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Wang B, Kobeissy F, Golpich M, Cai G, Li X, Abedi R, Haskins W, Tan W, Benner SA, Wang KKW. Aptamer Technologies in Neuroscience, Neuro-Diagnostics and Neuro-Medicine Development. Molecules 2024; 29:1124. [PMID: 38474636 DOI: 10.3390/molecules29051124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Aptamers developed using in vitro Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology are single-stranded nucleic acids 10-100 nucleotides in length. Their targets, often with specificity and high affinity, range from ions and small molecules to proteins and other biological molecules as well as larger systems, including cells, tissues, and animals. Aptamers often rival conventional antibodies with improved performance, due to aptamers' unique biophysical and biochemical properties, including small size, synthetic accessibility, facile modification, low production cost, and low immunogenicity. Therefore, there is sustained interest in engineering and adapting aptamers for many applications, including diagnostics and therapeutics. Recently, aptamers have shown promise as early diagnostic biomarkers and in precision medicine for neurodegenerative and neurological diseases. Here, we critically review neuro-targeting aptamers and their potential applications in neuroscience research, neuro-diagnostics, and neuro-medicine. We also discuss challenges that must be overcome, including delivery across the blood-brain barrier, increased affinity, and improved in vivo stability and in vivo pharmacokinetic properties.
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Affiliation(s)
- Bang Wang
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
- The Foundation for Applied Molecular Evolution, 1501 NW 68th Terrace, Gainesville, FL 32605, USA
| | - Firas Kobeissy
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
- Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, 1601 SW Archer Road, Gainesville, FL 32608, USA
- Center for Visual and Neurocognitive Rehabilitation (CVNR), Atlanta VA Health Care System, 1670 Clairmont Rd, Decatur, GA 30033, USA
| | - Mojtaba Golpich
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Guangzheng Cai
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Xiaowei Li
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Reem Abedi
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107-2020, Lebanon
| | - William Haskins
- Gryphon Bio, Inc., 611 Gateway Blvd. Suite 120 #253, South San Francisco, CA 94080, USA
| | - Weihong Tan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou 310022, China
| | - Steven A Benner
- The Foundation for Applied Molecular Evolution, 1501 NW 68th Terrace, Gainesville, FL 32605, USA
| | - Kevin K W Wang
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
- Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, 1601 SW Archer Road, Gainesville, FL 32608, USA
- Center for Visual and Neurocognitive Rehabilitation (CVNR), Atlanta VA Health Care System, 1670 Clairmont Rd, Decatur, GA 30033, USA
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2
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Di Mauro V, Lauta FC, Modica J, Appleton SL, De Franciscis V, Catalucci D. Diagnostic and Therapeutic Aptamers: A Promising Pathway to Improved Cardiovascular Disease Management. JACC Basic Transl Sci 2024; 9:260-277. [PMID: 38510714 PMCID: PMC10950404 DOI: 10.1016/j.jacbts.2023.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/29/2023] [Indexed: 03/22/2024]
Abstract
Despite advances in care, cardiovascular diseases remain the leading cause of death worldwide. As a result, identifying suitable biomarkers for early diagnosis and improving therapeutic and diagnostic strategies is crucial. Because of their significant advantages over other therapeutic approaches, nucleic-based therapies, particularly aptamers, are gaining increased attention. Aptamers are innovative synthetic polymers or oligomers of single-stranded DNA (ssDNA) or RNA molecules that can form 3-dimensional structures and thus interact with their targets with high specificity and affinity. Furthermore, they outperform classical protein-based antibodies in terms of in vitro selection, production, ease of modification and conjugation, high stability, low immunogenicity, and suitability for nanoparticle functionalization for targeted drug delivery. This work aims to review the advances made in the aptamers' field in biomarker detection, diagnosis, imaging, and targeted therapy, which highlight their huge potential in the management of cardiovascular diseases.
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Affiliation(s)
- Vittoria Di Mauro
- Veneto Institute of Molecular Medicine, Padua, Italy
- Institute of Genetic and Biomedical Research, Milan, Milan Italy
- Humanitas Cardio Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Jessica Modica
- Institute of Genetic and Biomedical Research, Milan, Milan Italy
- Humanitas Cardio Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Silvia Lucia Appleton
- Institute of Genetic and Biomedical Research, Milan, Milan Italy
- Humanitas Cardio Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Daniele Catalucci
- Institute of Genetic and Biomedical Research, Milan, Milan Italy
- Humanitas Cardio Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
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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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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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Aptamers Regulating the Hemostasis System. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238593. [PMID: 36500686 PMCID: PMC9739204 DOI: 10.3390/molecules27238593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
The hemostasis system is a complex structure that includes the fibrinolysis system, and Yes this is correct coagulation and anticoagulation parts. Due to the multicomponent nature, it becomes relevant to study the key changes in the functioning of signaling pathways, and develop new diagnostic methods and modern drugs with high selectivity. One of the ways to solve this problem is the development of molecular recognition elements capable of blocking one of the hemostasis systems and/or activating another. Aptamers can serve as ligands for targeting specific clinical needs, promising anticoagulants with minor side effects and significant biological activity. Aptamers with several clotting factors and platelet proteins are used for the treatment of thrombosis. This review is focused on the aptamers used for the correction of the hemostasis system, and their structural and functional features. G-rich nucleic acid aptamers, mostly versatile G-quadruplexes, recognize different components of the hemostasis system and are capable of correcting the functioning.
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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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Yoshitomi T, Wakui K, Miyakawa M, Yoshimoto K. Design strategy of antidote sequence for bivalent aptamer: Rapid neutralization of high-anticoagulant thrombin-binding bivalent DNA aptamer-linked M08 with HD22. Res Pract Thromb Haemost 2021; 5:e12503. [PMID: 34136744 PMCID: PMC8178692 DOI: 10.1002/rth2.12503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/09/2020] [Accepted: 12/19/2020] [Indexed: 11/10/2022] Open
Abstract
Background Bivalent thrombin-binding aptamers (TBAs) have great potential for the treatment of thrombosis because they exhibit high anticoagulant activity, and their complementary single-stranded DNA (ssDNA) sequences work as an antidote. However, a design strategy for antidote sequences against bivalent aptamers has not been established. Objectives To develop bivalent TBAs using M08, which exhibits higher anticoagulant activity than the previously reported exosite Ⅰ-binding DNA aptamers, such as HD1, an exosite Ⅱ-binding DNA aptamer (HD22) was linked to M08 with various types of linkers. In addition, short-length complementary ssDNAs were designed to neutralize the optimized bivalent aptamer effectively and rapidly. Results Among the bivalent aptamers of M08 linked to HD22 with various types of linkers, M08-T15-HD22 possessed approximately 5-fold higher anticoagulant activity than previously reported bivalent aptamers. To neutralize the activity of the 87-meric M08-T15-HD22, complementary ssDNA sequences with different lengths and hybridization segments were designed. The complementary sequence against the M08 moiety played a more important role in neutralizing than that against the HD22 moiety. Hybridization of the T15 linker in the M08-T15-HD22 with the A15 sequence in the antidote accelerated neutralization due to toehold-mediated strand displacement. Interestingly, some shorter-length antidotes showed higher neutralizing activity than the full complementary 87-meric antidote, and the shortest, 34-meric antidote, neutralized most effectively. Conclusions A pair comprising an 87-meric bivalent TBA containing M08 and a 34-meric short-length antidote with high anticoagulant and rapid neutralizing activities was developed. This design strategy of the DNA sequence can be used for other bivalent DNA aptamers and their antidotes.
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Affiliation(s)
- Toru Yoshitomi
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Tokyo Japan.,Research Center for Functional Materials National Institute for Materials Science Ibaraki Japan
| | - Koji Wakui
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Tokyo Japan
| | - Masato Miyakawa
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Tokyo Japan
| | - Keitaro Yoshimoto
- Department of Life Sciences Graduate School of Arts and Sciences The University of Tokyo Tokyo Japan.,JST PRESTO Tokyo Japan
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Overview of the Therapeutic Potential of Aptamers Targeting Coagulation Factors. Int J Mol Sci 2021; 22:ijms22083897. [PMID: 33918821 PMCID: PMC8069679 DOI: 10.3390/ijms22083897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 12/11/2022] Open
Abstract
Aptamers are single-stranded DNA or RNA sequences that bind target molecules with high specificity and affinity. Aptamers exhibit several notable advantages over protein-based therapeutics. Aptamers are non-immunogenic, easier to synthesize and modify, and can bind targets with greater affinity. Due to these benefits, aptamers are considered a promising therapeutic candidate to treat various conditions, including hematological disorders and cancer. An active area of research involves developing aptamers to target blood coagulation factors. These aptamers have the potential to treat cardiovascular diseases, blood disorders, and cancers. Although no aptamers targeting blood coagulation factors have been approved for clinical use, several aptamers have been evaluated in clinical trials and many more have demonstrated encouraging preclinical results. This review summarized our knowledge of the aptamers targeting proteins involved in coagulation, anticoagulation, fibrinolysis, their extensive applications as therapeutics and diagnostics tools, and the challenges they face for advancing to clinical use.
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Koudrina A, McConnell EM, Zurakowski JA, Cron GO, Chen S, Tsai EC, DeRosa MC. Exploring the Unique Contrast Properties of Aptamer-Gadolinium Conjugates in Magnetic Resonance Imaging for Targeted Imaging of Thrombi. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9412-9424. [PMID: 33395250 DOI: 10.1021/acsami.0c16666] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Objective: An important clinical question in the determination of the extent of thrombosis-related vascular conditions is the identification of blood clot location. Fibrin is a major molecular constituent of blood clots and can, therefore, be utilized in molecular imaging. In this proof-of-concept study, we sought to prepare a fibrin-targeting magnetic resonance imaging contrast agent, using a Gd(III)-loaded fibrinogen aptamer (FA) chelate conjugate (Gd(III)-NOTA-FA) (NOTA = 1,4,7-triazacyclononane-1,4,7-triacetic acid), to endow the ability to specifically accumulate at the location of blood clots, thereby enhancing contrast capabilities. Methods: The binding affinity of FA for fibrin was confirmed by fluorescence microscopy and microscale thermophoresis. The preparation and effective loading of the chelate-aptamer conjugates were confirmed by mass spectrometry and a xylenol orange colorimetric test. Longitudinal and transverse relaxivities and the effects of target binding were assessed using T1- and T2-map sequences at 7 T. T1- and T2-weighted images were acquired after blood clots were treated with Gd(III)-NOTA-FA. Collagen was used as the protein control, while an unrelated aptamer sequence, FB139, was used as the aptamer control. Results: FA demonstrated a high affinity and selectivity toward the polymeric protein, with a Kd of 16.6 nM, confirming an avidity over fibrinogen. The longitudinal (r1) and transverse (r2) relaxivities of Gd(III)-NOTA-FA demonstrated that conjugation to the long aptamer strand shortened T1 relaxation times and increased T2 relaxation times (3.04 and 38.7 mM-1 s-1, respectively). These effects were amplified by binding to the fibrin target (1.73 and 46.5 mM-1 s-1, respectively). In vitro studies with thrombin-polymerized human blood (clots) in whole blood showed an unexpected enhancement of signal intensity (hyperintense) produced exclusively at the location of the clot during the T2-weighted scan, while the presence of fibrinogen within a whole blood pool resulted in T1 signal intensity enhancement throughout the pool. This is advantageous, as simply reversing the type of a scan from a typical T1-weighted to a T2-weighted would allow to selectively highlight the location of blood clots. Conclusions: Gd(III)-NOTA-FA can be used for molecular imaging of thrombi, through fibrin-targeted delivery of contrast to the location of blood clots in T2-weighted scans.
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Affiliation(s)
- Anna Koudrina
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Erin M McConnell
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street W, Hamilton, ON L8S 4L8, Canada
| | - Joseph A Zurakowski
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Greg O Cron
- The Ottawa Hospital, Ottawa, ON K1Y 4E9, Canada
- Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada
- Department of Radiology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Suzan Chen
- The Ottawa Hospital, Ottawa, ON K1Y 4E9, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada
| | - Eve C Tsai
- The Ottawa Hospital, Ottawa, ON K1Y 4E9, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada
| | - Maria C DeRosa
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
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Recent Progress and Opportunities for Nucleic Acid Aptamers. Life (Basel) 2021; 11:life11030193. [PMID: 33671039 PMCID: PMC7997341 DOI: 10.3390/life11030193] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/20/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
Coined three decades ago, the term aptamer and directed evolution have now reached their maturity. The concept that nucleic acid could modulate the activity of target protein as ligand emerged from basic science studies of viruses. Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding, which allow for therapeutic and diagnostic applications. Compared to traditional antibodies, aptamers have several advantages, including small size, flexible structure, good biocompatibility, and low immunogenicity. In vitro selection method is used to isolate aptamers that are specific for a desired target from a randomized oligonucleotide library. The first aptamer drug, Macugen, was approved by FDA in 2004, which was accompanied by many studies and clinical investigations on various targets and diseases. Despite much promise, most aptamers have failed to meet the requisite safety and efficacy standards in human clinical trials. Amid these setbacks, the emergence of novel technologies and recent advances in aptamer and systematic evolution of ligands by exponential enrichment (SELEX) design are fueling hope in this field. The unique properties of aptamer are gaining renewed interest in an era of COVID-19. The binding performance of an aptamer and reproducibility are still the key issues in tackling current hurdles in clinical translation. A thorough analysis of the aptamer binding under varying conditions and the conformational dynamics is warranted. Here, the challenges and opportunities of aptamers are reviewed with recent progress.
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Tran PHL, Xiang D, Nguyen TNG, Tran TTD, Chen Q, Yin W, Zhang Y, Kong L, Duan A, Chen K, Sun M, Li Y, Hou Y, Zhu Y, Ma Y, Jiang G, Duan W. Aptamer-guided extracellular vesicle theranostics in oncology. Theranostics 2020; 10:3849-3866. [PMID: 32226524 PMCID: PMC7086349 DOI: 10.7150/thno.39706] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/20/2019] [Indexed: 12/14/2022] Open
Abstract
In the past decade, the study of exosomes, nanosized vesicles (50-150 nm) released into the extracellular space via the fusion of multivesicular bodies with the plasma membrane, has burgeoned with impressive achievements in theranostics applications. These nanosized vesicles have emerged as key players in homeostasis and in the pathogenesis of diseases owing to the variety of the cargos they can carry, the nature of the molecules packaged inside the vesicles, and the robust interactions between exosomes and target cells or tissues. Accordingly, the development of exosome-based liquid biopsy techniques for early disease detection and for monitoring disease progression marks a new era of precision medicine in the 21st century. Moreover, exosomes possess intrinsic properties - a nanosized structure and unique "homing effects" - that make them outstanding drug delivery vehicles. In addition, targeted exosome-based drug delivery systems can be further optimized using active targeting ligands such as nucleic acid aptamers. Indeed, the aptamers themselves can function as therapeutic and/or diagnostic tools based on their attributes of unique target-binding and non-immunogenicity. This review aims to provide readers with a current picture of the research on exosomes and aptamers and their applications in cancer theranostics, highlighting recent advances in their transition from the bench to the clinic.
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Affiliation(s)
- Phuong H-L Tran
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Victoria, Australia
| | - Dongxi Xiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, 77 Avenue Louise Pasteur, Boston, MA 02115, USA
| | - Tuong N-G Nguyen
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Victoria, Australia
| | - Thao T-D Tran
- Department for Management of Science and Technology Development, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Qian Chen
- Translational Medical Center, The Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian District, Beijing, China, 100853
| | - Wang Yin
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Victoria, Australia
| | - Yumei Zhang
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Victoria, Australia
| | - Lingxue Kong
- Institute for Frontier Materials, Deakin University, Waurn Ponds, Victoria, 3216, Australia
| | - Andrew Duan
- School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, 27 Rainforest Walk, Clayton VIC 3800, Australia
| | - Kuisheng Chen
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, He'nan Key Laboratory of Tumor Pathology, Zhengzhou 450052, China
| | - Miomio Sun
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, He'nan Key Laboratory of Tumor Pathology, Zhengzhou 450052, China
| | - Yong Li
- Cancer Care Centre, St George Hospital, Kogarah, and St George and Sutherland Clinical School, University of New South Wales, Kensington, NSW, Australia
| | - Yingchun Hou
- Laboratory of Tumor Molecular and Cellular Biology, College of Life Sciences, Shaanxi Normal University, 620 West Chang'an Avenue, Xi'an, Shaanxi 710119, China
| | - Yimin Zhu
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Yongchao Ma
- Clinical School, Luohe Medical College, 148, Daxue Road, Luohe City, Henan Province, 462000, China
| | - Guoqin Jiang
- Department of General Surgery, Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, P.R. China, 215004
| | - Wei Duan
- School of Medicine and Centre for Molecular and Medical Research, Deakin University, Waurn Ponds, Victoria, Australia
- GenePharma-Deakin Joint Laboratory of Aptamer Medicine, Suzhou 215123, China and Waurn Ponds, Victoria 3216, Australia
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12
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Guan B, Zhang X. Aptamers as Versatile Ligands for Biomedical and Pharmaceutical Applications. Int J Nanomedicine 2020; 15:1059-1071. [PMID: 32110008 PMCID: PMC7035142 DOI: 10.2147/ijn.s237544] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/10/2020] [Indexed: 12/14/2022] Open
Abstract
Aptamers are a class of targeting ligands that bind exclusively to biomarkers of interest. Aptamers have been identified as candidates for the construction of various smart systems for therapy, diagnosis, bioimaging, and drug delivery due to their high target affinity and specificity. Aptamers are accounted as chemical antibodies that can be readily linked to drugs, sensors, signal enhancers, or nanocarriers for functionalization. Use of aptamer-guided medications, especially nanomedicines, has resulted in encouraging outcomes compared to those use of aptamer-free counterparts. This article reviews recent advances in the use of aptamers as targeting ligands for various biomedical and pharmaceutical purposes. Special interests focus on aptamer-based theranostics, biosensing, bioimaging, drug potentiation, and targeted drug delivery.
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Affiliation(s)
- Baozhang Guan
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou 510630, People's Republic of China
| | - Xingwang Zhang
- Department of Pharmaceutics, College of Pharmacy, Jinan University, Guangzhou 510632, People's Republic of China
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13
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Gray BP, Requena MD, Nichols MD, Sullenger BA. Aptamers as Reversible Sorting Ligands for Preparation of Cells in Their Native State. Cell Chem Biol 2019; 27:232-244.e7. [PMID: 31879266 DOI: 10.1016/j.chembiol.2019.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/01/2019] [Accepted: 12/05/2019] [Indexed: 12/13/2022]
Abstract
Although antibodies are routinely used to label and isolate a desired cell type from a more complex mixture of cells, via either fluorescence-activated cell sorting (FACS) or magnetic-activated cell sorting (MACS), such antibody labeling is not easily reversible. We describe an FACS and MACS compatible method to reversibly label and purify cells using aptamers. Magnetic beads loaded with the epidermal growth factor receptor (EGFR)-binding antagonistic aptamer E07 specifically isolated EGFR-expressing cells, and pure, label-free cells were recovered via treatment with an "antidote" oligonucleotide complementary to the aptamer. Additionally, while FACS sorting cells with E07 or EGFR antibody yielded EGFR(+) cells with impeded EGFR signaling, stripping off the aptamer via antidote treatment restored receptor function, returning cells to their native state, which was not possible with the antibody. The ability to reversibly label or isolate cells without compromising their function is a valuable, versatile tool with important implications for both the laboratory and clinic.
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Affiliation(s)
- Bethany Powell Gray
- Department of Surgery, Duke University Medical Center, 2 Genome Ct, Durham, NC 27710, USA
| | - Martin D Requena
- Department of Surgery, Duke University Medical Center, 2 Genome Ct, Durham, NC 27710, USA
| | - Michael D Nichols
- Department of Biomedical Engineering, Duke University, 101 Science Dr, Durham, NC 27710, USA
| | - Bruce A Sullenger
- Department of Surgery, Duke University Medical Center, 2 Genome Ct, Durham, NC 27710, USA; Department of Biomedical Engineering, Duke University, 101 Science Dr, Durham, NC 27710, USA.
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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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15
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Serrano CM, Freeman R, Godbe J, Lewis JA, Stupp SI. DNA-Peptide Amphiphile Nanofibers Enhance Aptamer Function. ACS APPLIED BIO MATERIALS 2019; 2:2955-2963. [PMID: 32999996 DOI: 10.1021/acsabm.9b00310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The single stranded DNA oligonucleotides known as aptamers have the capacity to bind proteins and other molecules and offer great therapeutic potential. Further work is required to optimize their function and to diminish their susceptibility to nuclease degradation. We report here on the synthesis and supramolecular self-assembly of DNA-peptide amphiphiles that form high aspect ratio nanofibers and display aptamers for platelet-derived growth factor. The nanofibers were found to bind the growth factor with an affinity that was fivefold greater than the free aptamer. We also observed that the aptamer displayed by the supramolecular nanostructures was eight times more nuclease resistant than free aptamer. In order to highlight the therapeutic potential of these supramolecular systems, we demonstrated the improved inhibition of proliferation when the growth factor was bound to aptamers displayed by the nanofibers.
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Affiliation(s)
- Christopher M Serrano
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, USA.,Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA
| | - Ronit Freeman
- Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA
| | - Jacqueline Godbe
- Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Jacob A Lewis
- Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA.,Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Samuel I Stupp
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, USA.,Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Chicago, Illinois 60611, USA.,Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA.,Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA.,Department of Medicine, Northwestern University, 676 North Saint Clair Street, Chicago, Illinois 60611, United States
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16
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Moreno A, Pitoc GA, Ganson NJ, Layzer JM, Hershfield MS, Tarantal AF, Sullenger BA. Anti-PEG Antibodies Inhibit the Anticoagulant Activity of PEGylated Aptamers. Cell Chem Biol 2019; 26:634-644.e3. [PMID: 30827937 PMCID: PMC6707742 DOI: 10.1016/j.chembiol.2019.02.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 12/17/2018] [Accepted: 01/31/2019] [Indexed: 02/06/2023]
Abstract
Biopharmaceuticals have become increasingly attractive therapeutic agents and are often PEGylated to enhance their pharmacokinetics and reduce their immunogenicity. However, recent human clinical trials have demonstrated that administration of PEGylated compounds can evoke anti-PEG antibodies. Considering the ubiquity of PEG in commercial products and the presence of pre-existing anti-PEG antibodies in patients in large clinical trials evaluating a PEG-modified aptamer, we investigated how anti-PEG antibodies effect the therapeutic activities of PEGylated RNA aptamers. We demonstrate that anti-PEG antibodies can directly bind to and inhibit anticoagulant aptamer function in vitro and in vivo. Moreover, in parallel studies we detected the presence of anti-PEG antibodies in nonhuman primates after a single administration of a PEGylated aptamer. Our results suggest that anti-PEG antibodies can limit the activity of PEGylated drugs and potentially compromise the activity of otherwise effective therapeutic agents.
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Affiliation(s)
- Angelo Moreno
- Department of Molecular Genetics and Microbiology graduate program, Duke University, Durham, NC, USA,Department of Surgery, Duke University, Durham, NC, USA
| | | | - Nancy J. Ganson
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Juliana M. Layzer
- Department of Surgery, Duke University, Durham, NC, USA,Duke Clinical and Translational Science Institute, Durham, NC, USA
| | | | - Alice F. Tarantal
- Departments of Pediatrics and Cell Biology and Human Anatomy, School of Medicine, NHLBI Center for Gene Transfer for Heart, Lung, and Blood Disease, and California National Primate Research Center, University of California, Davis, CA, USA
| | - Bruce A. Sullenger
- Department of Molecular Genetics and Microbiology graduate program, Duke University, Durham, NC, USA,Department of Surgery, Duke University, Durham, NC, USA,Contact Info: Corresponding Author and Lead Contact:
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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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McConnell EM, Ventura K, Dwyer Z, Hunt V, Koudrina A, Holahan MR, DeRosa MC. In Vivo Use of a Multi-DNA Aptamer-Based Payload/Targeting System To Study Dopamine Dysregulation in the Central Nervous System. ACS Chem Neurosci 2019; 10:371-383. [PMID: 30160936 DOI: 10.1021/acschemneuro.8b00292] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The delivery of therapeutics across the blood-brain barrier remains a considerable challenge in investigating central nervous system related processes. In this work, a liposome vehicle was surface-modified with an aptamer that binds to the transferrin receptor and was loaded with two different dopamine-binding aptamer payloads. This system was effectively used to promote the delivery of the aptamer cargo from the peripheral injection site into the brain. The effect of these delivered aptamers on behavior was investigated in vivo in a locomotor task. The first dopamine binding aptamer assessed was a DNA aptamer, the binding of which had been previously validated through the aptamer-based biosensor development reported by several independent research groups. The second aptamer investigated was the result of a novel in vitro selection experiment described herein. Our data suggest that systemic administration of the modified liposomes led to delivery of the dopamine aptamers into the brain. Fluorescence microscopy revealed differential distribution of fluorescence based on the presence or absence of the transferrin receptor aptamer on the surface of fluorescently modified liposomes. In a behavioral experiment using cocaine administration to induce elevated concentrations of neural dopamine, systemic pretreatment with the dopamine aptamer-loaded liposomes reduced cocaine-induced hyperlocomotion. Multiple controls including a transferrin-negative liposome control and transferrin-positive liposomes loaded with either a nonbinding, base-substituted dopamine aptamer or a random oligonucleotide were investigated. None of these controls altered cocaine-induced hyperlocomotion. Chronic systemic administration of the modified liposomes produced no deleterious neurobehavioral or neural degenerative effects. Importantly, this work is one example of an application for this versatile multiaptamer payload/targeting system. Its general application is limited only by the availability of aptamers for specific neural targets.
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Affiliation(s)
- Erin M. McConnell
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Katelyn Ventura
- Department of Neuroscience, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Zach Dwyer
- Department of Neuroscience, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Vernon Hunt
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Anna Koudrina
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Matthew R. Holahan
- Department of Neuroscience, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Maria C. DeRosa
- Department of Chemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
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Gunaratne R, Kumar S, Frederiksen JW, Stayrook S, Lohrmann JL, Perry K, Bompiani KM, Chabata CV, Thalji NK, Ho MD, Arepally G, Camire RM, Krishnaswamy S, Sullenger BA. Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass. Nat Biotechnol 2018; 36:606-613. [PMID: 29863725 PMCID: PMC6349032 DOI: 10.1038/nbt.4153] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 03/27/2018] [Indexed: 02/05/2023]
Abstract
Unfractionated heparin (UFH), the standard anticoagulant for cardiopulmonary bypass (CPB) surgery, carries a risk of post-operative bleeding and is potentially harmful in patients with heparin-induced thrombocytopenia-associated antibodies. To improve the activity of an alternative anticoagulant, the RNA aptamer 11F7t, we solved X-ray crystal structures of the aptamer bound to factor Xa (FXa). The finding that 11F7t did not bind the catalytic site suggested that it could complement small-molecule FXa inhibitors. We demonstrate that combinations of 11F7t and catalytic-site FXa inhibitors enhance anticoagulation in purified reaction mixtures and plasma. Aptamer-drug combinations prevented clot formation as effectively as UFH in human blood circulated in an extracorporeal oxygenator circuit that mimicked CPB, while avoiding side effects of UFH. An antidote could promptly neutralize the anticoagulant effects of both FXa inhibitors. Our results suggest that drugs and aptamers with shared targets can be combined to exert more specific and potent effects than either agent alone.
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Affiliation(s)
- Ruwan Gunaratne
- Duke University, Department of Pharmacology and Cancer Biology, Durham, NC 27710
- Duke University, Medical Scientist Training Program, Durham, NC 27710
| | - Shekhar Kumar
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | | | - Steven Stayrook
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Kay Perry
- Northeastern Collaborative Access Team (NE-CAT) and Departments of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439
| | | | - Charlene V. Chabata
- Duke University, Department of Pharmacology and Cancer Biology, Durham, NC 27710
| | - Nabil K. Thalji
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104
| | - Michelle D. Ho
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | | | - Rodney M. Camire
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104
| | - Sriram Krishnaswamy
- Research Institute, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104
| | - Bruce A. Sullenger
- Duke University, Department of Pharmacology and Cancer Biology, Durham, NC 27710
- Duke University, Department of Surgery, Durham, NC 27710
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20
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Morita Y, Leslie M, Kameyama H, Volk DE, Tanaka T. Aptamer Therapeutics in Cancer: Current and Future. Cancers (Basel) 2018; 10:cancers10030080. [PMID: 29562664 PMCID: PMC5876655 DOI: 10.3390/cancers10030080] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 12/14/2022] Open
Abstract
Aptamer-related technologies represent a revolutionary advancement in the capacity to rapidly develop new classes of targeting ligands. Structurally distinct RNA and DNA oligonucleotides, aptamers mimic small, protein-binding molecules and exhibit high binding affinity and selectivity. Although their molecular weight is relatively small—approximately one-tenth that of monoclonal antibodies—their complex tertiary folded structures create sufficient recognition surface area for tight interaction with target molecules. Additionally, unlike antibodies, aptamers can be readily chemically synthesized and modified. In addition, aptamers’ long storage period and low immunogenicity are favorable properties for clinical utility. Due to their flexibility of chemical modification, aptamers are conjugated to other chemical entities including chemotherapeutic agents, siRNA, nanoparticles, and solid phase surfaces for therapeutic and diagnostic applications. However, as relatively small sized oligonucleotides, aptamers present several challenges for successful clinical translation. Their short plasma half-lives due to nuclease degradation and rapid renal excretion necessitate further structural modification of aptamers for clinical application. Since the US Food and Drug Administration (FDA) approval of the first aptamer drug, Macugen® (pegaptanib), which treats wet-age-related macular degeneration, several aptamer therapeutics for oncology have followed and shown promise in pre-clinical models as well as clinical trials. This review discusses the advantages and challenges of aptamers and introduces therapeutic aptamers under investigation and in clinical trials for cancer treatments.
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Affiliation(s)
- Yoshihiro Morita
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
| | - Macall Leslie
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
| | - Hiroyasu Kameyama
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
| | - David E Volk
- McGovern Medical School, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 1825 Hermann Pressler, Houston, TX 77030, USA.
| | - Takemi Tanaka
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, 975 NE 10th, BRC-W, Rm 1415, Oklahoma City, OK 73104, USA.
- Department of Pathology, College of Medicine, University of Oklahoma Health Sciences Center, 940 SL Young Blvd, Oklahoma City, OK 73104, USA.
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21
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Purvis SH, Keefer JR, Fortenberry YM, Barron-Casella EA, Casella JF. Identification of Aptamers That Bind to Sickle Hemoglobin and Inhibit Its Polymerization. Nucleic Acid Ther 2017; 27:354-364. [PMID: 29039727 DOI: 10.1089/nat.2016.0646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The pathophysiology of sickle cell disease (SCD) is dependent on the polymerization of deoxygenated sickle hemoglobin (HbS), leading to erythrocyte deformation (sickling) and vaso-occlusion within the microvasculature. Following deoxygenation, there is a delay time before polymerization is initiated, during which nucleation of HbS monomers occurs. An agent with the ability to extend this delay time or slow polymerization would therefore hold a therapeutic, possibly curative, potential. We used the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method to screen for HbS-binding RNA aptamers modified with nuclease-resistant 2'-fluoropyrimidines. Polymerization assays were employed to identify aptamers with polymerization-inhibitory properties. Two noncompeting aptamers, DE3A and OX3B, were found to bind hemoglobin, significantly increase the delay time, and reduce the rate of polymerization of HbS. These modifiable, nuclease-resistant aptamers are potential new therapeutic agents for SCD.
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Affiliation(s)
- Shirley H Purvis
- Division of Hematology, Department of Pediatrics, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Jeffrey R Keefer
- Division of Hematology, Department of Pediatrics, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Yolanda M Fortenberry
- Division of Hematology, Department of Pediatrics, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Emily A Barron-Casella
- Division of Hematology, Department of Pediatrics, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - James F Casella
- Division of Hematology, Department of Pediatrics, Johns Hopkins University School of Medicine , Baltimore, Maryland
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22
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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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Steen Burrell KA, Layzer J, Sullenger BA. A kallikrein-targeting RNA aptamer inhibits the intrinsic pathway of coagulation and reduces bradykinin release. J Thromb Haemost 2017; 15:1807-1817. [PMID: 28632925 PMCID: PMC5818257 DOI: 10.1111/jth.13760] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 01/29/2023]
Abstract
Essentials Kallikrein amplifies contact activation and is a potential target for preventing thrombosis. We developed and characterized a kallikrein aptamer using convergent evolution and kinetic assays. Kall1-T4 prolongs intrinsic clotting time by inhibiting factor XIIa-mediated prekallikrein activation. Kall1-T4 decreases high-molecular-weight kininogen cleavage and bradykinin release. SUMMARY Background Plasma kallikrein is a serine protease that plays an integral role in many biological processes, including coagulation, inflammation, and fibrinolysis. The main function of kallikrein in coagulation is the amplification of activated factor XII (FXIIa) production, which ultimately leads to thrombin generation and fibrin clot formation. Kallikrein is generated by FXIIa-mediated cleavage of the zymogen prekallikrein, which is usually complexed with the non-enzymatic cofactor high molecular weight kininogen (HK). HK also serves as a substrate for kallikrein to generate the proinflammatory peptide bradykinin (BK). Interestingly, prekallikrein-deficient mice are protected from thrombotic events while retaining normal hemostatic capacity. Therefore, therapeutic targeting of kallikrein may provide a safer alternative to traditional anticoagulants with anti-inflammatory benefits. Objectives To isolate and characterize an RNA aptamer that binds to and inhibits plasma kallikrein, and to elucidate its mechanism of action. Methods and Results Using convergent Systematic Evolution of Ligands by Exponential Enrichment (SELEX), we isolated an RNA aptamer that targets kallikrein. This aptamer, Kall1-T4, specifically binds to both prekallikrein and kallikrein with similar subnanomolar binding affinities, and dose-dependently prolongs fibrin clot formation in an activated partial thromboplastin time (APTT) coagulation assay. In a purified in vitro system, Kall1-T4 inhibits the reciprocal activation of prekallikrein and FXII primarily by reducing the rate of FXIIa-mediated prekallikrein activation. Additionally, Kall1-T4 significantly reduces kallikrein-mediated HK cleavage and subsequent BK release. Conclusions We have isolated a specific and potent inhibitor of prekallikrein/kallikrein activity that serves as a powerful tool for further elucidating the role of kallikrein in thrombosis and inflammation.
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Affiliation(s)
- K-A Steen Burrell
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - J Layzer
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - B A Sullenger
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
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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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25
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Chen K, Liu B, Yu B, Zhong W, Lu Y, Zhang J, Liao J, Liu J, Pu Y, Qiu L, Zhang L, Liu H, Tan W. Advances in the development of aptamer drug conjugates for targeted drug delivery. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2017; 9:10.1002/wnan.1438. [PMID: 27800663 PMCID: PMC5507701 DOI: 10.1002/wnan.1438] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 08/29/2016] [Accepted: 09/06/2016] [Indexed: 12/20/2022]
Abstract
A key goal of modern medicine is target-specific therapeutic intervention. However, most drugs lack selectivity, resulting in 'off-target' side effects. To address the requirements of 'targeted therapy,' aptamers, which are artificial oligonucleotides, have been used as novel targeting ligands to construct aptamer drug conjugates (ApDC) that can specifically bind to a broad spectrum of targets, including diseased cells. Accordingly, the application of aptamers in targeted drug delivery has attracted broad interest due to their impressive selectivity and affinity, low immunogenicity, easy synthesis with high reproducibility, facile modification, and relatively rapid tissue penetration with no toxicity. Functionally, aptamers themselves can be used as macromolecular drugs, and they are also commonly used in biomarker discovery and targeted drug delivery. In this review, we will highlight the most recent advances in the development of aptamers and aptamer conjugates, and discuss their potential in targeted therapy. WIREs Nanomed Nanobiotechnol 2017, 9:e1438. doi: 10.1002/wnan.1438 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ke Chen
- Xiangya Hospital, Central South University, Changsha, China
| | - Bo Liu
- Xiangya Hospital, Central South University, Changsha, China
| | - Bo Yu
- Xiangya Hospital, Central South University, Changsha, China
| | - Wen Zhong
- Xiangya Hospital, Central South University, Changsha, China
| | - Yi Lu
- Xiangya Hospital, Central South University, Changsha, China
| | - Jiani Zhang
- Xiangya Hospital, Central South University, Changsha, China
| | - Jie Liao
- Xiangya Hospital, Central South University, Changsha, China
| | - Jun Liu
- Xiangya Hospital, Central South University, Changsha, China
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha, China
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, Hunan University, Changsha, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Ying Pu
- Xiangya Hospital, Central South University, Changsha, China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha, China
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, Hunan University, Changsha, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
| | - Liqin Zhang
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha, China
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, Hunan University, Changsha, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Huixia Liu
- Xiangya Hospital, Central South University, Changsha, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, Hunan University, Changsha, China
- State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, Hunan University, Changsha, China
- College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
- College of Biology, Hunan University, Changsha, China
- Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, University of Florida, Gainesville, FL, USA
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26
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Abstract
Nucleic acid aptamers, often termed 'chemical antibodies', are functionally comparable to traditional antibodies, but offer several advantages, including their relatively small physical size, flexible structure, quick chemical production, versatile chemical modification, high stability and lack of immunogenicity. In addition, many aptamers are internalized upon binding to cellular receptors, making them useful targeted delivery agents for small interfering RNAs (siRNAs), microRNAs and conventional drugs. However, several crucial factors have delayed the clinical translation of therapeutic aptamers, such as their inherent physicochemical characteristics and lack of safety data. This Review discusses these challenges, highlighting recent clinical developments and technological advances that have revived the impetus for this promising class of therapeutics.
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Affiliation(s)
- Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - John Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
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27
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Vorobyeva M, Vorobjev P, Venyaminova A. Multivalent Aptamers: Versatile Tools for Diagnostic and Therapeutic Applications. Molecules 2016; 21:molecules21121613. [PMID: 27898020 PMCID: PMC6274531 DOI: 10.3390/molecules21121613] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/11/2016] [Accepted: 11/18/2016] [Indexed: 11/24/2022] Open
Abstract
Nucleic acid aptamers generated through an in vitro selection are currently extensively applied as very valuable biomolecular tools thanks to their prominent advantages. Diversity of spatial structures, ease of production through chemical synthesis and a large variety of chemical modifications make aptamers convenient building blocks for the generation of multifunctional constructs. An opportunity to combine different aptamer functionalities with other molecules of interest such as reporter groups, nanoparticles, chemotherapeutic agents, siRNA or antisense oligonucleotides provides a widest range of applications of multivalent aptamers. The present review summarizes approaches to the design of multivalent aptamers, various examples of multifunctional constructs and the prospects of employing them as components of biosensors, probes for affinity capture, tools for cell research and potential therapeutic candidates.
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Affiliation(s)
- Mariya Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia.
| | - Pavel Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia.
| | - Alya Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia.
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28
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Nimjee SM, Povsic TJ, Sullenger BA, Becker RC. Translation and Clinical Development of Antithrombotic Aptamers. Nucleic Acid Ther 2016; 26:147-55. [PMID: 26882082 PMCID: PMC4900189 DOI: 10.1089/nat.2015.0581] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 01/12/2016] [Indexed: 01/02/2023] Open
Abstract
Thrombosis is a necessary physiological process to protect the body from uncontrolled bleeding. Pathological thrombus formation can lead to devastating clinical events including heart attack, stroke, deep vein thrombosis, pulmonary embolism, and disseminated intravascular coagulation. Numerous drugs have been developed to inhibit thrombosis. These have been targeted to coagulation factors along with proteins and receptors that activate platelets. While these drugs are effective at preventing blood clotting, their major side effect is inadvertent hemorrhage that can result in significant morbidity and mortality. There exists a need for anticoagulants that are not only effective at preventing thrombosis but can also be readily reversed. Aptamers offer a potential solution, representing a new class of drug agents that can be isolated to any protein and where antidote oligonucleotides can be designed based on the sequence of the aptamer. We present a summary of the anticoagulant and antithrombotic aptamers that have been identified and their stage of development and comment on the future of aptamer-based drug development to treat thrombosis.
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Affiliation(s)
- Shahid M. Nimjee
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Thomas J. Povsic
- Duke Clinical Research Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Bruce A. Sullenger
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Richard C. Becker
- Department of Medicine, University of Cincinnati Medical Center, Cincinnati, Ohio
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