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Chen K, Zhu L, Li J, Zhang Y, Yu Y, Wang X, Wei W, Huang K, Xu W. High-content tailoring strategy to improve the multifunctionality of functional nucleic acids. Biosens Bioelectron 2024; 261:116494. [PMID: 38901394 DOI: 10.1016/j.bios.2024.116494] [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: 05/08/2024] [Revised: 05/30/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
Functional nucleic acids (FNAs) have attracted increasing attention in recent years due to their diverse physiological functions. The understanding of their conformational recognition mechanisms has advanced through nucleic acid tailoring strategies and sequence optimization. With the development of the FNA tailoring techniques, they have become a methodological guide for nucleic acid repurposing. Therefore, it is necessary to systematize the relationship between FNA tailoring strategies and the development of nucleic acid multifunctionality. This review systematically categorizes eight types of FNA multifunctionality, and introduces the traditional FNA tailoring strategy from five aspects, including deletion, substitution, splitting, fusion and elongation. Based on the current state of FNA modification, a new generation of FNA tailoring strategy, called the high-content tailoring strategy, was unprecedentedly proposed to improve FNA multifunctionality. In addition, the multiple applications of rational tailoring-driven FNA performance enhancement in various fields were comprehensively summarized. The limitations and potential of FNA tailoring and repurposing in the future are also explored in this review. In summary, this review introduces a novel tailoring theory, systematically summarizes eight FNA performance enhancements, and provides a systematic overview of tailoring applications across all categories of FNAs. The high-content tailoring strategy is expected to expand the application scenarios of FNAs in biosensing, biomedicine and materials science, thus promoting the synergistic development of various fields.
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Affiliation(s)
- Keren Chen
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jie Li
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yangzi Zhang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Yongxia Yu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Xiaofu Wang
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Wei Wei
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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Riccardi C, Pérez de Carvasal K, Platella C, Meyer A, Smietana M, Morvan F, Montesarchio D. Probing naphthalene diimide and 3-hydroxypropylphosphate as end-conjugating moieties for improved thrombin binding aptamers: Structural and biological effects. Bioorg Chem 2023; 141:106917. [PMID: 37865055 DOI: 10.1016/j.bioorg.2023.106917] [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: 09/04/2023] [Revised: 09/27/2023] [Accepted: 10/09/2023] [Indexed: 10/23/2023]
Abstract
The limitations associated with the in vivo use of the thrombin binding aptamer (TBA or TBA15) have dramatically stimulated the search of suitable chemically modified analogues in order to discover effective and reversible inhibitors of thrombin activity. In this context, we previously proposed cyclic and pseudo-cyclic TBA analogues with improved stability that proved to be more active than the parent aptamer. Herein, we have investigated a novel library of TBA derivatives carrying naphthalene diimide (NDI) moieties at the 3'- or 5'-end. In a subset of the investigated oligonucleotides, additional 3-hydroxypropylphosphate (HPP) groups were introduced at one or both ends of the TBA sequence. Evaluation of the G-quadruplex thermal stability, serum nuclease resistance and in vitro anticoagulant activity of the new TBA analogues allowed rationalizing the effect of these appendages on the activity of the aptamer on the basis of their relative position. Notably, most of the different TBA analogues tested were more potent thrombin inhibitors than unmodified TBA. Particularly, the analogue carrying an NDI group at the 5'-end and an HPP group at the 3'-end, named N-TBA-p, exhibited enhanced G-quadruplex thermal stability (ΔTm + 14° C) and ca. 10-fold improved nuclease resistance in serum compared to the native aptamer. N-TBA-p also induced prolonged and dose-dependent clotting times, showing a ca. 11-fold higher anticoagulant activity compared to unmodified TBA, as determined by spectroscopic methods. Overall, N-TBA-p proved to be in vitro a more efficient thrombin inhibitor than all the best ones previously investigated in our group. Its interesting features, associated with its easy preparation, make it a very promising candidate for future in vivo studies.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Kévan Pérez de Carvasal
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - François Morvan
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34095 Montpellier, France.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy.
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Virgilio A, Benigno D, Aliberti C, Vellecco V, Bucci M, Esposito V, Galeone A. Improving the Biological Properties of Thrombin-Binding Aptamer by Incorporation of 8-Bromo-2'-Deoxyguanosine and 2'-Substituted RNA Analogues. Int J Mol Sci 2023; 24:15529. [PMID: 37958511 PMCID: PMC10647374 DOI: 10.3390/ijms242115529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Thrombin-binding aptamer (TBA) is one of the best-known G-quadruplex (G4)-forming aptamers. By adopting its peculiar chair-like G4 structure, TBA can efficiently bind to thrombin, thus producing an anticoagulant effect. The major limit to its therapeutic application is represented by its poor thermal and biological resistance. Therefore, numerous research studies have been focused on the design of TBA analogues with chemical modifications to improve its pharmacokinetic and pharmacodynamic properties. To maintain the functional recognition to protein surface on which TBA anticoagulant activity depends, it is essential to preserve the canonical antiparallel topology of the TBA quadruplex core. In this paper, we have designed three TBA variants with modified G-tetrads to evaluate the effects of nucleobase and sugar moiety chemical modifications on biological properties of TBA, preserving its chair-like G-quadruplex structure. All derivatives contain 8-bromo-2'-deoxyguanosine (GBr) in syn positions, while in the anti-positions, locked nucleic acid guanosine (GLNA) in the analogue TBABL, 2'-O-methylguanosine (GOMe) in TBABM, and 2'-F-riboguanosine (GF) in TBABF is present. CD (Circular Dichroism), CD melting, 1H-NMR (Nuclear Magnetic Resonance), and non-denaturing PAGE (Polyacrylamide Gel Electrophoresis), nuclease stability, prothrombin time (PT) and fibrinogen-clotting assays have been performed to investigate the structural and biological properties of these TBA analogues. The most interesting results have been obtained with TBABF, which revealed extraordinary thermal stability (Tm approximately 40 °C higher than that of TBA), anticoagulant activity almost doubled compared to the original aptamer, and, above all, a never-observed resistance to nucleases, as 50% of its G4 species was still present in 50% FBS at 24 h. These data indicate TBABF as one of the best TBA analogue ever designed and investigated, to the best of our knowledge, overcoming the main limitations to therapeutic applications of this aptamer.
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Affiliation(s)
| | | | | | | | | | - Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, 80131 Napoli, Italy; (A.V.); (D.B.); (V.V.); (M.B.); (A.G.)
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Varizhuk IV, Tsvetkov VB, Toropygin IY, Stomakhin AA, Kolganova NA, Surzhikov SA, Timofeev EN. The Regioselective Conjugation of the 15-nt Thrombin Aptamer with an Optimized Tripeptide Sequence Greatly Increases the Anticoagulant Activity of the Aptamer. Pharmaceutics 2023; 15:pharmaceutics15020604. [PMID: 36839926 PMCID: PMC9967020 DOI: 10.3390/pharmaceutics15020604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Currently, oligonucleotide therapy has emerged as a new paradigm in the treatment of human diseases. In many cases, however, therapeutic oligonucleotides cannot be used directly without modification. Chemical modification or the conjugation of therapeutic oligonucleotides is required to increase their stability or specificity, improve their affinity or inhibitory characteristics, and address delivery issues. Recently, we proposed a conjugation strategy for a 15-nt G-quadruplex thrombin aptamer aimed at extending the recognition interface of the aptamer. In particular, we have prepared a series of designer peptide conjugates of the thrombin aptamer, showing improved anticoagulant activity. Herein, we report a new series of aptamer-peptide conjugates with optimized peptide sequences. The anti-thrombotic activity of aptamer conjugates was notably improved. The lead conjugate, TBA-GLE, was able to inhibit thrombin-induced coagulation approximately six-fold more efficiently than the unmodified aptamer. In terms of its anticoagulant activity, the TBA-GLE conjugate approaches NU172, one of the most potent G-quadruplex thrombin aptamers. Molecular dynamics studies have confirmed that the principles applied to the design of the peptide side chain are efficient instruments for improving aptamer characteristics for the proposed TBA conjugate model.
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Affiliation(s)
- Irina V. Varizhuk
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir B. Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Institute of Biodesign and Complex System Modeling, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Ilya Yu. Toropygin
- Department of Proteomics, V.N. Orekhovich Research Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow 119832, Russia
| | - Andrey A. Stomakhin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Natalia A. Kolganova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Edward N. Timofeev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Correspondence:
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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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Properties and Potential Antiproliferative Activity of Thrombin-Binding Aptamer (TBA) Derivatives with One or Two Additional G-Tetrads. Int J Mol Sci 2022; 23:ijms232314921. [PMID: 36499249 PMCID: PMC9736779 DOI: 10.3390/ijms232314921] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/09/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
In this paper, we study the biological properties of two TBA analogs containing one and two extra G-tetrads, namely TBAG3 and TBAG4, respectively, and two further derivatives in which one of the small loops at the bottom (TBAG41S) or the large loop at the top (TBAG4GS) of the TBAG4 structure has been completely modified by replacing all loop residues with abasic site mimics. The therapeutical development of the TBA was hindered by its low thermodynamic and nuclease stability, while its potential as an anticancer/antiproliferative molecule is also affected by the anticoagulant activity, being a side effect in this case. In order to obtain suitable TBA analogs and to explore the involvement of specific aptamer regions in biological activity, the antiproliferative capability against DU 145 and MDAMB 231 cancer cell lines (MTT), the anticoagulant properties (PT), the biological degradability (nuclease stability assay) and nucleolin (NCL) binding ability (SPR) of the above described TBA derivatives have been tested. Interestingly, none of the TBA analogs exhibits an anticoagulant activity, while all of them show antiproliferative properties to the same extent. Furthermore, TBAG4 displays extraordinary nuclease stability and promising antiproliferative properties against breast cancer cells binding NCL efficiently. These results expand the range of G4-structures targeting NCL and the possibility of developing novel anticancer and antiviral drugs.
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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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9
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Müller P, Sahlbach M, Gasper S, Mayer G, Müller J, Pötzsch B, Heckel A. Controlling Coagulation in Blood with Red Light. Angew Chem Int Ed Engl 2021; 60:22441-22446. [PMID: 34293228 PMCID: PMC8518524 DOI: 10.1002/anie.202108468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Indexed: 12/15/2022]
Abstract
Precise control of blood clotting and rapid reversal of anticoagulation are essential in many clinical situations. We were successful in modifying a thrombin-binding aptamer with a red-light photocleavable linker derived from Cy7 by Cu-catalyzed Click chemistry. We were able to show that we can successfully deactivate the modified aptamer with red light (660 nm) even in human blood-restoring the blood's natural coagulation capability.
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Affiliation(s)
- Patricia Müller
- Goethe University FrankfurtInstitute for Organic Chemistry and Chemical BiologyMax-von-Laue Str. 960438Frankfurt am MainGermany
| | - Marlen Sahlbach
- Goethe University FrankfurtInstitute for Organic Chemistry and Chemical BiologyMax-von-Laue Str. 960438Frankfurt am MainGermany
| | - Simone Gasper
- University Hospital BonnInstitute of Experimental Hematology and Transfusion MedicineVenusberg-Campus 153105BonnGermany
| | - Günter Mayer
- University of BonnLife and Medical Sciences InstituteCenter of Aptamer Research & DevelopmentGerhard-Domagk-Str. 153121BonnGermany
| | - Jens Müller
- University Hospital BonnInstitute of Experimental Hematology and Transfusion MedicineVenusberg-Campus 153105BonnGermany
| | - Bernd Pötzsch
- University Hospital BonnInstitute of Experimental Hematology and Transfusion MedicineVenusberg-Campus 153105BonnGermany
| | - Alexander Heckel
- Goethe University FrankfurtInstitute for Organic Chemistry and Chemical BiologyMax-von-Laue Str. 960438Frankfurt am MainGermany
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10
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Pérez de Carvasal K, Riccardi C, Russo Krauss I, Cavasso D, Vasseur JJ, Smietana M, Morvan F, Montesarchio D. Charge-Transfer Interactions Stabilize G-Quadruplex-Forming Thrombin Binding Aptamers and Can Improve Their Anticoagulant Activity. Int J Mol Sci 2021; 22:9510. [PMID: 34502432 PMCID: PMC8430690 DOI: 10.3390/ijms22179510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 02/07/2023] Open
Abstract
In the search for optimized thrombin binding aptamers (TBAs), we herein describe the synthesis of a library of TBA analogues obtained by end-functionalization with the electron-rich 1,5-dialkoxy naphthalene (DAN) and the electron-deficient 1,8,4,5-naphthalenetetra-carboxylic diimide (NDI) moieties. Indeed, when these G-rich oligonucleotides were folded into the peculiar TBA G-quadruplex (G4) structure, effective donor-acceptor charge transfer interactions between the DAN and NDI residues attached to the extremities of the sequence were induced, providing pseudo-cyclic structures. Alternatively, insertion of NDI groups at both extremities produced TBA analogues stabilized by π-π stacking interactions. All the doubly-modified TBAs were characterized by different biophysical techniques and compared with the analogues carrying only the DAN or NDI residue and unmodified TBA. These modified TBAs exhibited higher nuclease resistance, and their G4 structures were markedly stabilized, as evidenced by increased Tm values compared to TBA. These favorable properties were also associated with improved anticoagulant activity for one DAN/NDI-modified TBA, and for one NDI/NDI-modified TBA. Our results indicated that TBA pseudo-cyclic structuring by ad hoc designed end-functionalization represents an efficient approach to improve the aptamer features, while pre-organizing and stabilizing the G4 structure but allowing sufficient flexibility to the aptamer folding, which is necessary for optimal thrombin recognition.
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Affiliation(s)
- Kévan Pérez de Carvasal
- Institut des Biomolécules Max Mousseron, University Montpellier, CNRS, ENSCM, 34095 Montpellier, France; (K.P.d.C.); (J.-J.V.); (M.S.)
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy; (C.R.); (I.R.K.); (D.C.)
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy; (C.R.); (I.R.K.); (D.C.)
- CSGI—Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Domenico Cavasso
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy; (C.R.); (I.R.K.); (D.C.)
- CSGI—Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, University Montpellier, CNRS, ENSCM, 34095 Montpellier, France; (K.P.d.C.); (J.-J.V.); (M.S.)
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, University Montpellier, CNRS, ENSCM, 34095 Montpellier, France; (K.P.d.C.); (J.-J.V.); (M.S.)
| | - François Morvan
- Institut des Biomolécules Max Mousseron, University Montpellier, CNRS, ENSCM, 34095 Montpellier, France; (K.P.d.C.); (J.-J.V.); (M.S.)
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy; (C.R.); (I.R.K.); (D.C.)
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11
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Müller P, Sahlbach M, Gasper S, Mayer G, Müller J, Pötzsch B, Heckel A. Controlling Coagulation in Blood with Red Light. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Patricia Müller
- Goethe University Frankfurt Institute for Organic Chemistry and Chemical Biology Max-von-Laue Str. 9 60438 Frankfurt am Main Germany
| | - Marlen Sahlbach
- Goethe University Frankfurt Institute for Organic Chemistry and Chemical Biology Max-von-Laue Str. 9 60438 Frankfurt am Main Germany
| | - Simone Gasper
- University Hospital Bonn Institute of Experimental Hematology and Transfusion Medicine Venusberg-Campus 1 53105 Bonn Germany
| | - Günter Mayer
- University of Bonn Life and Medical Sciences Institute Center of Aptamer Research & Development Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Jens Müller
- University Hospital Bonn Institute of Experimental Hematology and Transfusion Medicine Venusberg-Campus 1 53105 Bonn Germany
| | - Bernd Pötzsch
- University Hospital Bonn Institute of Experimental Hematology and Transfusion Medicine Venusberg-Campus 1 53105 Bonn Germany
| | - Alexander Heckel
- Goethe University Frankfurt Institute for Organic Chemistry and Chemical Biology Max-von-Laue Str. 9 60438 Frankfurt am Main Germany
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12
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Structural and functional analysis of the simultaneous binding of two duplex/quadruplex aptamers to human α-thrombin. Int J Biol Macromol 2021; 181:858-867. [PMID: 33864869 DOI: 10.1016/j.ijbiomac.2021.04.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/23/2022]
Abstract
The long-range communication between the two exosites of human α-thrombin (thrombin) tightly modulates the protein-effector interactions. Duplex/quadruplex aptamers represent an emerging class of very effective binders of thrombin. Among them, NU172 and HD22 aptamers are at the forefront of exosite I and II recognition, respectively. The present study investigates the simultaneous binding of these two aptamers by combining a structural and dynamics approach. The crystal structure of the ternary complex formed by the thrombin with NU172 and HD22_27mer provides a detailed view of the simultaneous binding of these aptamers to the protein, inspiring the design of novel bivalent thrombin inhibitors. The crystal structure represents the starting model for molecular dynamics studies, which point out the cooperation between the binding at the two exosites. In particular, the binding of an aptamer to its exosite reduces the intrinsic flexibility of the other exosite, that preferentially assumes conformations similar to those observed in the bound state, suggesting a predisposition to interact with the other aptamer. This behaviour is reflected in a significant increase of the anticoagulant activity of NU172 when the inactive HD22_27mer is bound to exosite II, providing a clear evidence of the synergic action of the two aptamers.
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13
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Riccardi C, Napolitano E, Platella C, Musumeci D, Montesarchio D. G-quadruplex-based aptamers targeting human thrombin: Discovery, chemical modifications and antithrombotic effects. Pharmacol Ther 2020; 217:107649. [PMID: 32777331 DOI: 10.1016/j.pharmthera.2020.107649] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
First studies on thrombin-inhibiting DNA aptamers were reported in 1992, and since then a large number of anticoagulant aptamers has been discovered. TBA - also named HD1, a 15-mer G-quadruplex (G4)-forming oligonucleotide - is the best characterized thrombin binding aptamer, able to specifically recognize the protein exosite I, thus inhibiting the conversion of soluble fibrinogen into insoluble fibrin strands. Unmodified nucleic acid-based aptamers, in general, and TBA in particular, exhibit limited pharmacokinetic properties and are rapidly degraded in vivo by nucleases. In order to improve the biological performance of aptamers, a widely investigated strategy is the introduction of chemical modifications in their backbone at the level of the nucleobases, sugar moieties or phosphodiester linkages. Besides TBA, also other thrombin binding aptamers, able to adopt a well-defined G4 structure, e.g. mixed duplex/quadruplex sequences, as well as homo- and hetero-bivalent constructs, have been identified and optimized. Considering the growing need of new efficient anticoagulant agents associated with the strong therapeutic potential of these thrombin inhibitors, the research on thrombin binding aptamers is still a very hot and intriguing field. Herein, we comprehensively described the state-of-the-art knowledge on the DNA-based aptamers targeting thrombin, especially focusing on the optimized analogues obtained by chemically modifying the oligonucleotide backbone, and their biological performances in therapeutic applications.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Department of Advanced Medical and Surgical Sciences, 2(nd) Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy.
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
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14
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Application of Piezo-Based Measuring System for Evaluation of Nucleic Acid-Based Drugs Influencing the Coagulation. SENSORS 2019; 20:s20010152. [PMID: 31881749 PMCID: PMC6982813 DOI: 10.3390/s20010152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/15/2019] [Accepted: 12/21/2019] [Indexed: 11/16/2022]
Abstract
During open-heart surgery, the status of hemostasis has to be constantly monitored to quickly and reliably detect bleeding or coagulation disorders. In this study, a novel optimized piezo-based measuring system (PIEZ) for rheological monitoring of hemostasis was established. The applicability of the PIEZ for the evaluation of nucleic acid-based drugs influencing coagulation was analyzed. Thrombin aptamers such as NU172 might be used during extracorporeal circulation (ECC) in combination with a reduced heparin concentration or for patients with heparin-induced thrombocytopenia (HIT). Therefore, the effect of the coagulation inhibiting thrombin aptamer NU172 and the abrogation by its complementary antidote sequence (AD) were investigated by this rheological PIEZ system. After the addition of different NU172 concentrations, the coagulation of fresh human blood was analyzed under static conditions and using an in vitro rotation model under dynamic conditions (simulating ECC). The clotting times (CTs) detected by PIEZ were compared to those obtained with a medical reference device, a ball coagulometer. Additionally, after the circulation of blood samples for 30 min at 37 °C, blood cell numbers, thrombin markers (thrombin-antithrombin III (TAT) and fibrinopeptide A (FPA)) and a platelet activation marker (β-thromboglobulin (β-TG)) were analyzed by enzyme-linked immunosorbent assays (ELISAs). The increase of NU172 concentration resulted in prolonged CTs, which were comparable between the reference ball coagulometer and the PIEZ, demonstrating the reliability of the new measuring system. Moreover, by looking at the slope of the linear regression of the viscous and elastic components, PIEZ also could provide information on the kinetics of the coagulation reaction. The shear viscosity at the end of the measurements (after 300 s) was indicative of clot firmness. Furthermore, the PIEZ was able to detect the abrogation of coagulation inhibition after the equimolar addition of NU172 aptamer´s AD. The obtained results showed that the established PIEZ is capable to dynamically measure the hemostasis status in whole blood and can be applied to analyze nucleic acid-based drugs influencing the coagulation.
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15
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Roxo C, Kotkowiak W, Pasternak A. G-Quadruplex-Forming Aptamers-Characteristics, Applications, and Perspectives. Molecules 2019; 24:E3781. [PMID: 31640176 PMCID: PMC6832456 DOI: 10.3390/molecules24203781] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes constitute a unique class of nucleic acid structures formed by G-rich oligonucleotides of DNA- or RNA-type. Depending on their chemical nature, loops length, and localization in the sequence or structure molecularity, G-quadruplexes are highly polymorphic structures showing various folding topologies. They may be formed in the human genome where they are believed to play a pivotal role in the regulation of multiple biological processes such as replication, transcription, and translation. Thus, natural G-quadruplex structures became prospective targets for disease treatment. The fast development of systematic evolution of ligands by exponential enrichment (SELEX) technologies provided a number of G-rich aptamers revealing the potential of G-quadruplex structures as a promising molecular tool targeted toward various biologically important ligands. Because of their high stability, increased cellular uptake, ease of chemical modification, minor production costs, and convenient storage, G-rich aptamers became interesting therapeutic and diagnostic alternatives to antibodies. In this review, we describe the recent advances in the development of G-quadruplex based aptamers by focusing on the therapeutic and diagnostic potential of this exceptional class of nucleic acid structures.
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Affiliation(s)
- Carolina Roxo
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Weronika Kotkowiak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Anna Pasternak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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16
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Troisi R, Napolitano V, Spiridonova V, Russo Krauss I, Sica F. Several structural motifs cooperate in determining the highly effective anti-thrombin activity of NU172 aptamer. Nucleic Acids Res 2019; 46:12177-12185. [PMID: 30357392 PMCID: PMC6294562 DOI: 10.1093/nar/gky990] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/09/2018] [Indexed: 12/22/2022] Open
Abstract
Despite aptamers are very promising alternative to antibodies, very few of them are under clinical trials or are used as drugs. Among them, NU172 is currently in Phase II as anticoagulant in heart disease treatments. It inhibits thrombin activity much more effectively than TBA, the best-known thrombin binding aptamer. The crystal structure of thrombin-NU172 complex reveals a bimodular duplex/quadruplex architecture for the aptamer, which binds thrombin exosite I through a highly complementary surface involving all three loops of the G-quadruplex module. Although the duplex domain does not interact directly with thrombin, the features of the duplex/quadruplex junction and the solution data on two newly designed NU172 mutants indicate that the duplex moiety is important for the optimization of the protein-ligand interaction and for the inhibition of the enzyme activity. Our work discloses the structural features determining the inhibition of thrombin by NU172 and put the basis for the design of mutants with improved properties.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples 'Federico II', Naples 80126, Italy
| | - Valeria Napolitano
- Department of Chemical Sciences, University of Naples 'Federico II', Naples 80126, Italy
| | - Vera Spiridonova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples 'Federico II', Naples 80126, Italy.,CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Sesto Fiorentino, FI 50019, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples 'Federico II', Naples 80126, Italy
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17
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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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Roloff A, Carlini AS, Callmann CE, Gianneschi NC. Micellar Thrombin-Binding Aptamers: Reversible Nanoscale Anticoagulants. J Am Chem Soc 2017; 139:16442-16445. [PMID: 29135251 DOI: 10.1021/jacs.7b07799] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aptamers are nucleic acid-based ligands that exhibit promising features including specific and reversible target binding and inhibition. Aptamers can function as anticoagulants if they are directed against enzymes of the coagulation cascade. However, they typically suffer from nucleolytic digestion and fast clearance from the bloodstream. We present thrombin-binding aptamer amphiphiles that self-assemble into nanoscale polymeric micelles with a densely functionalized aptamer-displaying corona. We show that these micellar aptamers retain their native secondary structure in a crowded environment and are stabilized against degradation by nucleases in human serum. Moreover, they are effective inhibitors of human plasma clotting in vitro. The inhibitory effect can be rapidly reversed by complementary nucleic acids that break the aptamers' secondary structure upon hybridization. Compared to free aptamers, the increased molecular weight and size of the overall assembly promotes extended blood circulation times in vivo.
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Affiliation(s)
| | | | | | - Nathan C Gianneschi
- Department of Chemistry, Materials Science and Engineering, Biomedical Engineering, Northwestern University , Evanston, Illinois 60208, United States
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20
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Gómez-Outes A, García-Fuentes M, Suárez-Gea ML. Discovery methods of coagulation-inhibiting drugs. Expert Opin Drug Discov 2017; 12:1195-1205. [DOI: 10.1080/17460441.2017.1384811] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Antonio Gómez-Outes
- Division of Pharmacology and Clinical Drug Evaluation, Medicines for Human Use, Spanish Agency for Medicines and Medical Devices (AEMPS), Madrid, Spain
| | - Minerva García-Fuentes
- Division of Pharmacology and Clinical Drug Evaluation, Medicines for Human Use, Spanish Agency for Medicines and Medical Devices (AEMPS), Madrid, Spain
| | - Mª Luisa Suárez-Gea
- Division of Pharmacology and Clinical Drug Evaluation, Medicines for Human Use, Spanish Agency for Medicines and Medical Devices (AEMPS), Madrid, Spain
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21
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Stoll H, Steinle H, Wilhelm N, Hann L, Kunnakattu SJ, Narita M, Schlensak C, Wendel HP, Avci-Adali M. Rapid Complexation of Aptamers by Their Specific Antidotes. Molecules 2017; 22:molecules22060954. [PMID: 28594360 PMCID: PMC6152687 DOI: 10.3390/molecules22060954] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/04/2017] [Accepted: 06/05/2017] [Indexed: 11/06/2022] Open
Abstract
Nucleic acid ligands, aptamers, harbor the unique characteristics of small molecules and antibodies. The specificity and high affinity of aptamers enable their binding to different targets, such as small molecules, proteins, or cells. Chemical modifications of aptamers allow increased bioavailability. A further great benefit of aptamers is the antidote (AD)-mediated controllability of their effect. In this study, the AD-mediated complexation and neutralization of the thrombin binding aptamer NU172 and Toll-like receptor 9 (TLR9) binding R10-60 aptamer were determined. Thereby, the required time for the generation of aptamer/AD-complexes was analyzed at 37 °C in human serum using gel electrophoresis. Afterwards, the blocking of aptamers’ effects was analyzed by determining the activated clotting time (ACT) in the case of the NU172 aptamer, or the expression of immune activation related genes IFN-1β, IL-6, CXCL-10, and IL-1β in the case of the R10-60 aptamer. Gel electrophoresis analyses demonstrated the rapid complexation of the NU172 and R10-60 aptamers by complementary AD binding after just 2 min of incubation in human serum. A rapid neutralization of anticoagulant activity of NU172 was also demonstrated in fresh human whole blood 5 min after addition of AD. Furthermore, the TLR9-mediated activation of PMDC05 cells was interrupted after the addition of the R10-60 AD. Using these two different aptamers, the rapid antagonizability of the aptamers was demonstrated in different environments; whole blood containing numerous proteins, cells, and different small molecules, serum, or cell culture media. Thus, nucleic acid ADs are promising molecules, which offer several possibilities for different in vivo applications, such as antagonizing aptamer-based drugs, immobilization, or delivery of oligonucleotides to defined locations.
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Affiliation(s)
- Heidi Stoll
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, 72076 Tuebingen, Germany.
| | - Heidrun Steinle
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, 72076 Tuebingen, Germany.
| | - Nadja Wilhelm
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, 72076 Tuebingen, Germany.
| | - Ludmilla Hann
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, 72076 Tuebingen, Germany.
| | - Silju-John Kunnakattu
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, 72076 Tuebingen, Germany.
| | - Miwako Narita
- Laboratory of Hematology and Oncology, Graduate School of Health Sciences, Niigata University, Niigata 951-8518, Japan.
| | - Christian Schlensak
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, 72076 Tuebingen, Germany.
| | - Hans P Wendel
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, 72076 Tuebingen, Germany.
| | - Meltem Avci-Adali
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, 72076 Tuebingen, Germany.
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22
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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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23
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Rangnekar A, Nash JA, Goodfred B, Yingling YG, LaBean TH. Design of Potent and Controllable Anticoagulants Using DNA Aptamers and Nanostructures. Molecules 2016; 21:molecules21020202. [PMID: 26861277 PMCID: PMC6273181 DOI: 10.3390/molecules21020202] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/03/2016] [Indexed: 11/16/2022] Open
Abstract
The regulation of thrombin activity offers an opportunity to regulate blood clotting because of the central role played by this molecule in the coagulation cascade. Thrombin-binding DNA aptamers have been used to inhibit thrombin activity. In the past, to address the low efficacy reported for these aptamers during clinical trials, multiple aptamers have been linked using DNA nanostructures. Here, we modify that strategy by linking multiple copies of various thrombin-binding aptamers using DNA weave tiles. The resulting constructs have very high anticoagulant activity in functional assays owing to their improved cooperative binding affinity to thrombin due to optimized spacing, orientation, and the high local concentration of aptamers. We also report the results of molecular dynamics simulations to gain insight into the solution conformations of the tiles. Moreover, by using DNA strand displacement, we were able to turn the coagulation cascade off and on as desired, thereby enabling significantly better control over blood coagulation.
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Affiliation(s)
- Abhijit Rangnekar
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, NC 27695, USA.
| | - Jessica A Nash
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, NC 27695, USA.
| | - Bethany Goodfred
- Department of Molecular and Structural Biochemistry, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC 27695, USA.
| | - Yaroslava G Yingling
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, NC 27695, USA.
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, NC 27695, USA.
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24
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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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26
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Abstract
Coagulation and anticoagulation system is kept in balance by the orchestrated action of a variety of biological factors, and the disruption of this balance leads to the risk of hemorrhage or thrombosis. Oligonucleotide aptamers are single-stranded DNA (ssDNA) or RNA ligands that are synthesized in vitro and bind to target molecules through dimensional structure with high specificity and affinity, and thus represent attractive candidates for the development of agents to maintain the balance of coagulation and anticoagulation. In this review, we summarize recent progress in aptamer-based application in the modulation of coagulation. The aptamers with specific chemical and biological characteristics have great potential to be explored as agents for the treatment of blood coagulation abnormalities.
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McConnell EM, Holahan MR, DeRosa MC. Aptamers as promising molecular recognition elements for diagnostics and therapeutics in the central nervous system. Nucleic Acid Ther 2015; 24:388-404. [PMID: 25296265 DOI: 10.1089/nat.2014.0492] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Oligonucleotide aptamers are short, synthetic, single-stranded DNA or RNA able to recognize and bind to a multitude of targets ranging from small molecules to cells. Aptamers have emerged as valuable tools for fundamental research, clinical diagnosis, and therapy. Due to their small size, strong target affinity, lack of immunogenicity, and ease of chemical modification, aptamers are an attractive alternative to other molecular recognition elements, such as antibodies. Although it is a challenging environment, the central nervous system and related molecular targets present an exciting potential area for aptamer research. Aptamers hold promise for targeted drug delivery, diagnostics, and therapeutics. Here we review recent advances in aptamer research for neurotransmitter and neurotoxin targets, demyelinating disease and spinal cord injury, cerebrovascular disorders, pathologies related to protein aggregation (Alzheimer's, Parkinson's, and prions), brain cancer (glioblastomas and gliomas), and regulation of receptor function. Challenges and limitations posed by the blood brain barrier are described. Future perspectives for the application of aptamers to the central nervous system are also discussed.
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Affiliation(s)
- Erin M McConnell
- 1 Department of Chemistry, Carleton University , Ottawa, Ontario, Canada
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Savchik EY, Kalinina TB, Drozd NN, Makarov VA, Zav'yalova EG, Lapsheva EN, Mudrik NN, Babij AV, Pavlova GV, Golovin AV, Kopylov AM. Aptamer RA36 inhibits of human, rabbit, and rat plasma coagulation activated with thrombin or snake venom coagulases. Bull Exp Biol Med 2014; 156:44-8. [PMID: 24319726 DOI: 10.1007/s10517-013-2274-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
RA36 DNA aptamer is a direct anticoagulant prolonging clotting time of human, rabbit, and rat plasma in the thrombin time test. Anticoagulant activity of RA36 is lower than that of recombinant hirudin. During inhibition of human plasma clotting activated with echitox (coagulase from Echis multisquamatus venom), the aptamer presumably binds to meisothrombin exosite I. The sensitivity of human plasma to the aptamer 5-fold surpasses that of rat plasma. Analysis of RA36 binding to coagulase of Agkistrodon halys venom (ancistron) is required for proving the effect of aptamer on polymerization of human fibrinogen.
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Affiliation(s)
- E Yu Savchik
- Hematology Research Center, Ministry of Health and Social Development of the Russian Federation; APTO-PHARM, Moscow Region; Chemical Faculty, Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University; Institute of Gene Biology, Russian Academy of Sciences, Moscow.
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Rohrbach F, Schäfer F, Fichte MAH, Pfeiffer F, Müller J, Pötzsch B, Heckel A, Mayer G. Aptamerbasiertes Caging zur selektiven Maskierung von Proteindomänen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Rohrbach F, Schäfer F, Fichte MAH, Pfeiffer F, Müller J, Pötzsch B, Heckel A, Mayer G. Aptamer-guided caging for selective masking of protein domains. Angew Chem Int Ed Engl 2013; 52:11912-5. [PMID: 24127310 DOI: 10.1002/anie.201306686] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/30/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Falk Rohrbach
- Life and Medical Sciences Institute, Gerhard Domagk-Strasse 1, 53121 Bonn (Germany) http://www.mayerlab.de
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Banerjee J, Nilsen-Hamilton M. Aptamers: multifunctional molecules for biomedical research. J Mol Med (Berl) 2013; 91:1333-42. [PMID: 24045702 DOI: 10.1007/s00109-013-1085-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 08/14/2013] [Accepted: 09/04/2013] [Indexed: 12/28/2022]
Abstract
Aptamers are single-stranded oligonucleotides that fold into well-defined three-dimensional shapes, allowing them to bind their targets with high affinity and specificity. They can be generated through an in vitro process called "Systemic Evolution of Ligands by Exponential Enrichment" and applied for specific detection, inhibition, and characterization of various targets like small organic and inorganic molecules, proteins, and whole cells. Aptamers have also been called chemical antibodies because of their synthetic origin and their similar modes of action to antibodies. They exhibit significant advantages over antibodies in terms of their small size, synthetic accessibility, and ability to be chemically modified and thus endowed with new properties. The first generation of aptamer drug "Macugen" was available for public use within 25 years of the discovery of aptamers. With others in the pipeline for clinical trials, this emerging field of medical biotechnology is raising significant interest. However, aptamers pose different problems for their development than for antibodies that need to be addressed to achieve practical applications. It is likely that current developments in aptamer engineering will be the basis for the evolution of improved future bioanalytical and biomedical applications. The present review discusses the development of aptamers for therapeutics, drug delivery, target validation and imaging, and reviews some of the challenges to fully realizing the promise of aptamers in biomedical applications.
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Affiliation(s)
- Jayeeta Banerjee
- Biology Department, Indian Institute of Science Education and Research (IISER), 900 NCL Innovation Park, Dr. Homi Bhabha Road, Pune, 411008, India,
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Synthesis, characterization and in vitro activity of thrombin-binding DNA aptamers with triazole internucleotide linkages. Eur J Med Chem 2013; 67:90-7. [PMID: 23850569 DOI: 10.1016/j.ejmech.2013.06.034] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 06/11/2013] [Accepted: 06/14/2013] [Indexed: 11/23/2022]
Abstract
A series of DNA aptamers bearing triazole internucleotide linkages that bind to thrombin was synthesized. The novel aptamers are structurally analogous to the well-known thrombin-inhibiting G-quadruplexes TBA15 and TBA31. The secondary structure stability, binding affinity for thrombin and anticoagulant effects of the triazole-modified aptamers were measured. A modification in the central loop of the aptamer quadruplex resulted in increased nuclease resistance and an inhibition efficiency similar to that of TBA15. The likely aptamer-thrombin binding mode was determined by molecular dynamics simulations. Due to their relatively high activity and the increased resistance to nuclease digestion imparted by the triazole internucleotide linkages, the novel aptamers are a promising alternative to known DNA-based anticoagulant agents.
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Rohrbach F, Fatthalla MI, Kupper T, Pötzsch B, Müller J, Petersen M, Pedersen EB, Mayer G. Chemical maturation of a bivalent aptamer by single domain variation. Chembiochem 2012; 13:631-4. [PMID: 22331608 DOI: 10.1002/cbic.201200015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/1932] [Indexed: 01/28/2023]
Affiliation(s)
- Falk Rohrbach
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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