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Berzal-Herranz A, Romero-López C. Aptamers' Potential to Fill Therapeutic and Diagnostic Gaps. Pharmaceuticals (Basel) 2024; 17:105. [PMID: 38256938 PMCID: PMC10818422 DOI: 10.3390/ph17010105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
More than 30 years ago, in 1990, three independent research groups published several papers demonstrating that genetics could be performed in vitro in the absence of living organisms or cells [...].
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Affiliation(s)
- Alfredo Berzal-Herranz
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas. PTS Granada, Av. del Conocimiento 17, 18016 Granada, Spain
| | - Cristina Romero-López
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas. PTS Granada, Av. del Conocimiento 17, 18016 Granada, Spain
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2
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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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Troisi R, Balasco N, Autiero I, Sica F, Vitagliano L. New insight into the traditional model of the coagulation cascade and its regulation: illustrated review of a three-dimensional view. Res Pract Thromb Haemost 2023; 7:102160. [PMID: 37727847 PMCID: PMC10506138 DOI: 10.1016/j.rpth.2023.102160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 09/21/2023] Open
Abstract
The coagulation process relies on an intricate network of three-dimensional structural interactions and subtle biological regulations. In the present review, we illustrate the state of the art of the structural biology of the coagulation cascade by surveying the Protein Data Bank and the EBI AlphaFold databases. Investigations performed in the last decade have provided structural information on essentially all players involved in the process. Indeed, the initial characterization of specific and rather canonical domains has been progressively extended to complicated multidomain proteins. Recently, the application of cryogenic electron microscopy techniques has unraveled the structural features of highly complex coagulation factors, which has led to enhanced understanding. This review initially focuses on the structure of the individual factors as a function of their involvement in intrinsic, extrinsic, and common pathways. A specific emphasis is given to what is known or unknown on the structural basis of each step of the cascade. Available data providing clues on the structural recognition of the factors involved in the functional partnerships of the pathways are illustrated. Recent structures of important complexes formed by these proteins with regulators are described, focusing on the drugs used as anticoagulants and on their reversal agents. Finally, we highlight the different roles that innovative biomolecules such as aptamers may have in the regulation of the cascade.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Naples, Italy
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Department of Chemistry, University of Rome Sapienza, Rome, Italy
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant’Angelo, Naples, Italy
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Santostasi G, Denas G, Pengo V. New pharmacotherapeutic options for oral anticoagulant treatment in atrial fibrillation patients aged 65 and older: factor XIa inhibitors and beyond. Expert Opin Pharmacother 2023; 24:1335-1347. [PMID: 37243619 DOI: 10.1080/14656566.2023.2219391] [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: 03/15/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 05/29/2023]
Abstract
INTRODUCTION Although much progress has been made using anticoagulation for stroke prevention in patients with non-valvular atrial fibrillation, bleeding is still a major concern. AREAS COVERED This article reviews current pharmacotherapeutic options in this setting. Particular emphasis is placed on the ability of the new molecules to minimize the bleeding risk in elderly patients. A systematic search of PubMed, Web of Science, and the Cochrane Library up to March 2023 was carried out. EXPERT OPINION Contact phase of coagulation is a possible new target for anticoagulant therapy. Indeed, congenital or acquired deficiency of contact phase factors is associated with reduced thrombotic burden and limited risk of spontaneous bleeding. These new drugs seem particularly suitable for stroke prevention in elderly patients with non-valvular atrial fibrillation in whom the hemorrhagic risk is high. Most of anti Factor XI (FXI) drugs are for parenteral use only. A group of small molecules are for oral use and therefore are candidates to substitute direct oral anticoagulants (DOACs) for stroke prevention in elderly patients with atrial fibrillation. Doubts remain on the possibility of impaired hemostasis. Indeed, a fine calibration of inhibition of contact phase factors is crucial for an effective and safe treatment.
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Affiliation(s)
| | - Gentian Denas
- Cardiology Clinic, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Padua University Hospital, Padua, Italy
| | - Vittorio Pengo
- Cardiology Clinic, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Padua University Hospital, Padua, Italy
- Arianna Foundation on Anticoagulation, Bologna, Italy
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5
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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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6
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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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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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8
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Ozer I, Pitoc GA, Layzer JM, Moreno A, Olson LB, Layzer KD, Hucknall AM, Sullenger BA, Chilkoti A. PEG-Like Brush Polymer Conjugate of RNA Aptamer That Shows Reversible Anticoagulant Activity and Minimal Immune Response. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2107852. [PMID: 34994037 DOI: 10.1002/adma.202107852] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Ribonucleic acid (RNA) therapeutics are an emerging class of drugs. RNA aptamers are of significant therapeutic and clinical interest because their activity can be easily reversed in vivo-a useful feature that is difficult to achieve using other therapeutic modalities. Despite their therapeutic promise, RNA aptamers are limited by their poor blood circulation. The attachment of polyethylene glycol (PEG) to RNA aptamers addresses this limitation. However, an RNA aptamer-PEG conjugate that is a reversible anticoagulant fails in a clinical trial due to the reactivity of the conjugate with pre-existing PEG antibodies and has cast a pall over PEGylation of aptamers and other biologics, despite its long history of utility in drug delivery. Here, PEG antibody-reactivity of this RNA aptamer is eliminated by conjugating it to a next-generation PEG-like brush polymer-poly[(oligoethylene glycol) methyl ether methacrylate)] (POEGMA). The conjugate retained the drug's therapeutic action and the ability to be easily reversed. Importantly, this conjugate does not bind pre-existing PEG antibodies that are prevalent in humans and does not induce a humoral immune response against the polymer itself in mice. These findings suggest a path to rescuing the PEGylation of RNA therapeutics and vaccines from the deleterious side-effects of PEG.
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Affiliation(s)
- Imran Ozer
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - George A Pitoc
- Department of Surgery, Duke University Medical Center, Durham, NC, 27707, USA
| | - Juliana M Layzer
- Department of Surgery, Duke University Medical Center, Durham, NC, 27707, USA
- Duke Clinical and Translational Science Institute, Durham, NC, 27707, USA
| | - Angelo Moreno
- Department of Surgery, Duke University Medical Center, Durham, NC, 27707, USA
| | - Lyra B Olson
- Department of Surgery, Duke University Medical Center, Durham, NC, 27707, USA
| | - Kyle D Layzer
- Department of Surgery, Duke University Medical Center, Durham, NC, 27707, USA
| | - Angus M Hucknall
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Bruce A Sullenger
- Department of Surgery, Duke University Medical Center, Durham, NC, 27707, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
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Soule EE, Yu H, Olson L, Naqvi I, Kumar S, Krishnaswamy S, Sullenger BA. Generation of an anticoagulant aptamer that targets factor V/Va and disrupts the FVa-membrane interaction in normal and COVID-19 patient samples. Cell Chem Biol 2022; 29:215-225.e5. [PMID: 35114109 PMCID: PMC8808741 DOI: 10.1016/j.chembiol.2022.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/11/2021] [Accepted: 01/11/2022] [Indexed: 11/29/2022]
Abstract
Coagulation cofactors profoundly regulate hemostasis and are appealing targets for anticoagulants. However, targeting such proteins has been challenging because they lack an active site. To address this, we isolate an RNA aptamer termed T18.3 that binds to both factor V (FV) and FVa with nanomolar affinity and demonstrates clinically relevant anticoagulant activity in both plasma and whole blood. The aptamer also shows synergy with low molecular weight heparin and delivers potent anticoagulation in plasma collected from patients with coronavirus disease 2019 (COVID-19). Moreover, the aptamer's anticoagulant activity can be rapidly and efficiently reversed using protamine sulfate, which potentially allows fine-tuning of aptamer's activity post-administration. We further show that the aptamer achieves its anticoagulant activity by abrogating FV/FVa interactions with phospholipid membranes. Our success in generating an anticoagulant aptamer targeting FV/Va demonstrates the feasibility of using cofactor-binding aptamers as therapeutic protein inhibitors and reveals an unconventional working mechanism of an aptamer by interrupting protein-membrane interactions.
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Affiliation(s)
- Erin E. Soule
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC 27710, USA,Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Haixiang Yu
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Lyra Olson
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC 27710, USA,Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Ibtehaj Naqvi
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Shekhar Kumar
- The Children’s Hospital of Philadelphia, Division of Hematology, Department of Pediatrics, The University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sriram Krishnaswamy
- The Children’s Hospital of Philadelphia, Division of Hematology, Department of Pediatrics, The University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Bruce A. Sullenger
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC 27710, USA,Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA,Corresponding author
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10
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Serumula W, Fernandez G, Gonzalez VM, Parboosing R. Anti-HIV Aptamers: Challenges and Prospects. Curr HIV Res 2022; 20:7-19. [PMID: 34503417 DOI: 10.2174/1570162x19666210908114825] [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: 02/19/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
Human Immunodeficiency Virus (HIV) infection continues to be a significant health burden in many countries around the world. Current HIV treatment through a combination of different antiretroviral drugs (cART) effectively suppresses viral replication, but drug resistance and crossresistance are significant challenges. This has prompted the search for novel targets and agents, such as nucleic acid aptamers. Nucleic acid aptamers are oligonucleotides that attach to the target sites with high affinity and specificity. This review provides a target-by-target account of research into anti-HIV aptamers and summarises the challenges and prospects of this therapeutic strategy, specifically in the unique context of HIV infection.
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Affiliation(s)
- William Serumula
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, c/o Inkosi Albert Luthuli Central Hospital, 5th Floor Laboratory Building, 800 Bellair Road, Mayville, Durban 4091, South Africa
| | - Geronimo Fernandez
- Departamento de Bioquímica-Investigación, Aptus Biotech SL, Avda. Cardenal Herrera Oria, 298-28035 Madrid. Spain
| | - Victor M Gonzalez
- Departamento de Bioquímica-Investigación, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)-Hospital Ramón y Cajal, 28034 Madrid, Spain
| | - Raveen Parboosing
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, c/o Inkosi Albert Luthuli Central Hospital, 5th Floor Laboratory Building, 800 Bellair Road, Mayville, Durban 4091, South Africa
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11
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Krissanaprasit A, Key CM, Pontula S, LaBean TH. Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers. Chem Rev 2021; 121:13797-13868. [PMID: 34157230 DOI: 10.1021/acs.chemrev.0c01332] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carson M Key
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Sahil Pontula
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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12
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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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13
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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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14
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Krissanaprasit A, Key CM, Froehlich K, Pontula S, Mihalko E, Dupont DM, Andersen ES, Kjems J, Brown AC, LaBean TH. Multivalent Aptamer-Functionalized Single-Strand RNA Origami as Effective, Target-Specific Anticoagulants with Corresponding Reversal Agents. Adv Healthc Mater 2021; 10:e2001826. [PMID: 33882195 DOI: 10.1002/adhm.202001826] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/23/2021] [Indexed: 12/15/2022]
Abstract
Anticoagulants are commonly utilized during surgeries and to treat thrombotic diseases like stroke and deep vein thrombosis. However, conventional anticoagulants have serious side-effects, narrow therapeutic windows, and lack safe reversal agents (antidotes). Here, an alternative RNA origami displaying RNA aptamers as target-specific anticoagulant is described. Improved design and construction techniques for self-folding, single-molecule RNA origami as a platform for displaying pre-selected RNA aptamers with precise orientational and spatial control are reported. Nuclease resistance is added using 2'-fluoro-modified pyrimidines during in vitro transcription. When four aptamers are displayed on the RNA origami platform, the measured thrombin inhibition and anticoagulation activity is higher than observed for free aptamers, ssRNA-linked RNA aptamers, and RNA origami displaying fewer aptamers. Importantly, thrombin inhibition is immediately switched off by addition of specific reversal agents. Results for single-stranded DNA (ssDNA) and single-stranded peptide nucleic acid (PNA) antidotes show restoration of 63% and 95% coagulation activity, respectively. To demonstrate potential for practical, long-term storage for clinical use, RNA origami is freeze-dried, and stored at room temperature. Freshly produced and freeze-dried RNA show identical levels of activity in coagulation assays. Compared to current commercial intravenous anticoagulants, RNA origami-based molecules show promise as safer alternatives with rapid activity switching for future therapeutic applications.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering College of Engineering North Carolina State University Raleigh NC 27695 USA
| | - Carson M. Key
- Department of Materials Science and Engineering College of Engineering North Carolina State University Raleigh NC 27695 USA
| | - Kristen Froehlich
- Joint Department of Biomedical Engineering College of Engineering North Carolina State University and University of North Carolina – Chapel Hill Raleigh NC 27695 USA
| | | | - Emily Mihalko
- Joint Department of Biomedical Engineering College of Engineering North Carolina State University and University of North Carolina – Chapel Hill Raleigh NC 27695 USA
| | - Daniel M. Dupont
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Aarhus C Aarhus 8000 Denmark
| | - Ebbe S. Andersen
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Aarhus C Aarhus 8000 Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Aarhus C Aarhus 8000 Denmark
| | - Ashley C. Brown
- Joint Department of Biomedical Engineering College of Engineering North Carolina State University and University of North Carolina – Chapel Hill Raleigh NC 27695 USA
- Comparative Medicine Institute North Carolina State University and University of North Carolina – Chapel Hill Raleigh NC 27695 USA
| | - Thomas H. LaBean
- Department of Materials Science and Engineering College of Engineering North Carolina State University Raleigh NC 27695 USA
- Comparative Medicine Institute North Carolina State University and University of North Carolina – Chapel Hill Raleigh NC 27695 USA
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15
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Hu J, Hodgkinson CP, Pratt RE, Lee J, Sullenger BA, Dzau VJ. Enhancing cardiac reprogramming via synthetic RNA oligonucleotides. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 23:55-62. [PMID: 33335792 PMCID: PMC7723775 DOI: 10.1016/j.omtn.2020.10.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 10/21/2020] [Indexed: 11/08/2022]
Abstract
Reprogramming scar fibroblasts into new heart muscle cells has the potential to restore function to the injured heart. However, the effectiveness of reprogramming is notably low. We have recently demonstrated that the effectiveness of reprogramming fibroblasts into heart muscle cells (cardiomyocytes) is increased by the addition of RNA-sensing receptor ligands. Clinical use of these ligands is problematic due to their ability to induce adverse inflammatory events. To overcome this issue, we sought to determine whether synthetic analogs of natural RNA-sensing receptor ligands, which avoid generating inflammatory insults and are nuclease resistant, would similarly enhance fibroblast reprogramming into cardiomyocytes. Indeed, one such stabilized RNA, ICR2, increased the expression of cardiomyocyte-specific mRNAs in reprogrammed fibroblasts. Moreover, ICR2 enhanced the ability of reprogramming factors to produce cardiomyocytes with mature sarcomeres. Knockdown assays indicated that the effects of ICR2 were mediated by the RNA-sensing receptors Rig-I and TLR3. In addition, ICR2 reduced the effective dose and number of reprogramming factors needed for efficient reprogramming. In summary, the synthetic RNA oligonucleotide ICR2 is a potential therapeutic agent to enhance cardiac reprogramming efficiency.
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Affiliation(s)
- Jiabiao Hu
- Mandel Center for Heart and Vascular Research, and the Duke Cardiovascular Research Center, Duke University Medical Center, Durham, NC 27710, USA
| | - Conrad P Hodgkinson
- Mandel Center for Heart and Vascular Research, and the Duke Cardiovascular Research Center, Duke University Medical Center, Durham, NC 27710, USA
| | - Richard E Pratt
- Mandel Center for Heart and Vascular Research, and the Duke Cardiovascular Research Center, Duke University Medical Center, Durham, NC 27710, USA
| | - JaeWoo Lee
- Department of Surgery, Duke University, Durham, NC 27710, USA
| | | | - Victor J Dzau
- Mandel Center for Heart and Vascular Research, and the Duke Cardiovascular Research Center, Duke University Medical Center, Durham, NC 27710, USA
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16
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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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17
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Shao Q, Chen T, Sheng K, Liu Z, Zhang Z, Romesberg FE. Selection of Aptamers with Large Hydrophobic 2'-Substituents. J Am Chem Soc 2020; 142:2125-2128. [PMID: 31961667 DOI: 10.1021/jacs.9b10538] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Previously, we evolved a DNA polymerase, SFM4-3, for the recognition of substrates modified at their 2' positions with a fluoro, O-methyl, or azido substituent. Here we use SFM4-3 to synthesize 2'-azido-modified DNA; we then use the azido group to attach different, large hydrophobic groups via click chemistry. We show that SFM4-3 recognizes the modified templates under standard conditions, producing natural DNA and thereby allowing amplification. To demonstrate the utility of this remarkable property, we use SFM4-3 to select aptamers with large hydrophobic 2' substituents that bind human neutrophil elastase or the blood coagulation protein factor IXa. The results indicate that SFM4-3 should facilitate the discovery of aptamers that adopt novel and perhaps more protein-like folds with hydrophobic cores that in turn allow them to access novel activities.
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Affiliation(s)
- Qian Shao
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Tingjian Chen
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Kai Sheng
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Zhixia Liu
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Zhuochen Zhang
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Floyd E Romesberg
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
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18
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Al-Horani RA. Factor XI(a) inhibitors for thrombosis: an updated patent review (2016-present). Expert Opin Ther Pat 2019; 30:39-55. [PMID: 31847619 DOI: 10.1080/13543776.2020.1705783] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: Anticoagulation without bleeding is an ideal goal in treating thrombosis, however, this goal has not been achieved. All current anticoagulants are associated with significant bleeding which limits their safe use. Genetic and pharmacological findings indicate that factor XIa is a key player in thrombosis, yet it is a relatively marginal one in hemostasis. Thus, factor XIa and its zymogen offer a unique opportunity to develop anticoagulants with low bleeding risk.Areas covered: A survey of patent literature has retrieved more than 50 patents on the discovery of novel therapeutics targeting factor XI(a) since 2016. Small molecules, monoclonal antibodies, oligonucleotides, and polypeptides have been developed to inhibit factor XI(a). Many inhibitors are in early development and few have been evaluated in clinical trials.Expert opinion: Factor XI(a) is being actively pursued as a drug target for the development of effective and safer anticoagulants. Although many patents claiming factor XI(a) inhibitors were filed prior to 2016, recent literature reveals a moderately declining trend. Nevertheless, more agents have entered different levels of clinical trials. These agents exploit diverse mechanistic strategies for inhibition. Although further development is warranted, reaching one or more of these agents to the clinic will transform the anticoagulation therapy.
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Affiliation(s)
- Rami A Al-Horani
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, USA
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19
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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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20
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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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21
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Alieva RR, Zavyalova EG, Tashlitsky VN, Kopylov AM. Quantitative characterization of oligomeric state of G-quadruplex antithrombin aptamers by size exclusion HPLC. MENDELEEV COMMUNICATIONS 2019. [DOI: 10.1016/j.mencom.2019.07.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
PURPOSE OF REVIEW Since the selection of the first thrombin-binding aptamer in 1992, the use of nucleic acid aptamers to target specific coagulation factors has emerged as a valuable approach for generating novel anticoagulant and procoagulant therapeutics. Herein, we highlight the most recent discoveries involving application of aptamers for those purposes. RECENT FINDINGS Learning from the successes and pitfalls of the FIXa-targeting aptamer pegnivacogin in preclinical and clinical studies, the latest efforts to develop antidote-controllable anticoagulation strategies for cardiopulmonary bypass that avoid unfractionated heparin involve potentiation of the exosite-binding factor X (FX)a aptamer 11F7t by combination with either a small molecule FXa catalytic site inhibitor or a thrombin aptamer. Recent work has also focused on identifying aptamer inhibitors of contact pathway factors such as FXIa and kallikrein, which may prove to be well tolerated and effective antithrombotic agents in certain clinical settings. Finally, new approaches to develop procoagulant aptamers to control bleeding associated with hemophilia and other coagulopathies involve targeting activated protein C and tissue plasminogen activator. SUMMARY Overall, these recent findings exemplify the versatility of aptamers to modulate a variety of procoagulant and anticoagulant factors, along with their capacity to be used complementarily with other aptamers or drugs for wide-ranging applications.
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23
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Putative Mechanisms Underlying High Inhibitory Activities of Bimodular DNA Aptamers to Thrombin. Biomolecules 2019; 9:biom9020041. [PMID: 30682825 PMCID: PMC6406280 DOI: 10.3390/biom9020041] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 01/10/2023] Open
Abstract
Nucleic acid aptamers are prospective molecular recognizing elements. Similar to antibodies, aptamers are capable of providing specific recognition due to their spatial structure. However, the apparent simplicity of oligonucleotide folding is often elusive, as there is a balance between several conformations and, in some cases, oligomeric structures. This research is focused on establishing a thermodynamic background and the conformational heterogeneity of aptamers taking a series of thrombin DNA aptamers having G-quadruplex and duplex modules as an example. A series of aptamers with similar modular structures was characterized with spectroscopic and chromatographic techniques, providing examples of the conformational homogeneity of aptamers with high inhibitory activity, as well as a mixture of monomeric and oligomeric species for aptamers with low inhibitory activity. Thermodynamic parameters for aptamer unfolding were calculated, and their correlation with aptamer functional activity was found. Detailed analysis of thrombin complexes with G-quadruplex aptamers bound to exosite I revealed the similarity of the interfaces of aptamers with drastically different affinities to thrombin. It could be suggested that there are some events during complex formation that have a larger impact on the affinity than the states of initial and final macromolecules. Possible mechanisms of the complex formation and a role of the duplex module in the association process are discussed.
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24
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Bruno JG. Potential Inherent Stimulation of the Innate Immune System by Nucleic Acid Aptamers and Possible Corrective Approaches. Pharmaceuticals (Basel) 2018; 11:ph11030062. [PMID: 29937498 PMCID: PMC6161019 DOI: 10.3390/ph11030062] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 01/25/2023] Open
Abstract
It is well known that unmethylated 2′-deoxycytidine-phosphate-2′-guanine (CpG) sequences alone or in longer DNA and RNA oligonucleotides can act like pathogen-associated molecular patterns (PAMPs) and trigger the innate immune response leading to deleterious cytokine production via Toll-like receptors (TLRs). Clearly, such CpG or CpG-containing sequences in aptamers intended for therapy could present very damaging side effects to patients. Previous antisense oligonucleotide developers were faced with the same basic CpG dilemma and devised not only avoidance, but other effective strategies from which current aptamer developers can learn to ameliorate or eliminate damaging CpG effects. These strategies include obvious methylation of cytosines in the aptamer structure, as long as it does not affect aptamer binding in vivo, truncation of the aptamer to its essential binding site, backbone modifications, co-administration of antagonistic or suppressive oligonucleotides, or other novel drugs under development to lessen the toxic CpG effect on innate immunity.
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Affiliation(s)
- John G Bruno
- Operational Technologies Corporation, 4100 NW Loop 410, Suite 100, San Antonio, TX 78229, USA.
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25
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Bala J, Chinnapaiyan S, Dutta RK, Unwalla H. Aptamers in HIV research diagnosis and therapy. RNA Biol 2018; 15:327-337. [PMID: 29431588 PMCID: PMC5927724 DOI: 10.1080/15476286.2017.1414131] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/07/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022] Open
Abstract
Aptamers are high affinity single-stranded nucleic acid or protein ligands which exhibit specificity and avidity comparable to, or exceeding that of antibodies and can be generated against most targets. The functionality of aptamers is based on their unique tertiary structure, complexity and their ability to attain unique binding pockets by folding. Aptamers are selected in vitro by a process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). The Kd values for the selected aptamer are often in the picomolar to low nanomolar range. Stable and nontoxic aptamers could be selected for a wide range of ligands including small molecules to large proteins. Aptamers have shown tremendous potential and have found multipurpose application in the field of therapeutic, diagnostic, biosensor and bio-imaging. While their mechanism of action can be similar to that of monoclonal antibodies, aptamers provide additional advantages in terms of production cost, simpler regulatory approval and lower immunogenicity as they are synthesized chemically. Human immunodeficiency virus (HIV) is the primary cause of acquired immune deficiency syndrome (AIDS), which causes significant morbidity and mortality with a significant consequent decrease in the quality of patient's lives. While cART has led to good viral control, people living with HIV now suffer from non-HIV comorbidities due to viral protein expression that cannot be controlled by cART. Hence pathophysiological mechanisms that govern these comorbidities with a focus on therapies that neutralize these HIV effects gained increased attention. Recent advances in HIV/AIDS research have identified several molecular targets and for the development of therapeutic and diagnostic using aptamers against HIV/AIDS. This review presents recent advances in aptamers technology for potential application in HIV diagnostics and therapeutics towards improving the quality of life of people living with HIV.
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Affiliation(s)
- Jyoti Bala
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Srinivasan Chinnapaiyan
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Rajib Kumar Dutta
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Hoshang Unwalla
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
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Kotkowiak W, Lisowiec-Wachnicka J, Grynda J, Kierzek R, Wengel J, Pasternak A. Thermodynamic, Anticoagulant, and Antiproliferative Properties of Thrombin Binding Aptamer Containing Novel UNA Derivative. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 10:304-316. [PMID: 29499943 PMCID: PMC5862132 DOI: 10.1016/j.omtn.2017.12.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 12/25/2022]
Abstract
Thrombin is a serine protease that plays a crucial role in hemostasis, fibrinolysis, cell proliferation, and migration. Thrombin binding aptamer (TBA) is able to inhibit the activity of thrombin molecule via binding to its exosite I. This 15-nt DNA oligonucleotide forms an intramolecular, antiparallel G-quadruplex structure with a chair-like conformation. In this paper, we report on our investigations on the influence of certain modified nucleotide residues on thermodynamic stability, folding topology, and biological properties of TBA variants. In particular, the effect of single incorporation of a novel 4-thiouracil derivative of unlocked nucleic acid (UNA), as well as single incorporation of 4-thiouridine and all four canonical UNAs, was evaluated. The studies presented herein have shown that 4-thiouridine in RNA and UNA series, as well as all four canonical UNAs, can efficiently modulate G-quadruplex thermodynamic and biological stability, and that the effect is strongly position dependent. Interestingly, TBA variants containing the modified nucleotide residues are characterized by unchanged folding topology. Thrombin time assay revealed that incorporation of certain UNA residues may improve G-quadruplex anticoagulant properties. Noteworthy, some TBA variants, characterized by decreased ability to inhibit thrombin activity, possess significant antiproliferative properties reducing the viability of the HeLa cell line even by 95% at 10 μM concentration.
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Affiliation(s)
- Weronika Kotkowiak
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Jolanta Lisowiec-Wachnicka
- Department of Nucleic Acids Bioengineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jakub Grynda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gabriela Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Ryszard Kierzek
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Jesper Wengel
- Department of Physics, Chemistry and Pharmacy, Biomolecular Nanoscale Engineering Center, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - 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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27
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Zavyalova E, Samoylenkova N, Revishchin A, Turashev A, Gordeychuk I, Golovin A, Kopylov A, Pavlova G. The Evaluation of Pharmacodynamics and Pharmacokinetics of Anti-thrombin DNA Aptamer RA-36. Front Pharmacol 2017; 8:922. [PMID: 29311929 PMCID: PMC5735248 DOI: 10.3389/fphar.2017.00922] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/05/2017] [Indexed: 11/13/2022] Open
Abstract
Anticoagulants are a vital class of drugs, which are applied for short-term surgical procedures, and for long-term treatments for thrombosis prevention in high risk groups. Several anticoagulant drugs are commercially available, but all have intrinsic disadvantages, e.g., bleeding risks, as well as specific ones, e.g., immune response to peptide/protein drugs. Therefore, the search for novel, efficient and safe anticoagulants is essential. Nucleic acid aptamers are an emerging class of contemporary pharmaceuticals which are fully biocompatible and biodegradable; they have low toxicity, and are as efficient as many protein-based drugs. The anti-thrombin DNA aptamer RA-36 has been created using a combination of rational design and molecular dynamics, showing several extra-features over existing aptamers. Aptamer RA-36 has a bimodular structure; the first G-quadruplex binds and inhibits thrombin, whereas the second G-quadruplex varies the properties of the first. This bimodular structure provides a favorable dose-effect dependence allowing the risk of bleeding to be potentially decreased. Here, the results of efficiency trials of the aptamer are presented. The aptamer RA-36 has a distinctive species specificity; therefore, the careful selection of experimental animals was required. The anticoagulant activity was characterized in rats and monkeys in vivo. Antithrombotic activity was evaluated in the live murine model of the induced thrombosis. Pharmacokinetics was estimated by tracking radionuclide labeled aptamer in rats. The aptamer was thoroughly characterized using bivalirudin as a reference drug. Despite the different profiles of anticoagulant activity, these two compounds could refer to each other, and the corresponding doses could be estimated. Bivalirudin turned out to have 10-fold higher anticoagulant and antithrombotic activity. The difference in activity is easy to explain due to the pharmacokinetic profiles of the substances: the aptamer RA-36 has 20-fold faster elimination from blood with a half-life of 1 min. The entire dataset revealed that the non-modified DNA aptamer could be an alternative to the currently used bivalent peptide inhibitor; the dosage profile could be improved by manipulating aptamer pharmacokinetics. The study has revealed aptamer RA-36 to be one of the most promising candidates for further development as a new generation of anticoagulants.
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Affiliation(s)
- Elena Zavyalova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Apto-Pharm Ltd., Moscow, Russia
| | - Nadezhda Samoylenkova
- Apto-Pharm Ltd., Moscow, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Ilya Gordeychuk
- Chumakov Federal Scientific Center for Research and Development of Immune-and- Biological Products (RAS), Moscow, Russia.,I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Andrey Golovin
- Apto-Pharm Ltd., Moscow, Russia.,Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Kopylov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Apto-Pharm Ltd., Moscow, Russia
| | - Galina Pavlova
- Apto-Pharm Ltd., Moscow, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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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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Lamba V, Yabukarski F, Herschlag D. An Activator-Blocker Pair Provides a Controllable On-Off Switch for a Ketosteroid Isomerase Active Site Mutant. J Am Chem Soc 2017; 139:11089-11095. [PMID: 28719738 DOI: 10.1021/jacs.7b03547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Control of enzyme activity is fundamental to biology and represents a long-term goal in bioengineering and precision therapeutics. While several powerful molecular strategies have been developed, limitations remain in their generalizability and dynamic range. We demonstrate a control mechanism via separate small molecules that turn on the enzyme (activator) and turn off the activation (blocker). We show that a pocket created near the active site base of the enzyme ketosteriod isomerase (KSI) allows efficient and saturable base rescue when the enzyme's natural general base is removed. Binding a small molecule with similar properties but lacking general-base capability in this pocket shuts off rescue. The ability of small molecules to directly participate in and directly block catalysis may afford a broad controllable dynamic range. This approach may be amenable to numerous enzymes and to engineering and screening approaches to identify activators and blockers with strong, specific binding for engineering and therapeutic applications.
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Affiliation(s)
- Vandana Lamba
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Filip Yabukarski
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Daniel Herschlag
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
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Abstract
Aptamers are nucleic acids referred to as chemical antibodies as they bind to their specific targets with high affinity and selectivity. They are selected via an iterative process known as ‘selective evolution of ligands by exponential enrichment’ (SELEX). Aptamers have been developed against numerous cancer targets and among them, many tumor cell-membrane protein biomarkers. The identification of aptamers targeting cell-surface proteins has mainly been performed by two different strategies: protein- and cell-based SELEX, when the targets used for selection were proteins and cells, respectively. This review aims to update the literature on aptamers targeting tumor cell surface protein biomarkers, highlighting potentials, pitfalls of protein- and cell-based selection processes and applications of such selected molecules. Aptamers as promising agents for diagnosis and therapeutic approaches in oncology are documented, as well as aptamers in clinical development.
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Woodruff RS, Ivanov I, Verhamme IM, Sun MF, Gailani D, Sullenger BA. Generation and characterization of aptamers targeting factor XIa. Thromb Res 2017. [PMID: 28644959 DOI: 10.1016/j.thromres.2017.06.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND The plasma protease factor XIa (FXIa) has become a target of interest for therapeutics designed to prevent or treat thrombotic disorders. METHODS We used a solution-based, directed evolution approach called systematic evolution of ligands by exponential enrichment (SELEX) to isolate RNA aptamers that target the FXIa catalytic domain. RESULTS Two aptamers, designated 11.16 and 12.7, were identified that bound to previously identified anion binding and serpin bindings sites on the FXIa catalytic domain. The aptamers were non-competitive inhibitors of FXIa cleavage of a tripeptide chromogenic substrate and of FXIa activation of factor IX. In normal human plasma, aptamer 12.7 significantly prolonged the aPTT clotting time. CONCLUSIONS The results show that novel inhibitors of FXIa can be prepared using SELEX techniques. RNA aptamers can bind to distinct sites on the FXIa catalytic domain and noncompetitively inhibit FXIa activity toward its primary macromolecular substrate factor IX with different levels of potency. Such compounds can be developed for use as therapeutic inhibitors.
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Affiliation(s)
- R S Woodruff
- Department of Surgery, Duke University Medical Center, Durham, NC, United States; University Program in Genetics and Genomics, Duke University, Durham, NC, United States
| | - I Ivanov
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - I M Verhamme
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - M-F Sun
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - D Gailani
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - B A Sullenger
- Department of Surgery, Duke University Medical Center, Durham, NC, United States.
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Wheeler AP, Gailani D. The Intrinsic Pathway of Coagulation as a Target for Antithrombotic Therapy. Hematol Oncol Clin North Am 2017; 30:1099-114. [PMID: 27637310 DOI: 10.1016/j.hoc.2016.05.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Plasma coagulation in the activated partial thromboplastin time assay is initiated by sequential activation of coagulation factors XII, XI, and IX. While this series of proteolytic reactions is not an accurate model for hemostasis in vivo, there is mounting evidence that factor XI and factor XII contribute to thrombosis, and that inhibiting them can produce an antithrombotic effect with a small effect on hemostasis. This article discusses the contributions of components of the intrinsic pathway to thrombosis in animal models and humans, and results of early clinical trials of drugs targeting factors IX, XI, and XII.
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Affiliation(s)
- Allison P Wheeler
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, C-3321A Medical Center North, 1161 21st Avenue, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University, 397 Preston Research Building, 2220 Pierce Ave, Nashville, TN 37232, USA.
| | - David Gailani
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, C-3321A Medical Center North, 1161 21st Avenue, Nashville, TN 37232, USA; Hematology/Oncology Division, Department of Medicine, Vanderbilt University, 777 Preston Research Building, 2220 Pierce Avenue, Nashville, TN 37232, USA
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Evolution of Complex Target SELEX to Identify Aptamers against Mammalian Cell-Surface Antigens. Molecules 2017; 22:molecules22020215. [PMID: 28146093 PMCID: PMC5572134 DOI: 10.3390/molecules22020215] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/24/2017] [Indexed: 01/10/2023] Open
Abstract
The demand has increased for sophisticated molecular tools with improved detection limits. Such molecules should be simple in structure, yet stable enough for clinical applications. Nucleic acid aptamers (NAAs) represent a class of molecules able to meet this demand. In particular, aptamers, a class of small nucleic acid ligands that are composed of single-stranded modified/unmodified RNA/DNA molecules, can be evolved from a complex library using Systematic Evolution of Ligands by EXponential enrichment (SELEX) against almost any molecule. Since its introduction in 1990, in stages, SELEX technology has itself undergone several modifications, improving selection and broadening the repertoire of targets. This review summarizes these milestones that have pushed the field forward, allowing researchers to generate aptamers that can potentially be applied as therapeutic and diagnostic agents.
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Chu H, Kohane DS, Langer R. RNA therapeutics - The potential treatment for myocardial infarction. Regen Ther 2016; 4:83-91. [PMID: 31245491 PMCID: PMC6581817 DOI: 10.1016/j.reth.2016.03.002] [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: 11/06/2015] [Revised: 03/05/2016] [Accepted: 03/05/2016] [Indexed: 01/19/2023] Open
Abstract
RNA therapeutics mainly control gene expression at the transcript level. In contrast to conventional gene therapy which solely increases production of a protein, delivered RNAs can enhance, reduce or abolish synthesis of a particular protein, which control its relevant activities in a more diverse fashion. Thus, they hold promise to treat many human diseases including myocardial infarction (MI). MI is a serious health burden that causes substantial morbidity and mortality. An unmet clinical need for treating MI is the recovery of cardiac function, which requires regeneration of the functional tissues including the vasculature, nerves, and myocardium. Several classes of RNA therapeutics have been investigated in preclinical MI models, and the results have demonstrated their benefits and encourage their future development. In this review, we summarize the common RNA therapeutic approaches and highlight their application in MI therapy.
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Affiliation(s)
- Hunghao Chu
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Daniel S. Kohane
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115, United States
| | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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Patel KA, Sethi R, Dhara AR, Roy I. Challenges with osmolytes as inhibitors of protein aggregation: Can nucleic acid aptamers provide an answer? Int J Biol Macromol 2016; 100:75-88. [PMID: 27156694 DOI: 10.1016/j.ijbiomac.2016.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 02/07/2023]
Abstract
Protein aggregation follows some common motifs. Whether in the formation of inclusion bodies in heterologous overexpression systems or inclusions in protein conformational diseases, or aggregation during storage or transport of protein formulations, aggregates form cross beta-sheet structures and stain with amyloidophilic dyes like Thioflavin T and Congo Red, irrespective of the concerned protein. Traditionally, osmolytes are used to stabilize proteins against stress conditions. They are employed right from protein expression, through production and purification, to formulation and administration. As osmolytes interact with the solvent, the differential effect of the stress condition on the solvent mostly determines the effect of the osmolyte on protein stability. Nucleic acid aptamers, on the other hand, are highly specific for their targets. When selected against monomeric, natively folded proteins, they bind to them with very high affinity. This binding inhibits the unfolding of the protein and/or monomer-monomer interaction which are the initial common steps of protein aggregation. Thus, by changing the approach to a protein-centric model, aptamers are able to function as universal stabilizers of proteins. The review discusses cases where osmolytes were unable to provide stabilization to proteins against different stress conditions, a gap which the aptamers seem to be able to fill.
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Affiliation(s)
- Kinjal A Patel
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ratnika Sethi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Anita R Dhara
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India.
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36
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Pre-existing anti-polyethylene glycol antibody linked to first-exposure allergic reactions to pegnivacogin, a PEGylated RNA aptamer. J Allergy Clin Immunol 2015; 137:1610-1613.e7. [PMID: 26688515 PMCID: PMC5819876 DOI: 10.1016/j.jaci.2015.10.034] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/22/2015] [Accepted: 10/12/2015] [Indexed: 12/25/2022]
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