoire de Biochimie Théorique, UPR9080, CNRS, Université de Paris, 13 rue Pierre et Marie Curie, F-75005 Paris, France.,Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, 75005 Paris, France
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam.,Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
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20
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Nguyen NT, Nguyen TH, Pham TNH, Huy NT, Bay MV, Pham MQ, Nam PC, Vu VV, Ngo ST. Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity. J Chem Inf Model 2019; 60:204-211. [DOI: 10.1021/acs.jcim.9b00778] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nguyen Thanh Nguyen
- Department of Theoretical Physics, Ho Chi Minh City University of Science, Ho Chi Minh City 700000, Vietnam
| | - Trung Hai Nguyen
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - T. Ngoc Han Pham
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - Nguyen Truong Huy
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - Mai Van Bay
- Department of Chemical Engineering, The University of Da Nang, University of Science and Technology, Da Nang City 550000, Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi 100000, Vietnam
| | - Pham Cam Nam
- Department of Chemical Engineering, The University of Da Nang, University of Science and Technology, Da Nang City 550000, Vietnam
| | - Van V. Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
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21
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High-throughput genome-wide phenotypic screening via immunomagnetic cell sorting. Nat Biomed Eng 2019; 3:796-805. [DOI: 10.1038/s41551-019-0454-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023]
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22
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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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23
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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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