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Wang Z, Xie X, Jin K, Xia D, Zhu J, Zhang J. Amplified and Specific Staining of Protein Dimerization on Cell Membrane Catalyzed by Responsively Installed DNA Nanomachines for Cancer Diagnosis. Adv Healthc Mater 2024; 13:e2303398. [PMID: 38183379 DOI: 10.1002/adhm.202303398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/27/2023] [Indexed: 01/08/2024]
Abstract
In situ staining of protein dimerization on cell membrane has an important significance in accurate diagnosis during perioperative period, yet facile integration of specific recognition function and local signal conversion/amplification abilities on membrane surface remains a great challenge. Herein, a two-stage catalytic strategy is developed by installing DNA nanomachines and employing. Specifically, dual-aptamer-assisted DNA scaffold perform a "bispecific recognition-then-computing" operation and the output signal initiate a membrane-anchored biocatalysis for self-assembly of DNA catalytic converters, that is, G-quadruplex nanowire/hemin DNAzyme. Then, localized-deposition of chromogenic polydopamine is chemically catalyzed by horseradish peroxidase-mimicking DNAzyme and guided by supramolecular interactions between conjugate rigid plane of G-tetrad and polydopamine oligomer. The catalytic products exhibit nanofiber morphology with a diameter of 80-120 nm and a length of 1-10 µm, and one-to-one localize on DNA scaffold for amplified and specific staining of protein dimers. The bispecific staining leads to a higher (≈3.4-fold) signal intensity than traditional immunohistochemistry, which is beneficial for direct visualization. Moreover, an efficient discrimination ability of the bispecific staining strategy is observed in co-culture model staining. This study provides a novel catalytic method for controlling deposition of chromogens and paves a new avenue to sensitively stain of protein-protein interactions in disease diagnosis.
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Affiliation(s)
- Zhenqiang Wang
- Department of Pharmacy, The Second Affiliated Hospital, Army Medical University, No. 183 Xinqiao Road, Chongqing, 400037, China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No.174 Shazheng Road, Chongqing, 400044, China
| | - Xiyue Xie
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No.174 Shazheng Road, Chongqing, 400044, China
| | - Kaifei Jin
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No.174 Shazheng Road, Chongqing, 400044, China
| | - Daqing Xia
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No.174 Shazheng Road, Chongqing, 400044, China
| | - Jing Zhu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No.174 Shazheng Road, Chongqing, 400044, China
| | - Jixi Zhang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, No.174 Shazheng Road, Chongqing, 400044, China
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Xie S, Yang G, Wu J, Jiang L, Yuan C, Xu P, Huang M, Liu Y, Li J. In silico screening of natural products as uPAR inhibitors via multiple structure-based docking and molecular dynamics simulations. J Biomol Struct Dyn 2023:1-12. [PMID: 38111151 DOI: 10.1080/07391102.2023.2295386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/07/2023] [Indexed: 12/20/2023]
Abstract
Cancer remains one of the most pressing challenges to global healthcare, exerting a significant impact on patient life expectancy. Cancer metastasis is a critical determinant of the lethality and treatment resistance of cancer. The urokinase-type plasminogen activator receptor (uPAR) shows great potential as a target for anticancer and antimetastatic therapies. In this work, we aimed to identify potential uPAR inhibitors by structural dynamics-based virtual screenings against a natural product library on four representative apo-uPAR structural models recently derived from long-timescale molecular dynamics (MD) simulations. Fifteen potential inhibitors (NP1-NP15) were initially identified through molecular docking, consensus scoring, and visual inspection. Subsequently, we employed MD-based molecular mechanics-generalized Born surface area (MM-GBSA) calculations to evaluate their binding affinities to uPAR. Structural dynamics analyses further indicated that all of the top 6 compounds exhibited stable binding to uPAR and interacted with the critical residues in the binding interface between uPAR and its endogenous ligand uPA, suggesting their potential as uPAR inhibitors by interrupting the uPAR-uPA interaction. We finally predicted the ADMET properties of these compounds. The natural products NP5, NP12, and NP14 with better binding affinities to uPAR than the uPAR inhibitors previously discovered by us were proven to be potentially orally active in humans. This work offers potential uPAR inhibitors that may contribute to the development of novel effective anticancer and antimetastatic therapeutics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Song Xie
- College of Chemistry, Fuzhou University, Fuzhou, China
| | - Guiqian Yang
- College of Chemistry, Fuzhou University, Fuzhou, China
| | - Juhong Wu
- College of Chemistry, Fuzhou University, Fuzhou, China
| | | | - Cai Yuan
- College of Chemistry, Fuzhou University, Fuzhou, China
| | - Peng Xu
- College of Chemistry, Fuzhou University, Fuzhou, China
| | | | - Yichang Liu
- School of Pharmacy, Nantong University, Nantong, China
| | - Jinyu Li
- College of Chemistry, Fuzhou University, Fuzhou, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, China
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3
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Ismail A, Hayek SS. Role of Soluble Urokinase-Type Plasminogen Activator Receptor in Cardiovascular Disease. Curr Cardiol Rep 2023; 25:1797-1810. [PMID: 37948017 DOI: 10.1007/s11886-023-01991-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/01/2023] [Indexed: 11/12/2023]
Abstract
PURPOSE OF REVIEW Chronic inflammation is a major contributor to cardiovascular disease (CVD) risk. Soluble urokinase plasminogen activator receptor (suPAR) is an immune-derived glycoprotein that is strongly associated with atherosclerotic disease. This review summarizes evidence on suPAR's role in CVD pathogenesis and its potential as a prognostic indicator and therapeutic target. RECENT FINDINGS Clinical, genetic, and experimental evidence supports suPAR's role as a pathogenic factor in atherosclerosis. suPAR promotes atherosclerosis through modulation of monocyte activation and function. Clinically, elevated suPAR levels are linked to increased cardiovascular risk across diverse populations. Ongoing clinical trials are evaluating therapies targeting suPAR signaling. Current evidence positions suPAR as a regulator of myeloid cell function that contributes to vascular inflammation and subsequent cardiovascular events. Additional research is needed to determine whether suPAR measurement can improve CVD risk prediction and enable personalized management. Overall, suPAR is a promising immune-derived biomarker and target for reducing inflammation and cardiovascular risk.
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Affiliation(s)
- Anis Ismail
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, 1500 E Medical Center Dr, CVC #2709, Ann Arbor, 48109, MI, USA
| | - Salim S Hayek
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, 1500 E Medical Center Dr, CVC #2709, Ann Arbor, 48109, MI, USA.
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4
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Torres-Paris C, Chen Y, Xiao L, Song HJ, Chen P, Komives EA. The autoactivation of human single-chain urokinase-type plasminogen activator (uPA). J Biol Chem 2023; 299:105179. [PMID: 37607618 PMCID: PMC10520878 DOI: 10.1016/j.jbc.2023.105179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/29/2023] [Accepted: 08/15/2023] [Indexed: 08/24/2023] Open
Abstract
Most serine proteases are synthesized as inactive zymogens that are activated by cleavage by another protease in a tightly regulated mechanism. The urokinase-type plasminogen activator (uPA) and plasmin cleave and activate each other, constituting a positive feedback loop. How this mutual activation cycle begins has remained a mystery. We used hydrogen deuterium exchange mass spectrometry to characterize the dynamic differences between the inactive single-chain uPA (scuPA) and its active form two-chain uPA (tcuPA). The results show that the C-terminal β-barrel and the area around the new N terminus have significantly reduced dynamics in tcuPA as compared with scuPA. We also show that the zymogen scuPA is inactive but can, upon storage, become active in the absence of external proteases. In addition to plasmin, the tcuPA can activate scuPA by cleavage at K158, a process called autoactivation. Unexpectedly, tcuPA can cleave at position 158 even when this site is mutated. TcuPA can also cleave scuPA after K135 or K136 in the disordered linker, which generates the soluble protease domain of uPA. Plasmin cleaves scuPA exclusively after K158 and at a faster rate than tcuPA. We propose a mechanism by which the uPA receptor dimerization could promote autoactivation of scuPA on cell surfaces. These results resolve long-standing controversies in the literature surrounding the mechanism of uPA activation.
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Affiliation(s)
- Constanza Torres-Paris
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Yueyi Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Lufan Xiao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Harriet J Song
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Pingyu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.
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Zhou Y, Song M, Xie D, Yan S, Yu S, Xie S, Cai M, Li H, Shang L, Jiang L, Yuan C, Huang M, Li J, Xu P. Structural Dynamics-Driven Discovery of Anticancer and Antimetastatic Effects of Diltiazem and Glibenclamide Targeting Urokinase Receptor. J Med Chem 2023; 66:5415-5426. [PMID: 36854648 DOI: 10.1021/acs.jmedchem.2c01663] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Diltiazem and glibenclamide are commonly used hypotensive and antidiabetic drugs. This study reports the discovery of the potential antitumor and antimetastatic effects of these two drugs using a structural dynamics-driven virtual screening targeting urokinase receptor (uPAR). Owing to uPAR's high flexibility, currently resolved crystal structures of uPAR, all in ligand-bound states, provide limited representations of its physiological conformation. To improve the accuracy of screening, we performed a long-timescale molecular dynamics simulation and obtained the representative conformations of apo-uPAR as the targets for our screening. Experimentally, we demonstrated that diltiazem and glibenclamide bound uPAR with KD values in the micromolar range. In addition, both compounds effectively suppressed tumor growth and metastasis in a uPAR-dependent manner in vitro and in vivo. This work not only provides two potent uPAR inhibitors but also reports a proof-of-concept study on the potential off-label antitumor and antimetastatic uses of diltiazem and glibenclamide.
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Affiliation(s)
- Yang Zhou
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, P. R. China.,College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, P. R. China
| | - Meiru Song
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, P. R. China.,Henan Academy of Sciences, Zhengzhou, Henan 450046, P. R. China
| | - Daoqing Xie
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, P. R. China
| | - Shufeng Yan
- Sanming University, Sanming, Fujian 365004, P. R. China
| | - Shujuan Yu
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, P. R. China
| | - Song Xie
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, P. R. China
| | - Meiqin Cai
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, P. R. China
| | - Hanlin Li
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, P. R. China
| | - Le Shang
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Science, Fuzhou, Fujian 350109, P. R. China
| | - Longguang Jiang
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, P. R. China
| | - Cai Yuan
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, P. R. China
| | - Mingdong Huang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, P. R. China.,College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, P. R. China
| | - Jinyu Li
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, P. R. China
| | - Peng Xu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350108, P. R. China.,Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, Fujian 350108, P. R. China
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6
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Yatsenko T, Skrypnyk M, Troyanovska O, Tobita M, Osada T, Takahashi S, Hattori K, Heissig B. The Role of the Plasminogen/Plasmin System in Inflammation of the Oral Cavity. Cells 2023; 12:cells12030445. [PMID: 36766787 PMCID: PMC9913802 DOI: 10.3390/cells12030445] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/03/2023] Open
Abstract
The oral cavity is a unique environment that consists of teeth surrounded by periodontal tissues, oral mucosae with minor salivary glands, and terminal parts of major salivary glands that open into the oral cavity. The cavity is constantly exposed to viral and microbial pathogens. Recent studies indicate that components of the plasminogen (Plg)/plasmin (Pm) system are expressed in tissues of the oral cavity, such as the salivary gland, and contribute to microbial infection and inflammation, such as periodontitis. The Plg/Pm system fulfills two major functions: (a) the destruction of fibrin deposits in the bloodstream or damaged tissues, a process called fibrinolysis, and (b) non-fibrinolytic actions that include the proteolytic modulation of proteins. One can observe both functions during inflammation. The virus that causes the coronavirus disease 2019 (COVID-19) exploits the fibrinolytic and non-fibrinolytic functions of the Plg/Pm system in the oral cavity. During COVID-19, well-established coagulopathy with the development of microthrombi requires constant activation of the fibrinolytic function. Furthermore, viral entry is modulated by receptors such as TMPRSS2, which is necessary in the oral cavity, leading to a derailed immune response that peaks in cytokine storm syndrome. This paper outlines the significance of the Plg/Pm system for infectious and inflammatory diseases that start in the oral cavity.
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Affiliation(s)
- Tetiana Yatsenko
- Department of Research Support Utilizing Bioresource Bank, Graduate School of Medicine, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Maksym Skrypnyk
- Department of Research Support Utilizing Bioresource Bank, Graduate School of Medicine, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Olga Troyanovska
- Department of Research Support Utilizing Bioresource Bank, Graduate School of Medicine, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Morikuni Tobita
- Department of Oral and Maxillofacial Surgery, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan
| | - Taro Osada
- Department of Gastroenterology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka, Urayasu-Shi 279-0021, Japan
| | - Satoshi Takahashi
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ku, Tokyo 108-8639, Japan
| | - Koichi Hattori
- Center for Genome and Regenerative Medicine, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan
- Correspondence: (K.H.); (B.H.); Tel.: +81-3-3813-3111 (switchboard 2115) (B.H.)
| | - Beate Heissig
- Department of Research Support Utilizing Bioresource Bank, Graduate School of Medicine, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo 113-8421, Japan
- Correspondence: (K.H.); (B.H.); Tel.: +81-3-3813-3111 (switchboard 2115) (B.H.)
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Shmakova AA, Popov VS, Romanov IP, Khabibullin NR, Sabitova NR, Karpukhina AA, Kozhevnikova YA, Kurilina EV, Tsokolaeva ZI, Klimovich PS, Rubina KA, Vassetzky YS, Semina EV. Urokinase System in Pathogenesis of Pulmonary Fibrosis: A Hidden Threat of COVID-19. Int J Mol Sci 2023; 24:ijms24021382. [PMID: 36674896 PMCID: PMC9867169 DOI: 10.3390/ijms24021382] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/04/2023] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Pulmonary fibrosis is a common and threatening post-COVID-19 complication with poorly resolved molecular mechanisms and no established treatment. The plasminogen activator system, including urokinase (uPA) and urokinase receptor (uPAR), is involved in the pathogenesis of COVID-19 and contributes to the development of lung injury and post-COVID-19 pulmonary fibrosis, although their cellular and molecular underpinnings still remain obscure. The aim of the current study was to assess the role of uPA and uPAR in the pathogenesis of pulmonary fibrosis. We analyzed uPA and uPAR expression in human lung tissues from COVID-19 patients with pulmonary fibrosis using single-cell RNA-seq and immunohistochemistry. We modeled lung fibrosis in Plau-/- and Plaur-/- mice upon bleomycin instillation and explored the effect of uPAR downregulation in A549 and BEAS-2B lung epithelial cells. We found that uPAR expression drastically decreased in the epithelial airway basal cells and monocyte/macrophage cells, whereas uPA accumulation significantly increased in tissue samples of COVID-19 patients. Lung injury and fibrosis in Plaur-/- vs. WT mice upon bleomycin instillation revealed that uPAR deficiency resulted in pro-fibrogenic uPA accumulation, IL-6 and ACE2 upregulation in lung tissues and was associated with severe fibrosis, weight loss and poor survival. uPAR downregulation in A549 and BEAS-2B was linked to an increased N-cadherin expression, indicating the onset of epithelial-mesenchymal transition and potentially contributing to pulmonary fibrosis. Here for the first time, we demonstrate that plasminogen treatment reversed lung fibrosis in Plaur-/- mice: the intravenous injection of 1 mg of plasminogen on the 21st day of bleomycin-induced fibrosis resulted in a more than a two-fold decrease in the area of lung fibrosis as compared to non-treated mice as evaluated by the 42nd day. The expression and function of the plasminogen activator system are dysregulated upon COVID-19 infection, leading to excessive pulmonary fibrosis and worsening the prognosis. The potential of plasminogen as a life-saving treatment for non-resolving post-COVID-19 pulmonary fibrosis warrants further investigation.
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Affiliation(s)
- Anna A. Shmakova
- Institute of Experimental Cardiology, National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Vladimir S. Popov
- Faculty of Medicine, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Iliya P. Romanov
- Faculty of Medicine, Lomonosov Moscow State University, 119192 Moscow, Russia
| | | | - Nailya R. Sabitova
- Faculty of Medicine, Lomonosov Moscow State University, 119192 Moscow, Russia
| | | | | | - Ella V. Kurilina
- Institute of Experimental Cardiology, National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
| | - Zoya I. Tsokolaeva
- Institute of Experimental Cardiology, National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
| | - Polina S. Klimovich
- Institute of Experimental Cardiology, National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Kseniya A. Rubina
- Faculty of Medicine, Lomonosov Moscow State University, 119192 Moscow, Russia
| | | | - Ekaterina V. Semina
- Institute of Experimental Cardiology, National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 119192 Moscow, Russia
- Correspondence:
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