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Krause KD, Rees K, Darwish GH, Bernal-Escalante J, Algar WR. Bait and Cleave: Exosite-Binding Peptides on Quantum Dots Selectively Accelerate Protease Activity for Sensing with Enhanced Sensitivity. ACS NANO 2024; 18:17018-17030. [PMID: 38845136 DOI: 10.1021/acsnano.4c03265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
The advantageous optical properties of quantum dots (QDs) motivate their use in a wide variety of applications related to imaging and bioanalysis, including the detection of proteases and their activity. Recent studies have shown that surface chemistry on QDs is able to modulate protease activity, but only nonspecifically. Here, we present a strategy to selectively accelerate the activity of a particular target protease by as much as two orders of magnitude. Exosite-binding "bait" peptides were derived from proteins that span a range of biological roles─substrate, receptor, and inhibitor─and were used to increase the affinity of the QD-peptide conjugates for either thrombin or factor Xa, resulting in increased rates of proteolysis for coconjugated substrates. Unlike effects from QD surface chemistry, the acceleration was specific to the target protease with negligible acceleration of other proteases. Benefits of this "bait and cleave" sensing approach included detection limits that improved by more than an order of magnitude, reenabled detection of target protease against an overwhelming background of nontarget proteolysis, and mitigation of the action of inhibitors. The cumulative results point to a generalizable strategy, where the mechanism of acceleration, considerations for the design of bait peptides and conjugates, and routes to expanding the scope of this approach are discussed. Overall, this research represents a major step forward in the rational design of nanoparticle-based enzyme sensors that enhance sensitivity and selectivity.
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Affiliation(s)
- Katherine D Krause
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver , BC V6T 1Z1, Canada
| | - Kelly Rees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver , BC V6T 1Z1, Canada
| | - Ghinwa H Darwish
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver , BC V6T 1Z1, Canada
| | - Jasmine Bernal-Escalante
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver , BC V6T 1Z1, Canada
| | - W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver , BC V6T 1Z1, Canada
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Wu X, Li L, Lu Z, Hu X, Lu Y, Liu Y, Xu G, Ding Q, Wang X, Wu W, Jin P, Dai J. Heterozygous Prothrombin Mutation-Associated Thrombophilia. Thromb Haemost 2024. [PMID: 38914130 DOI: 10.1055/a-2350-8338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
BACKGROUND Venous thromboembolism (VTE) is predisposed by thrombotic mutations in patients with hereditary thrombophilia. Although prothrombin deficiencies caused by homozygous or compound heterozygous mutations are associated with bleeding diathesis, rare cases have shown a correlation between heterozygous prothrombin mutations and thrombosis. MATERIALS AND METHODS We surveyed genetic variants involved in thrombosis and hemostasis in 347 patients with unprovoked VTE or having a positive family history of thrombosis. For patients identified with heterozygous prothrombin mutations, we conducted family investigations and performed a thrombin generation test (TGT) to elucidate the thrombotic risk. Novel mutants were expressed and subjected to functional assays to clarify the underlying thrombotic mechanisms. RESULTS Heterozygous prothrombin mutations were identified in 3.5% of patients (12/347), including three novel mutations Phe382Ser, Phe382Leu, and Asp597Tyr found in one patient each, as well as previously reported Arg541Trp mutation in four patients and Arg596Gln mutation in five patients. A total of 42 mutation carriers were identified within the 12 pedigrees, among whom 64.3% (27/42) had experienced thrombotic events. TGT results demonstrated hypercoagulability for carriers of the five mutations, with Arg596Gln showing the highest thrombin generation potential followed by Arg541Trp. The Phe382-associated mutations severely impaired thrombomodulin-binding ability of thrombin, resulting in obviously reduced protein C (PC) activation. The Asp597Tyr mutation exhibited a mild reduction in both inactivation by antithrombin and PC activation reactions. CONCLUSION The presence of heterozygous prothrombin mutations represents a potential genetic predisposition for VTE. All thrombosis-associated mutations potentiate coagulation activity by either conferring antithrombin resistance and/or impairing PC pathway activity.
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Affiliation(s)
- Xi Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengjing Lu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaobo Hu
- Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Yeling Lu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Liu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guanqun Xu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Laboratory Medicine, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenman Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Laboratory Medicine, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Peipei Jin
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Dai
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Dai Y, Kretz CA, Kim PY, Gross PL. A specific fluorescence resonance energy quenching-based biosensor for measuring thrombin activity in whole blood. J Thromb Haemost 2024; 22:1627-1639. [PMID: 38382740 DOI: 10.1016/j.jtha.2024.02.007] [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: 10/17/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND At sites of vessel injury, thrombin acts as the central mediator of coagulation by catalyzing fibrin clot formation and platelet activation. Thrombin generation is most frequently measured in plasma samples using small-molecule substrates; however, these have low specificity for thrombin and limited utility in whole blood. Plasma assays are limited because they ignore the hemostatic contributions of blood cells and require anticoagulation and the addition of supraphysiological concentrations of calcium. OBJECTIVES To overcome these limitations, we designed and characterized a fluorescence resonance energy quenching-based thrombin sensor (FTS) protein. METHODS The fluorescence resonance energy quenching pair of mAmetrine and tTomato, separated by a thrombin recognition sequence, was developed. The protein was expressed using Escherichia coli, and purity was assessed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The cleavage of FTS was monitored by fluorescence using excitation at 406 nm and emission at 526 nm and 581 nm. RESULTS Compared with small-molecule substrates, the FTS demonstrated high specificity for thrombin; it is not cleaved by thrombin or inhibited by α2-macroglobulin and interacts with thrombin's anion-binding exosite I. The FTS can effectively measure thrombin generation in plasma and in finger-prick whole blood, which allows it to be developed into a point-of-care test of thrombin generation. The FTS does not inhibit standard thrombin-generation assays. Lastly, FTS-based thrombin generation in nonanticoagulated finger-prick blood was delayed but enhanced compared with that in citrated plasma. CONCLUSION The FTS will broaden our understanding of thrombin generation in ways that are not attainable with current methods.
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Affiliation(s)
- Ying Dai
- Hamilton Health Sciences and Departments of Medicine and Medical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Colin A Kretz
- Hamilton Health Sciences and Departments of Medicine and Medical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Paul Y Kim
- Hamilton Health Sciences and Departments of Medicine and Medical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Peter L Gross
- Hamilton Health Sciences and Departments of Medicine and Medical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada.
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Aleksandrowicz K, Hempel D, Polityńska B, Wojtukiewicz AM, Honn KV, Tang DG, Wojtukiewicz MZ. The Complex Role of Thrombin in Cancer and Metastasis: Focus on Interactions with the Immune System. Semin Thromb Hemost 2024; 50:462-473. [PMID: 37984359 DOI: 10.1055/s-0043-1776875] [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: 11/22/2023]
Abstract
Thrombin, a pleiotropic enzyme involved in coagulation, plays a crucial role in both procoagulant and anticoagulant pathways. Thrombin converts fibrinogen into fibrin, initiates platelet activation, and promotes clot formation. Thrombin also activates anticoagulant pathways, indirectly inhibiting factors involved in coagulation. Tissue factor triggers thrombin generation, and the overexpression of thrombin in various cancers suggests that it is involved in tumor growth, angiogenesis, and metastasis. Increased thrombin generation has been observed in cancer patients, especially those with metastases. Thrombin exerts its effects through protease-activated receptors (PARs), particularly PAR-1 and PAR-2, which are involved in cancer progression, angiogenesis, and immunological responses. Thrombin-mediated signaling promotes angiogenesis by activating endothelial cells and platelets, thereby releasing proangiogenic factors. These functions of thrombin are well recognized and have been widely described. However, in recent years, intriguing new findings concerning the association between thrombin activity and cancer development have come to light, which justifies a review of this research. In particular, there is evidence that thrombin-mediated events interact with the immune system, and may regulate its response to tumor growth. It is also worth reevaluating the impact of thrombin on thrombocytes in conjunction with its multifaceted influence on tumor progression. Understanding the role of thrombin/PAR-mediated signaling in cancer and immunological responses is crucial, particularly in the context of developing immunotherapies. In this systematic review, we focus on the impact of the thrombin-related immune system response on cancer progression.
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Affiliation(s)
- Karolina Aleksandrowicz
- Department of Clinical Oncology, Medical University, Białystok, Poland
- Comprehensive Cancer Center, Bialystok, Poland
| | - Dominika Hempel
- Department of Clinical Oncology, Medical University, Białystok, Poland
- Comprehensive Cancer Center, Bialystok, Poland
| | - Barbara Polityńska
- Department of Psychology and Philosophy, Medical University of Białystok, Białystok, Poland
| | - Anna M Wojtukiewicz
- Department of Psychology and Philosophy, Medical University of Białystok, Białystok, Poland
| | - Kenneth V Honn
- Department of Pathology-School of Medicine, Bioactive Lipids Research Program, Detroit, Michigan
- Department of Chemistry, Wayne State University, Detroit, Michigan
- Department of Oncology, Wayne State University, Detroit, Michigan
| | - Dean G Tang
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Marek Z Wojtukiewicz
- Department of Clinical Oncology, Medical University, Białystok, Poland
- Comprehensive Cancer Center, Bialystok, Poland
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Acquasaliente L, Pierangelini A, Pagotto A, Pozzi N, De Filippis V. From haemadin to haemanorm: Synthesis and characterization of full-length haemadin from the leech Haemadipsa sylvestris and of a novel bivalent, highly potent thrombin inhibitor (haemanorm). Protein Sci 2023; 32:e4825. [PMID: 37924304 PMCID: PMC10683372 DOI: 10.1002/pro.4825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
Hirudin from Hirudo medicinalis is a bivalent α-Thrombin (αT) inhibitor, targeting the enzyme active site and exosite-I, and is currently used in anticoagulant therapy along with its simplified analogue hirulog. Haemadin, a small protein (57 amino acids) isolated from the land-living leech Haemadipsa sylvestris, selectively inhibits αT with a potency identical to that of recombinant hirudin (KI = 0.2 pM), with which it shares a common disulfide topology and overall fold. At variance with hirudin, haemadin targets exosite-II and therefore (besides the free protease) it also blocks thrombomodulin-bound αT without inhibiting the active intermediate meizothrombin, thus offering potential advantages over hirudin. Here, we produced in reasonably high yields and pharmaceutical purity (>98%) wild-type haemadin and the oxidation resistant Met5 → nor-Leucine analogue, both inhibiting αT with a KI of 0.2 pM. Thereafter, we used site-directed mutagenesis, spectroscopic, ligand-displacement, and Hydrogen/Deuterium Exchange-Mass Spectrometry techniques to map the αT regions relevant for the interaction with full-length haemadin and with the synthetic N- and C-terminal peptides Haem(1-10) and Haem(45-57). Haem(1-10) competitively binds to/inhibits αT active site (KI = 1.9 μM) and its potency was enhanced by 10-fold after Phe3 → β-Naphthylalanine exchange. Conversely to full-length haemadin, haem(45-57) displays intrinsic affinity for exosite-I (KD = 1.6 μM). Hence, we synthesized a peptide in which the sequences 1-9 and 45-57 were joined together through a 3-Glycine spacer to yield haemanorm, a highly potent (KI = 0.8 nM) inhibitor targeting αT active site and exosite-I. Haemanorm can be regarded as a novel class of hirulog-like αT inhibitors with potential pharmacological applications.
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Affiliation(s)
- Laura Acquasaliente
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Andrea Pierangelini
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Anna Pagotto
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
| | - Nicola Pozzi
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
- Department of Biochemistry and Molecular Biology, Edward A. Doisy Research CenterSaint Louis UniversitySt. LouisMissouriUSA
| | - Vincenzo De Filippis
- Laboratory of Protein Chemistry & Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of MedicineUniversity of PadovaPaduaItaly
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Balakrishnan N, Katkar R, Pham PV, Downey T, Kashyap P, Anastasiu DC, Ramasubramanian AK. Prospection of Peptide Inhibitors of Thrombin from Diverse Origins Using a Machine Learning Pipeline. Bioengineering (Basel) 2023; 10:1300. [PMID: 38002424 PMCID: PMC10669389 DOI: 10.3390/bioengineering10111300] [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: 09/14/2023] [Revised: 10/30/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Thrombin is a key enzyme involved in the development and progression of many cardiovascular diseases. Direct thrombin inhibitors (DTIs), with their minimum off-target effects and immediacy of action, have greatly improved the treatment of these diseases. However, the risk of bleeding, pharmacokinetic issues, and thrombotic complications remain major concerns. In an effort to increase the effectiveness of the DTI discovery pipeline, we developed a two-stage machine learning pipeline to identify and rank peptide sequences based on their effective thrombin inhibitory potential. The positive dataset for our model consisted of thrombin inhibitor peptides and their binding affinities (KI) curated from published literature, and the negative dataset consisted of peptides with no known thrombin inhibitory or related activity. The first stage of the model identified thrombin inhibitory sequences with Matthew's Correlation Coefficient (MCC) of 83.6%. The second stage of the model, which covers an eight-order of magnitude range in KI values, predicted the binding affinity of new sequences with a log room mean square error (RMSE) of 1.114. These models also revealed physicochemical and structural characteristics that are hidden but unique to thrombin inhibitor peptides. Using the model, we classified more than 10 million peptides from diverse sources and identified unique short peptide sequences (<15 aa) of interest, based on their predicted KI. Based on the binding energies of the interaction of the peptide with thrombin, we identified a promising set of putative DTI candidates. The prediction pipeline is available on a web server.
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Affiliation(s)
- Nivedha Balakrishnan
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
| | - Rahul Katkar
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
| | - Peter V. Pham
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
| | - Taylor Downey
- Department of Computer Science and Engineering, Santa Clara University, Santa Clara, CA 95053, USA (D.C.A.)
| | - Prarthna Kashyap
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
| | - David C. Anastasiu
- Department of Computer Science and Engineering, Santa Clara University, Santa Clara, CA 95053, USA (D.C.A.)
| | - Anand K. Ramasubramanian
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
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7
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Yasmin R, Chanchal S, Ashraf MZ, Doley R. Daboxin P, a phospholipase A 2 of Indian Daboia russelii venom, modulates thrombin-mediated platelet aggregation. J Biochem Mol Toxicol 2023; 37:e23476. [PMID: 37466159 DOI: 10.1002/jbt.23476] [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: 12/10/2022] [Revised: 03/12/2023] [Accepted: 07/08/2023] [Indexed: 07/20/2023]
Abstract
Daboxin P, reported earlier from the venom of Daboia russellii, disturbs the blood coagulation cascade by targeting factor X and factor Xa. The present study exhibits that Daboxin P also inhibits platelet aggregation induced by various agonists. The thrombin-induced platelet aggregation was inhibited maximum whereas inhibition of collagen-induced platelet aggregation was found to be 50% and no inhibition of adenosine diphosphate (ADP) and arachidonic acid-induced aggregation was observed. Daboxin P dose-dependently inhibited the thrombin-induced platelet aggregation with Anti-Aggregation 50 (AD50 ) dose of 55.166 nM and also reduced the thrombin-mediated calcium influx. In-silico interaction studies suggested that Daboxin P binds to thrombin and blocks its interaction with its receptor on the platelet surface. Quenching of thrombin's emission spectrum by Daboxin P and electrophoretic profiles of pull-down assay further reveals the binding between Daboxin P and thrombin. Thus, the present study demonstrates that Daboxin P inhibits thrombin-induced platelet aggregation by binding to thrombin.
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Affiliation(s)
- Rafika Yasmin
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Shankar Chanchal
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, New Delhi, India
| | - Mohammad Zahid Ashraf
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, New Delhi, India
| | - Robin Doley
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
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Yuan F, Li S, Huang B, Hu Y, Zeng X, Peng Y, Du C, Rong M. Molecular mechanism by which spider-driving peptide potentiates coagulation factors. Biomed Pharmacother 2023; 166:115421. [PMID: 37660649 DOI: 10.1016/j.biopha.2023.115421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023] Open
Abstract
Hemostasis is a crucial process that quickly forms clots at injury sites to prevent bleeding and infections. Dysfunctions in this process can lead to hemorrhagic disorders, such as hemophilia and thrombocytopenia purpura. While hemostatic agents are used in clinical treatments, there is still limited knowledge about potentiators targeting coagulation factors. Recently, LCTx-F2, a procoagulant spider-derived peptide, was discovered. This study employed various methods, including chromogenic substrate analysis and dynamic simulation, to investigate how LCTx-F2 enhances the activity of thrombin and FXIIa. Our findings revealed that LCTx-F2 binds to thrombin and FXIIa in a similar manner, with the N-terminal penetrating the active-site cleft of the enzymes and the intermediate section reinforcing the peptide-enzyme connection. Interestingly, the C-terminal remained at a considerable distance from the enzymes, as evidenced by the retention of affinity for both enzymes using truncated peptide T-F2. Furthermore, results indicated differences in the bonding relationship of critical residues between thrombin and FXIIa, with His13 facilitating binding to thrombin and Arg7 being required for binding to FXIIa. Overall, our study sheds light on the molecular mechanism by which LCTx-F2 potentiates coagulation factors, providing valuable insights that may assist in designing drugs targeting procoagulation factors.
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Affiliation(s)
- Fuchu Yuan
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410006, China
| | - Shuwan Li
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410006, China
| | - Biao Huang
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410006, China
| | - Ya Hu
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410006, China
| | - Xiongzhi Zeng
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410006, China
| | - Yanmei Peng
- Institute of Innovative Medicine, Hunan Academy of Chinese Medicine, Changsha, Hunan 410006, China
| | - Canwei Du
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan 411201, Hunan, China; Institute of Innovative Medicine, Hunan Academy of Chinese Medicine, Changsha, Hunan 410006, China.
| | - Mingqiang Rong
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410006, China.
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Paszek E, Malinowski KP, Ząbczyk M, Butenas S, Undas A. Elevated factor XIa as a modulator of plasma fibrin clot properties in coronary artery disease. Eur J Clin Invest 2023; 53:e14007. [PMID: 37042848 DOI: 10.1111/eci.14007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/12/2023] [Accepted: 04/11/2023] [Indexed: 04/13/2023]
Abstract
INTRODUCTION Patients with coronary artery disease (CAD) display a prothrombotic fibrin clot phenotype, involving low permeability and resistance to lysis. The determinants of this phenotype remain elusive. Circulating tissue factor (TF) and activated factor XI (FXIa) are linked to arterial thromboembolism. We investigated whether detectable active TF and FXIa influence fibrin clot properties in CAD. METHODS In 118 CAD patients (median age 65 years, 78% men), we assessed Ks, an indicator of clot permeability, and clot lysis time (CLT) in plasma-based assays, along with the presence of active TF and FXIa. We also analysed proteins involved in clotting and thrombolysis, including fibrinogen, plasminogen activator inhibitor-1 (PAI-1) and thrombin activatable thrombolysis inhibitor (TAFI). During a median 106 month (interquartile range 95-119) follow-up, myocardial infarction (MI), stroke, systemic thromboembolism (SE) and cardiovascular (CV) death were recorded. RESULTS Circulating TF and FXIa, detected in 20.3% and 39.8% of patients, respectively, were associated with low Ks and prolonged CLT. Solely FXIa remained an independent predictor of low Ks and high CLT on multivariable analysis. Additionally, fibrinogen and PAI-1 were associated with low Ks, while PAI-1 and TAFI-with prolonged CLT. During follow-up low Ks and prolonged CLT increased the risk of MI and the latter also a composite endpoint of MI, stroke/SE or CV death. CONCLUSIONS To our knowledge, this study is the first to show that circulating FXIa is associated with prothrombotic fibrin clot properties in CAD, suggesting additional mechanisms through which FXIa inhibitors could act as novel antithrombotic agents in CAD.
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Affiliation(s)
- Elżbieta Paszek
- Clinical Department of Interventional Cardiology, John Paul II Hospital, Krakow, Poland
- Department of Thromboembolic Disorders, Institute of Cardiology, Jagiellonian University Medical College, Krakow, Poland
| | - Krzysztof P Malinowski
- Department of Bioinformatics and Telemedicine, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland
- Center for Digital Medicine and Robotics, Jagiellonian University Medical College, Krakow, Poland
| | - Michał Ząbczyk
- Department of Thromboembolic Disorders, Institute of Cardiology, Jagiellonian University Medical College, Krakow, Poland
- Krakow Center for Medical Research and Technologies, John Paul II Hospital, Krakow, Poland
| | - Saulius Butenas
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
| | - Anetta Undas
- Department of Thromboembolic Disorders, Institute of Cardiology, Jagiellonian University Medical College, Krakow, Poland
- Krakow Center for Medical Research and Technologies, John Paul II Hospital, Krakow, Poland
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Li K, O'Dwyer R, Yang F, Cymerman J, Li J, Feldman JD, Simon M, Rafailovich M. Enhancement of acellular biomineralization, dental pulp stem cell migration, and differentiation by hybrid fibrin gelatin scaffolds. Dent Mater 2023; 39:305-319. [PMID: 36746694 DOI: 10.1016/j.dental.2023.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 01/16/2023] [Accepted: 01/31/2023] [Indexed: 02/06/2023]
Abstract
OBJECTIVE The current in vitro study aims to evaluate cross-linked hydrogels with and without the addition of fibrin that could potentially be used in endodontic regeneration as a scaffold material. METHODS Synthesis of gelatin/fibrin scaffold, and performing nanoscale characterization using cryo-electron microscopy, dynamic rheology, and XRF for structure property relations; plating dental pulp stem cells and determining mineralization, migration, and differentiation using rt-PCR, XRF, and Raman spectroscopy. RESULTS Cryo electron imaging shows gelatin and fibrin, when gelled separately to form classical rectangular cross-linked networks, where the modulus scales inversely with the cube root of the mesh size. When gelled together, a network with a fundamentally different structure is formed, which has higher ductility and when placed as a scaffold in osteogenic media, produces twice the mineral content. Immunofluorescence, RT-PCR and Rahman Spectroscopy indicate that the hybrid gel enhances cell migration, induces odontogenic differentiation of dental pulp stem cells, and promotes formation of dentin. SIGNIFICANCE The mechanical properties of the hybrid gel scaffold enhance in-migration of stem cells and subsequent differentiation, which are critical for regenerative procedures. Under acellular conditions, placement of the hybrid gel enhances biomineralization, which would strengthen the root if used as a scaffold for endodontic regeneration. Our in vitro findings are consistent with previous in vivo studies which show improved mineralization when bleeding is induced into the canal, given that fibrin is a primary component in blood clotting. Therefore, insertion of the hybrid gelatin-fibrin scaffold could enable more reproducible and consistent outcomes if used for regenerative endodontic treatment (RET).
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Affiliation(s)
- Kao Li
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, NY 11794, USA; Shandong Institute of Petroleum and Chemical Technology, Doying, Shandong 257061, China
| | - Rita O'Dwyer
- Department of Periodontology, Division of Endodontics, School of Dental Medicine, Stony Brook University, NY 11794, USA; Department of Oral Biology and Pathology, Stony Brook University Medical Center, Stony Brook, NY 11794, USA
| | - Fan Yang
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jerome Cymerman
- Department of Periodontology, Division of Endodontics, School of Dental Medicine, Stony Brook University, NY 11794, USA; Department of Oral Biology and Pathology, Stony Brook University Medical Center, Stony Brook, NY 11794, USA
| | - Juyi Li
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jake D Feldman
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marcia Simon
- Department of Oral Biology and Pathology, Stony Brook University Medical Center, Stony Brook, NY 11794, USA
| | - Miriam Rafailovich
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, NY 11794, USA.
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11
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Li S, Wang W, Lin L, Yang L, Cai Y, Yang X, Zhang T, Xiao C, Yan H, Gao N, Zhao J. Oligosaccharide Blocks PAR1 (Proteinase-Activated Receptor 1)-PAR4-Mediated Platelet Activation by Binding to Thrombin Exosite II and Impairs Thrombosis. Arterioscler Thromb Vasc Biol 2023; 43:253-266. [PMID: 36519467 DOI: 10.1161/atvbaha.122.318085] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Inappropriate activation and aggregation of platelets can lead to arterial thrombosis. Thrombin is the most potent platelet agonist that activates human platelets via two PARs (proteinase-activated receptors), PAR1 and PAR4. The aim is to study the activity and mechanism of an oligosaccharide HS-11 (the undecasaccharide, derived from sea cucumber Holothuria fuscopunctata) in inhibiting thrombin-mediated platelet activation and aggregation and to evaluate its antithrombotic activity. METHODS Platelet activation was analyzed by detecting CD62P/P-selectin expression using flow cytometry. The HS-11-thrombin interaction and the binding site were studied by biolayer interferometry. Intracellular Ca2+ mobilization of platelets was measured by FLIPR Tetra System using Fluo-4 AM (Fluo-4 acetoxymethyl). Platelet aggregation, thrombus formation, and bleeding Assay were assessed. RESULTS An oligosaccharide HS-11, depolymerized from fucosylated glycosaminoglycan from sea cucumber Holothuria fuscopunctata blocks the interaction of thrombin with PAR1 and PAR4 complex by directly binding to thrombin exosite II, and completely inhibits platelet signal transduction, including intracellular Ca2+ mobilization and protein phosphorylation. Furthermore, HS-11 potently inhibits thrombin-PARs-mediated platelet aggregation and reduces thrombus formation in a model of ex vivo thrombosis. CONCLUSIONS The study firstly report that the fucosylated glycosaminoglycan oligosaccharide has antiplatelet activity by binding to thrombin exosite II, and demonstrates that thrombin exosite II plays an important role in the simultaneous activation of PAR1 and PAR4, which may be a potential antithrombotic target for effective treatment of arterial thrombosis.
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Affiliation(s)
- Sujuan Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.).,University of Chinese Academy of Sciences, Beijing, China (S.L., W.W., L.L., Y.C., T.Z.)
| | - Weili Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.).,University of Chinese Academy of Sciences, Beijing, China (S.L., W.W., L.L., Y.C., T.Z.)
| | - Lisha Lin
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.).,University of Chinese Academy of Sciences, Beijing, China (S.L., W.W., L.L., Y.C., T.Z.)
| | - Lian Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.)
| | - Ying Cai
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.).,University of Chinese Academy of Sciences, Beijing, China (S.L., W.W., L.L., Y.C., T.Z.)
| | - Xingzhi Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.)
| | - Taocui Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.).,University of Chinese Academy of Sciences, Beijing, China (S.L., W.W., L.L., Y.C., T.Z.)
| | - Chuang Xiao
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, China (C.X.)
| | - Hui Yan
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.)
| | - Na Gao
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China (N.G., J.Z.)
| | - Jinhua Zhao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.).,School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China (N.G., J.Z.)
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12
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Krissanaprasit A, Key C, Froehlich K, LaBean TH. Production and Testing of RNA Origami Anticoagulants. Methods Mol Biol 2023; 2639:339-350. [PMID: 37166725 DOI: 10.1007/978-1-0716-3028-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Nucleic acid nanotechnology provides the ability to create unprecedented nanostructures with diverse architectures and functions that can be utilized in myriad fields. A set of self-folding, single-stranded RNA origami structures bearing thrombin RNA aptamers have been demonstrated to act as anticoagulants. Here, we describe the detailed methods of producing and testing of such RNA origami anticoagulants. This method highlights the potential of RNA origami for biomedical applications.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, USA
| | - Carson Key
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, USA
| | - Kristen Froehlich
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, USA
| | - Thomas H LaBean
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, USA.
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13
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A combined computational and experimental approach predicts thrombin adsorption to zeolites. Colloids Surf B Biointerfaces 2023; 221:113007. [DOI: 10.1016/j.colsurfb.2022.113007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 11/08/2022]
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14
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Allosteric modulation of exosite 1 attenuates polyphosphate-catalyzed activation of factor XI by thrombin. JOURNAL OF THROMBOSIS AND HAEMOSTASIS : JTH 2023; 21:83-93. [PMID: 36695400 DOI: 10.1016/j.jtha.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 10/05/2022] [Accepted: 10/31/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Polyphosphate (polyP) promotes feedback activation of factor (F) XI by thrombin by serving as a template. The contribution of thrombin's exosites to these interactions is unclear. OBJECTIVES To determine the contribution of thrombin exosites 1 and 2 to polyP-induced potentiation of FXI activation by thrombin. METHODS The affinities of α-thrombin; K109E/110E-thrombin, an exosite 1 variant, or R93E-thrombin, an exosite 2 variant; FXI; and FXIa for polyP-70 were quantified using surface plasmon resonance in the absence or presence of exosite ligands. FXI was activated with α-thrombin or thrombin variants in the absence or presence of polyP-70 and exosite ligands. RESULTS α-Thrombin, K109/110E-thrombin, FXI, and FXIa bound polyP-70, whereas R93E-thrombin exhibited minimal binding. Exosite 1 and exosite 2 ligands attenuated thrombin binding to polyP-70. PolyP-70 accelerated the rate of FXI activation by α-thrombin and K109E/110E-thrombin but not R93E-thrombin up to 1500-fold in a bell-shaped, concentration-responsive manner. Exosite 1 and exosite 2 ligands had no impact on FXI activation by thrombin in the absence of polyP-70; however, in its presence, they attenuated activation by 40% to 65%. CONCLUSION PolyP-70 binds FXI and thrombin and promotes their interaction. Exosite 2 ligands attenuate activation because thrombin binds polyP-70 via exosite 2. Attenuation of FXI activation by exosite 1 ligands likely reflects allosteric modulation of exosite 2 and/or the active site of thrombin because exosite 1 is not directly involved in FXI activation. Therefore, allosteric modulation of thrombin's exosites may represent a novel strategy for downregulating FXI activation.
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15
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Chang LH, Chi NF, Chen CY, Lin YS, Hsu SL, Tsai JY, Huang HC, Lin CJ, Chung CP, Tung CY, Jeng CJ, Lee YC, Liu YT, Lee IH. Monogenic Causes in Familial Stroke Across Intracerebral Hemorrhage and Ischemic Stroke Subtypes Identified by Whole-Exome Sequencing. Cell Mol Neurobiol 2022:10.1007/s10571-022-01315-3. [PMID: 36580209 DOI: 10.1007/s10571-022-01315-3] [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: 09/09/2022] [Accepted: 12/20/2022] [Indexed: 12/30/2022]
Abstract
Whole exome sequencing (WES) has been used to detect rare causative variants in neurological diseases. However, the efficacy of WES in genetic diagnosis of clinically heterogeneous familial stroke remains inconclusive. We prospectively searched for disease-causing variants in unrelated probands with defined familial stroke by candidate gene/hotspot screening and/or WES, depending on stroke subtypes and neuroimaging features at a referral center. The clinical significance of each variant was determined according to the American College of Medical Genetics guidelines. Among 161 probands (mean age at onset 53.2 ± 13.7 years; male 63.4%), 33 participants (20.5%) had been identified with 19 pathogenic/likely pathogenic variants (PVs; WES applied 152/161 = 94.4%). Across subtypes, the highest hit rate (HR) was intracerebral hemorrhage (ICH, 7/18 = 38.9%), particularly with the etiological subtype of structural vasculopathy (4/4 = 100%, PVs in ENG, KRIT1, PKD1, RNF213); followed by ischemic small vessel disease (SVD, 15/48 = 31.3%; PVs in NOTCH3, HTRA1, HBB). In contrast, large artery atherosclerosis (LAA, 4/44 = 9.1%) and cardioembolism (0/11 = 0%) had the lowest HR. NOTCH3 was the most common causative gene (16/161 = 9.9%), presenting with multiple subtypes of SVD (n = 13), ICH (n = 2), or LAA (n = 1). Importantly, we disclosed two previously unreported PVs, KRIT1 p.E379* in a familial cerebral cavernous malformation, and F2 p.F382L in a familial cerebral venous sinus thrombosis. The contribution of monogenic etiologies was particularly high in familial ICH and SVD subtypes in our Taiwanese cohort. Utilizing subtype-guided hotspot screening and/or subsequent WES, we unraveled monogenic causes in 20.5% familial stroke probands, including 1.2% novel PVs. Genetic diagnosis may enable early diagnosis, management and lifestyle modification. Among 161 familial stroke probands, 33 (20.5%) had been identified pathogenic or likely pathogenic monogenic variants related to stroke. The positive hit rate among all subtypes was high in intracerebral hemorrhage (ICH) and ischemic small vessel disease (SVD). Notably, two previously unreported variants, KRIT1 p.E379* in a familial cerebral cavernous malformation and F2 p.F382L in familial cerebral venous sinus thrombosis, were disclosed. CVT cerebral venous thrombosis; HTN Hypertensive subtype; LAA large artery atherosclerosis; SV structural vasculopathy; U Undetermined.
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Affiliation(s)
- Li-Hsin Chang
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Nai-Fang Chi
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chun-Yu Chen
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan
| | - Yung-Shuan Lin
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan
| | - Shao-Lun Hsu
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan
| | - Jui-Yao Tsai
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan
| | - Hui-Chi Huang
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan
| | - Chun-Jen Lin
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chih-Ping Chung
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chien-Yi Tung
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chung-Jiuan Jeng
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Anatomy and Cell Biology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Chung Lee
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yo-Tsen Liu
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan. .,Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan. .,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan. .,Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - I-Hui Lee
- Institute of Brain Science, National Yang Ming Chiao Tung University, Taipei, Taiwan. .,Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, No. 201, Sec. 2, Shipai Rd., Beitou District, 11217, Taipei City, Taiwan. .,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan. .,Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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16
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Mo Z, Xiao Z, He C. Functional expression of a thrombin exosite I inhibitor triabin in Escherichia coli and elucidation of the role of key residues in its inhibitory activity. Biochimie 2022; 208:13-19. [PMID: 36580989 DOI: 10.1016/j.biochi.2022.12.013] [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: 09/16/2022] [Revised: 12/03/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Triabin, a lipocalin-like thrombin inhibitor from the saliva of the blood-sucking triatomine bug Triatoma pallidipennis, exhibits effective inhibition comparable to hirudin despite binding exclusively at exosite I. Interestingly, it was reported that higher triabin doses would not inhibit thrombin completely, which makes it a promising antithrombotic candidate agent with a larger therapeutic window. However, few structural and functional studies about triabin have been reported in the past three decades, mostly due to the lack of a reliable and practicable recombinant expression technology for this seemingly small protein. In this work, we have adopted the SUMO fusion technology for the expression of triabin in E. coli cells-with facile refolding and purification procedures-and the bioactive triabin was produced in ∼12 mg/L culture medium. Subsequently, the structure-function studies through extensive site-directed mutagenesis reveal that triabin's Phe-106 involved in the hydrophobic contacts plays a surprisingly important role in the thrombin inhibition, in contrast to the negatively charged residues Asp-135 or Glu-128 involved in the salt-bridge interaction. As such, this study complements our understanding of the interaction mechanism of natural thrombin inhibitors, which should facilitate the development of anticoagulant drugs with a novel mode of action against thrombin.
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Affiliation(s)
- Zeyuan Mo
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Zhenbang Xiao
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Chunmao He
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, PR China.
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17
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Saad AA. Unveiling the Great Therapeutic Potential of MASPs as Hemostatic Agents. J Hematol 2022; 11:240-245. [PMID: 36632573 PMCID: PMC9822654 DOI: 10.14740/jh1060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/31/2022] [Indexed: 01/04/2023] Open
Affiliation(s)
- Ashraf Abdullah Saad
- Unit of Pediatric Hematologic Oncology and BMT, Sultan Qaboos University Hospital, Muscat, Oman.
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18
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Zhu M, Xu F, Miao S, Xie C, Li H, Li S, Xia F. Incorporation of a Multi-Valent Aptamer into Electrochemical Biosensors to Achieve an Improved Performance for Thrombin Analysis in Blood Serum. Chempluschem 2022; 87:e202200325. [PMID: 36410784 DOI: 10.1002/cplu.202200325] [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: 09/19/2022] [Revised: 10/10/2022] [Indexed: 11/23/2022]
Abstract
The electrochemical aptamer-based (E-AB) biosensor usually has a long reaction time when detecting thrombin. This work reports the design of an E-AB biosensor with dual recognition sites to quickly detect thrombin. Specifically, two specific recognition sites of thrombin were used to design three aptamer sequences (TBA-15, TBA-29 and TBA-U), followed by fabrication of corresponding sensors. First, we tested these three types of biosensors in tris buffer solution, and found that the response time of the TBA-U sensor to the same concentration of thrombin was about 2 hours, which is shorter than TBA-15 and TBA-29 sensors. Then, we also did the same test in 50 % diluted serum with 500 nM thrombin. The response time of the TBA-U sensor was about 2 hours, which is still faster than the 3 hours of TBA-15 sensor and the 5.5 hours for TBA-29 sensor. In addition, in terms of dynamic range and specificity, TBA-U has good performance.
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Affiliation(s)
- Man Zhu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Fan Xu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Siyuan Miao
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Chongyu Xie
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Hui Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Shaoguang Li
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, P. R. China
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19
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Tang Y, Kay A, Jiang Z, Arkin MR. LC3B Binds to the Autophagy Protease ATG4b with High Affinity Using a Bipartite Interface. Biochemistry 2022; 61:2295-2302. [PMID: 36264309 PMCID: PMC9631991 DOI: 10.1021/acs.biochem.2c00482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/23/2022] [Indexed: 11/29/2022]
Abstract
Autophagy is a catabolic cellular process in which unwanted proteins and organelles are degraded by lysosomes. It is characterized by the formation of the double-membrane autophagosome decorated with LC3B, a protein that mediates autophagosomal fusion with lysosomes. The cysteine protease ATG4b acts at two stages in the life cycle of LC3B. We set out to characterize the protein-protein interaction between LC3B and ATG4b. Through biochemical and biophysical studies, we show that the ubiquitin-like core of LC3B (residues 1-115; "LC3B-115"), which lacks the C-terminal cleavage site (between residue 120 and 121), binds to full-length ATG4b with a surprisingly tight dissociation constant (KD) in the low nanomolar range; 10-30-fold tighter than that of the substrate pro-LC3B (residues 1-125) or the product LC3B-I (residues 1-120). Consequently, LC3B-115 is a potent inhibitor of the ATG4b-mediated cleavage of pro-LC3B (IC50 = 15 nM). Binding of the LC3B-115 has no effect on the conformation of the active site of ATG4b, as judged by the turnover of a peptide substrate ("substrate-33"), derived from LC3B-I residues 116-120. Conversely, truncations of ATG4b show that binding and proteolysis of LC3B critically depend on the C-terminal tail of ATG4b, whereas proteolysis of the peptide substrate-33 does not require the C-terminal tail of ATG4b. These results support a bipartite model for LC3B-ATG4b binding in which the core of LC3B binds to ATG4b and the C-terminal tail of pro-LC3B organizes the ATG4b active site; additionally, the C-terminal tail of ATG4b contributes at least 1000-fold higher binding affinity to the LC3B-ATG4b interaction and likely wraps around the LC3B-ubiquitin core. PPIs are often described as containing an energetic "hot spot" for binding; in the case of LC3B-ATG4b, however, the substrate-enzyme complex contains multiple, energetically relevant domains that differentially affect binding affinity and catalytic efficiency.
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Affiliation(s)
- Yinyan Tang
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Amber Kay
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Ziwen Jiang
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, California 94158, United States
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20
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Bhargavan B, Kanmogne GD. SARS-CoV-2 Spike Proteins and Cell-Cell Communication Inhibits TFPI and Induces Thrombogenic Factors in Human Lung Microvascular Endothelial Cells and Neutrophils: Implications for COVID-19 Coagulopathy Pathogenesis. Int J Mol Sci 2022; 23:10436. [PMID: 36142345 PMCID: PMC9499475 DOI: 10.3390/ijms231810436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022] Open
Abstract
In SARS-CoV-2-infected humans, disease progression is often associated with acute respiratory distress syndrome involving severe lung injury, coagulopathy, and thrombosis of the alveolar capillaries. The pathogenesis of these pulmonary complications in COVID-19 patients has not been elucidated. Autopsy study of these patients showed SARS-CoV-2 virions in pulmonary vessels and sequestrated leukocytes infiltrates associated with endotheliopathy and microvascular thrombosis. Since SARS-CoV-2 enters and infects target cells by binding its spike (S) protein to cellular angiotensin-converting enzyme 2 (ACE2), and there is evidence that vascular endothelial cells and neutrophils express ACE2, we investigated the effect of S-proteins and cell-cell communication on primary human lung microvascular endothelial cells (HLMEC) and neutrophils expression of thrombogenic factors and the potential mechanisms. Using S-proteins of two different SARS-CoV-2 variants (Wuhan and Delta), we demonstrate that exposure of HLMEC or neutrophils to S-proteins, co-culture of HLMEC exposed to S-proteins with non-exposed neutrophils, or co-culture of neutrophils exposed to S-proteins with non-exposed HLMEC induced transcriptional upregulation of tissue factor (TF), significantly increased the expression and secretion of factor (F)-V, thrombin, and fibrinogen and inhibited tissue factor pathway inhibitor (TFPI), the primary regulator of the extrinsic pathway of blood coagulation, in both cell types. Recombinant (r)TFPI and a thiol blocker (5,5'-dithio-bis-(2-nitrobenzoic acid)) prevented S-protein-induced expression and secretion of Factor-V, thrombin, and fibrinogen. Thrombomodulin blocked S-protein-induced expression and secretion of fibrinogen but had no effect on S-protein-induced expression of Factor-V or thrombin. These results suggests that following SARS-CoV-2 contact with the pulmonary endothelium or neutrophils and endothelial-neutrophil interactions, viral S-proteins induce coagulopathy via the TF pathway and mechanisms involving functional thiol groups. These findings suggest that using rTFPI and/or thiol-based drugs could be a viable therapeutic strategy against SARS-CoV-2-induced coagulopathy and thrombosis.
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Affiliation(s)
| | - Georgette D. Kanmogne
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5800, USA
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21
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Shestopal SA, Parunov LA, Olivares P, Chun H, Ovanesov MV, Pettersson JR, Sarafanov AG. Isolated Variable Domains of an Antibody Can Assemble on Blood Coagulation Factor VIII into a Functional Fv-like Complex. Int J Mol Sci 2022; 23:ijms23158134. [PMID: 35897712 PMCID: PMC9330781 DOI: 10.3390/ijms23158134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 11/29/2022] Open
Abstract
Single-chain variable fragments (scFv) are antigen-recognizing variable fragments of antibodies (FV) where both subunits (VL and VH) are connected via an artificial linker. One particular scFv, iKM33, directed against blood coagulation factor VIII (FVIII) was shown to inhibit major FVIII functions and is useful in FVIII research. We aimed to investigate the properties of iKM33 enabled with protease-dependent disintegration. Three variants of iKM33 bearing thrombin cleavage sites within the linker were expressed using a baculovirus system and purified by two-step chromatography. All proteins retained strong binding to FVIII by surface plasmon resonance, and upon thrombin cleavage, dissociated into VL and VH as shown by size-exclusion chromatography. However, in FVIII activity and low-density lipoprotein receptor-related protein 1 binding assays, the thrombin-cleaved iKM33 variants were still inhibitory. In a pull-down assay using an FVIII-affinity sorbent, the isolated VH, a mixture of VL and VH, and intact iKM33 were carried over via FVIII analyzed by electrophoresis. We concluded that the isolated VL and VH assembled into scFv-like heterodimer on FVIII, and the isolated VH alone also bound FVIII. We discuss the potential use of both protease-cleavable scFvs and isolated Fv subunits retaining high affinity to the antigens in various practical applications such as therapeutics, diagnostics, and research.
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22
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Dong H, Yang D, Hu Y, Song X. Recent advances in smart nanoplatforms for tumor non-interventional embolization therapy. J Nanobiotechnology 2022; 20:337. [PMID: 35858896 PMCID: PMC9301833 DOI: 10.1186/s12951-022-01548-w] [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: 05/23/2022] [Accepted: 07/10/2022] [Indexed: 11/10/2022] Open
Abstract
Tumor embolization therapy has attracted great attention due to its high efficiency in inhibiting tumor growth by cutting off tumor nutrition and oxygen supply by the embolic agent. Although transcatheter arterial embolization (TAE) is the mainstream technique in the clinic, there are still some limitations to be considered, especially the existence of high risks and complications. Recently, nanomaterials have drawn wide attention in disease diagnosis, drug delivery, and new types of therapies, such as photothermal therapy and photodynamic therapy, owing to their unique optical, thermal, convertible and in vivo transport properties. Furthermore, the utilization of nanoplatforms in tumor non-interventional embolization therapy has attracted the attention of researchers. Herein, the recent advances in this area are summarized in this review, which revealed three different types of nanoparticle strategies: (1) nanoparticles with active targeting effects or stimuli responsiveness (ultrasound and photothermal) for the safe delivery and responsive release of thrombin; (2) tumor microenvironment (copper and phosphate, acidity and GSH/H2O2)-responsive nanoparticles for embolization therapy with high specificity; and (3) peptide-based nanoparticles with mimic functions and excellent biocompatibility for tumor embolization therapy. The benefits and limitations of each kind of nanoparticle in tumor non-interventional embolization therapy will be highlighted. Investigations of nanoplatforms are undoubtedly of great significance, and some advanced nanoplatform systems have arrived at a new height and show potential applications in practical applications.
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Affiliation(s)
- Heng Dong
- Nanjing Stomatological Hospital, Medical School of Nanjing University Jiangsu, 30 Zhongyang Road, 210008, Nanjing, China
| | - Dongliang Yang
- School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), 30 South Puzhu Road, 211816, Nanjing, China
| | - Yanling Hu
- School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), 30 South Puzhu Road, 211816, Nanjing, China. .,Nanjing Polytechnic Institute, 210048, Nanjing, China.
| | - Xuejiao Song
- School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), 30 South Puzhu Road, 211816, Nanjing, China.
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23
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Stewart V, Ronald PC. Sulfotyrosine residues: interaction specificity determinants for extracellular protein-protein interactions. J Biol Chem 2022; 298:102232. [PMID: 35798140 PMCID: PMC9372746 DOI: 10.1016/j.jbc.2022.102232] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
Tyrosine sulfation, a post-translational modification, can determine and often enhance protein–protein interaction specificity. Sulfotyrosyl residues (sTyrs) are formed by the enzyme tyrosyl-protein sulfotransferase during protein maturation in the Golgi apparatus and most often occur singly or as a cluster within a six-residue span. With both negative charge and aromatic character, sTyr facilitates numerous atomic contacts as visualized in binding interface structural models, thus there is no discernible binding site consensus. Found exclusively in secreted proteins, in this review, we discuss the four broad sequence contexts in which sTyr has been observed: first, a solitary sTyr has been shown to be critical for diverse high-affinity interactions, such as between peptide hormones and their receptors, in both plants and animals. Second, sTyr clusters within structurally flexible anionic segments are essential for a variety of cellular processes, including coreceptor binding to the HIV-1 envelope spike protein during virus entry, chemokine interactions with receptors, and leukocyte rolling cell adhesion. Third, a subcategory of sTyr clusters is found in conserved acidic sequences termed hirudin-like motifs that enable proteins to interact with thrombin; consequently, many proven and potential therapeutic proteins derived from blood-consuming invertebrates depend on sTyrs for their activity. Finally, several proteins that interact with collagen or similar proteins contain one or more sTyrs within an acidic residue array. Refined methods to direct sTyr incorporation in peptides synthesized both in vitro and in vivo, together with continued advances in mass spectrometry and affinity detection, promise to accelerate discoveries of sTyr occurrence and function.
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Affiliation(s)
- Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, USA.
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, USA; Genome Center, University of California, Davis, USA.
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24
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Acquasaliente L, Pontarollo G, Radu CM, Peterle D, Artusi I, Pagotto A, Uliana F, Negro A, Simioni P, De Filippis V. Exogenous human α-Synuclein acts in vitro as a mild platelet antiaggregant inhibiting α-thrombin-induced platelet activation. Sci Rep 2022; 12:9880. [PMID: 35701444 PMCID: PMC9198058 DOI: 10.1038/s41598-022-12886-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 05/18/2022] [Indexed: 11/29/2022] Open
Abstract
α-Synuclein (αSyn) is a small disordered protein, highly conserved in vertebrates and involved in the pathogenesis of Parkinson’s disease (PD). Indeed, αSyn amyloid aggregates are present in the brain of patients with PD. Although the pathogenic role of αSyn is widely accepted, the physiological function of this protein remains elusive. Beyond the central nervous system, αSyn is expressed in hematopoietic tissue and blood, where platelets are a major cellular host of αSyn. Platelets play a key role in hemostasis and are potently activated by thrombin (αT) through the cleavage of protease-activated receptors. Furthermore, both αT and αSyn could be found in the same spatial environment, i.e. the platelet membrane, as αT binds to and activates platelets that can release αSyn from α-granules and microvesicles. Here, we investigated the possibility that exogenous αSyn could interfere with platelet activation induced by different agonists in vitro. Data obtained from distinct experimental techniques (i.e. multiple electrode aggregometry, rotational thromboelastometry, immunofluorescence microscopy, surface plasmon resonance, and steady-state fluorescence spectroscopy) on whole blood and platelet-rich plasma indicate that exogenous αSyn has mild platelet antiaggregating properties in vitro, acting as a negative regulator of αT-mediated platelet activation by preferentially inhibiting P-selectin expression on platelet surface. We have also shown that both exogenous and endogenous (i.e. cytoplasmic) αSyn preferentially bind to the outer surface of activated platelets. Starting from these findings, a coherent model of the antiplatelet function of αSyn is proposed.
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Affiliation(s)
- Laura Acquasaliente
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy
| | - Giulia Pontarollo
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy.,Center for Thrombosis and Hemostasis (CTH) University Medical Center Mainz, Langenbeckstraße 1, 55131, Mainz, Germany
| | - Claudia Maria Radu
- Department of Women's & Children's Health, University of Padua, Padua, Italy.,Thrombotic and Hemorrhagic Diseases Unit, Department of Medicine, University of Padua, via Giustiniani, 2, 35128, Padua, Italy
| | - Daniele Peterle
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy.,Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave. 02115, Boston, MA, USA
| | - Ilaria Artusi
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy
| | - Anna Pagotto
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy
| | - Federico Uliana
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy.,Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Alessandro Negro
- Department of Biomedical Sciences, University of Padua, viale G. Colombo 3, 35100, Padua, Italy.
| | - Paolo Simioni
- Thrombotic and Hemorrhagic Diseases Unit, Department of Medicine, University of Padua, via Giustiniani, 2, 35128, Padua, Italy.
| | - Vincenzo De Filippis
- Laboratory of Protein Chemistry and Molecular Hematology, Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padua, via Marzolo, 5, 35131, Padua, Italy. .,Biotechnology Center, CRIBI, University of Padua, Padua, Italy.
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25
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Vecchio FL, Bisceglia P, Imbimbo BP, Lozupone M, Latino RR, Resta E, Leone M, Solfrizzi V, Greco A, Daniele A, Watling M, Panza F, Seripa D. Are apolipoprotein E fragments a promising new therapeutic target for Alzheimer’s disease? Ther Adv Chronic Dis 2022; 13:20406223221081605. [PMID: 35321401 PMCID: PMC8935560 DOI: 10.1177/20406223221081605] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/28/2022] [Indexed: 11/17/2022] Open
Abstract
Human apolipoprotein E (ApoE) is a 299-amino acid secreted glycoprotein that binds cholesterol and phospholipids. ApoE exists as three common isoforms (ApoE2, ApoE3, and ApoE4) and heterozygous carriers of the ε4 allele of the gene encoding ApoE (APOE) have a fourfold greater risk of developing Alzheimer’s disease (AD). The enzymes thrombin, cathepsin D, α-chymotrypsin-like serine protease, and high-temperature requirement serine protease A1 are responsible for ApoE proteolytic processing resulting in bioactive C-terminal-truncated fragments that vary depending on ApoE isoforms, brain region, aging, and neural injury. The objectives of the present narrative review were to describe ApoE processing, discussing current hypotheses about the potential role of various ApoE fragments in AD pathophysiology, and reviewing the current development status of different anti-ApoE drugs. The exact mechanism by which APOE gene variants increase/decrease AD risk and the role of ApoE fragments in the deposition are not fully understood, but APOE is known to directly affect tau-mediated neurodegeneration. ApoE fragments co-localize with neurofibrillary tangles and amyloid β (Aβ) plaques, and may cause neurodegeneration. Among anti-ApoE approaches, a fascinating strategy may be to therapeutically overexpress ApoE2 in APOE ε4/ε4 carriers through vector administration or liposomal delivery systems. Another approach involves reducing ApoE4 expression by intracerebroventricular antisense oligonucleotides that significantly decreased Aβ pathology in transgenic mice. Differences in the proteolytic processing of distinct ApoE isoforms and the use of ApoE fragments as mimetic peptides in AD treatment are also under investigation. Treatment with peptides that mimic the structural and biological properties of native ApoE may reduce Aβ deposition, tau hyperphosphorylation, and glial activation in mouse models of Aβ pathology. Alternative strategies involve the use of ApoE4 structure correctors, passive immunization to target a certain form of ApoE, conversion of the ApoE4 aminoacid sequence into that of ApoE3 or ApoE2, and inhibition of the ApoE-Aβ interaction.
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Affiliation(s)
- Filomena Lo Vecchio
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia 71013, Italy
| | - Paola Bisceglia
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Madia Lozupone
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Raffaela Rita Latino
- Complex Structure of Neurology, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Emanuela Resta
- Translational Medicine and Management of Health Systems, University of Foggia, Foggia, Italy
| | - Maurizio Leone
- Complex Structure of Neurology, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Vincenzo Solfrizzi
- ‘Cesare Frugoni’ Internal and Geriatric Medicine and Memory Unit, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Antonio Greco
- Department of Neuroscience, Catholic University of the Sacred Heart, Rome, Italy; Neurology Unit, IRCCS Fondazione Policlinico Universitario A. Gemelli, Rome, Italy
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Mark Watling
- CNS & Pain Department, TranScrip Ltd, Reading, UK
| | - Francesco Panza
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
- Population Health Unit, Healthy Aging Phenotypes Research Unit, ‘Salus in Apulia Study’, National Institute of Gastroenterology ‘Saverio de Bellis’, Research Hospital, Castellana Grotte, Bari 70013, Italy
| | - Davide Seripa
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Hematology and Stem Cell Transplant Unit, ‘Vito Fazzi’ Hospital, Lecce, Italy
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26
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Ito T, Akamatsu K, Hasegawa H, Sakatani Y, Miyamura M, Hoshiga M. Relationship of warfarin versus DOACs with thrombogenic milieu in the left atrium among patients with nonvalvular atrial fibrillation. Echocardiography 2022; 39:483-489. [PMID: 35137446 DOI: 10.1111/echo.15319] [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: 10/20/2021] [Revised: 01/25/2022] [Accepted: 01/30/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Thrombogenic milieu (TM) within the left atrium plays a pivotal role in the pathogenesis of thromboembolic events, for which anticoagulation treatment is indicated typically on the mandatory basis. Little is known, however, about which regimen of anticoagulation, warfarin or direct oral anticoagulants (DOACs), is more likely associated with TM. We evaluated relative relationship of the two treatment options with concurrently-observed TM in patients with nonvalvular atrial fibrillation (AF) who underwent transesophageal echocardiography. METHODS TM was defined as the presence of either left atrial spontaneous echo contrast (SEC) or thrombus, or both. To determine which regimen was more likely related to TM, we firstly compared the prevalence of TM in 208 patients taking warfarin (Warfarin group) versus 486 patients taking DOACs (DOAC group); and secondly, did the same analysis after propensity score matching. RESULTS Warfarin group was more likely associated with TM compared with DOAC group (46% vs 29%, p < 0.001). Similar findings were observed for dense SEC (18% vs 7%, p < 0.001) and thrombus (4% vs 1%, p = 0.057). The propensity score matching (198 patients for each group), where several baseline parameters were matched including age, gender, chronicity of AF, estimated glomerular filtration rate and B-type natriuretic peptide as well as the left ventricular ejection fraction, resulted in similar findings to the original groups (TM, 47% vs 32%, p = 0.002; dense SEC, 18% vs 7%, p = 0.001; thrombus, 4% vs 1%, p = 0.047). CONCLUSIONS This study may strengthen the data on randomized trials that DOACs are superior to warfarin in preventing thromboembolic events in nonvalvular AF patients. Further studies are required to elucidate the details behind this difference.
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Affiliation(s)
- Takahide Ito
- Department of Cardiology, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan
| | - Kanako Akamatsu
- Department of Cardiology, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan
| | - Hitomi Hasegawa
- Department of Cardiology, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan
| | - Yuka Sakatani
- Department of Cardiology, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan
| | - Masatoshi Miyamura
- Department of Cardiology, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan
| | - Masaaki Hoshiga
- Department of Cardiology, Osaka Medical and Pharmaceutical University, Takatsuki, Osaka, Japan
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27
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Shearin S, Venkateswarlu D. Structural insights into the activation of blood coagulation factor XI zymogen by thrombin: A computational molecular dynamics study. Biophys Chem 2022; 281:106737. [PMID: 34923393 PMCID: PMC8741744 DOI: 10.1016/j.bpc.2021.106737] [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: 08/01/2021] [Revised: 11/28/2021] [Accepted: 12/02/2021] [Indexed: 02/03/2023]
Abstract
Activation of human blood coagulation factor XI zymogen to factor XIa plays a significant role in the upstream coagulation pathway, in which factor XIa activates factor IX zymogen. The mechanistic details of the proteolytic activation of factor XI by the activating enzyme thrombin are not well-understood at atomic level. In this study, we employed a combination of molecular docking and microsecond time-scale molecular dynamics simulations to identify the key regions of interaction between fXI and thrombin. The activating complex between the substrate and enzyme was modeled to represent the initial acylation step of the serine-protease hydrolysis mechanism. The proposed solution structural complex, fIX:fIIa, obtained from 3 microseconds of MD refinement, suggests that the activation of factor XI is mediated by thrombin's anion binding exosite-II interactions with A3 and A4 domains. We predict that the two positively charged arginine residues (Arg409 and Arg413) in the exosite-2 region, the β- and γ-insertion loops of thrombin play an important structural role in the initial activating complex between fXI and thrombin.
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28
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Kosinski R, Perez JM, Schöneweiß EC, Ruiz-Blanco YB, Ponzo I, Bravo-Rodriguez K, Erkelenz M, Schlücker S, Uhlenbrock G, Sanchez-Garcia E, Saccà B. The role of DNA nanostructures in the catalytic properties of an allosterically regulated protease. SCIENCE ADVANCES 2022; 8:eabk0425. [PMID: 34985948 PMCID: PMC8730604 DOI: 10.1126/sciadv.abk0425] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/10/2021] [Indexed: 06/04/2023]
Abstract
DNA-scaffolded enzymes typically show altered kinetic properties; however, the mechanism behind this phenomenon is still poorly understood. We address this question using thrombin, a model of allosterically regulated serine proteases, encaged into DNA origami cavities with distinct structural and electrostatic features. We compare the hydrolysis of substrates that differ only in their net charge due to a terminal residue far from the cleavage site and presumably involved in the allosteric activation of thrombin. Our data show that the reaction rate is affected by DNA/substrate electrostatic interactions, proportionally to the degree of DNA/enzyme tethering. For substrates of opposite net charge, this leads to an inversion of the catalytic response of the DNA-scaffolded thrombin when compared to its freely diffusing counterpart. Hence, by altering the electrostatic environment nearby the encaged enzyme, DNA nanostructures interfere with charge-dependent mechanisms of enzyme-substrate recognition and may offer an alternative tool to regulate allosteric processes through spatial confinement.
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Affiliation(s)
- Richard Kosinski
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Joel Mieres Perez
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Elisa-C. Schöneweiß
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Irene Ponzo
- Dynamic Biosensors GmbH, 82152 Martinsried, Germany
| | | | - Michael Erkelenz
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Sebastian Schlücker
- Physical Chemistry, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | | | - Elsa Sanchez-Garcia
- Computational Biochemistry, ZMB, University of Duisburg-Essen, 45117 Essen, Germany
| | - Barbara Saccà
- Bionanotechnology, CENIDE and ZMB, University of Duisburg-Essen, 45117 Essen, Germany
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29
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Cheng S, Wu D, Liu H, Xu X, Zhu B, Du M. A novel anticoagulant peptide discovered from Crassostrea gigas by combining bioinformatics with the enzymolysis strategy: inhibitory kinetics and mechanisms. Food Funct 2021; 12:10136-10146. [PMID: 34528647 DOI: 10.1039/d1fo02148f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A novel anticoagulant peptide (IEELEEELEAER) derived from oyster (Crassostrea gigas) was discovered by combining the emerging bioinformatics with the classical enzymolysis approach. The anticoagulant peptide drastically reduced the extrinsic clotting activity (49% residual PT activity) and impaired the intrinsic clotting activity (77% residual PT activity). Consistent with the clotting data, the thrombin peak height reduced to 88.7 from 123.4 nM, and the thrombin generation time delayed to 5.32 from 4.42 min when an extrinsic trigger was applied. The inhibitory kinetics of FXIa, FIXa, FXa, FIIa, and APC in a purified component system rationally explained the reduction of the extrinsic clotting activity and impairment of thrombin generation. Besides the inhibition of FXa and FIIa activity, the activation processes of FX and FII by an intrinsic/extrinsic tenase complex and prothrombinase were also damaged. The anticoagulant activity in the plasma system was the result of comprehensive inhibition of various factors. The research provided a frame for anticoagulant evaluation and inhibitory mechanism of bioactive peptides from food products.
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Affiliation(s)
- Shuzhen Cheng
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, 116034, Liaoning, China. .,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Di Wu
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, 116034, Liaoning, China.
| | - Hanxiong Liu
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, 116034, Liaoning, China.
| | - Xianbing Xu
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, 116034, Liaoning, China.
| | - Beiwei Zhu
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, 116034, Liaoning, China. .,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Ming Du
- Department of Food Science and Engineering, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, 116034, Liaoning, China.
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30
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Dowman LJ, Agten SM, Ripoll-Rozada J, Calisto BM, Pereira PJB, Payne RJ. Synthesis and evaluation of peptidic thrombin inhibitors bearing acid-stable sulfotyrosine analogues. Chem Commun (Camb) 2021; 57:10923-10926. [PMID: 34596182 DOI: 10.1039/d1cc04742f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tyrosine sulfation is an important post-translational modification of peptides and proteins which underpins and modulates many protein-protein interactions. In order to overcome the inherent instability of the native modification, we report the synthesis of two sulfonate analogues and their incorporation into two thrombin-inhibiting sulfopeptides. The effective mimicry of these sulfonate analogues for native sulfotyrosine was validated in the context of their thrombin inhibitory activity and binding mode, as determined by X-ray crystallography.
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Affiliation(s)
- Luke J Dowman
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia. .,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydne, NSW 2006, Australia
| | - Stijn M Agten
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Jorge Ripoll-Rozada
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | | | - Pedro José Barbosa Pereira
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia. .,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydne, NSW 2006, Australia
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Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands. Int J Mol Sci 2021; 22:ijms221910803. [PMID: 34639143 PMCID: PMC8509272 DOI: 10.3390/ijms221910803] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
Thrombin is the key enzyme of the entire hemostatic process since it is able to exert both procoagulant and anticoagulant functions; therefore, it represents an attractive target for the developments of biomolecules with therapeutic potential. Thrombin can perform its many functional activities because of its ability to recognize a wide variety of substrates, inhibitors, and cofactors. These molecules frequently are bound to positively charged regions on the surface of protein called exosites. In this review, we carried out extensive analyses of the structural determinants of thrombin partnerships by surveying literature data as well as the structural content of the Protein Data Bank (PDB). In particular, we used the information collected on functional, natural, and synthetic molecular ligands to define the anatomy of the exosites and to quantify the interface area between thrombin and exosite ligands. In this framework, we reviewed in detail the specificity of thrombin binding to aptamers, a class of compounds with intriguing pharmaceutical properties. Although these compounds anchor to protein using conservative patterns on its surface, the present analysis highlights some interesting peculiarities. Moreover, the impact of thrombin binding aptamers in the elucidation of the cross-talk between the two distant exosites is illustrated. Collectively, the data and the work here reviewed may provide insights into the design of novel thrombin inhibitors.
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Hassankalhori M, Bolcato G, Bissaro M, Sturlese M, Moro S. Shedding Light on the Molecular Recognition of Sub-Kilodalton Macrocyclic Peptides on Thrombin by Supervised Molecular Dynamics. Front Mol Biosci 2021; 8:707661. [PMID: 34532343 PMCID: PMC8438215 DOI: 10.3389/fmolb.2021.707661] [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: 05/10/2021] [Accepted: 07/15/2021] [Indexed: 11/25/2022] Open
Abstract
Macrocycles are attractive structures for drug development due to their favorable structural features, potential in binding to targets with flat featureless surfaces, and their ability to disrupt protein–protein interactions. Moreover, large novel highly diverse libraries of low-molecular-weight macrocycles with therapeutically favorable characteristics have been recently established. Considering the mentioned facts, having a validated, fast, and accurate computational protocol for studying the molecular recognition and binding mode of this interesting new class of macrocyclic peptides deemed to be helpful as well as insightful in the quest of accelerating drug discovery. To that end, the ability of the in-house supervised molecular dynamics protocol called SuMD in the reproduction of the X-ray crystallography final binding state of a macrocyclic non-canonical tetrapeptide—from a novel library of 8,988 sub-kilodalton macrocyclic peptides—in the thrombin active site was successfully validated. A comparable binding mode with the minimum root-mean-square deviation (RMSD) of 1.4 Å at simulation time point 71.6 ns was achieved. This method validation study extended the application domain of the SuMD sampling method for computationally cheap, fast but accurate, and insightful macrocycle–protein molecular recognition studies.
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Affiliation(s)
- Mahdi Hassankalhori
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Giovanni Bolcato
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Maicol Bissaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
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Yang Z, Wan Y, E J, Luo Z, Guan S, Wang S, Zhang H. Structural basis of different surface-modified fullerene derivatives as novel thrombin inhibitors: insight into the inhibitory mechanism through molecular modelling studies. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1943028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Zhijie Yang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Yongfeng Wan
- Institute of Atomic and Molecular Physics, Jilin University, Changchun, People’s Republic of China
| | - Jingwen E
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Zhijian Luo
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Shanshan Guan
- College of Biology and Food Engineering, Jilin Engineering Normal University, Changchun, People’s Republic of China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Hao Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
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[Thrombin generation assay in autoimmune disease]. Rev Med Interne 2021; 42:862-868. [PMID: 34175144 DOI: 10.1016/j.revmed.2021.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 05/18/2021] [Accepted: 06/06/2021] [Indexed: 01/05/2023]
Abstract
Thrombin generation assay (TGA) is a useful tool to evaluate the initiation, propagation and inhibition of coagulation. TGA is a global test that is used to assess hemorrhagic risk in hemophilia patients, but it can also be used to study hypercoagulable states. The interest of TGA is to screen for cardiovascular risk, which is regularly associated with autoimmune disease (AID) such as antiphospholipid syndrome. Indeed, TGA has been used to evaluate hypercoagulability in patients with antiphospholipid syndrome treated with rivaroxaban versus warfarin. In other AIDs without thrombotic events, TGA measurement is elevated, mainly in rheumatoid arthritis (RA), systemic lupus erythematosus and Behçet's disease. These findings in RA are correlated with the inflammatory activity of the disease. In systemic lupus erythematosus and Behçet's disease, TGA appears to reflect disease activity. In conclusion, TGA remains relatively under used in the clinical evaluation of AID, but it could play a greater role in the evaluation of certain potentially thrombogenic treatments in AID. Finally, TGA helps measuring AID activity, due to the clearlink between coagulation and inflammation, despite some limitations of interpretation mainly due to a lack of standardization.
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2D titanium carbide nanosheets based fluorescent aptasensor for sensitive detection of thrombin. Talanta 2021; 228:122219. [PMID: 33773725 DOI: 10.1016/j.talanta.2021.122219] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/02/2021] [Accepted: 02/13/2021] [Indexed: 01/06/2023]
Abstract
The emerging two-dimensional titanium carbides (MXenes) have a large potential in biomedical sensing owing to their excellent electrical and optical properties. Herein, a fluorescence resonance energy transfer (FRET) aptasensor with high sensitivity and specificity was constructed with single layer Ti3C2 MXene for quantitative detection of thrombin. The dye labelled thrombin-binding aptamer (TBA) was deposited on the surface of Ti3C2, and the fluorescence of which was efficiently quenched owing to the FRET between the dye and Ti3C2. The fact that thrombin forms quadruplex with TBA on Ti3C2 surface is due to the high electronic affinity between thrombin and Ti3C2. This process will cause the subsequent detachment of dye from the surface of Ti3C2, resulting in the recovery of fluorescence. Because of the special structure and high fluorescence quenching efficiency of Ti3C2 MXene, the aptasensor shows a high sensitivity with a low detection limit for thrombin at 5.27 pM. Three different aptamers were compared, and the aptamer HD22 is most sensitive for detection of thrombin originated from its great specificity in the human plasma. Importantly, this Ti3C2 MXene-based FRET aptasensor can detect thrombin in human serum accurately. These results suggest that the Ti3C2 MXene-based FRET aptasensor hold a great prospect in clinical diagnosis in the real-world applications.
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Shlobin NA, Har-Even M, Itsekson-Hayosh Z, Harnof S, Pick CG. Role of Thrombin in Central Nervous System Injury and Disease. Biomolecules 2021; 11:562. [PMID: 33921354 PMCID: PMC8070021 DOI: 10.3390/biom11040562] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 12/16/2022] Open
Abstract
Thrombin is a Na+-activated allosteric serine protease of the chymotrypsin family involved in coagulation, inflammation, cell protection, and apoptosis. Increasingly, the role of thrombin in the brain has been explored. Low concentrations of thrombin are neuroprotective, while high concentrations exert pathological effects. However, greater attention regarding the involvement of thrombin in normal and pathological processes in the central nervous system is warranted. In this review, we explore the mechanisms of thrombin action, localization, and functions in the central nervous system and describe the involvement of thrombin in stroke and intracerebral hemorrhage, neurodegenerative diseases, epilepsy, traumatic brain injury, and primary central nervous system tumors. We aim to comprehensively characterize the role of thrombin in neurological disease and injury.
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Affiliation(s)
- Nathan A. Shlobin
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Meirav Har-Even
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Sylvan Adams Sports Institute, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ze’ev Itsekson-Hayosh
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel;
- Department of Neurology and Joseph Sagol Neuroscience Center, The Chaim Sheba Medical Center, Tel HaShomer 5262000, Israel
| | - Sagi Harnof
- Department of Neurosurgery, Beilinson Hospital, Rabin Medical Center, Tel Aviv University, Petah Tikva 4941492, Israel;
| | - Chaim G. Pick
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Sylvan Adams Sports Institute, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Biology of Addictive Diseases, Tel Aviv University, Tel Aviv 6997801, Israel
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38
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Prolongation of clot lysis time by a direct thrombin inhibitor melagatran mediated by paradoxical enhancement of thrombin generation: comparison with a direct factor Xa inhibitor edoxaban. Blood Coagul Fibrinolysis 2021; 32:209-215. [PMID: 33560005 DOI: 10.1097/mbc.0000000000001020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Previously, we reported that a direct thrombin inhibitor melagatran paradoxically increased thrombin generation in human plasma in the presence of thrombomodulin. The aim of this study is to test the hypothesis that melagatran may exert a deleterious effect on tissue-type plasminogen activator (t-PA)-induced fibrinolysis via enhancement of thrombin generation and subsequent activation of thrombin-activatable fibrinolysis inhibitor (TAFI) and factor XIII (FXIII). Clot formation in human plasma containing t-PA and thrombomodulin was induced by tissue factor. The absorbance at 405 nm was measured to obtain clot lysis time. Effects of melagatran and a factor Xa inhibitor edoxaban on clot lysis time were determined. In the presence of thrombomodulin, melagatran significantly prolonged clot lysis time, but edoxaban shortened it. In the absence of thrombomodulin, melagatran did not inhibit fibrinolysis. Prolongation of clot lysis time by melagatran was reversed by activated protein C (which suppressed thrombin generation increased by melagatran) and a TAFIa inhibitor. Melagatran significantly suppressed plasmin generation, while edoxaban significantly increased it. However, both melagatran and edoxaban suppressed FXIII activation. In the clot formed in the presence of melagatran and edoxaban, the fibrin fibre was thin compared with control, showing no clear difference in the clot structures between melagatran and edoxaban. These results indicated that melagatran, not edoxaban, prolonged clot lysis time through the paradoxical enhancement of thrombin generation, and subsequent TAFI activation and inhibition of plasmin generation. Neither FXIII activation nor change in fibrin clot structure contributed to the inhibition of fibrinolysis by melagatran.
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Watanabe Y, Oguri R, Suzuki R, Meng Q, Ishikawa Y, Tatsukawa H, Hashimoto H, Hitomi K. Thrombin-deficient mutant of medaka, a model fish, displays serious retardation in blood coagulation. Biosci Biotechnol Biochem 2021; 85:824-833. [PMID: 33589932 DOI: 10.1093/bbb/zbaa098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/24/2020] [Indexed: 12/27/2022]
Abstract
At the last stage of the blood coagulation cascade, thrombin plays a central role in the processing of fibrinogen for the polymerization and in the additional activation of Factor XIII for the stable cross-linking of fibrin. In addition, thrombin carries out possible multiple roles via processing or interaction with various functional proteins. Several studies conducted in order to elucidate additional physiological significance are ongoing. To clarify further significance of thrombin and to establish an associated disease model, we characterized the orthologue gene for medaka (Oryzias latipes), a research model fish. Tissue distribution of medaka prothrombin has been immunotechnically analyzed. Furthermore, thrombin-deficient medaka mutants were viably established by utilizing a genome-editing method. The established gene-deficient mutants exhibited retarded blood coagulation even in the heterozygous fish. Taking advantage of their ease of handling, this specific model is useful for further investigation in medical research areas on human coagulation diseases.
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Affiliation(s)
- Yuko Watanabe
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Rina Oguri
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Risa Suzuki
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Qi Meng
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Yuta Ishikawa
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Hideki Tatsukawa
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | | | - Kiyotaka Hitomi
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
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40
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Yum JH, Ishizuka T, Fukumoto K, Hori D, Bao HL, Xu Y, Sugiyama H, Park S. Systematic Approach to DNA Aptamer Design Using Amino Acid-Nucleic Acid Hybrids (ANHs) Targeting Thrombin. ACS Biomater Sci Eng 2021; 7:1338-1343. [PMID: 33756075 DOI: 10.1021/acsbiomaterials.1c00060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chemical modifications of innate DNA/RNA aptamers facilitate the improvement of their function. Herein, we report our modular strategy to manipulate a thrombin-binding DNA aptamer (TBA) to improve its anticoagulation activity and binding affinity. A set of amino acid conjugates, termed amino acid-nucleic acid hybrids or ANHs, was synthesized and incorporated into a TBA loop sequences. We found that substitutions with hydrophobic amino acids in the loop region possessed significantly enhanced antithrombin activity, up to 3-fold higher than the native TBA. We investigated the correlations between thrombin-binding affinity and the features of our amino-acid conjugates using experimental techniques including circular dichroism spectroscopy, surface plasmon resonance assay, and molecular modeling. The present study demonstrates a systematic approach to aptamer design based on amino-acid characteristics, allowing the development of advanced aptamers.
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Affiliation(s)
- Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takumi Ishizuka
- Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Koyuki Fukumoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Daisuke Hori
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hong-Liang Bao
- Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Yan Xu
- Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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41
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Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen. Nat Commun 2021; 12:1693. [PMID: 33727531 PMCID: PMC7966775 DOI: 10.1038/s41467-021-21754-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Proteases are among the largest protein families and critical regulators of biochemical processes like apoptosis and blood coagulation. Knowledge of proteases has been expanded by the development of proteomic approaches, however, technology for multiplexed screening of proteases within native environments is currently lacking behind. Here we introduce a simple method to profile protease activity based on isolation of protease products from native lysates using a 96FASP filter, their analysis in a mass spectrometer and a custom data analysis pipeline. The method is significantly faster, cheaper, technically less demanding, easy to multiplex and produces accurate protease fingerprints. Using the blood cascade proteases as a case study, we obtain protease substrate profiles that can be used to map specificity, cleavage entropy and allosteric effects and to design protease probes. The data further show that protease substrate predictions enable the selection of potential physiological substrates for targeted validation in biochemical assays. Characterizing proteases in their native environment is still challenging. Here, the authors develop a proteomics workflow for analyzing protease-specific peptides from cell lysates in 96-well format, providing mechanistic insights into blood proteases and enabling the prediction of protease substrates.
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42
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Romero Díaz C, Mayoral LPC, Hernández Huerta MT, Majluf-Cruz AS, Plascencia Mora SE, Pérez-Campos Mayoral E, Mayoral Andrade G, Martínez Cruz M, Zenteno E, Matias Cervantes CA, Vásquez Martínez G, Martínez Cruz R, Ángel Reyes Franco M, Cruz Parada E, Pina Canseco S, Mayoral EPC. The influence of hydrogen ions on coagulation in traumatic brain injury, explored by molecular dynamics. Brain Inj 2021; 35:842-849. [PMID: 33678100 DOI: 10.1080/02699052.2021.1895312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Background: Patients in intensive care units with traumatic brain injuries (TBI) frequently present acid-base abnormalities and coagulability disorders, which complicate their condition.Objective: To identify protonation through in silico simulations of molecules involved in the process of coagulation in standard laboratory tests.Materials and methods: Ten patients with TBI were selected from the intensive care unit in addition to ten "healthy control subjects", and another nine patients as "disease control subjects"; the latter being a comparative group, corresponding to subjects with diabetes mellitus 2 (DM2). Fibrinogen, FVII, FVIII, FIX, FX, and D-dimer in the presence of acidification were evaluated in 20 healthy subjects in order to compare clinical results with molecular dynamics (MD), and to explain proton interactions and coagulation molecules.Results: The TBI group presented a slight, non-significant increase in D-dimer; but this was not present in "disease control subjects". Levels of fibrinogen, FVII, FIX, FX, and D-dimer were affected in the presence of acidification. We observed that various specific residues of coagulation factors "trap" ions.Conclusion: Protonation of tissue factor and factor VIIa may favor anticoagulant mechanisms, and protonation does not affect ligand binding sites of GPIIb/IIIa (PAC1) suggesting other causes for the low affinity to PAC1.
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Affiliation(s)
| | - Laura Pérez Campos Mayoral
- Research Centre Medicine UNAM-UABJO, Faculty of Medicine, Benito Juárez Autonomous University of Oaxaca, Oaxaca, Mexico
| | | | - Abraham Salvador Majluf-Cruz
- Medical Research Unit in Thrombosis, Haemostasis and Atherogenesis, Mexican Institute of Social Security/IMSS, Mexico City, Mexico
| | | | - Eduardo Pérez-Campos Mayoral
- Research Centre Medicine UNAM-UABJO, Faculty of Medicine, Benito Juárez Autonomous University of Oaxaca, Oaxaca, Mexico
| | - Gabriel Mayoral Andrade
- Research Centre Medicine UNAM-UABJO, Faculty of Medicine, Benito Juárez Autonomous University of Oaxaca, Oaxaca, Mexico
| | | | - Edgar Zenteno
- School of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
| | | | | | - Ruth Martínez Cruz
- Research Centre Medicine UNAM-UABJO, Faculty of Medicine, Benito Juárez Autonomous University of Oaxaca, Oaxaca, Mexico
| | | | | | - Socorro Pina Canseco
- Research Centre Medicine UNAM-UABJO, Faculty of Medicine, Benito Juárez Autonomous University of Oaxaca, Oaxaca, Mexico
| | - Eduardo Pérez-Campos Mayoral
- National Technological of Mexico/ITOaxaca, Oaxaca, Mexico.,Clinical Pathology Laboratory, "Dr. Eduardo Pérez Ortega", Oaxaca, Mexico
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43
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Agten SM, Watson EE, Ripoll‐Rozada J, Dowman LJ, Wu MCL, Alwis I, Jackson SP, Pereira PJB, Payne RJ. Potent Trivalent Inhibitors of Thrombin through Hybridization of Salivary Sulfopeptides from Hematophagous Arthropods. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stijn M. Agten
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Sydney Sydney NSW 2006 Australia
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM) Maastricht University Universiteitssingel 50 6229 ER Maastricht The Netherlands
| | - Emma E. Watson
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Sydney Sydney NSW 2006 Australia
| | - Jorge Ripoll‐Rozada
- IBMC—Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde Universidade do Porto 4200-135 Porto Portugal
| | - Luke J. Dowman
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Sydney Sydney NSW 2006 Australia
| | - Mike C. L. Wu
- Charles Perkins Centre The University of Sydney Sydney NSW 2006 Australia
- Heart Research Institute Sydney NSW 2042 Australia
| | - Imala Alwis
- Charles Perkins Centre The University of Sydney Sydney NSW 2006 Australia
- Heart Research Institute Sydney NSW 2042 Australia
| | - Shaun P. Jackson
- Charles Perkins Centre The University of Sydney Sydney NSW 2006 Australia
- Heart Research Institute Sydney NSW 2042 Australia
| | - Pedro José Barbosa Pereira
- IBMC—Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde Universidade do Porto 4200-135 Porto Portugal
| | - Richard J. Payne
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Sydney Sydney NSW 2006 Australia
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44
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Agten SM, Watson EE, Ripoll-Rozada J, Dowman LJ, Wu MCL, Alwis I, Jackson SP, Pereira PJB, Payne RJ. Potent Trivalent Inhibitors of Thrombin through Hybridization of Salivary Sulfopeptides from Hematophagous Arthropods. Angew Chem Int Ed Engl 2021; 60:5348-5356. [PMID: 33345438 DOI: 10.1002/anie.202015127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/14/2020] [Indexed: 12/20/2022]
Abstract
Blood feeding arthropods, such as leeches, ticks, flies and mosquitoes, provide a privileged source of peptidic anticoagulant molecules. These primarily operate through inhibition of the central coagulation protease thrombin by binding to the active site and either exosite I or exosite II. Herein, we describe the rational design of a novel class of trivalent thrombin inhibitors that simultaneously block both exosites as well as the active site. These engineered hybrids were synthesized using tandem diselenide-selenoester ligation (DSL) and native chemical ligation (NCL) reactions in one-pot. The most potent trivalent inhibitors possessed femtomolar inhibition constants against α-thrombin and were selective over related coagulation proteases. A lead hybrid inhibitor possessed potent anticoagulant activity, blockade of both thrombin generation and platelet aggregation in vitro and efficacy in a murine thrombosis model at 1 mg kg-1 . The rational engineering approach described here lays the foundation for the development of potent and selective inhibitors for a range of other enzymatic targets that possess multiple sites for the disruption of protein-protein interactions, in addition to an active site.
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Affiliation(s)
- Stijn M Agten
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, 2006, NSW, Australia
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Emma E Watson
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, 2006, NSW, Australia
| | - Jorge Ripoll-Rozada
- IBMC-Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Luke J Dowman
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, 2006, NSW, Australia
| | - Mike C L Wu
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Heart Research Institute, Sydney, NSW, 2042, Australia
| | - Imala Alwis
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Heart Research Institute, Sydney, NSW, 2042, Australia
| | - Shaun P Jackson
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- Heart Research Institute, Sydney, NSW, 2042, Australia
| | - Pedro José Barbosa Pereira
- IBMC-Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Richard J Payne
- School of Chemistry and ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, 2006, NSW, Australia
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45
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Saravanan R, Choong YK, Lim CH, Lim LM, Petrlova J, Schmidtchen A. Cell-Free DNA Promotes Thrombin Autolysis and Generation of Thrombin-Derived C-Terminal Fragments. Front Immunol 2021; 12:593020. [PMID: 33717072 PMCID: PMC7943729 DOI: 10.3389/fimmu.2021.593020] [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: 08/09/2020] [Accepted: 01/07/2021] [Indexed: 12/21/2022] Open
Abstract
Cell-free DNA (cfDNA) is the major structural component of neutrophil extracellular traps (NETs), an innate immune response to infection. Antimicrobial proteins and peptides bound to cfDNA play a critical role in the bactericidal property of NETs. Recent studies have shown that NETs have procoagulant activity, wherein cfDNA triggers thrombin generation through activation of the intrinsic pathway of coagulation. We have recently shown that thrombin binds to NETs in vitro and consequently can alter the proteome of NETs. However, the effect of NETs on thrombin is still unknown. In this study, we report that DNA binding leads to thrombin autolysis and generation of multiple thrombin-derived C-terminal peptides (TCPs) in vitro. Employing a 25-residue prototypic TCP, GKY25 (GKYGFYTHVFRLKKWIQKVIDQFGE), we show that TCPs bind NETs, thus conferring mutual protection against nuclease and protease degradation. Together, our results demonstrate the complex interplay between coagulation, NET formation, and thrombin cleavage and identify a previously undisclosed mechanism for formation of TCPs.
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Affiliation(s)
- Rathi Saravanan
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Yeu Khai Choong
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Chun Hwee Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore.,Interdisciplinary Graduate School, NTU Institute for Health Technologies, Nanyang Technological University Singapore, Singapore, Singapore.,Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Li Ming Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Jitka Petrlova
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Artur Schmidtchen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Lund, Sweden.,Wound Healing Centre, Bispebjerg Hospital, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
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Smirnov I, Kolganova N, Troisi R, Sica F, Timofeev E. Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:863-871. [PMID: 33614235 PMCID: PMC7868722 DOI: 10.1016/j.omtn.2021.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/08/2021] [Indexed: 01/11/2023]
Abstract
Post-SELEX modification of DNA aptamers is an established strategy to improve their affinity or inhibitory characteristics. In this study, we examined the possibility of increasing the recognition interface between the thrombin-binding aptamer HD1 (TBA) and thrombin by adding a chemically modified side chain to selected nucleotide residues. A panel of 22 TBA variants with N3-modified residues T3 and T12 was prepared by a two-step modification procedure. Aptamers were characterized by a combination of biophysical and biochemical methods. We identified mutants with enhanced affinity and improved anticoagulant activity. The crystal structures of thrombin complexes with three selected modified variants revealed that the modified pyrimidine base invariably allocates in proximity to thrombin residues Tyr76 and Ile82 due to the directing role of the unmodified TT loop. The modifications induced an increase in the contact areas between thrombin and the modified TBAs. Comparative analysis of the structural, biochemical, and biophysical data suggests that the non-equivalent binding modes of the mutants with thrombin in the T3- and T12-modified series account for the observed systematic differences in their affinity characteristics. In this study, we show that extending the recognition surface between the protein and modified aptamers is a promising approach that may improve characteristics of aptamer ligands.
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Affiliation(s)
- Igor Smirnov
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Natalia Kolganova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Edward Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Riccardi C, Napolitano E, Musumeci D, Montesarchio D. Dimeric and Multimeric DNA Aptamers for Highly Effective Protein Recognition. Molecules 2020; 25:E5227. [PMID: 33182593 PMCID: PMC7698228 DOI: 10.3390/molecules25225227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/14/2022] Open
Abstract
Multivalent interactions frequently occur in biological systems and typically provide higher binding affinity and selectivity in target recognition than when only monovalent interactions are operative. Thus, taking inspiration by nature, bivalent or multivalent nucleic acid aptamers recognizing a specific biological target have been extensively studied in the last decades. Indeed, oligonucleotide-based aptamers are suitable building blocks for the development of highly efficient multivalent systems since they can be easily modified and assembled exploiting proper connecting linkers of different nature. Thus, substantial research efforts have been put in the construction of dimeric/multimeric versions of effective aptamers with various degrees of success in target binding affinity or therapeutic activity enhancement. The present review summarizes recent advances in the design and development of dimeric and multimeric DNA-based aptamers, including those forming G-quadruplex (G4) structures, recognizing different key proteins in relevant pathological processes. Most of the designed constructs have shown improved performance in terms of binding affinity or therapeutic activity as anti-inflammatory, antiviral, anticoagulant, and anticancer agents and their number is certainly bound to grow in the next future.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
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Yang X, Xiang Y, Wang F, Cai G, Li Y, Zhong L, Pu L, Yang Y, Song E. Expressions and relationship of Krüppel-like factor 15 and endothelial nitric oxide synthase in experimental deep venous thrombosis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1090. [PMID: 33145309 PMCID: PMC7575959 DOI: 10.21037/atm-20-5828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Background Deep vein thrombosis (DVT) is an early postoperative complication. Thrombosis formation, which is potentially life-threatening, seriously affects the rehabilitation of patients after surgery. We aimed to establish a C57 mouse model of DVT and to examine the changes in the expression of Krüppel-like factor 15 (KLF15) and endothelial nitric oxide synthase (eNOS) in venous wall tissues, and we also investigated the regulatory relationship of KLF15 and eNOS in the thrombin-induced human umbilical vein endothelial cell (HUVEC) injury cell model. Methods The DVT model was established using the inferior vena cava (IVC) stenosis method. The expression levels of KLF15 and eNOS were analyzed using quantitative reverse transcription–polymerase chain reaction (qRT-PCR). In cell experiments, the expression of KLF15 and eNOS was analyzed in the model of thrombin-induced HUVEC injury with KLF15 siRNA. Results Compared to the control and sham-operated groups, KLF15 in the DVT group was upregulated, while eNOS was downregulated. The results of cell experiments revealed that KLF15 was downregulated in the thrombin+KLF15 siRNA group compared with the thrombin group. Meanwhile, eNOS was upregulated in the thrombin+KLF15 siRNA group compared with the thrombin group. These findings suggested that KLF15 regulated the expression of eNOS in the DVT model. Conclusions We successfully constructed a DVT mouse model. In the early stage of DVT formation, KLF15 regulated the expression and inhibited the antithrombotic effect of eNOS, resulting in thrombi formation.
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Affiliation(s)
- Xianguang Yang
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yaoyu Xiang
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Fuke Wang
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Guofeng Cai
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yanlin Li
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ling Zhong
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li Pu
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yang Yang
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - En Song
- Department of Sports Medicine, the First Affiliated Hospital of Kunming Medical University, Kunming, China
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Curran CS, Rivera DR, Kopp JB. COVID-19 Usurps Host Regulatory Networks. Front Pharmacol 2020; 11:1278. [PMID: 32922297 PMCID: PMC7456869 DOI: 10.3389/fphar.2020.01278] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/03/2020] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes coronavirus disease 2019 (COVID-19). SARS-CoV-2 binds the angiotensin-converting enzyme 2 (ACE2) on the cell surface and this complex is internalized. ACE2 serves as an endogenous inhibitor of inflammatory signals associated with four major regulator systems: the renin-angiotensin-aldosterone system (RAAS), the complement system, the coagulation cascade, and the kallikrein-kinin system (KKS). Understanding the pathophysiological effects of SARS-CoV-2 on these pathways is needed, particularly given the current lack of proven, effective treatments. The vasoconstrictive, prothrombotic and pro-inflammatory conditions induced by SARS-CoV-2 can be ascribed, at least in part, to the activation of these intersecting physiological networks. Moreover, patients with immune deficiencies, hypertension, diabetes, coronary heart disease, and kidney disease often have altered activation of these pathways, either due to underlying disease or to medications, and may be more susceptible to SARS-CoV-2 infection. Certain characteristic COVID-associated skin, sensory, and central nervous system manifestations may also be linked to viral activation of the RAAS, complement, coagulation, and KKS pathways. Pharmacological interventions that target molecules along these pathways may be useful in mitigating symptoms and preventing organ or tissue damage. While effective anti-viral therapies are critically needed, further study of these pathways may identify effective adjunctive treatments and patients most likely to benefit.
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Affiliation(s)
- Colleen S Curran
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Donna R Rivera
- Surveillance Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Rockville, MD, United States
| | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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Riccardi C, Napolitano E, Platella C, Musumeci D, Montesarchio D. G-quadruplex-based aptamers targeting human thrombin: Discovery, chemical modifications and antithrombotic effects. Pharmacol Ther 2020; 217:107649. [PMID: 32777331 DOI: 10.1016/j.pharmthera.2020.107649] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
First studies on thrombin-inhibiting DNA aptamers were reported in 1992, and since then a large number of anticoagulant aptamers has been discovered. TBA - also named HD1, a 15-mer G-quadruplex (G4)-forming oligonucleotide - is the best characterized thrombin binding aptamer, able to specifically recognize the protein exosite I, thus inhibiting the conversion of soluble fibrinogen into insoluble fibrin strands. Unmodified nucleic acid-based aptamers, in general, and TBA in particular, exhibit limited pharmacokinetic properties and are rapidly degraded in vivo by nucleases. In order to improve the biological performance of aptamers, a widely investigated strategy is the introduction of chemical modifications in their backbone at the level of the nucleobases, sugar moieties or phosphodiester linkages. Besides TBA, also other thrombin binding aptamers, able to adopt a well-defined G4 structure, e.g. mixed duplex/quadruplex sequences, as well as homo- and hetero-bivalent constructs, have been identified and optimized. Considering the growing need of new efficient anticoagulant agents associated with the strong therapeutic potential of these thrombin inhibitors, the research on thrombin binding aptamers is still a very hot and intriguing field. Herein, we comprehensively described the state-of-the-art knowledge on the DNA-based aptamers targeting thrombin, especially focusing on the optimized analogues obtained by chemically modifying the oligonucleotide backbone, and their biological performances in therapeutic applications.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Department of Advanced Medical and Surgical Sciences, 2(nd) Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy.
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
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