1
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Yu H, Kumar S, Frederiksen JW, Kolyadko VN, Pitoc G, Layzer J, Yan A, Rempel R, Francis S, Krishnaswamy S, Sullenger BA. Aptameric hirudins as selective and reversible EXosite-ACTive site (EXACT) inhibitors. Nat Commun 2024; 15:3977. [PMID: 38730234 PMCID: PMC11087511 DOI: 10.1038/s41467-024-48211-6] [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: 12/20/2023] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Potent and selective inhibition of the structurally homologous proteases of coagulation poses challenges for drug development. Hematophagous organisms frequently accomplish this by fashioning peptide inhibitors combining exosite and active site binding motifs. Inspired by this biological strategy, we create several EXACT inhibitors targeting thrombin and factor Xa de novo by linking EXosite-binding aptamers with small molecule ACTive site inhibitors. The aptamer component within the EXACT inhibitor (1) synergizes with and enhances the potency of small-molecule active site inhibitors by many hundred-fold (2) can redirect an active site inhibitor's selectivity towards a different protease, and (3) enable efficient reversal of inhibition by an antidote that disrupts bivalent binding. One EXACT inhibitor, HD22-7A-DAB, demonstrates extraordinary anticoagulation activity, exhibiting great potential as a potent, rapid onset anticoagulant to support cardiovascular surgeries. Using this generalizable molecular engineering strategy, selective, potent, and rapidly reversible EXACT inhibitors can be created against many enzymes through simple oligonucleotide conjugation for numerous research and therapeutic applications.
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Affiliation(s)
- Haixiang Yu
- Department of Surgery, Duke University, Durham, NC, USA
| | - Shekhar Kumar
- Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Vladimir N Kolyadko
- Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - George Pitoc
- Department of Surgery, Duke University, Durham, NC, USA
| | | | - Amy Yan
- Department of Surgery, Duke University, Durham, NC, USA
| | - Rachel Rempel
- Department of Surgery, Duke University, Durham, NC, USA
| | - Samuel Francis
- Department of Emergency Medicine, Duke University Hospital, Durham, NC, USA
| | - Sriram Krishnaswamy
- Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Bruce A Sullenger
- Department of Surgery, Duke University, Durham, NC, USA.
- Departments of Pharmacology & Cancer Biology and Biomedical Engineering, Duke University, Durham, NC, USA.
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2
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Nagano M, Kubota K, Sakata A, Nakamura R, Yoshitomi T, Wakui K, Yoshimoto K. A neutralizable dimeric anti-thrombin aptamer with potent anticoagulant activity in mice. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:762-772. [PMID: 37621412 PMCID: PMC10445101 DOI: 10.1016/j.omtn.2023.07.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023]
Abstract
Heparin-induced thrombocytopenia (HIT) is a complication caused by administration of the anticoagulant heparin. Although the number of patients with HIT has drastically increased because of coronavirus disease 2019 (COVID-19), the currently used thrombin inhibitors for HIT therapy do not have antidotes to arrest the severe bleeding that occurs as a side effect; therefore, establishment of safer treatments for HIT patients is imperative. Here, we devised a potent thrombin inhibitor based on bivalent aptamers with a higher safety profile via combination with the antidote. Using an anti-thrombin DNA aptamer M08s-1 as a promising anticoagulant, its homodimer and heterodimer with TBA29 linked by a conformationally flexible linker or a rigid duplex linker were designed. The dimerized M08s-1-based aptamers had about 100-fold increased binding affinity to human and mouse thrombin compared with the monomer counterparts. Administration of these bivalent aptamers into mice revealed that the anticoagulant activity of the dimers significantly surpassed that of an approved drug for HIT treatment, argatroban. Moreover, adding protamine sulfate as an antidote against the most potent bivalent aptamer completely suppressed the anticoagulant activity of the dimer. Emerging potent and neutralizable anticoagulant aptamers will be promising candidates for HIT treatment with a higher safety profile.
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Affiliation(s)
- Masanobu Nagano
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Kazuki Kubota
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Asuka Sakata
- Medicinal Biology of Thrombosis and Hemostasis, Nara Medical University, 840 Shijo-cho, Kashihara, Nara 634-8521, Japan
| | - Rei Nakamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Toru Yoshitomi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Koji Wakui
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
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3
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Ayass MA, Griko N, Pashkov V, Tripathi T, Zhang J, Ramankutty Nair R, Okyay T, Zhu K, Abi-Mosleh L. New High-Affinity Thrombin Aptamers for Advancing Coagulation Therapy: Balancing Thrombin Inhibition for Clot Prevention and Effective Bleeding Management with Antidote. Cells 2023; 12:2230. [PMID: 37759453 PMCID: PMC10526462 DOI: 10.3390/cells12182230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Thrombin is a key enzyme involved in blood clotting, and its dysregulation can lead to thrombotic diseases such as stroke, myocardial infarction, and deep vein thrombosis. Thrombin aptamers have the potential to be used as therapeutic agents to prevent or treat thrombotic diseases. Thrombin DNA aptamers developed in our laboratory exhibit high affinity and specificity to thrombin. In vitro assays have demonstrated their efficacy by significantly decreasing Factor II activity and increasing PT and APTT times in both plasma and whole blood. Aptamers AYA1809002 and AYA1809004, the two most potent aptamers, exhibit high affinity for their target, with affinity constants (Kd) of 10 nM and 13 nM, respectively. Furthermore, the in vitro activity of these aptamers displays dose-dependent behavior, highlighting their efficacy in a concentration-dependent manner. In vitro stability assessments reveal that the aptamers remain stable in plasma and whole blood for up to 24 h. This finding is crucial for their potential application in clinical settings. Importantly, the thrombin inhibitory activity of the aptamers can be reversed by employing reverse complement sequences, providing a mechanism to counteract their anticoagulant effects when necessary to avoid excessive bleeding. These thrombin aptamers have been determined to be safe, with no observed mutagenic or immunogenic effects. Overall, these findings highlight the promising characteristics of these newly developed thrombin DNA aptamers, emphasizing their potential for therapeutic applications in the field of anticoagulation therapy. Moreover, the inclusion of an antidote in the coagulation therapy regimen can improve patient safety, ensure greater therapeutic efficacy, and minimize risk during emergency situations.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lina Abi-Mosleh
- Ayass Bioscience LLC, 8501 Wade Blvd, Building 9, Frisco, TX 75034, USA
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4
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Yu H, Frederiksen J, Sullenger BA. Applications and future of aptamers that achieve rapid-onset anticoagulation. RNA (NEW YORK, N.Y.) 2023; 29:455-462. [PMID: 36697262 PMCID: PMC10019365 DOI: 10.1261/rna.079503.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
In this short Perspective, we discuss the history of, and recent progress toward, the development of aptamers that can serve as rapid onset anticoagulants during cardiopulmonary bypass (CPB), extracorporeal membrane oxygenation (ECMO), and catheter-based diagnostic and interventional procedures, several million of which are performed each year worldwide. Aptamer anticoagulants provide potent and antidote-controllable anticoagulation and have low immunogenicity. New methods of aptamer isolation and engineering have not only improved the quality of aptamers, but also accelerated their development. Unfortunately, no aptamer identified to date can produce an anticoagulant effect as potent as that produced by unfractionated heparin (UFH), the standard anticoagulant for CPB. We have suggested several possible strategies to amplify the anticoagulant potency of existing aptamer anticoagulants.
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Affiliation(s)
- Haixiang Yu
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - James Frederiksen
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Bruce A Sullenger
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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5
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Rolband LA, Ke W, Afonin KA. Aptamer Conjugated RNA/DNA Hybrid Nanostructures Designed for Efficient Regulation of Blood Coagulation. Methods Mol Biol 2023; 2709:277-286. [PMID: 37572288 PMCID: PMC10498824 DOI: 10.1007/978-1-0716-3417-2_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Disruptions to the hemostatic pathway can cause a variety of serious or even life-threatening complications. Situations in which the coagulation of blood has become disturbed necessitate immediate care. Thrombin-binding aptamers are single-stranded nucleic acids that bind to thrombin with high specificity and affinity. While they can effectively inhibit thrombin, they suffer from rapid degradation and clearance in vivo. These issues are resolved, however, by attaching the therapeutic aptamer to a nucleic acid nanostructure. The increased size of the nanostructure-aptamer complex elongates the post-infusion half-life of the aptamer. These complexes are also immunoquiescent. A significant benefit of using nucleic acids as anticoagulants is their rapid deactivation by the introduction of a nanostructure made fully from the reverse complement of the therapeutically active nanostructure. These advantages make nanoparticle conjugated antithrombin aptamers a promising candidate for a rapidly reversible anticoagulant therapy.
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Affiliation(s)
- Lewis A Rolband
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Weina Ke
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Kirill A Afonin
- University of North Carolina at Charlotte, Charlotte, NC, USA.
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6
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de Freitas Saito R, Barion BG, da Rocha TRF, Rolband A, Afonin KA, Chammas R. Anticoagulant Activity of Nucleic Acid Nanoparticles (NANPs) Assessed by Thrombin Generation Dynamics on a Fully Automated System. Methods Mol Biol 2023; 2709:319-332. [PMID: 37572292 PMCID: PMC10482313 DOI: 10.1007/978-1-0716-3417-2_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Rapidly reversible anticoagulant agents have great clinical potential. Oligonucleotide-based anticoagulant agents are uniquely positioned to fill this clinical niche, as they are able to be deactivated through the introduction of the reverse complement oligo. Once the therapeutic and the antidote oligos meet in solution, they are able to undergo isothermal reassociation to form short, inactive, duplexes that are rapidly secreted via filtration by the kidneys. The formation of the duplexes interrupts the structure of the anticoagulant oligo, allowing normal coagulation to be restored. To effectively assess these new anticoagulants, a variety of methods may be employed. The measurement of thrombin generation (TG) reflects the overall capacity of plasma to produce active thrombin and provides a strong contribution to identifying new anticoagulant drugs, including DNA/RNA thrombin binding aptamer carrying fibers which are used through this chapter as an example. Here we describe the TG assessed by Calibrated Automated Thrombogram (CAT) assay in a fully automated system. This method is based on the detection of TG in plasma samples by measuring fluorescent signals released from a quenched fluorogenic thrombin substrate and the subsequent conversion of these signals in TG curves.
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Affiliation(s)
- Renata de Freitas Saito
- Comprehensive Center for Precision Oncology, Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil.
| | - Bárbara Gomes Barion
- Laboratório de Hemostasia do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Tania Rubia Flores da Rocha
- Laboratório de Hemostasia do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Alex Rolband
- University of North Carolina, Charlotte, NC, USA
| | | | - Roger Chammas
- Comprehensive Center for Precision Oncology, Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil.
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7
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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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8
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Wang Y, Wang D, Lin J, Lyu Z, Chen P, Sun T, Xue C, Mojtabavi M, Vedadghavami A, Zhang Z, Wang R, Zhang L, Park C, Heo GS, Liu Y, Dong SS, Zhang K. A Long-Circulating Vector for Aptamers Based upon Polyphosphodiester-Backboned Molecular Brushes. Angew Chem Int Ed Engl 2022; 61:e202204576. [PMID: 35979844 PMCID: PMC9529849 DOI: 10.1002/anie.202204576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 11/11/2022]
Abstract
Aptamers face challenges for use outside the ideal conditions in which they are developed. These difficulties are most palpable in vivo due to nuclease activities, rapid clearance, and off-target binding. Herein, we demonstrate that a polyphosphodiester-backboned molecular brush can suppress enzymatic digestion, reduce non-specific cell uptake, enable long blood circulation, and rescue the bioactivity of a conjugated aptamer in vivo. The backbone along with the aptamer is assembled via solid-phase synthesis, followed by installation of poly(ethylene glycol) (PEG) side chains using a two-step process with near-quantitative efficiency. The synthesis allows for precise control over polymer size and architecture. Consisting entirely of building blocks that are generally recognized as safe for therapeutics, this novel molecular brush is expected to provide a highly translatable route for aptamer-based therapeutics.
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Affiliation(s)
- Yuyan Wang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Dali Wang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jiachen Lin
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Zidi Lyu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Peiru Chen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Tingyu Sun
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Chenyang Xue
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Mehrnaz Mojtabavi
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
| | - Armin Vedadghavami
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
| | - Zheyu Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Ruimeng Wang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Lei Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Christopher Park
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Gyu Seong Heo
- Department of Radiology, Washington University, St. Louis, MO 63110, USA
| | - Yongjian Liu
- Department of Radiology, Washington University, St. Louis, MO 63110, USA
| | - Sijia S Dong
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Ke Zhang
- Departments of Chemistry and Chemical Biology, Chemical Engineering, and Bioengineering, Northeastern University, Boston, MA 02115, USA
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9
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Kelley MA, Leiderman K. Mathematical modeling to understand the role of bivalent thrombin-fibrin binding during polymerization. PLoS Comput Biol 2022; 18:e1010414. [PMID: 36107837 PMCID: PMC9477365 DOI: 10.1371/journal.pcbi.1010414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Thrombin is an enzyme produced during blood coagulation that is crucial to the formation of a stable clot. Thrombin cleaves soluble fibrinogen into fibrin, which polymerizes and forms an insoluble, stabilizing gel around the growing clot. A small fraction of circulating fibrinogen is the variant γA/γ′, which has been associated with high-affinity thrombin binding and implicated as a risk factor for myocardial infarctions, deep vein thrombosis, and coronary artery disease. Thrombin is also known to be strongly sequestered by polymerized fibrin for extended periods of time in a way that is partially regulated by γA/γ′. However, the role of γA/γ′-thrombin interactions during fibrin polymerization is not fully understood. Here, we present a mathematical model of fibrin polymerization that considered the interactions between thrombin, fibrinogen, and fibrin, including those with γA/γ′. In our model, bivalent thrombin-fibrin binding greatly increased thrombin residency times and allowed for thrombin-trapping during fibrin polymerization. Results from the model showed that early in fibrin polymerization, γ′ binding to thrombin served to localize the thrombin to the fibrin(ogen), which effectively enhanced the enzymatic conversion of fibrinogen to fibrin. When all the fibrin was fully generated, however, the fibrin-thrombin binding persisted but the effect of fibrin on thrombin switched quickly to serve as a sink, essentially removing all free thrombin from the system. This dual role for γ′-thrombin binding during polymerization led to a paradoxical decrease in trapped thrombin as the amount of γ′ was increased. The model highlighted biochemical and biophysical roles for fibrin-thrombin interactions during polymerization and agreed well with experimental observations.
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Affiliation(s)
- Michael A. Kelley
- Department of Applied Mathematics and Statistics, Colorado School of Mines, Golden, Colorado, United States of America
| | - Karin Leiderman
- Department of Applied Mathematics and Statistics, Colorado School of Mines, Golden, Colorado, United States of America
- * E-mail:
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10
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Wang Y, Wang D, Lin J, Lyu Z, Chen P, Sun T, Xue C, Mojtabavi M, Vedadghavami A, Zhang Z, Wang R, Zhang L, Park C, Heo GS, Liu Y, Dong SS, Zhang K. A Long‐Circulating Vector for Aptamers Based upon Polyphosphodiester‐Backboned Molecular Brushes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yuyan Wang
- Northeastern University Chemistry and chemical biology UNITED STATES
| | - Dali Wang
- Northeastern University Chemistry and chemical biology UNITED STATES
| | - Jiachen Lin
- Northeastern University Chemistry and chemical biology UNITED STATES
| | - Zidi Lyu
- Northeastern University Chemistry and chemical biology UNITED STATES
| | - Peiru Chen
- Northeastern University Chemistry and chemical biology UNITED STATES
| | - Tingyu Sun
- Northeastern University Chemistry and chemical biology UNITED STATES
| | - Chenyang Xue
- Northeastern University Chemistry and chemical biology UNITED STATES
| | | | | | - Zheyu Zhang
- Northeastern University Chemistry and chemical biology UNITED STATES
| | - Ruimeng Wang
- Northeastern University Chemistry and chemical biology UNITED STATES
| | - Lei Zhang
- Northeastern University Chemistry and chemical biology UNITED STATES
| | - Christopher Park
- Northeastern University Chemistry and chemical biology UNITED STATES
| | - Gyu Seong Heo
- Washington University in St Louis Department of radiology UNITED STATES
| | - Yongjian Liu
- Washington University in St Louis Department of radiology UNITED STATES
| | - Sijia S. Dong
- Northeastern University Chemistry and chemical biology UNITED STATES
| | - Ke Zhang
- Northeastern University Chemistry and Chemical Biology 360 Huntington AveHT 102 02115 Boston UNITED STATES
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11
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Ke W, Chandler M, Cedrone E, Saito RF, Rangel MC, de Souza Junqueira M, Wang J, Shi D, Truong N, Richardson M, Rolband LA, Dréau D, Bedocs P, Chammas R, Dokholyan NV, Dobrovolskaia MA, Afonin KA. Locking and Unlocking Thrombin Function Using Immunoquiescent Nucleic Acid Nanoparticles with Regulated Retention In Vivo. NANO LETTERS 2022; 22:5961-5972. [PMID: 35786891 PMCID: PMC9511123 DOI: 10.1021/acs.nanolett.2c02019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The unbalanced coagulation of blood is a life-threatening event that requires accurate and timely treatment. We introduce a user-friendly biomolecular platform based on modular RNA-DNA anticoagulant fibers programmed for reversible extracellular communication with thrombin and subsequent control of anticoagulation via a "kill-switch" mechanism that restores hemostasis. To demonstrate the potential of this reconfigurable technology, we designed and tested a set of anticoagulant fibers that carry different thrombin-binding aptamers. All fibers are immunoquiescent, as confirmed in freshly collected human peripheral blood mononuclear cells. To assess interindividual variability, the anticoagulation is confirmed in the blood of human donors from the U.S. and Brazil. The anticoagulant fibers reveal superior anticoagulant activity and prolonged renal clearance in vivo in comparison to free aptamers. Finally, we confirm the efficacy of the "kill-switch" mechanism in vivo in murine and porcine models.
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Affiliation(s)
- Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Edward Cedrone
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Renata F Saito
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 01246-903, Brazil
| | - Maria Cristina Rangel
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 01246-903, Brazil
| | - Mara de Souza Junqueira
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 01246-903, Brazil
| | - Jian Wang
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Da Shi
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Nguyen Truong
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Melina Richardson
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Lewis A Rolband
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Didier Dréau
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Peter Bedocs
- Department of Anesthesiology, School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland 20817, United States
| | - Roger Chammas
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP 01246-903, Brazil
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland 21702, United States
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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12
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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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13
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Overview of the Therapeutic Potential of Aptamers Targeting Coagulation Factors. Int J Mol Sci 2021; 22:ijms22083897. [PMID: 33918821 PMCID: PMC8069679 DOI: 10.3390/ijms22083897] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 12/11/2022] Open
Abstract
Aptamers are single-stranded DNA or RNA sequences that bind target molecules with high specificity and affinity. Aptamers exhibit several notable advantages over protein-based therapeutics. Aptamers are non-immunogenic, easier to synthesize and modify, and can bind targets with greater affinity. Due to these benefits, aptamers are considered a promising therapeutic candidate to treat various conditions, including hematological disorders and cancer. An active area of research involves developing aptamers to target blood coagulation factors. These aptamers have the potential to treat cardiovascular diseases, blood disorders, and cancers. Although no aptamers targeting blood coagulation factors have been approved for clinical use, several aptamers have been evaluated in clinical trials and many more have demonstrated encouraging preclinical results. This review summarized our knowledge of the aptamers targeting proteins involved in coagulation, anticoagulation, fibrinolysis, their extensive applications as therapeutics and diagnostics tools, and the challenges they face for advancing to clinical use.
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14
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Spiridonova VA, Novikova TM, Sizov VA, Shashkovskaya VS, Titaeva EV, Dobrovolsky AB, Zharikova EB, Mazurov AV. DNA Aptamers to Thrombin Exosite I. Structure-Function Relationships and Antithrombotic Effects. BIOCHEMISTRY (MOSCOW) 2020; 84:1521-1528. [PMID: 31870256 DOI: 10.1134/s0006297919120113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
DNA aptamers (oligonucleotides) interacting with thrombin exosite I contain G-quadruplex, two T-T, and one T-G-T loops in their structure. They prevent exosite I binding with fibrinogen and thrombin receptors on platelet surface, thereby suppressing thrombin-stimulated formation of fibrin from fibrinogen and platelet aggregation. Earlier, we synthesized original antithrombin aptamer RE31 (5'-GTGACGTAGGTTGGTGTGGTTGGGGCGTCAC-3') that contained (in addition to G-quadruplex) a hinge region connected to six pairs of complementary bases (duplex region). In this study, we compared properties of RE31 aptamer and its analogues containing varying number of bases in the duplex region and nucleotide insertions in the hinge region. Reduction in the number of nucleotides in the duplex region by 1 to 4 pairs (in comparison with RE31 aptamer) resulted in the decrease of the structural stability of aptamers (manifested as lower melting temperatures) and their ability to inhibit thrombin-stimulated fibrin formation in human blood plasma in tests of thrombin, prothrombin, and activated partial thromboplastin times. However, an increase in the number of bases by 1 to 2 pairs did not cause significant changes in the stability and antithrombin activity of the aptamers. Insertions into the hinge region of RE31 aptamer decreased its antithrombin activity. Investigation of RE31 antithrombotic properties demonstrated that RE31 (i) slowed down thrombin formation in human blood plasma (thrombin generation test), (ii) accelerated lysis of fibrin clot by tissue plasminogen activator in in vitro model, and (iii) suppressed arterial thrombosis in in vivo model. Based on the obtained data, RE31 aptamer can be considered as a potentially effective antithrombotic compound.
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Affiliation(s)
- V A Spiridonova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - T M Novikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - V A Sizov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - V S Shashkovskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - E V Titaeva
- National Medical Research Center for Cardiology, Russian Ministry of Health, Moscow, 121552, Russia
| | - A B Dobrovolsky
- National Medical Research Center for Cardiology, Russian Ministry of Health, Moscow, 121552, Russia
| | - E B Zharikova
- National Medical Research Center for Cardiology, Russian Ministry of Health, Moscow, 121552, Russia
| | - A V Mazurov
- National Medical Research Center for Cardiology, Russian Ministry of Health, Moscow, 121552, Russia.
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15
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Zhou Y, Qi X, Liu Y, Zhang F, Yan H. DNA-Nanoscaffold-Assisted Selection of Femtomolar Bivalent Human α-Thrombin Aptamers with Potent Anticoagulant Activity. Chembiochem 2019; 20:2494-2503. [PMID: 31083763 DOI: 10.1002/cbic.201900265] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Indexed: 11/11/2022]
Abstract
Multivalent aptamers that interact with their target proteins through multiple sites exhibit much stronger binding strengths than their monovalent counterparts. In this work, we have designed a single-stranded DNA (ssDNA) library (1015 molecules, each 145 nt) based on a predefined DNA nanostructure designed to present two random-loop sites for bivalent aptamer evolution. From this library, a group of ultra-strong bivalent aptamers against human α-thrombin (with apparent KD values of ≈340 fm) were easily identified through a simple seven-round conventional systematic evolution of ligands by exponential enrichment (SELEX) procedure. The dominant bivalent aptamers consist of two components, one binding to exosite I and the other to exosite II. The best of these bivalent aptamers show strong allosteric attenuation of the thrombin cleavage activity and also display an extremely potent anticoagulation effect in human plasma, demonstrating their great potential in therapeutic applications. The method developed here can easily be adapted to conventional SELEX techniques, opening a new route for fast selection of multivalent aptamers with superior binding affinity for other targets.
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Affiliation(s)
- Yu Zhou
- The Biodesign Institute and School of Molecular Science, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85281, USA
| | - Xiaodong Qi
- The Biodesign Institute and School of Molecular Science, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85281, USA
| | - Yan Liu
- The Biodesign Institute and School of Molecular Science, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85281, USA
| | - Fei Zhang
- The Biodesign Institute and School of Molecular Science, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85281, USA
| | - Hao Yan
- The Biodesign Institute and School of Molecular Science, Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85281, USA
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16
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Kelley M, Leiderman K. A Mathematical Model of Bivalent Binding Suggests Physical Trapping of Thrombin within Fibrin Fibers. Biophys J 2019; 117:1442-1455. [PMID: 31586524 DOI: 10.1016/j.bpj.2019.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/14/2019] [Accepted: 09/06/2019] [Indexed: 01/21/2023] Open
Abstract
Thrombin is an enzyme that plays many important roles in the blood clotting process; it activates platelets, cleaves coagulation proteins within feedback loops, and cleaves fibrinogen into fibrin, which polymerizes into fibers to form a stabilizing gel matrix in and around growing clots. Thrombin also binds to the formed fibrin matrix, but this interaction is not well understood. Thrombin-fibrin binding is often described as two independent, single-step binding events, one high-affinity and one low-affinity. However, kinetic schemes describing these single-step binding events do not explain experimentally-observed residency times of fibrin-bound thrombin. In this work, we study a bivalent, sequential-step binding scheme as an alternative to the high-affinity event and, in addition to the low-affinity one. We developed mathematical models for the single- and sequential-step schemes consisting of reaction-diffusion equations to compare to each other and to experimental data. We then used Bayesian inference, in the form of Markov chain Monte Carlo, to learn model parameter distributions from previously published experimental data. For the model to best fit the data, we made an additional assumption that thrombin was irreversibly sequestered; we hypothesized that this could be due to thrombin becoming physically trapped within fibrin fibers as they formed. We further estimated that ∼30% of thrombin in the experiments to which we compare our model output became physically trapped. The notion of physically trapped thrombin may provide new insights into conflicting observations regarding the speed of fibrinolysis. Finally, we show that our new model can be used to further probe scenarios dealing with thrombin allostery.
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Affiliation(s)
- Michael Kelley
- Department of Applied Mathematics and Statistics, Colorado School of Mines, Golden, Colorado
| | - Karin Leiderman
- Department of Applied Mathematics and Statistics, Colorado School of Mines, Golden, Colorado.
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Chai Z, Guo L, Jin H, Li Y, Du S, Shi Y, Wang C, Shi W, He J. TBA loop mapping with 3'-inverted-deoxythymidine for fine-tuning of the binding affinity for α-thrombin. Org Biomol Chem 2019; 17:2403-2412. [PMID: 30735210 DOI: 10.1039/c9ob00053d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
TBA is a 15-mer DNA aptamer for human α-thrombin, and its three T-rich loops are involved in the binding interactions with thrombin differently. In order to clarify their specific spatial locations in the binding interactions and search for more favourable positions, here a systematic investigation of all the loop residues was conducted with 3'-inverted thymidine (iT), by which both unnatural 3'-3'- and 5'-5'-linkages for each incorporation were introduced in the tertiary structure. The changes in Tm values and CD spectra revealed that motifs T3T12 and T4T13 are structurally distinct. Longer anti-clotting time was obtained for the T3 and T12 modifications, respectively, while T4 and T13 were completely intolerant with such changes, in terms of stability and binding to thrombin. In particular, the increased affinity bindings and longer anti-clotting time were obtained with the replacement on the central loop T7G8T9, which were closely related to the existence of a monovalent ion, K+ or Na+, consistently with the supposed binding site of these ions in TBA. It is worthwhile to note that both the subtle variations of the loop residues induced by iT and the monovalent ions determined the interacting residues of TBA and the binding strength rather than the thermal stability of the TBA structure.
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Affiliation(s)
- Zhilong Chai
- School of Pharmaceutical Sciences, Guizhou University, Guizhou 550025, China
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18
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Derszniak K, Przyborowski K, Matyjaszczyk K, Moorlag M, de Laat B, Nowakowska M, Chlopicki S. Comparison of Effects of Anti-thrombin Aptamers HD1 and HD22 on Aggregation of Human Platelets, Thrombin Generation, Fibrin Formation, and Thrombus Formation Under Flow Conditions. Front Pharmacol 2019; 10:68. [PMID: 30842734 PMCID: PMC6391317 DOI: 10.3389/fphar.2019.00068] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/18/2019] [Indexed: 11/13/2022] Open
Abstract
HD1 and HD22 are two of the most-studied aptamers binding to thrombin exosite I and exosite, respectively. To complete of their pharmacological profiles, the effects of HD1 and HD22 on thrombin-, ristocetin-, and collagen-induced human platelet aggregation, on thrombin generation and fibrin formation in human plasma, as well as on thrombus formation in human whole blood under flow conditions were assessed. The dissociation constants for HD1 and HD22 complexes with thrombin in simulated plasma ionic buffer were also evaluated. HD1 was more potent than HD22 in terms of inhibiting thrombin-induced platelet aggregation in platelet-rich plasma (PRP; 0.05-3 μM) and in washed platelets (WPs; 0.005-3 μM): approximately 8.31% (±6.99% SD) and 89.53% (±11.38% SD) for HD1 (0.5 μM) and HD22 (0.5 μM), respectively. Neither HD1 nor HD22 (3 μM) did influence platelets aggregation induced by collagen. Both of them inhibited ristocetin-induced aggregation in PRP. Surprisingly, HD1 and HD22 aptamers (3 μM) potentiated ristocetin-induced platelet aggregation in WP. HD1 reduced thrombin generation in a concentration-dependent manner [ETP at 3 μM: 1677.53 ± 55.77 (nM⋅min) vs. control 2271.71 ± 423.66 (nM⋅min)], inhibited fibrin formation (lag time at 3 μM: 33.70 min ± 8.01 min vs. control 7.91 min ± 0.91 min) and reduced thrombus formation under flow conditions [AUC30 at 3 μM: 758.30 ± 344.23 (kPa⋅min) vs. control 1553.84 ± 118.03 (kPa⋅min)]. HD22 (3 μM) also delayed thrombin generation but increased the thrombin peak. HD22 (3 μM) shortened the lag time of fibrin generation (5.40 min ± 0.26 min vs. control 7.58 min ± 1.14 min) but did not modify thrombus formation (3, 15 μM). K d values for the HD1 complex with thrombin was higher (257.8 ± 15.0 nM) than the K d for HD22 (97.6 ± 2.2 nM). In conclusion, HD1 but not HD22 represents a potent anti-thrombotic agent, confirming the major role of exosite I in the action of thrombin. HD22 aptamer blocking exosite II displays weaker anti-platelet and anti-coagulant activity, with surprising activating effects on thrombin and fibrin generation most likely induced by HD22-induced allosteric changes in thrombin dynamic structure.
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Affiliation(s)
- Katarzyna Derszniak
- Faculty of Chemistry, Jagiellonian University, Kraków, Poland
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, Kraków, Poland
| | - Kamil Przyborowski
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, Kraków, Poland
| | - Karolina Matyjaszczyk
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, Kraków, Poland
- Department of Toxicology, Jagiellonian University Medical College, Kraków, Poland
| | - Martijn Moorlag
- Cardiovascular Research Institute Maastricht, Maastricht University Medical Centre, Maastricht, Netherlands
- Synapse Research Institute, Maastricht, Netherlands
| | - Bas de Laat
- Cardiovascular Research Institute Maastricht, Maastricht University Medical Centre, Maastricht, Netherlands
- Synapse Research Institute, Maastricht, Netherlands
| | | | - Stefan Chlopicki
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, Kraków, Poland
- Department of Pharmacology, Jagiellonian University Medical College, Kraków, Poland
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19
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Khurshid H, Shi Y, Berwin BL, Weaver JB. Evaluating blood clot progression using magnetic particle spectroscopy. Med Phys 2018; 45:3258-3263. [PMID: 29772078 DOI: 10.1002/mp.12983] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 04/16/2018] [Accepted: 04/16/2018] [Indexed: 02/04/2023] Open
Abstract
PURPOSE To evaluate the thrombus maturity noninvasively providing the promise of much earlier and more accurate diagnosis of diseases ranging from stroke to myocardial infarction to deep vein thrombosis. METHODS Magnetic spectroscopy of nanoparticle Brownian rotation (MSB), a form of magnetic particle spectroscopy sensitive to Brownian rotation of magnetic nanoparticles, was used for the detection and characterization of blood clots. The nanoparticles' relaxation time was quantified by scaling the MSB spectra in frequency to match the spectra from nanoparticles in a reference state. The nanoparticles' relaxation time, in the bound state, was used to characterize the nanoparticle binding to thrombin on the blood clot. The number of nanoparticles bound to the clot was also estimated. Both the relaxation time and the weight of bound nanoparticles were obtained for clots of several ages, reflecting different stages of development and organization. The impact of clot development was explored using functionalized nanoparticles present during clot formation. RESULTS The relaxation time of the bound nanoparticles decreases for more mature, organized clots. The number of nanoparticles able to bind the clot diminishes quantitatively with clot age. On mature clots, the nanoparticles bind the thrombin on the surface while for developing clots the nanoparticles bind several thrombin molecules or become trapped in the clot matrix during formation. CONCLUSIONS By estimating the magnetic nanoparticles' relaxation time the clot age and organization can be predicted. The purposed methods are quick and minimally invasive for in vivo applications.
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Affiliation(s)
- Hafsa Khurshid
- Department of Radiology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA.,Department of Applied Physics and Astronomy, University of Sharjah, Sharjah, 27272, UAE
| | - Yipeng Shi
- Department of Physics, Dartmouth College, Hanover, NH, 03755, USA
| | - Brent L Berwin
- Department of Microbiology and Immunology, Geisel School of Medicine, Hanover, NH, 03755, USA
| | - John B Weaver
- Department of Radiology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA.,Department of Physics, Dartmouth College, Hanover, NH, 03755, USA.,Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
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20
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Kim PY, Yeh CH, Dale BJ, Leslie BA, Stafford AR, Fredenburgh JC, Hirsh J, Weitz JI. Mechanistic Basis for the Differential Effects of Rivaroxaban and Apixaban on Global Tests of Coagulation. TH OPEN 2018; 2:e190-e201. [PMID: 31249942 PMCID: PMC6524873 DOI: 10.1055/s-0038-1649507] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/26/2018] [Indexed: 02/07/2023] Open
Abstract
Rivaroxaban and apixaban are both small molecules that reversibly inhibit factor Xa. Compared with rivaroxaban, apixaban has minimal effects on the prothrombin time and activated partial thromboplastin time. To investigate this phenomenon, we used a factor Xa-directed substrate in a buffer system. Although rivaroxaban and apixaban inhibited factor Xa with similar K i values at equilibrium, kinetic measurements revealed that rivaroxaban inhibited factor Xa up to 4-fold faster than apixaban ( p < 0.001). Using a discontinuous chromogenic assay to monitor thrombin production by prothrombinase in a purified system, rivaroxaban was 4-fold more potent than apixaban (K i values of 0.7 ± 0.3 and 2.9 ± 0.5 nM, respectively; p = 0.02). Likewise, in thrombin generation assays in plasma, rivaroxaban prolonged the lag time and suppressed endogenous thrombin potential to a greater extent than apixaban. To characterize how the two inhibitors differ in recognizing factor Xa, inhibition of prothrombinase was monitored in real-time using a fluorescent probe for thrombin. The data were fit using a mixed-inhibition model and the individual association and dissociation rate constants were determined. The association rates for the binding of rivaroxaban to either free factor Xa or factor Xa incorporated into the prothrombinase complex were 10- and 1,193-fold faster than those for apixaban, respectively, whereas dissociation rates were about 3-fold faster. Collectively, these findings suggest that rivaroxaban and apixaban differ in their capacity to inhibit factor Xa and provide a plausible explanation for the observation that rivaroxaban has a greater effect on global tests of coagulation than apixaban.
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Affiliation(s)
- Paul Y Kim
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - Calvin H Yeh
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Brian J Dale
- Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Beverly A Leslie
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - Alan R Stafford
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - James C Fredenburgh
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada
| | - Jack Hirsh
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jeffrey I Weitz
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada.,Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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21
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Billur R, Ban D, Sabo TM, Maurer MC. Deciphering Conformational Changes Associated with the Maturation of Thrombin Anion Binding Exosite I. Biochemistry 2017; 56:6343-6354. [PMID: 29111672 DOI: 10.1021/acs.biochem.7b00970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Thrombin participates in procoagulation, anticoagulation, and platelet activation. This enzyme contains anion binding exosites, ABE I and ABE II, which attract regulatory biomolecules. As prothrombin is activated to thrombin, pro-ABE I is converted into mature ABE I. Unexpectedly, certain ligands can bind to pro-ABE I specifically. Moreover, knowledge of changes in conformation and affinity that occur at the individual residue level as pro-ABE I is converted to ABE I is lacking. Such changes are transient and were not captured by crystallography. Therefore, we employed nuclear magnetic resonance (NMR) titrations to monitor development of ABE I using peptides based on protease-activated receptor 3 (PAR3). Proton line broadening NMR revealed that PAR3 (44-56) and more weakly binding PAR3G (44-56) could already interact with pro-ABE I on prothrombin. 1H-15N heteronuclear single-quantum coherence NMR titrations were then used to probe binding of individual 15N-labeled PAR3G residues (F47, E48, L52, and D54). PAR3G E48 and D54 could interact electrostatically with prothrombin and tightened upon thrombin maturation. The higher affinity for PAR3G D54 suggests the region surrounding thrombin R77a is better oriented to bind D54 than the interaction between PAR3G E48 and thrombin R75. Aromatic PAR3G F47 and aliphatic L52 both reported on significant changes in the chemical environment upon conversion of prothrombin to thrombin. The ABE I region surrounding the 30s loop was more affected than the hydrophobic pocket (F34, L65, and I82). Our NMR titrations demonstrate that PAR3 residues document structural rearrangements occurring during exosite maturation that are missed by reported X-ray crystal structures.
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Affiliation(s)
- Ramya Billur
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40292, United States
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville , Louisville, Kentucky 40202, United States
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville , Louisville, Kentucky 40202, United States
| | - Muriel C Maurer
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40292, United States
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22
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Chen K, Stafford AR, Wu C, Yeh CH, Kim PY, Fredenburgh JC, Weitz JI. Exosite 2-Directed Ligands Attenuate Protein C Activation by the Thrombin–Thrombomodulin Complex. Biochemistry 2017; 56:3119-3128. [DOI: 10.1021/acs.biochem.7b00250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kai Chen
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Alan R. Stafford
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Chengliang Wu
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Calvin H. Yeh
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Paul Y. Kim
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - James C. Fredenburgh
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Jeffrey I. Weitz
- Department of Medicine, ‡Department of Biochemistry
and Biomedical Sciences, and §Thrombosis and
Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
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23
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Dabigatran and Argatroban Diametrically Modulate Thrombin Exosite Function. PLoS One 2016; 11:e0157471. [PMID: 27305147 PMCID: PMC4909201 DOI: 10.1371/journal.pone.0157471] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/31/2016] [Indexed: 11/23/2022] Open
Abstract
Thrombin is a highly plastic molecule whose activity and specificity are regulated by exosites 1 and 2, positively-charged domains that flank the active site. Exosite binding by substrates and cofactors regulates thrombin activity by localizing thrombin, guiding substrates, and by inducing allosteric changes at the active site. Although inter-exosite and exosite-to-active-site allostery have been demonstrated, the impact of active site ligation on exosite function has not been examined. To address this gap, we used surface plasmon resonance to determine the effects of dabigatran and argatroban, active site-directed inhibitors, on thrombin binding to immobilized γA/γA-fibrin or glycoprotein Ibα peptide via exosite 1 and 2, respectively, and thrombin binding to γA/γ′-fibrin or factor Va, which is mediated by both exosites. Whereas dabigatran attenuated binding, argatroban increased thrombin binding to γA/γA- and γA/γ′-fibrin and to factor Va. The results with immobilized fibrin were confirmed by examining the binding of radiolabeled thrombin to fibrin clots. Thus, dabigatran modestly accelerated the dissociation of thrombin from γA/γA-fibrin clots, whereas argatroban attenuated dissociation. Dabigatran had no effect on thrombin binding to glycoprotein Ibα peptide, whereas argatroban promoted binding. These findings not only highlight functional effects of thrombin allostery, but also suggest that individual active site-directed thrombin inhibitors uniquely modulate exosite function, thereby identifying potential novel mechanisms of action.
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24
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Trends in the Design and Development of Specific Aptamers Against Peptides and Proteins. Protein J 2016; 35:81-99. [DOI: 10.1007/s10930-016-9653-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Zavyalova E, Kopylov A. Exploring potential anticoagulant drug formulations using thrombin generation test. Biochem Biophys Rep 2016; 5:111-119. [PMID: 28955812 PMCID: PMC5600416 DOI: 10.1016/j.bbrep.2015.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/05/2015] [Accepted: 11/13/2015] [Indexed: 01/20/2023] Open
Abstract
Many anticoagulant drugs inhibiting proteins of the coagulation cascade have been developed. The main targets of anticoagulant drugs are thrombin and factor Xa; inhibiting these factors delays thrombus growth, thus preventing thrombosis while increasing bleeding risk. A balance between thrombosis and bleeding is ensured in the ‘therapeutic window’ of the anticoagulant drug concentration range. Novel anticoagulant drugs and combinations thereof are being developed. We rank coagulation factors as potential anticoagulant drug targets in combination with thrombin inhibitors, aptamer HD1 and bivalirudin, providing a background for several promising dual target treatment strategies. The thrombin generation test was used to assess the whole coagulation cascade in normal and factor-deficient human blood plasma. Potential therapeutic windows were estimated for coagulation factors, ranking them as targets for anticoagulant drugs. Thrombin and factor Xa have been revealed as the most promising targets, which fully agrees with the current drug development strategy. Inhibitors of factors Va and VIIa are expected to have narrow therapeutic windows. Inhibitors of factors VIIIa and IXa are expected to have a moderate anticoagulant effect. Factors XI and XII are poor targets for anticoagulant drugs. Compared with plasma that is deficient in factor II, the thrombin inhibitors bivalirudin and aptamer HD1 had increased activity. Both inhibitors were tested in deficient plasma providing a model of potential drug combination. The most promising combinations were anti-thrombin with anti-V/Va and also anti-thrombin with anti-IX/IXa. Each combination had an incremental dose-effect dependence that is promising from the standpoint of the therapeutic window. Coagulation factors are ranked as anticoagulant targets. Several promising combinations of anticoagulant and thrombin inhibitor are proposed. The most promising combinations are anti-thrombin with anti-V/Va or anti-IX/IXa.
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Affiliation(s)
- Elena Zavyalova
- Chemistry Department of Lomonosov Moscow State University, 'Apto-Pharm' LTD, Moscow, Russian Federation
| | - Alexey Kopylov
- Chemistry Department of Lomonosov Moscow State University, 'Apto-Pharm' LTD, Moscow, Russian Federation
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26
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Trapaidze A, Hérault JP, Herbert JM, Bancaud A, Gué AM. Investigation of the selectivity of thrombin-binding aptamers for thrombin titration in murine plasma. Biosens Bioelectron 2015; 78:58-66. [PMID: 26594887 DOI: 10.1016/j.bios.2015.11.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/26/2015] [Accepted: 11/08/2015] [Indexed: 11/26/2022]
Abstract
Detection of thrombin in plasma raises timely challenges to enable therapeutic management of thrombosis in patients under vital threat. Thrombin binding aptamers represent promising candidates as sensing elements for the development of real-time thrombin biosensors; however implementation of such biosensor requires the clear understanding of thrombin-aptamer interaction properties in real-like environment. In this study, we used Surface Plasmon Resonance technique to answer the questions of specificity and sensitivity of thrombin detection by the thrombin-binding aptamers HD1, NU172 and HD22. We systematically characterized their properties in the presence of thrombin, as well as interfering molecular species such as the thrombin precursor prothrombin, thrombin in complex with some of its natural inhibitors, nonspecific serum proteins, and diluted plasma. Kinetic experiments show the multiple binding modes of HD1 and NU172, which both interact with multiple sites of thrombin with low nanomolar affinities and show little specificity of interaction for prothrombin vs. thrombin. HD22, on the other hand, binds specifically to thrombin exosite II and has no affinity to prothrombin at all. While thrombin in complex with some of its inhibitors could not be recognized by any aptamer, the binding of HD1 and NU172 properties is compromised by thrombin inhibitors alone, as well as with serum albumin. Finally, the complex nature of plasma was overwhelming for HD1, but we define conditions for the thrombin detection at 10nM range in 100-fold diluted plasma by HD22. Consequently HD22 showed key advantage over HD1 and NU172, and appears as the only alternative to design an aptasensor.
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Affiliation(s)
- Ana Trapaidze
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France; Université de Toulouse, LAAS, F-31400 Toulouse, France.
| | | | | | - Aurélien Bancaud
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France; Université de Toulouse, LAAS, F-31400 Toulouse, France.
| | - Anne-Marie Gué
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France; Université de Toulouse, LAAS, F-31400 Toulouse, France
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Woodruff RS, Sullenger BA. Modulation of the Coagulation Cascade Using Aptamers. Arterioscler Thromb Vasc Biol 2015; 35:2083-91. [PMID: 26315404 PMCID: PMC5304947 DOI: 10.1161/atvbaha.115.300131] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/19/2015] [Indexed: 11/16/2022]
Abstract
As a novel class of therapeutics, aptamers, or nucleic acid ligands, have garnered clinical interest because of the ease of isolating a highly specific aptamer against a wide range of targets, their chemical flexibility and synthesis, and their inherent ability to have their function reversed. The following review details the development and molecular mechanisms of aptamers targeting specific proteases in the coagulation cascade. The ability of these anticoagulant aptamers to bind to and inhibit exosite function rather than binding within the active site highlights the importance of exosites in blocking protein function. As both exosite inhibitors and reversible agents, the use of aptamers is a promising strategy for future therapeutics.
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Affiliation(s)
- Rebecca S Woodruff
- From the Bloodworks Northwest Research Institute, Seattle, WA (R.S.W.); Department of Medicine, University of Washington, Seattle (R.S.W.); and Duke Translational Research Institute, Department of Surgery, Duke University Medical Center, Durham, NC (B.A.S.)
| | - Bruce A Sullenger
- From the Bloodworks Northwest Research Institute, Seattle, WA (R.S.W.); Department of Medicine, University of Washington, Seattle (R.S.W.); and Duke Translational Research Institute, Department of Surgery, Duke University Medical Center, Durham, NC (B.A.S.).
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28
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Scuotto M, Rivieccio E, Varone A, Corda D, Bucci M, Vellecco V, Cirino G, Virgilio A, Esposito V, Galeone A, Borbone N, Varra M, Mayol L. Site specific replacements of a single loop nucleoside with a dibenzyl linker may switch the activity of TBA from anticoagulant to antiproliferative. Nucleic Acids Res 2015; 43:7702-16. [PMID: 26250112 PMCID: PMC4652776 DOI: 10.1093/nar/gkv789] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/23/2015] [Indexed: 12/20/2022] Open
Abstract
Many antiproliferative G-quadruplexes (G4s) arise from the folding of GT-rich strands. Among these, the Thrombin Binding Aptamer (TBA), as a rare example, adopts a monomolecular well-defined G4 structure. Nevertheless, the potential anticancer properties of TBA are severely hampered by its anticoagulant action and, consequently, no related studies have appeared so far in the literature. We wish to report here that suitable chemical modifications in the TBA sequence can preserve its antiproliferative over anticoagulant activity. Particularly, we replaced one residue of the TT or TGT loops with a dibenzyl linker to develop seven new quadruplex-forming TBA based sequences (TBA-bs), which were studied for their structural (CD, CD melting, 1D NMR) and biological (fibrinogen, PT and MTT assays) properties. The three-dimensional structures of the TBA-bs modified at T13 (TBA-bs13) or T12 (TBA-bs12), the former endowed with selective antiproliferative activity, and the latter acting as potently as TBA in both coagulation and MTT assays, were further studied by 2D NMR restrained molecular mechanics. The comparative structural analyses indicated that neither the stability, nor the topology of the G4s, but the different localization of the two benzene rings of the linker was responsible for the loss of the antithrombin activity for TBA-bs13.
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Affiliation(s)
- Maria Scuotto
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Elisa Rivieccio
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Alessia Varone
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Daniela Corda
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Mariarosaria Bucci
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Valentina Vellecco
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Giuseppe Cirino
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Michela Varra
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
| | - Luciano Mayol
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, Naples, Italy
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Spiridonova VA, Barinova KV, Glinkina KA, Melnichuk AV, Gainutdynov AA, Safenkova IV, Dzantiev BB. A family of DNA aptamers with varied duplex region length that forms complexes with thrombin and prothrombin. FEBS Lett 2015; 589:2043-9. [PMID: 26143256 DOI: 10.1016/j.febslet.2015.06.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 06/06/2015] [Accepted: 06/22/2015] [Indexed: 01/25/2023]
Abstract
Structural properties determine binding affinities of DNA aptamers specific to thrombin. Our paper is the first to focus on a family of eight G-quadruplex-based aptamers with varied duplex region length (from two to eight base pairs). We have shown that the duplex, which is not the main binding domain, greatly influences the interaction with thrombin and prothrombin. Furthermore, the affinity of an aptamer to thrombin and prothrombin increases (respectively from 2.7×10⁻⁸ M to 5.6×10⁻¹⁰ M and from 1.8×10⁻⁵ M to 7.1×10⁻⁹ M) with an increase in the number of nucleotide pairs in the duplex region.
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Affiliation(s)
- V A Spiridonova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - K V Barinova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - K A Glinkina
- Chemistry Department, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - A V Melnichuk
- Chemistry Department, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - A A Gainutdynov
- Chemistry Department, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - I V Safenkova
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - B B Dzantiev
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia.
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30
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Daniel C, Roupioz Y, Livache T, Buhot A. On the use of aptamer microarrays as a platform for the exploration of human prothrombin/thrombin conversion. Anal Biochem 2015; 473:66-71. [PMID: 25582304 DOI: 10.1016/j.ab.2014.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/07/2014] [Accepted: 12/24/2014] [Indexed: 11/28/2022]
Abstract
Microarrays are particular biosensors with multiple grafted probes that are generally used for parallel and simultaneous detection of various targets. In this study, we used microarrays with aptamer probes in order to follow up the different biomolecular interactions of a single enzyme, the thrombin protein, involved in the complex coagulation cascade. More precisely, thanks to label-free surface plasmon resonance imaging, we were able to monitor in real time an important step in the firing of the coagulation cascade in situ-the enzymatic transformation of prothrombin into thrombin, catalyzed by factor Xa. We were also able to appraise the influence of other biochemical factors and their corresponding inhibiting or enhancing behaviors on thrombin activation. Our study opens the door for the development of a complete microarray-based platform not only for the whole coagulation cascade analysis but also for novel drug screening assays in pharmacology.
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Affiliation(s)
- Camille Daniel
- Université Grenoble Alpes, INAC-SPrAM, F-38000 Grenoble, France; Centre National de la Recherche Scientifique (CNRS), SPrAM, F-38000 Grenoble, France; Centre d'Etudes Atomiques (CEA), INAC-SPrAM, F-38000 Grenoble, France
| | - Yoann Roupioz
- Université Grenoble Alpes, INAC-SPrAM, F-38000 Grenoble, France; Centre National de la Recherche Scientifique (CNRS), SPrAM, F-38000 Grenoble, France; Centre d'Etudes Atomiques (CEA), INAC-SPrAM, F-38000 Grenoble, France.
| | - Thierry Livache
- Université Grenoble Alpes, INAC-SPrAM, F-38000 Grenoble, France; Centre National de la Recherche Scientifique (CNRS), SPrAM, F-38000 Grenoble, France; Centre d'Etudes Atomiques (CEA), INAC-SPrAM, F-38000 Grenoble, France
| | - Arnaud Buhot
- Université Grenoble Alpes, INAC-SPrAM, F-38000 Grenoble, France; Centre National de la Recherche Scientifique (CNRS), SPrAM, F-38000 Grenoble, France; Centre d'Etudes Atomiques (CEA), INAC-SPrAM, F-38000 Grenoble, France
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31
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Unusual Chair-Like G-Quadruplex Structures: Heterochiral TBA Analogues Containing Inversion of Polarity Sites. J CHEM-NY 2015. [DOI: 10.1155/2015/473051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterochiral oligodeoxynucleotides based on the thrombin binding aptamer sequence, namely, 5′gg3′-3′TT5′-5′ggtgtgg3′-3′TT5′-5′gg3′ (H1), 5′gg3′-3′TT5′-5′gg3′-3′TGT5′-5′gg3′-3′TT5′-5′gg3′ (H2), and 5′gGTTGgtgtgGTTGg3′ (H3), where lower case letters indicate L-residues, have been investigated in their ability to fold in G-quadruplex structures through a combination of gel electrophoresis, circular dichroism, and UV spectroscopy techniques. InH1andH2inversions of polarity sites have been introduced to control the strand direction in the loop regions. Collected data suggest that all modified sequences are able to fold in chair-like G-quadruplexes mimicking the originalTBAstructure.
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32
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Wu M, Petryayeva E, Algar WR. Quantum dot-based concentric FRET configuration for the parallel detection of protease activity and concentration. Anal Chem 2014; 86:11181-8. [PMID: 25361050 DOI: 10.1021/ac502600a] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protease expression, activity, and inhibition play crucial roles in a multitude of biological processes; however, these three aspects of their function are difficult for any one bioanalytical probe to measure. To help address this challenge, we report a multifunctional concentric Förster resonance energy transfer (FRET) configuration that combines two modes of biorecognition using aptamers and peptide substrates coassembled to a central semiconductor quantum dot (QD). The aptamer is sensitive to the concentration of protease and the peptide is sensitive to its hydrolytic activity. The role of the QD is to serve as a nanoscale scaffold and initial donor for energy transfer with both Cyanine 3 (Cy3) and Alexa Fluor 647 (A647) fluorescent dyes associated with the aptamer and peptide, respectively. Using thrombin as a model protease, we show that a ratiometric analysis of the emission from the QD, Cy3, and A647 permits discrimination between thrombin and thrombin-like activity, and distinguishes between active, reversibly inhibited, and irreversibly inhibited thrombin. Reliable quantitative results were obtained from a kinetic analysis of the changes in FRET. This concentric FRET format, which capitalizes on both the physical and optical properties of QDs, should be adaptable to other protease targets for which both peptide substrates and binding aptamers are known. It is thus expected to become valuable a tool for the real-time analysis of protease activity and regulation.
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Affiliation(s)
- Miao Wu
- Department of Chemistry, University of British Columbia , 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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33
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Virgilio A, Petraccone L, Scuotto M, Vellecco V, Bucci M, Mayol L, Varra M, Esposito V, Galeone A. 5-Hydroxymethyl-2'-deoxyuridine residues in the thrombin binding aptamer: investigating anticoagulant activity by making a tiny chemical modification. Chembiochem 2014; 15:2427-34. [PMID: 25214456 DOI: 10.1002/cbic.201402355] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Indexed: 11/07/2022]
Abstract
We report an investigation into analogues of the thrombin binding aptamer (TBA). Individual thymidines were replaced by the unusual residue 5-hydroxymethyl-2'-deoxyuridine (hmU). This differs from the canonical thymidine by a hydroxyl group on the 5-methyl group. NMR and CD data clearly indicate that all TBA derivatives retain the ability to fold into the "chair-like" quadruplex structure. The presence of the hmU residue does not significantly affect the thermal stability of the modified aptamers compared to the parent, except for analogue H9, which showed a marked increase in melting temperature. Although all TBA analogues showed decreased affinities to thrombin, H3, H7, and H9 proved to have improved anticoagulant activities. Our data open up the possibility to enhance TBA biological properties, simply by introducing small chemical modifications.
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Affiliation(s)
- Antonella Virgilio
- Dipartimento di Farmacia, Università degli Studi di Napoli "Federico II", Via D. Montesano 49, 80131 Napoli (Italy)
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34
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Shcherbinin DS, Veselovsky AV. Investigation of interaction of thrombin-binding aptamer with thrombin and prethrombin-2 by simulation of molecular dynamics. Biophysics (Nagoya-shi) 2013. [DOI: 10.1134/s0006350913030160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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35
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Denas G, Pengo V. Investigational anticoagulants for hematological conditions: a new generation of therapies. Expert Opin Investig Drugs 2013; 22:1281-94. [PMID: 23876036 DOI: 10.1517/13543784.2013.821463] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The introduction of novel anticoagulants has had contrasting effects on the agents in the pipeline, fueling the development of some and sinking the others. The complexity of the coagulation cascade offers interesting inhibition choices that might become valid treatment options. AREAS COVERED This review will highlight some of the anticoagulants in the pipeline. Following the success of the direct thrombin and FXa inhibitors already in the market, new agents are being tested. These include AZD0837, betrixaban, letaxaban, darexaban, and LY517717. Targeting other components of the hemostatic pathway might lead to better safety profiles without influencing efficacy. Inhibitors to FVIIa-tissue factor (FVIIa/TF) complex, FIX, FXI, and FXII are being assessed. New inspiring inhibitors are antisense oligonucleotides (ASOs) and aptamers. These are highly specific agents with readily reversible effect and might be engineered to inhibit any coagulation factor. Currently tested ASOs and aptamers are inhibitors of FXI, FXII, thrombin, FIXa, and platelet GPIV. EXPERT OPINION Some of the agents in the pipeline offer valid treatment option for long-term therapy, overcoming some of the drawbacks of the novel anticoagulants. Research is being driven by an expanding market in the anticoagulation field that has been unexploited for a long time.
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Affiliation(s)
- Gentian Denas
- Padua University Hospital, Cardiology Clinic, Department of Cardiac, Thoracic, and Vascular Sciences , Via Giustiniani 2, 35128 Padova , Italy +390498215658 ; +390498215658 ;
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36
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Wilson R, Cossins A, Nicolau DV, Missailidis S. The selection of DNA aptamers for two different epitopes of thrombin was not due to different partitioning methods. Nucleic Acid Ther 2012; 23:88-92. [PMID: 23216233 DOI: 10.1089/nat.2012.0386] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Nearly all aptamers identified so far for any given target molecule have been specific for the same binding site (epitope). The most notable exception to the 1 aptamer per target molecule rule is the pair of DNA aptamers that bind to different epitopes of thrombin. This communication refutes the suggestion that these aptamers exist because different partitioning methods were used when they were selected. The possibility that selection of these aptamers was biased by conflicting secondary structures was also investigated and found not to contribute. The preparation of protein-coated magnetic beads for systematic evolution of ligands by exponential enrichment (SELEX) and the different specificities of the thrombin aptamers for the α and β forms of thrombin are also reported.
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Affiliation(s)
- Robert Wilson
- Institute of Integrative Biology, Liverpool University, Liverpool, United Kingdom.
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37
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Borbone N, Bucci M, Oliviero G, Morelli E, Amato J, D'Atri V, D'Errico S, Vellecco V, Cirino G, Piccialli G, Fattorusso C, Varra M, Mayol L, Persico M, Scuotto M. Investigating the role of T7 and T12 residues on the biological properties of thrombin-binding aptamer: enhancement of anticoagulant activity by a single nucleobase modification. J Med Chem 2012; 55:10716-28. [PMID: 23126678 DOI: 10.1021/jm301414f] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An acyclic pyrimidine analogue, containing a five-member cycle fused on the pyrimidine ring, was synthesized and introduced at position 7 or 12 of the 15-mer oligodeoxynucleotide GGTTGGTGTGGTTGG, known as thrombin-binding aptamer (TBA). Characterization by 1H NMR and CD spectroscopies of the resulting aptamers, TBA-T7b and TBA-T12b, showed their ability to fold into the typical antiparallel chairlike G-quadruplex structure formed by TBA. The apparent CD melting temperatures indicated that the introduction of the acyclic residue, mainly at position 7, improves the thermal stability of resulting G-quadruplexes with respect to TBA. The anticoagulant activity of the new molecules was then valued in PT assay, and it resulted that TBA-T7b is more potent than TBA in prolonging clotting time. On the other hand, in purified fibrinogen assay the thrombin inhibitory activity of both modified sequences was lower than that of TBA using human enzyme, whereas the potency trend was again reversed using bovine enzyme. Obtained structure-activity relationships were investigated by structural and computational studies. Taken together, these results reveal the active role of TBA residues T7 and T12 and the relevance of some amino acids located in the anion binding exosite I of the protein in aptamer-thrombin interaction.
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Affiliation(s)
- Nicola Borbone
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
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38
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Botkjaer KA, Deryugina EI, Dupont DM, Gårdsvoll H, Bekes EM, Thuesen CK, Chen Z, Chen Z, Ploug M, Quigley JP, Andreasen PA. Targeting tumor cell invasion and dissemination in vivo by an aptamer that inhibits urokinase-type plasminogen activator through a novel multifunctional mechanism. Mol Cancer Res 2012; 10:1532-43. [PMID: 23038812 DOI: 10.1158/1541-7786.mcr-12-0349] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Data accumulated over the latest two decades have established that the serine protease urokinase-type plasminogen activator (uPA) is a potential therapeutic target in cancer. When designing inhibitors of the proteolytic activity of serine proteases, obtaining sufficient specificity is problematic, because the topology of the proteases' active sites are highly similar. In an effort to generate highly specific uPA inhibitors with new inhibitory modalities, we isolated uPA-binding RNA aptamers by screening a library of 35 nucleotides long 2'-fluoro-pyrimidine RNA molecules using a version of human pro-uPA lacking the epidermal growth factor-like and kringle domains as bait. One pro-uPA-binding aptamer sequence, referred to as upanap-126, proved to be highly specific for human uPA. Upanap-126 delayed the proteolytic conversion of human pro-uPA to active uPA, but did not inhibit plasminogen activation catalyzed by two-chain uPA. The aptamer also inhibited the binding of pro-uPA to uPAR and the binding of vitronectin to the preformed pro-uPA/uPAR complex, both in cell-free systems and on cell surfaces. Furthermore, upanap-126 inhibited human tumor cell invasion in vitro in the Matrigel assay and in vivo in the chick embryo assay of cell escape from microtumors. Finally, upanap-126 significantly reduced the levels of tumor cell intravasation and dissemination in the chick embryo model of spontaneous metastasis. Together, our findings show that usage of upanap-126 represents a novel multifunctional mechanistic modality for inhibition of uPA-dependent processes involved in tumor cell spread.
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Affiliation(s)
- Kenneth A Botkjaer
- Department of Molecular Biology and Genetics, Aarhus University, Copenhagen, Denmark
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39
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Fredenburgh JC, Kretz CA, Weitz JI. A Protease TAMER: a nucleic acid-based anticoagulant. J Thromb Haemost 2012; 10:867-9. [PMID: 22405195 DOI: 10.1111/j.1538-7836.2012.04684.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J C Fredenburgh
- Department of Medicine and Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
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40
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Bompiani K, Monroe D, Church F, Sullenger B. A high affinity, antidote-controllable prothrombin and thrombin-binding RNA aptamer inhibits thrombin generation and thrombin activity. J Thromb Haemost 2012; 10:870-80. [PMID: 22385910 PMCID: PMC3636572 DOI: 10.1111/j.1538-7836.2012.04679.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
BACKGROUND The conversion of prothrombin to thrombin is one of two non-duplicated enzymatic reactions during coagulation. Thrombin has long been considered an optimal anticoagulant target because it plays a crucial role in fibrin clot formation by catalyzing the cleavage of fibrinogen, upstream coagulation cofactors and platelet receptors. Although a number of anti-thrombin therapeutics exist, it is challenging to use them clinically due to their propensity to induce bleeding. Previously, we isolated a modified RNA aptamer (R9D-14) that binds prothrombin with high affinity and is a potent anticoagulant in vitro. OBJECTIVES We sought to explore the structure of R9D-14 and elucidate its anticoagulant mechanism(s). In addition to designing an optimized aptamer (RNA(R9D-14T)), we also explored whether complementary antidote oligonucleotides can rapidly modulate the optimized aptamer's anticoagulant activity. METHODS AND RESULTS RNA(R9D-14T) binds prothrombin and thrombin pro/exosite I with high affinity and inhibits both thrombin generation and thrombin exosite I-mediated activity (i.e. fibrin clot formation, feedback activity and platelet activation). RNA(R9D-14T) significantly prolongs the aPTT, PT and TCT clotting assays, and is a more potent inhibitor than the thrombin exosite I DNA aptamer ARC-183. Moreover, a complementary oligonucleotide antidote can rapidly (< 2 min) and durably (>2 h) reverse RNA(R9D-14T) anticoagulation in vitro. CONCLUSIONS Powerful anticoagulation, in conjunction with antidote reversibility, suggests that RNA(R9D-14T) may be ideal for clinical anticoagulation in settings that require rapid and robust anticoagulation, such as cardiopulmonary bypass, deep vein thrombosis, stroke or percutaneous coronary intervention.
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Affiliation(s)
- K.M. Bompiani
- Department of Surgery, Duke University Medical Center, Durham, NC 27710
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710
| | - D.M. Monroe
- Division of Hematology and Oncology, University of North Carolina, Chapel Hill, NC 27599
| | - F.C. Church
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599
| | - B.A. Sullenger
- Department of Surgery, Duke University Medical Center, Durham, NC 27710
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41
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Mayer G, Rohrbach F, Pötzsch B, Müller J. Aptamer-based modulation of blood coagulation. Hamostaseologie 2012; 31:258-63. [PMID: 22065102 DOI: 10.5482/ha-1156] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 06/06/2011] [Indexed: 11/05/2022] Open
Abstract
Nucleic acid based aptamers are single-stranded oligonucleotide ligands isolated from random libraries by an in-vitro selection procedure. Through the formation of unique three-dimensional structures, aptamers are able to selectively interact with a variety of target molecules and are therefore also promising candidates for the development of anticoagulant drugs. While thrombin represents the most prominent enzymatic target in this field, also aptamers directed against other coagulation proteins and proteases have been identified with some currently being tested in clinical trials. In this review, we summarize recent developments in the design and evaluation of aptamers for anticoagulant therapy and research.
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Affiliation(s)
- G Mayer
- University of Bonn, Life & Medical Sciences Institute, Bonn, Germany.
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42
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Zavyalova EG, Protopopova AD, Yaminsky IV, Kopylov AM. Kinetic characterization of inhibition of human thrombin with DNA aptamers by turbidimetric assay. Anal Biochem 2011; 421:234-9. [PMID: 22056408 DOI: 10.1016/j.ab.2011.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 10/16/2022]
Abstract
A sensitive turbidimetric method for detecting fibrin association was used to study the kinetics of fibrinogen hydrolysis with thrombin. The data were complemented by high-performance liquid chromatography (HPLC) measurements of the peptide products, fibrinopeptides released during hydrolysis. Atomic force microscopy (AFM) data showed that the fibril diameter is the main geometric parameter influencing the turbidity. The turbidimetric assay was validated using thrombin with the standard activity. To study thrombin inhibitors, a kinetic model that allows estimating the inhibition constants and the type of inhibition was proposed. The kinetic model was used to study the inhibitory activity of the two DNA aptamers 15-TBA (thrombin-binding aptamer) and 31-TBA, which bind to thrombin exosites. For the first time, 31-TBA was shown to possess the competitive inhibition type, whereas the shortened aptamer 15-TBA has the noncompetitive inhibition type.
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Affiliation(s)
- Elena G Zavyalova
- Department of Chemistry, M V Lomonosov Moscow State University, Moscow 119991, Russian Federation.
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43
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Vu TT, Stafford AR, Leslie BA, Kim PY, Fredenburgh JC, Weitz JI. Histidine-rich glycoprotein binds fibrin(ogen) with high affinity and competes with thrombin for binding to the gamma'-chain. J Biol Chem 2011; 286:30314-30323. [PMID: 21757718 DOI: 10.1074/jbc.m111.253831] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Histidine-rich glycoprotein (HRG) is an abundant protein that binds fibrinogen and other plasma proteins in a Zn(2+)-dependent fashion but whose function is unclear. HRG has antimicrobial activity, and its incorporation into fibrin clots facilitates bacterial entrapment and killing and promotes inflammation. Although these findings suggest that HRG contributes to innate immunity and inflammation, little is known about the HRG-fibrin(ogen) interaction. By immunoassay, HRG-fibrinogen complexes were detected in Zn(2+)-supplemented human plasma, a finding consistent with a high affinity interaction. Surface plasmon resonance determinations support this concept and show that in the presence of Zn(2+), HRG binds the predominant γ(A)/γ(A)-fibrinogen and the γ-chain elongated isoform, γ(A)/γ'-fibrinogen, with K(d) values of 9 nm. Likewise, (125)I-labeled HRG binds γ(A)/γ(A)- or γ(A)/γ'-fibrin clots with similar K(d) values when Zn(2+) is present. There are multiple HRG binding sites on fibrin(ogen) because HRG binds immobilized fibrinogen fragment D or E and γ'-peptide, an analog of the COOH terminus of the γ'-chain that mediates the high affinity interaction of thrombin with γ(A)/γ'-fibrin. Thrombin competes with HRG for γ'-peptide binding and displaces (125)I-HRG from γ(A)/γ'-fibrin clots and vice versa. Taken together, these data suggest that (a) HRG circulates in complex with fibrinogen and that the complex persists upon fibrin formation, and (b) by competing with thrombin for γ(A)/γ'-fibrin binding, HRG may modulate coagulation. Therefore, the HRG-fibrin interaction may provide a novel link between coagulation, innate immunity, and inflammation.
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Affiliation(s)
- Trang T Vu
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario L8L 2X2, Canada; the Departments of Medical Sciences, McMaster University, Hamilton, Ontario L8L 2X2, Canada
| | - Alan R Stafford
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario L8L 2X2, Canada; Medicine, McMaster University, Hamilton, Ontario L8L 2X2, Canada
| | - Beverly A Leslie
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario L8L 2X2, Canada; Medicine, McMaster University, Hamilton, Ontario L8L 2X2, Canada
| | - Paul Y Kim
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario L8L 2X2, Canada; Medicine, McMaster University, Hamilton, Ontario L8L 2X2, Canada
| | - James C Fredenburgh
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario L8L 2X2, Canada; Medicine, McMaster University, Hamilton, Ontario L8L 2X2, Canada
| | - Jeffrey I Weitz
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario L8L 2X2, Canada; the Departments of Medical Sciences, McMaster University, Hamilton, Ontario L8L 2X2, Canada; Medicine, McMaster University, Hamilton, Ontario L8L 2X2, Canada.
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44
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Binding of alpha-thrombin to surface-anchored platelet glycoprotein Ib(alpha) sulfotyrosines through a two-site mechanism involving exosite I. Proc Natl Acad Sci U S A 2011; 108:8628-33. [PMID: 21555542 DOI: 10.1073/pnas.1017042108] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The involvement of exosite I in α-thrombin (FIIa) binding to platelet glycoprotein Ibα (GPIbα), which could influence interactions with other substrates, remains undefined. To address the problem, we generated the GPIbα amino terminal domain (GPIbα-N) fully sulfated on three tyrosine residues and solved the structure of its complex with FIIa. We found that sulfotyrosine (Tys) 278 enhances the interaction mainly by establishing contacts with exosite I. We then evaluated how substituting tyrosine with phenylalanine, which cannot be sulfated, affects FIIa binding to soluble or surface-immobilized GPIbα-N. Mutating Tyr(276), which mostly contacts exosite II residues, markedly reduced FIIa interaction with both soluble and immobilized GPIbα-N; mutating Tyr(278) or Tyr(279), which mostly contact exosite I residues, reduced FIIa complexing in solution by 0-20% but affinity for immobilized GPIbα-N 2 to 6-fold, respectively. Moreover, three exosite I ligands--aptamer HD1, hirugen, and lepirudin--did not interfere with soluble FIIa complexing to GPIbα-N, excluding that their binding caused allosteric effects influencing the interaction; nonetheless, all impaired FIIa binding to immobilized GPIbα-N and platelet GPIb nearly as much as aptamer HD22 and heparin, both exosite II ligands. Bound HD1 and hirugen alter Trp(148) orientation in a loop near exosite I preventing contacts with the sulfate oxygen atoms of Tys(279). These results support a mechanism in which binding occurs when the two exosites of one FIIa molecule independently interact with two immobilized GPIbα molecules. Through exosite engagement, GPIbα may influence FIIa-dependent processes relevant to hemostasis and thrombosis.
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45
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Vitamin-K-abhängige Gerinnungsfaktoren. Hamostaseologie 2010. [DOI: 10.1007/978-3-642-01544-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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46
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Lee W, Obubuafo A, Lee YI, Davis LM, Soper SA. Single-pair fluorescence resonance energy transfer (spFRET) for the high sensitivity analysis of low-abundance proteins using aptamers as molecular recognition elements. J Fluoresc 2010; 20:203-13. [PMID: 19802688 PMCID: PMC2863098 DOI: 10.1007/s10895-009-0540-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 09/15/2009] [Indexed: 10/20/2022]
Abstract
We have developed a strategy for the detection of single protein molecules, which uses single-pair fluorescence resonance energy transfer (spFRET) as the readout modality and provides exquisite analytical sensitivity and reduced assay turn-around-time by eliminating various sample pre-processing steps. The single-protein detection assay uses two independent aptamer recognition events to form an assembly conducive to intramolecular hybridization of oligonucleotide complements that are tethered to the aptamers. This hybridization brings a donor-acceptor pair within the Förster distance to create a fluorescence signature indicative of the presence of the protein-aptamer(s) association complex. As an example of spFRET, we demonstrate the technique for the analysis of serum thrombin. The assay requires co-association of two distinct epitope-binding aptamers, each of which is labeled with a donor or acceptor fluorescent dye (Cy3 or Cy5, respectively) to produce a FRET response. The FRET response between Cy3 and Cy5 was monitored by single-molecule photon-burst detection, which provides high analytical sensitivity when the number of single-molecule events is plotted versus the target concentration. We are able to identify thrombin with high efficiency based on photon burst events transduced in the Cy5 detection channel. We also demonstrate that the technique can discriminate thrombin molecules from its analogue prothrombin. The analytical sensitivity was >200-fold better than an ensemble measurement.
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Affiliation(s)
- Wonbae Lee
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803-1804, USA
| | - Anne Obubuafo
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803-1804, USA
| | - Yong-Ill Lee
- Department of Chemistry, Changwon National University, Changwon, 641-773, South Korea
| | - Lloyd M. Davis
- Center for Laser Applications, University of Tennessee Space Institute, Tullahoma, TN 37388, USA
| | - Steven A. Soper
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803-1804, USA
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47
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Bifunctional combined aptamer for simultaneous separation and detection of thrombin. Biosens Bioelectron 2009; 25:1487-92. [PMID: 19959350 DOI: 10.1016/j.bios.2009.11.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2009] [Revised: 11/03/2009] [Accepted: 11/05/2009] [Indexed: 11/21/2022]
Abstract
Here we report on the construction and evaluation of a bifunctional combined aptamer (BCA) that consists of a DNA streptavidin-binding aptamer (SBA), a DNA thrombin-binding aptamer (TBA) and a fluorophore. The BCA adopts a new conformation that is very different from simply linking the conformations of the two individual aptamers together, so that it does not bind to streptavidin in the absence of thrombin. Binding of this novel DNA aptamer to streptavidin is triggered by the thrombin binding and depends on the concentration of thrombin. Meanwhile, fluorescence from the streptavidin captured BCA reflects the quantity of the target molecule in the sample. This aptamer combination strategy based on the SBA holds good potential for applications in simultaneous detection and separation of targets of aptamers or certain DNA and RNA targets.
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48
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Grohe B, Taller A, Vincent PL, Tieu LD, Rogers KA, Heiss A, Sørensen ES, Mittler S, Goldberg HA, Hunter GK. Crystallization of calcium oxalates is controlled by molecular hydrophilicity and specific polyanion-crystal interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:11635-11646. [PMID: 19725562 DOI: 10.1021/la901145d] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
To gain more insight into protein structure-function relationships that govern ectopic biomineralization processes in kidney stone formation, we have studied the ability of urinary proteins (Tamm-Horsfall protein, osteopontin (OPN), prothrombin fragment 1 (PTF1), bikunin, lysozyme, albumin, fetuin-A), and model compounds (a bikunin fragment, recombinant-, milk-, bone osteopontin, poly-L-aspartic acid (poly asp), poly-L-glutamic acid (poly glu)) in modulating precipitation reactions of kidney stone-related calcium oxalate mono- and dihydrates (COM, COD). Combining scanning confocal microscopy and fluorescence imaging, we determined the crystal faces of COM with which these polypeptides interact; using scanning electron microscopy, we characterized their effects on crystal habits and precipitated volumes. Our findings demonstrate that polypeptide adsorption to COM crystals is dictated first by the polypeptide's affinity for the crystal followed by its preference for a crystal face: basic and relatively hydrophobic macromolecules show no adsorption, while acidic and more hydrophilic polypeptides adsorb either nonspecifically to all faces of COM or preferentially to {100}/{121} edges and {100} faces. However, investigating calcium oxalates grown in the presence of these polypeptides showed that some acidic proteins that adsorb to crystals do not affect crystallization, even if present in excess of physiological concentrations. These proteins (albumin, bikunin, PTF1, recombinant OPN) have estimated total hydrophilicities from 200 to 850 kJ/mol and net negative charges from -9 to -35, perhaps representing a "window" in which proteins adsorb and coat urinary crystals (support of excretion) without affecting crystallization. Strongest effects on crystallization were observed for polypeptides that are either highly hydrophilic (>950 kJ/mol) and highly carboxylated (poly asp, poly glu), or else highly hydrophilic and highly phosphorylated (native OPN isoforms), suggesting that highly hydrophilic proteins strongly affect precipitation processes in the urinary tract. Therefore, the level of hydrophilicity and net charge is a critical factor in the ability of polypeptides to affect crystallization and to regulate biomineralization processes.
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Affiliation(s)
- Bernd Grohe
- CIHR Group in Skeletal Development and Remodeling, School of Dentistry, University of Western Ontario, London, Ontario, Canada
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49
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Petrera NS, Stafford AR, Leslie BA, Kretz CA, Fredenburgh JC, Weitz JI. Long range communication between exosites 1 and 2 modulates thrombin function. J Biol Chem 2009; 284:25620-9. [PMID: 19589779 DOI: 10.1074/jbc.m109.000042] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although exosites 1 and 2 regulate thrombin activity by binding substrates and cofactors and by allosterically modulating the active site, it is unclear whether there is direct allosteric linkage between the two exosites. To begin to address this, we first titrated a thrombin variant fluorescently labeled at exosite 1 with exosite 2 ligands, HD22 (a DNA aptamer), gamma'-peptide (an analog of the COOH terminus of the gamma'-chain of fibrinogen) or heparin. Concentration-dependent and saturable changes in fluorescence were elicited, supporting inter-exosite linkage. To explore the functional consequences of this phenomenon, we evaluated the capacity of exosite 2 ligands to inhibit thrombin binding to gamma(A)/gamma(A)-fibrin, an interaction mediated solely by exosite 1. When gamma(A)/gamma(A)-fibrinogen was clotted with thrombin in the presence of HD22, gamma'-peptide, or prothrombin fragment 2 there was a dose-dependent and saturable decrease in thrombin binding to the resultant fibrin clots. Furthermore, HD22 reduced the affinity of thrombin for gamma(A)/gamma(A)-fibrin 6-fold and accelerated the dissociation of thrombin from preformed gamma(A)/gamma(A)-fibrin clots. Similar responses were obtained when surface plasmon resonance was used to monitor the interaction of thrombin with gamma(A)/gamma(A)-fibrinogen or fibrin. There is bidirectional communication between the exosites, because exosite 1 ligands, HD1 (a DNA aptamer) or hirudin-(54-65) (an analog of the COOH terminus of hirudin), inhibited the exosite 2-mediated interaction of thrombin with immobilized gamma'-peptide. These findings provide evidence for long range allosteric linkage between exosites 1 and 2 on thrombin, revealing further complexity to the mechanisms of thrombin regulation.
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Affiliation(s)
- Nicolas S Petrera
- Department of Medicine, McMaster University, and Henderson Research Center, Hamilton, Ontario L8V 1C3, Canada
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50
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An exosite-specific ssDNA aptamer inhibits the anticoagulant functions of activated protein C and enhances inhibition by protein C inhibitor. ACTA ACUST UNITED AC 2009; 16:442-51. [PMID: 19389630 DOI: 10.1016/j.chembiol.2009.03.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 02/25/2009] [Accepted: 03/05/2009] [Indexed: 11/22/2022]
Abstract
Activated protein C (APC) is a serine protease with anticoagulant, anti-inflammatory, and cytoprotective properties. Using recombinant APC, we identified a class of single-stranded DNA aptamers (HS02) that selectively bind to APC with high affinity. Interaction of HS02 with APC modulates the protease activity in a way such that the anticoagulant functions of APC are inhibited and its reactivity toward the protein C inhibitor is augmented in a glysoaminoglycan-like fashion, whereas APC's antiapoptotic and cytoprotective functions remain unaffected. Based on these data, the binding site of HS02 was localized to the basic exosite of APC. These characteristics render the exosite-specific aptamers a promising tool for the development of APC assays and a potential therapeutic agent applicable for the selective control of APC's anticoagulant activity.
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