1
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García-Fernández J, Rivadulla Costa L, Pinto-Díez C, Elena Martín M, González VM, de la Fuente Freire M. Chemical conjugation of aptamer-sphingomyelin nanosystems and their potential as inhibitors of tumour cell proliferation in breast cancer cells. NANOSCALE 2023; 15:19110-19127. [PMID: 37990926 DOI: 10.1039/d3nr03022a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Breast cancer is a complex and heterogeneous disease with a high mortality rate due to non-specific cytotoxicity, low intratumoral accumulation and drug resistance associated with the ineffectiveness of chemotherapy. In recent years, all efforts have been focused on finding new markers and therapeutic targets, protein kinase MNK1b being a promising candidate. Recently, an aptamer known as apMNK2F showed a highly specific interaction with this protein kinase, leading to a significant reduction in tumour cell proliferation, migration and colony formation. However, as aptamers are unable to penetrate the cell membrane and reach the target, these small biomolecules need to be conjugated to suitable vectors that can transport and protect them inside the cells. In this work, covalent conjugation between biocompatible and non-harmful nanoemulsions of vitamin E and sphingomyelin and the aptamer was performed to facilitate intracellular delivery of the therapeutic aptamer apMNK2F. All strategies employed were based on 2-step bioconjugation and optimized to get the simplest and most reproducible vehicle with the highest association efficiency (about 70% in all cases). The ability of the nanosystems to successfully deliver the conjugated therapeutic aptamer was demonstrated and compared to other commercial transfection agents such as Lipofectamine 2000, leading to an effective decrease of breast cancer cell proliferation in the MDA-MB-231 cell line. The proliferation inhibition of the aptamer nanoconjugates compared to the non-conjugated aptamer provides evidence that the antitumoral capacity derived from kinase interaction is improved in a dose-dependent manner. Furthermore, various experiments including cell migration and colony formation assays, along with apoptosis induction experiments, emphasize the significant antitumoral potential. Overall, the obtained results indicate that the developed formulation could be a promising therapy for the treatment of breast cancer.
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Affiliation(s)
- Jenifer García-Fernández
- Nano-Oncology and Translational Therapeutics Unit, Health Research Institute of Santiago de Compostel (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, 15706, Spain.
| | - Laura Rivadulla Costa
- Nano-Oncology and Translational Therapeutics Unit, Health Research Institute of Santiago de Compostel (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, 15706, Spain.
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, 15782, Spain
| | | | | | - Víctor M González
- Aptus Biotech S.L., Madrid, Spain
- IRYcis-Hospital Ramón y Cajal, Madrid, Spain
| | - María de la Fuente Freire
- Nano-Oncology and Translational Therapeutics Unit, Health Research Institute of Santiago de Compostel (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, 15706, Spain.
- Biomedical Research Networking Centre on Oncology (CIBERONC), Madrid, Spain
- DIVERSA Technologies S.L, Santiago de Compostela, Spain
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2
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Narwade M, Shaikh A, Gajbhiye KR, Kesharwani P, Gajbhiye V. Advanced cancer targeting using aptamer functionalized nanocarriers for site-specific cargo delivery. Biomater Res 2023; 27:42. [PMID: 37149607 PMCID: PMC10164340 DOI: 10.1186/s40824-023-00365-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/20/2023] [Indexed: 05/08/2023] Open
Abstract
The non-specificity of standard anticancer therapies has profound detrimental consequences in clinical treatment. Therapeutic specificity can be precisely achieved using cutting-edge ligands. Small synthetic oligonucleotide-ligands chosen through Systematic evolution of ligands by exponential enrichment (SELEX) would be an unceasing innovation in using nucleic acids as aptamers, frequently referred to as "chemical antibodies." Aptamers act as externally controlled switching materials that can attach to various substrates, for example, membrane proteins or nucleic acid structures. Aptamers pose excellent specificity and affinity for target molecules and can be used as medicines to suppress tumor cell growth directly. The creation of aptamer-conjugated nanoconstructs has recently opened up innovative options in cancer therapy that are more effective and target tumor cells with minor toxicity to healthy tissues. This review focuses on a comprehensive description of the most capable classes of aptamer-tethered nanocarriers for precise recognition of cancer cells with significant development in proficiency, selectivity, and targetability for cancer therapy. Existing theranostic applications with the problems and future directions are also highlighted.
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Affiliation(s)
- Mahavir Narwade
- Department of Pharmaceutics, Poona College of Pharmacy, Bharati Vidyapeeth, Pune, India
| | - Aazam Shaikh
- Nanobioscience Group, Agharkar Research Institute, Pune, 411004, India
- Savitribai Phule Pune University, Ganeshkhind, Pune, 411 007, India
| | - Kavita R Gajbhiye
- Department of Pharmaceutics, Poona College of Pharmacy, Bharati Vidyapeeth, Pune, India
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India.
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Science, Chennai, India.
| | - Virendra Gajbhiye
- Nanobioscience Group, Agharkar Research Institute, Pune, 411004, India.
- Savitribai Phule Pune University, Ganeshkhind, Pune, 411 007, India.
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3
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Zhu Y, Zhu L, Wang X, Jin H. RNA-based therapeutics: an overview and prospectus. Cell Death Dis 2022; 13:644. [PMID: 35871216 PMCID: PMC9308039 DOI: 10.1038/s41419-022-05075-2] [Citation(s) in RCA: 152] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 01/21/2023]
Abstract
The growing understanding of RNA functions and their crucial roles in diseases promotes the application of various RNAs to selectively function on hitherto "undruggable" proteins, transcripts and genes, thus potentially broadening the therapeutic targets. Several RNA-based medications have been approved for clinical use, while others are still under investigation or preclinical trials. Various techniques have been explored to promote RNA intracellular trafficking and metabolic stability, despite significant challenges in developing RNA-based therapeutics. In this review, the mechanisms of action, challenges, solutions, and clinical application of RNA-based therapeutics have been comprehensively summarized.
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Affiliation(s)
- Yiran Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Liyuan Zhu
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Xian Wang
- grid.13402.340000 0004 1759 700XDepartment of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
| | - Hongchuan Jin
- grid.13402.340000 0004 1759 700XLaboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China
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4
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Dai Z, Saksena SD, Horny G, Banholzer C, Ewert S, Gifford DK. Ultra-high-diversity factorizable libraries for efficient therapeutic discovery. Genome Res 2022; 32:gr.276593.122. [PMID: 35738900 PMCID: PMC9528983 DOI: 10.1101/gr.276593.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 06/22/2022] [Indexed: 01/13/2023]
Abstract
The successful discovery of novel biological therapeutics by selection requires highly diverse libraries of candidate sequences that contain a high proportion of desirable candidates. Here we propose the use of computationally designed factorizable libraries made of concatenated segment libraries as a method of creating large libraries that meet an objective function at low cost. We show that factorizable libraries can be designed efficiently by representing objective functions that describe sequence optimality as an inner product of feature vectors, which we use to design an optimization method we call stochastically annealed product spaces (SAPS). We then use this approach to design diverse and efficient libraries of antibody CDR-H3 sequences with various optimized characteristics.
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Affiliation(s)
- Zheng Dai
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sachit D Saksena
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Geraldine Horny
- Novartis Institutes for BioMedical Research (NIBR), CH-4056 Basel, Switzerland
| | - Christine Banholzer
- Novartis Institutes for BioMedical Research (NIBR), CH-4056 Basel, Switzerland
| | - Stefan Ewert
- Novartis Institutes for BioMedical Research (NIBR), CH-4056 Basel, Switzerland
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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5
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Van Simaeys D, De La Fuente A, Zilio S, Zoso A, Kuznetsova V, Alcazar O, Buchwald P, Grilli A, Caroli J, Bicciato S, Serafini P. RNA aptamers specific for transmembrane p24 trafficking protein 6 and Clusterin for the targeted delivery of imaging reagents and RNA therapeutics to human β cells. Nat Commun 2022; 13:1815. [PMID: 35383192 PMCID: PMC8983715 DOI: 10.1038/s41467-022-29377-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/08/2022] [Indexed: 12/20/2022] Open
Abstract
The ability to detect and target β cells in vivo can substantially refine how diabetes is studied and treated. However, the lack of specific probes still hampers a precise characterization of human β cell mass and the delivery of therapeutics in clinical settings. Here, we report the identification of two RNA aptamers that specifically and selectively recognize mouse and human β cells. The putative targets of the two aptamers are transmembrane p24 trafficking protein 6 (TMED6) and clusterin (CLUS). When given systemically in immune deficient mice, these aptamers recognize the human islet graft producing a fluorescent signal proportional to the number of human islets transplanted. These aptamers cross-react with endogenous mouse β cells and allow monitoring the rejection of mouse islet allografts. Finally, once conjugated to saRNA specific for X-linked inhibitor of apoptosis (XIAP), they can efficiently transfect non-dissociated human islets, prevent early graft loss, and improve the efficacy of human islet transplantation in immunodeficient in mice.
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Affiliation(s)
- Dimitri Van Simaeys
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Adriana De La Fuente
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Serena Zilio
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Alessia Zoso
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Victoria Kuznetsova
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Oscar Alcazar
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Peter Buchwald
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Andrea Grilli
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Jimmy Caroli
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Silvio Bicciato
- Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Paolo Serafini
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, USA. .,Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL, USA. .,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA.
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6
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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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7
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Dillen A, Lammertyn J. Paving the way towards continuous biosensing by implementing affinity-based nanoswitches on state-dependent readout platforms. Analyst 2022; 147:1006-1023. [DOI: 10.1039/d1an02308j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combining affinity-based nanoswitches with state-dependent readout platforms allows for continuous biosensing and acquisition of real-time information about biochemical processes occurring in the environment of interest.
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Affiliation(s)
- Annelies Dillen
- KU Leuven, Department of Biosystems – Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
| | - Jeroen Lammertyn
- KU Leuven, Department of Biosystems – Biosensors Group, Willem de Croylaan 42, Box 2428, 3001, Leuven, Belgium
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8
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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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9
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Identification and Engineering of Aptamers for Theranostic Application in Human Health and Disorders. Int J Mol Sci 2021; 22:ijms22189661. [PMID: 34575825 PMCID: PMC8469434 DOI: 10.3390/ijms22189661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/25/2021] [Accepted: 07/31/2021] [Indexed: 02/07/2023] Open
Abstract
An aptamer is a short sequence of synthetic oligonucleotides which bind to their cognate target, specifically while maintaining similar or higher sensitivity compared to an antibody. The in-vitro selection of an aptamer, applying a conjoining approach of chemistry and molecular biology, is referred as Systematic Evolution of Ligands by Exponential enrichment (SELEX). These initial products of SELEX are further modified chemically in an attempt to make them stable in biofluid, avoiding nuclease digestion and renal clearance. While the modification is incorporated, enough care should be taken to maintain its sensitivity and specificity. These modifications and several improvisations have widened the window frame of aptamer applications that are currently not only restricted to in-vitro systems, but have also been used in molecular imaging for disease pathology and treatment. In the food industry, it has been used as sensor for detection of different diseases and fungal infections. In this review, we have discussed a brief history of its journey, along with applications where its role as a therapeutic plus diagnostic (theranostic) tool has been demonstrated. We have also highlighted the potential aptamer-mediated strategies for molecular targeting of COVID-19. Finally, the review focused on its future prospective in immunotherapy, as well as in identification of novel biomarkers in stem cells and also in single cell proteomics (scProteomics) to study intra or inter-tumor heterogeneity at the protein level. Small size, chemical synthesis, low batch variation, cost effectiveness, long shelf life and low immunogenicity provide advantages to the aptamer over the antibody. These physical and chemical properties of aptamers render them as a strong biomedical tool for theranostic purposes over the existing ones. The significance of aptamers in human health was the key finding of this review.
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10
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Yu AM, Tu MJ. Deliver the promise: RNAs as a new class of molecular entities for therapy and vaccination. Pharmacol Ther 2021; 230:107967. [PMID: 34403681 PMCID: PMC9477512 DOI: 10.1016/j.pharmthera.2021.107967] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/19/2022]
Abstract
The concepts of developing RNAs as new molecular entities for therapies have arisen again and again since the discoveries of antisense RNAs, direct RNA-protein interactions, functional noncoding RNAs, and RNA-directed gene editing. The feasibility was demonstrated with the development and utilization of synthetic RNA agents to selectively control target gene expression, modulate protein functions or alter the genome to manage diseases. Rather, RNAs are labile to degradation and cannot cross cell membrane barriers, making it hard to develop RNA medications. With the development of viable RNA technologies, such as chemistry and pharmaceutics, eight antisense oligonucleotides (ASOs) (fomivirsen, mipomersen, eteplirsen, nusinersen, inotersen, golodirsen, viltolarsen and casimersen), one aptamer (pegaptanib), and three small interfering RNAs (siRNAs) (patisiran, givosiran and lumasiran) have been approved by the United States Food and Drug Administration (FDA) for therapies, and two mRNA vaccines (BNT162b2 and mRNA-1273) under Emergency Use Authorization for the prevention of COVID-19. Therefore, RNAs have become a great addition to small molecules, proteins/antibodies, and cell-based modalities to improve the public health. In this article, we first summarize the general characteristics of therapeutic RNA agents, including chemistry, common delivery strategies, mechanisms of actions, and safety. By overviewing individual RNA medications and vaccines approved by the FDA and some agents under development, we illustrate the unique compositions and pharmacological actions of RNA products. A new era of RNA research and development will likely lead to commercialization of more RNA agents for medical use, expanding the range of therapeutic targets and increasing the diversity of molecular modalities.
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA.
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA
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11
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Srivastava S, Abraham PR, Mukhopadhyay S. Aptamers: An Emerging Tool for Diagnosis and Therapeutics in Tuberculosis. Front Cell Infect Microbiol 2021; 11:656421. [PMID: 34277465 PMCID: PMC8280756 DOI: 10.3389/fcimb.2021.656421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) has been plaguing human civilization for centuries, and currently around one-third of the global population is affected with TB. Development of novel intervention tools for early diagnosis and therapeutics against Mycobacterium tuberculosis (M.tb) is the main thrust area in today's scenario. In this direction global efforts were made to use aptamers, the chemical antibodies as tool for TB diagnostics and therapeutics. This review describes the various aptamers introduced for targeting M.tb and highlights the need for development of novel aptamers to selectively target virulent proteins of M.tb for vaccine and anti-TB drugs. The objective of this review is to highlight the diagnostic and therapeutic application of aptamers used for tuberculosis. The discovery of aptamers, SELEX technology, different types of SELEX development processes, DNA and RNA aptamers reported for diseases and pathogenic agents as well have also been described in detail. But the emphasis of this review is on the development of aptamers which can block the function of virulent mycobacterial components for developing newer TB vaccine candidates and/or drug targets. Aptamers designed to target M.tb cell wall proteins, virulent factors, secretory proteins, or combination could orchestrate advanced diagnosis and therapeutic measures for tuberculosis.
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Affiliation(s)
- Shruti Srivastava
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Philip Raj Abraham
- Unit of OMICS, ICMR-Vector Control Research Centre (VCRC), Puducherry, India
| | - Sangita Mukhopadhyay
- Laboratory of Molecular Cell Biology, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
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12
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Niederlender S, Fontaine JJ, Karadjian G. Potential applications of aptamers in veterinary science. Vet Res 2021; 52:79. [PMID: 34078451 PMCID: PMC8172000 DOI: 10.1186/s13567-021-00948-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/23/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are small nucleic acids that fold in a three-dimensional conformation allowing them to bind specifically to a target. This target can be an organic molecule, free or carried in cells or tissues, or inorganic components, such as metal ions. Analogous to monoclonal antibodies, aptamers however have certain advantages over the latter: e.g., high specificity for their target, no to low immunogenicity and easy in vitro selection. Since their discovery more than 30 years ago, aptamers have led to various applications, although mainly restricted to basic research. This work reviews the applications of aptamers in veterinary science to date. First, we present aptamers, how they are selected and their properties, then we give examples of applications in food and environmental safety, as well as in diagnosis and medical treatment in the field of veterinary medicine. Because examples of applications in veterinary medicine are scarce, we explore the potential avenues for future applications based on discoveries made in human medicine. Aptamers may offer new possibilities for veterinarians to diagnose certain diseases—particularly infectious diseases—more rapidly or “at the patient’s bedside”. All the examples highlight the growing interest in aptamers and the premises of a potential market. Aptamers may benefit animals as well as their owners, breeders and even public health in a “One Health” approach.
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Affiliation(s)
- Solène Niederlender
- École Nationale Vétérinaire d'Alfort, Université Paris-Est Sup, 7 avenue du Général de Gaulle, 94700, Maisons-Alfort, France
| | - Jean-Jacques Fontaine
- UMR BIPAR 956, ANSES, INRAE, École Nationale Vétérinaire d'Alfort, Université Paris-Est Sup, 7 avenue du Général de Gaulle, 94700, Maisons-Alfort, France
| | - Grégory Karadjian
- UMR BIPAR, Laboratoire de Santé Animale, ANSES, INRAE, École Nationale Vétérinaire d'Alfort, Université Paris-Est Sup, 94700, Maisons-Alfort, France.
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13
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Eguchi A, Ueki A, Hoshiyama J, Kuwata K, Chikaoka Y, Kawamura T, Nagatoishi S, Tsumoto K, Ueki R, Sando S. A DNA Aptamer That Inhibits the Aberrant Signaling of Fibroblast Growth Factor Receptor in Cancer Cells. JACS AU 2021; 1:578-585. [PMID: 34467321 PMCID: PMC8395645 DOI: 10.1021/jacsau.0c00121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 06/13/2023]
Abstract
Growth factor receptors are activated through dimerization by the binding of their ligands and play pivotal roles in normal cell function. However, the aberrant activity of the receptors has been associated with cancer malignancy. One of the main causes of the aberrant receptor activation is the overexpression of receptors and the resultant formation of unliganded receptor dimers, which can be activated in the absence of external ligand molecules. Thus, the unliganded receptor dimer is a promising target to inhibit aberrant signaling in cancer. Here, we report an aptamer that specifically binds to fibroblast growth factor receptor 2b and inhibits the aberrant receptor activation and signaling. Our investigation suggests that this aptamer inhibits the formation of the receptor dimer occurring in the absence of external ligand molecules. This work presents a new inhibitory function of aptamers and the possibility of oligonucleotide-based therapeutics for cancer.
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Affiliation(s)
- Akihiro Eguchi
- Department of Chemistry and Biotechnology andDepartment of Bioengineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ayaka Ueki
- Department of Chemistry and Biotechnology andDepartment of Bioengineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Junya Hoshiyama
- Department of Chemistry and Biotechnology andDepartment of Bioengineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Keiko Kuwata
- Institute
of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Yoko Chikaoka
- Proteomics
Laboratory, Isotope Science Center, The
University of Tokyo, 2-11-16, Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Takeshi Kawamura
- Proteomics
Laboratory, Isotope Science Center, The
University of Tokyo, 2-11-16, Yayoi, Bunkyo-Ku, Tokyo 113-0032, Japan
| | - Satoru Nagatoishi
- The
Institute of Medical Science, The University
of Tokyo, 4-6-1 Shirokanedai,
Minato-ku, Tokyo 108-8639, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology andDepartment of Bioengineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- The
Institute of Medical Science, The University
of Tokyo, 4-6-1 Shirokanedai,
Minato-ku, Tokyo 108-8639, Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology andDepartment of Bioengineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology andDepartment of Bioengineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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14
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Ni S, Zhuo Z, Pan Y, Yu Y, Li F, Liu J, Wang L, Wu X, Li D, Wan Y, Zhang L, Yang Z, Zhang BT, Lu A, Zhang G. Recent Progress in Aptamer Discoveries and Modifications for Therapeutic Applications. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9500-9519. [PMID: 32603135 DOI: 10.1021/acsami.0c05750] [Citation(s) in RCA: 244] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Aptamers are oligonucleotide sequences with a length of about 25-80 bases which have abilities to bind to specific target molecules that rival those of monoclonal antibodies. They are attracting great attention in diverse clinical translations on account of their various advantages, including prolonged storage life, little batch-to-batch differences, very low immunogenicity, and feasibility of chemical modifications for enhancing stability, prolonging the half-life in serum, and targeted delivery. In this Review, we demonstrate the emerging aptamer discovery technologies in developing advanced techniques for producing aptamers with high performance consistently and efficiently as well as requiring less cost and resources but offering a great chance of success. Further, the diverse modifications of aptamers for therapeutic applications including therapeutic agents, aptamer-drug conjugates, and targeted delivery materials are comprehensively summarized.
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Affiliation(s)
- Shuaijian Ni
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Zhenjian Zhuo
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Yufei Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuanyuan Yu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Fangfei Li
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Jin Liu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Luyao Wang
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Xiaoqiu Wu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Dijie Li
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Youyang Wan
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Bao-Ting Zhang
- School of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Aiping Lu
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
| | - Ge Zhang
- Institute of Precision Medicine and Innovative Drug Discovery, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong 999077, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong 999077, China
- HKBU and IncreasePharm Joint Centre for Nucleic Acid Drug Discovery, Hong Kong 999077, China
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15
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Al-Sudani B, Ragazzon-Smith AH, Aziz A, Alansari R, Ferry N, Krstic-Demonacos M, Ragazzon PA. Circular and linear: a tale of aptamer selection for the activation of SIRT1 to induce death in cancer cells. RSC Adv 2020; 10:45008-45018. [PMID: 35516259 PMCID: PMC9058605 DOI: 10.1039/d0ra07857c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/30/2020] [Indexed: 11/21/2022] Open
Abstract
It is a challenge to select the right target to treat conditions without affecting non-diseased cells. Cancer belongs to the top 10 causes of death in the world and it remains difficult to treat. Amongst cancer emerging targets, silent information regulator 1 (SIRT1) - a histone deacetylase - has shown many roles in cancer, ageing and metabolism. Here we report novel SIRT1 ligands that bind and modulate the activity of SIRT1 within cells and enhance its enzymatic activity. We developed a modified aptamer capable of binding to and forming a complex with SIRT1. Our ligands are aptamers, they can be made of DNA or RNA oligonucleotides, their binding domain can recognise a target with very high affinity and specificity. We used the systematic evolution of ligands by exponential enrichment (SELEX) technique to develop circular and linear aptamers selectively binding to SIRT1. Cellular consequences of the interaction were monitored by fluorescence microscopy, cell viability assay, stability and enzymatic assays. Our results indicate that from our pool of aptamers, circular AC3 penetrates cancerous cells and is recruited to modulate the SIRT1 activity. This modulation of SIRT1 resulted in anticancer activity on different cancer cell lines. Furthermore, this modified aptamer showed no toxicity on one non-cancerous cell line and was stable in human plasma. We have demonstrated that aptamers are efficient tools for localisation of internal cell targets, and in this particular case, anticancer activity through modulation of SIRT1.
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Affiliation(s)
- Basma Al-Sudani
- College of Pharmacy, Branch of Clinical Laboratory Sciences, University of Mustansiriya UK
- Biomedical Research Centre, School of Environment and Life Sciences, University of Salford UK
| | | | - Athar Aziz
- Biomedical Research Centre, School of Environment and Life Sciences, University of Salford UK
| | - Rania Alansari
- School of Pharmacy and Bioengineering, Keele University Hornbeam Building (2.26) Keele ST5 5BG UK
| | - Natalie Ferry
- Biomedical Research Centre, School of Environment and Life Sciences, University of Salford UK
| | - Marija Krstic-Demonacos
- Biomedical Research Centre, School of Environment and Life Sciences, University of Salford UK
| | - Patricia A Ragazzon
- School of Pharmacy and Bioengineering, Keele University Hornbeam Building (2.26) Keele ST5 5BG UK
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16
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Riccardi C, Napolitano E, Musumeci D, Montesarchio D. Dimeric and Multimeric DNA Aptamers for Highly Effective Protein Recognition. Molecules 2020; 25:E5227. [PMID: 33182593 PMCID: PMC7698228 DOI: 10.3390/molecules25225227] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/14/2022] Open
Abstract
Multivalent interactions frequently occur in biological systems and typically provide higher binding affinity and selectivity in target recognition than when only monovalent interactions are operative. Thus, taking inspiration by nature, bivalent or multivalent nucleic acid aptamers recognizing a specific biological target have been extensively studied in the last decades. Indeed, oligonucleotide-based aptamers are suitable building blocks for the development of highly efficient multivalent systems since they can be easily modified and assembled exploiting proper connecting linkers of different nature. Thus, substantial research efforts have been put in the construction of dimeric/multimeric versions of effective aptamers with various degrees of success in target binding affinity or therapeutic activity enhancement. The present review summarizes recent advances in the design and development of dimeric and multimeric DNA-based aptamers, including those forming G-quadruplex (G4) structures, recognizing different key proteins in relevant pathological processes. Most of the designed constructs have shown improved performance in terms of binding affinity or therapeutic activity as anti-inflammatory, antiviral, anticoagulant, and anticancer agents and their number is certainly bound to grow in the next future.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Department of Advanced Medical and Surgical Sciences, 2nd Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
- Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (E.N.); (D.M.); (D.M.)
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17
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Chandana SR, Babiker HM, Mahadevan D. Clinical complexity of utilizing FGFR inhibitors in cancer therapeutics. Expert Opin Investig Drugs 2020; 29:1413-1429. [PMID: 33074030 DOI: 10.1080/13543784.2020.1838484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Fibroblast growth factor receptors (FGFR 1-4) are a highly conserved family of receptor tyrosine kinases, involved in several physiological processes. Genetic aberrations of FGFRs and their ligands, fibroblast growth factors (FGFs) are involved in several pathological processes including cancer. The FGF-FGFR axis has emerged as a treatment target in oncology. Because these aberrations drive cancer progression, the development of FGFR targeted therapies have been accelerated. AREAS COVERED In this comprehensive review, we evaluate molecular pathology and targeted therapies to FGFRs. We reviewed the evidence for safety and efficacy from preclinical and clinical studies (phase I-III) of FGFR targeted therapies. We also discuss potential challenges in bringing these targeted therapies from bench to bedside and the potential opportunities. EXPERT OPINION Despite the challenges of the clinical development of FGFR targeted therapies, two FGFR small-molecule inhibitors, namely Erdafitinib and Pemigatinib, are FDA approved for urothelial cancer and cholangiocarcinoma, respectively. Understanding and detection of FGFR genomic aberrations, protein overexpression and the development of isoform-specific inhibitors are factors in the clinical success of these therapies. An enhanced understanding of patient selection based on a gene signatures or biomarkers is key to success of FGFR targeted therapies.
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Affiliation(s)
- Sreenivasa R Chandana
- Phase I Program, START Midwest , Grand Rapids, MI, USA.,Department of Medical Oncology, Cancer and Hematology Centers of Western Michigan , Grand Rapids, MI, USA.,Department of Medicine, College of Human Medicine, Michigan State University , East Lansing, MI, USA
| | - Hani M Babiker
- Early Phase Clinical Trials Program, University of Arizona Cancer Center , Tucson, AZ, USA
| | - Daruka Mahadevan
- Early Phase Clinical Trials Program, University of Arizona Cancer Center , Tucson, AZ, USA.,Division of Hematology-Oncology, Mays Cancer Center, University of Texas Health San Antonio , San Antonio, TX, USA
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18
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Attwood MM, Jonsson J, Rask-Andersen M, Schiöth HB. Soluble ligands as drug targets. Nat Rev Drug Discov 2020; 19:695-710. [PMID: 32873970 DOI: 10.1038/s41573-020-0078-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2020] [Indexed: 02/07/2023]
Abstract
Historically, the main classes of drug targets have been receptors, enzymes, ion channels and transporters. However, owing largely to the rise of antibody-based therapies in the past two decades, soluble protein ligands such as inflammatory cytokines have become an increasingly important class of drug targets. In this Review, we analyse drugs targeting ligands that have reached clinical development at some point since 1992. We identify 291 drugs that target 99 unique ligands, and we discuss trends in the characteristics of the ligands, drugs and indications for which they have been tested. In the last 5 years, the number of ligand-targeting drugs approved by the FDA has doubled to 34, while the number of clinically validated ligand targets has doubled to 22. Cytokines and growth factors are the predominant types of targeted ligands (70%), and inflammation and autoimmune disorders, cancer and ophthalmological diseases are the top therapeutic areas for both approved agents and agents in clinical studies, reflecting the central role of cytokine and/or growth factor pathways in such diseases.
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Affiliation(s)
- Misty M Attwood
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Jörgen Jonsson
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Mathias Rask-Andersen
- Medical Genetics and Genomics, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Helgi B Schiöth
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden. .,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia.
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19
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Duffy K, Arangundy-Franklin S, Holliger P. Modified nucleic acids: replication, evolution, and next-generation therapeutics. BMC Biol 2020; 18:112. [PMID: 32878624 PMCID: PMC7469316 DOI: 10.1186/s12915-020-00803-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are now increasingly amenable to in vitro evolution, accelerating lead discovery. Here, we review the most recent discoveries in this dynamic field with a focus on progress in the enzymatic replication and functional exploration of XNAs.
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Affiliation(s)
- Karen Duffy
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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20
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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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21
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Zhou X, Zhu Q, Yang Y. Aptamer-integrated nucleic acid circuits for biosensing: Classification, challenges and perspectives. Biosens Bioelectron 2020; 165:112422. [PMID: 32729540 DOI: 10.1016/j.bios.2020.112422] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/28/2020] [Accepted: 07/01/2020] [Indexed: 12/27/2022]
Abstract
Owing to their high programmability and modularity, autonomous enzyme-free nucleic acid circuits are attracting ever-growing interest as signal amplifiers with potential applications in developing highly sensitive biosensing techniques. Besides nucleic acid input, the biosensing scope of aptamer-integrated nucleic acids could be further expanded to non-nucleic targets by integrating nucleic acid circuits with aptamers-a class of functional oligonucleotides with binding capabilities toward specific targets. By coupling upstream target recognition with downstream signal amplification, aptamer-integrated nucleic acid circuits enable aptasensors with increased sensitivity and enhanced performances, which may act as powerful tools in various fields including environment monitoring, personal care, clinical diagnosis, etc. In designing aptamer-integrated nucleic acid circuits, smart integration between aptamer and nucleic acid circuits plays a crucial role in developing reliable circuits with good performances. To date, although there are plenty of published researches adopting aptamer-integrated nucleic acid circuits as amplifiers in biosensing systems, deep discussion or systematic review on rational design strategies for aptamer-integrated nucleic acid circuits is still lacking. To fill this gap, rational aptamer-nucleic acid circuits integration modes were classified and summarized for the first time based on reviewing the state of art of existing aptamer-integrated nucleic acid circuits. Moreover, theoretical updates in nucleic acid circuits designs and major challenges to be overcome in developing highly sensitive aptamer-integrated nucleic acids based biosensing systems are discussed in this review.
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Affiliation(s)
- Xiaohong Zhou
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University, Beijing, 100084, China.
| | - Qian Zhu
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yihan Yang
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University, Beijing, 100084, China
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22
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Kumar Kulabhusan P, Hussain B, Yüce M. Current Perspectives on Aptamers as Diagnostic Tools and Therapeutic Agents. Pharmaceutics 2020; 12:E646. [PMID: 32659966 PMCID: PMC7407196 DOI: 10.3390/pharmaceutics12070646] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022] Open
Abstract
Aptamers are synthetic single-stranded DNA or RNA sequences selected from combinatorial oligonucleotide libraries through the well-known in vitro selection and iteration process, SELEX. The last three decades have witnessed a sudden boom in aptamer research, owing to their unique characteristics, like high specificity and binding affinity, low immunogenicity and toxicity, and ease in synthesis with negligible batch-to-batch variation. Aptamers can specifically bind to the targets ranging from small molecules to complex structures, making them suitable for a myriad of diagnostic and therapeutic applications. In analytical scenarios, aptamers are used as molecular probes instead of antibodies. They have the potential in the detection of biomarkers, microorganisms, viral agents, environmental pollutants, or pathogens. For therapeutic purposes, aptamers can be further engineered with chemical stabilization and modification techniques, thus expanding their serum half-life and shelf life. A vast number of antagonistic aptamers or aptamer-based conjugates have been discovered so far through the in vitro selection procedure. However, the aptamers face several challenges for its successful clinical translation, and only particular aptamers have reached the marketplace so far. Aptamer research is still in a growing stage, and a deeper understanding of nucleic acid chemistry, target interaction, tissue distribution, and pharmacokinetics is required. In this review, we discussed aptamers in the current diagnostics and theranostics applications, while addressing the challenges associated with them. The report also sheds light on the implementation of aptamer conjugates for diagnostic purposes and, finally, the therapeutic aptamers under clinical investigation, challenges therein, and their future directions.
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Affiliation(s)
| | - Babar Hussain
- Faculty of Life Sciences, University of Central Punjab, Lahore 54000, Pakistan;
| | - Meral Yüce
- SUNUM Nanotechnology Research and Application Centre, Sabanci University, Istanbul 34956, Turkey
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23
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Diagnostic and Therapeutic Value of Aptamers in Envenomation Cases. Int J Mol Sci 2020; 21:ijms21103565. [PMID: 32443562 PMCID: PMC7278915 DOI: 10.3390/ijms21103565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 02/07/2023] Open
Abstract
It is now more than a century since Albert Calmette from the Institut Pasteur changed the world of envenomation by demonstrating that antibodies raised against animal venoms have the ability to treat human victims of previously fatal bites or stings. Moreover, the research initiated at that time effectively launched the discipline of toxicology, first leading to the search for toxic venom components, followed by the demonstration of venoms that also contained compounds of therapeutic value. Interest from pharmaceutical companies to treat envenomation is, however, declining, mainly for economic reasons, and hence, the World Health Organization has reclassified this public health issue to be a highest priority concern. While the production, storage, and safety of antivenom sera suffer from major inconveniences, alternative chemical and technological approaches to the problem of envenomation need to be considered that bypass the use of antibodies for toxin neutralization. Herein, we review an emerging strategy that relies on the use of aptamers and discuss how close—or otherwise—we are to finding a viable alternative to the use of antibodies for the therapy of human envenomation.
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24
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Aptamers as a novel diagnostic and therapeutic tool and their potential use in parasitology. ACTA ACUST UNITED AC 2020; 40:148-165. [PMID: 32463617 PMCID: PMC7449109 DOI: 10.7705/biomedica.4765] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Indexed: 02/07/2023]
Abstract
Los aptámeros son secuencias de ADN o ARN de cadena sencilla que adoptan la forma de estructuras tridimensionales únicas, lo cual les permite reconocer un blanco específico con gran afinidad. Sus usos potenciales abarcan, entre otros, el diagnóstico de enfermedades, el desarrollo de nuevos agentes terapéuticos, la detección de riesgos alimentarios, la producción de biosensores, la detección de toxinas, el transporte de fármacos en el organismo y la señalización de nanopartículas. El pegaptanib es el único aptámero aprobado para uso comercial por la Food and Drug Administration (FDA). Otros aptámeros para el tratamiento de enfermedades están en la fase clínica de desarrollo. En parasitología, se destacan los estudios que se vienen realizando en Leishmania spp., con la obtención de aptámeros que reconocen la proteína de unión a poliA (LiPABP) y que pueden tener potencial utilidad en la investigación, el diagnóstico y el tratamiento de la leishmaniasis. En cuanto a la malaria, se han obtenido aptámeros que permiten identificar eritrocitos infectados e inhiben la formación de rosetas, y otros que prometen ser alternativas para el diagnóstico al detectar de forma específica la proteína lactato deshidrogenasa (PfLDH). Para Cryptosporidium parvuum se han seleccionado aptámeros que detectan ooquistes a partir de alimentos o aguas contaminadas. Para Entamoeba histolytica se han aislado dos aptámeros llamados C4 y C5, que inhiben la proliferación in vitro de los trofozoítos y tienen potencial terapéutico. Los aptámeros contra Trypanosoma cruzi inhiben la invasión de células LLC-MK2 (de riñón de mono) en un 50 a 70 % y aquellos contra T. brucei transportan moléculas tóxicas al lisosoma parasitario como una novedosa estrategia terapéutica. Los datos recopilados en esta revisión destacan los aptámeros como una alternativa para la investigación, el diagnóstico y el tratamiento contra parásitos de interés nacional.
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Abstract
Aptamers are synthetic DNA or RNA oligonucleotide ligands with great potential for therapeutic applications. A vast number of disease-related targets have been used to identify agonistic, antagonistic, or inhibitory aptamers, or aptamer-based targeting ligands. However, only a few aptamers have reached late-stage clinical trials so far and the commercial infrastructure is still far behind that of other therapeutic agents such as monoclonal antibodies. The desirable properties of aptamers such as selectivity, chemical flexibility, or cost-efficiency are faced by challenges, including a short half-life in vivo, immunogenicity, and entrapment in cellular organelles. Aptamer research is still in an early stage, and a deeper understanding of their structure, target interactions, and pharmacokinetics is necessary to catch up to the clinical market. In this review, we will discuss the benefits and limitations in the development of therapeutic aptamers, as well as the advances and future directions of aptamer research. The progress towards effective therapies seems to be slow, but it has not stopped and the best is yet to come.
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Nsairat H, Mahmoud IS, Odeh F, Abuarqoub D, Al-Azzawi H, Zaza R, Qadri MI, Ismail S, Al Bawab A, Awidi A, Alshaer W. Grafting of anti-nucleolin aptamer into preformed and remotely loaded liposomes through aptamer-cholesterol post-insertion. RSC Adv 2020; 10:36219-36229. [PMID: 35517091 PMCID: PMC9056972 DOI: 10.1039/d0ra07325c] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
A new combination strategy of an active loading and active targeting approach was applied in this work. The liposomes actively loaded with Curcumin (CRM) (LipCRM) were decorated with cholesterol tagged-anti-nucleolin AS1411 aptamer (NCL) via a new post-insertion approach, utilizing the cholesterol as a wedge to incorporate aptamer into the surface of the liposome bilayer. A successful NCL post-insertion was verified by agarose gel electrophoresis and dynamic light scattering (DLS). The cellular uptake of AptNCL-Lip was investigated using flow cytometry and Confocal Laser Scanning Microscopy (CLSM) on two different human breast cancer cell lines (MCF-7 and MDA-MB-231). The uptake and cytotoxicity of loaded CRM were investigated using flow cytometry and MTT assay. Our results showed successful post insertion of NCL aptamer to the surface of Lip. Also, higher cellular uptake was noted for AptNCL-Alexa-LipRhod compared to blank LipRhod in both cell lines. Moreover, CLSM showed prominent endocytosis and uptake of AptNCL-Alexa–LipRhod into the cytoplasm of breast cancer cells. Furthermore, the results showed a significant increase in the uptake and cytotoxicity of AptNCL-LipCRM compared to LipCRM in both cell lines. Overall, our results demonstrate a successful post-insertion of cholesterol-tagged aptamer into liposomes and the possible combination between active loading and active targeting. A new combination strategy of an active loading and active targeting approach was applied in this work.![]()
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Eremeeva E, Fikatas A, Margamuljana L, Abramov M, Schols D, Groaz E, Herdewijn P. Highly stable hexitol based XNA aptamers targeting the vascular endothelial growth factor. Nucleic Acids Res 2019; 47:4927-4939. [PMID: 30968117 PMCID: PMC6547419 DOI: 10.1093/nar/gkz252] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 01/22/2023] Open
Abstract
Biomedical applications of nucleic acid aptamers are limited by their rapid degradation in biological fluids and generally demand tedious post-selection modifications that might compromise binding. One possible solution to warrant biostability is to directly evolve chemically modified aptamers from xenobiotic nucleic acids (XNAs). We have isolated fully modified 2'-O-methyl-ribose-1,5-anhydrohexitol nucleic acid (MeORNA-HNA) aptamers targeting the rat vascular endothelial growth factor 164 (rVEGF164). Three sequences have been identified that interact with the target protein with affinities in the low-nanomolar range and HNA modifications appeared to be mandatory for their tight binding. The evolution of these XNA aptamers was accomplished using an in vitro selection procedure starting from a fully sugar-modified library containing a 20mer 2'-OMe-ribonucleotide region followed by a 47mer HNA sequence. The high binding affinity and selectivity of the selected aptamers were confirmed by several methods including gel-shift, fluorescence polarisation, and enzyme-linked oligonucleotide assays. The isolated HNA ligands exhibited higher specificity to the rVEGF164 and human VEGF165 isoforms compared to rat VEGF120, while very low binding efficiencies were observed to streptavidin and thrombin. Furthermore, it was clearly demonstrated that the resulting aptamers possessed a superior stability to degradation in human serum and DNase I solutions.
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Affiliation(s)
- Elena Eremeeva
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Antonios Fikatas
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1043, 3000 Leuven, Belgium
| | - Lia Margamuljana
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Mikhail Abramov
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1043, 3000 Leuven, Belgium
| | - Elisabetta Groaz
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49 - Box 1041, 3000 Leuven, Belgium
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Riccardi C, Musumeci D, Trifuoggi M, Irace C, Paduano L, Montesarchio D. Anticancer Ruthenium(III) Complexes and Ru(III)-Containing Nanoformulations: An Update on the Mechanism of Action and Biological Activity. Pharmaceuticals (Basel) 2019; 12:E146. [PMID: 31561546 PMCID: PMC6958509 DOI: 10.3390/ph12040146] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/22/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
The great advances in the studies on metal complexes for the treatment of different cancer forms, starting from the pioneering works on platinum derivatives, have fostered an increasingly growing interest in their properties and biomedical applications. Among the various metal-containing drugs investigated thus far, ruthenium(III) complexes have emerged for their selective cytotoxic activity in vitro and promising anticancer properties in vivo, also leading to a few candidates in advanced clinical trials. Aiming at addressing the solubility, stability and cellular uptake issues of low molecular weight Ru(III)-based compounds, some research groups have proposed the development of suitable drug delivery systems (e.g., taking advantage of nanoparticles, liposomes, etc.) able to enhance their activity compared to the naked drugs. This review highlights the unique role of Ru(III) complexes in the current panorama of anticancer agents, with particular emphasis on Ru-containing nanoformulations based on the incorporation of the Ru(III) complexes into suitable nanocarriers in order to enhance their bioavailability and pharmacokinetic properties. Preclinical evaluation of these nanoaggregates is discussed with a special focus on the investigation of their mechanism of action at a molecular level, highlighting their pharmacological potential in tumour disease models and value for biomedical 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.
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy.
| | - Marco Trifuoggi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy.
| | - Carlo Irace
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy.
| | - Luigi Paduano
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy.
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Kamatkar N, Levy M, Hébert JM. Development of a Monomeric Inhibitory RNA Aptamer Specific for FGFR3 that Acts as an Activator When Dimerized. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 17:530-539. [PMID: 31357131 PMCID: PMC6661505 DOI: 10.1016/j.omtn.2019.06.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/12/2019] [Accepted: 06/22/2019] [Indexed: 12/11/2022]
Abstract
There have been limited options for people who suffer from fibroblast growth factor receptor (FGFR) signaling disorders. In this study, we developed RNA aptamers specific for FGFR3 as potential therapeutic agents. Using a structured aptamer library, we performed ten rounds of SELEX (systematic evolution of ligands by exponential enrichment) against mouse FGFR3c protein. Using an engineered BaF3 cell line, one aptamer clone from round 6 of the selection inhibited FGF-dependent cell growth with a concentration at which 50% of growth is observed (IC50) of ∼260 nM and bound both mouse and human FGFR3 but not FGFR1 or FGFR2. This inhibitor of FGFR3 signaling (iR3), when dimerized using a template-driven approach, resulted in a functional activator of FGFR3 (aR3). We validated the activity and specificity of iR3 and aR3 on engineered BaF3 cell lines, mouse and human FGFR protein, and primary cultures of neuroepithelial precursor cells.
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Affiliation(s)
- Nachiket Kamatkar
- Departments of Neuroscience and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Matthew Levy
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Jean M Hébert
- Departments of Neuroscience and Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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Amato T, Virgilio A, Pirone L, Vellecco V, Bucci M, Pedone E, Esposito V, Galeone A. Investigating the properties of TBA variants with twin thrombin binding domains. Sci Rep 2019; 9:9184. [PMID: 31235717 PMCID: PMC6591170 DOI: 10.1038/s41598-019-45526-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/07/2019] [Indexed: 02/04/2023] Open
Abstract
In this paper, we report studies concerning thrombin binding aptamer (TBA) dimeric derivatives in which the 3′-ends of two TBA sequences have been joined by means of linkers containing adenosine or thymidine residues and/or a glycerol moiety. CD and electrophoretic investigations indicate that all modified aptamers are able to form G-quadruplex domains resembling that of the parent TBA structure. However, isothermal titration calorimetry measurements of the aptamer/thrombin interaction point to different affinities to the target protein, depending on the type of linker. Consistently, the best ligands for thrombin show anticoagulant activities higher than TBA. Interestingly, two dimeric aptamers with the most promising properties also show far higher resistances in biological environment than TBA.
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Affiliation(s)
- Teresa Amato
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Antonella Virgilio
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Luciano Pirone
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Valentina Vellecco
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Mariarosaria Bucci
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Emilia Pedone
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Veronica Esposito
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy.
| | - Aldo Galeone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131, Napoli, Italy.
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Paulmurugan R, Malhotra M, Massoud TF. The protean world of non-coding RNAs in glioblastoma. J Mol Med (Berl) 2019; 97:909-925. [PMID: 31129756 DOI: 10.1007/s00109-019-01798-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/05/2019] [Accepted: 05/13/2019] [Indexed: 12/12/2022]
Abstract
Non-coding ribonucleic acids (ncRNAs) are a diverse group of RNA molecules that are mostly not translated into proteins following transcription. We review the role of ncRNAs in the pathobiology of glioblastoma (GBM), and their potential applications for GBM therapy. Significant advances in our understanding of the protean manifestations of ncRNAs have been made, allowing us to better decipher the molecular complexity of GBM. A large number of regulatory ncRNAs appear to have a greater influence on the molecular pathology of GBM than thought previously. Importantly, also, a range of therapeutic approaches are emerging whereby ncRNA-based systems may be used to molecularly target GBM. The most successful of these is RNA interference, and some of these strategies are being evaluated in ongoing clinical trials. However, a number of limitations exist in the clinical translation of ncRNA-based therapeutic systems, such as delivery mechanisms and cytotoxicity; concerted research endeavors are currently underway in an attempt to overcome these. Ongoing and future studies will determine the potential practical role for ncRNA-based therapeutic systems in the clinical management of GBM. These applications may be especially promising, given that current treatment options are limited and prognosis remains poor for this challenging malignancy.
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Affiliation(s)
- Ramasamy Paulmurugan
- Cellular Pathway Imaging Laboratory (CPIL), Molecular Imaging Program at Stanford, Stanford University School of Medicine, 3155 Porter Drive, Palo Alto, CA, 94305, USA.
| | - Meenakshi Malhotra
- Laboratory of Experimental and Molecular Neuroimaging (LEMNI), Molecular Imaging Program at Stanford, Stanford University School of Medicine, 300 Pasteur Drive, Grant S-031, Stanford, CA, 94305-5105, USA
| | - Tarik F Massoud
- Laboratory of Experimental and Molecular Neuroimaging (LEMNI), Molecular Imaging Program at Stanford, Stanford University School of Medicine, 300 Pasteur Drive, Grant S-031, Stanford, CA, 94305-5105, USA.
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Yang S, Wen J, Li H, Xu L, Liu Y, Zhao N, Zeng Z, Qi J, Jiang W, Han W, Zu Y. Aptamer-Engineered Natural Killer Cells for Cell-Specific Adaptive Immunotherapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900903. [PMID: 31026116 PMCID: PMC6541510 DOI: 10.1002/smll.201900903] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/04/2019] [Indexed: 05/28/2023]
Abstract
Natural killer (NK) cells are a key component of the innate immune system as they can attack cancer cells without prior sensitization. However, due to lack of cell-specific receptors, NK cells are not innately able to perform targeted cancer immunotherapy. Aptamers are short single-stranded oligonucleotides that specifically recognize their targets with high affinity in a similar manner to antibodies. To render NK cells with target-specificity, synthetic CD30-specific aptamers are anchored on cell surfaces to produce aptamer-engineered NK cells (ApEn-NK) without genetic alteration or cell damage. Under surface-anchored aptamer guidance, ApEn-NK specifically bind to CD30-expressing lymphoma cells but do not react to off-target cells. The resulting specific cell binding of ApEn-NK triggers higher apoptosis/death rates of lymphoma cells compared to parental NK cells. Additionally, experiments with primary human NK cells demonstrate the potential of ApEn-NK to specifically target and kill lymphoma cells, thus presenting a potential new approach for targeted immunotherapy by NK cells.
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Affiliation(s)
- Shuanghui Yang
- Department of Hematology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Jianguo Wen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Huan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Ling Xu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
- Department of Hematology, First Affiliated Hospital, Jinan University, Guangzhou 510632, Guangdong, China
| | - Yanting Liu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Nianxi Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Zihua Zeng
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Jianjun Qi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Wenqi Jiang
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Wei Han
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
- Department of Hematology, First Hospital of Jilin University, Changchun 130021, Jilin, China
| | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
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Lee J, Oh J, Lee ES, Kim YP, Lee M. Conjugation of prostate cancer-specific aptamers to polyethylene glycol-grafted polyethylenimine for enhanced gene delivery to prostate cancer cells. J IND ENG CHEM 2019. [DOI: 10.1016/j.jiec.2019.01.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Abstract
This chapter provides a brief introduction to followed by discussion of recent preclinical studies on potential aptamer drugs grouped into two broad categories, namely, “aptamer structures” and “non-ocular diseases.” Examples of aptamer-based targeting of drugs are then described. Next is an overview of the status of nearly 30 clinical trials of aptamer drugs currently listed in ClinicalTrials.gov, which is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world, and is a service of the US National Institutes of Health. This overview includes brief descriptions of each study sponsor, aptamer drug, disease(s), and type of study, as well as separate tables for completed studies, withdrawn or terminated studies, and active studies. The final section discusses Conclusions and Prospects.
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Affiliation(s)
- G. Zon
- TriLink BioTechnologies 9955 Mesa Rim Road San Diego 92121 USA
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Acquah C, Agyei D, Obeng EM, Pan S, Tan KX, Danquah MK. Aptamers: an emerging class of bioaffinity ligands in bioactive peptide applications. Crit Rev Food Sci Nutr 2019; 60:1195-1206. [PMID: 30714390 DOI: 10.1080/10408398.2018.1564234] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The food and health applications of bioactive peptides have grown remarkably in the past few decades. Current elucidations have shown that bioactive peptides have unique structural arrangement of amino acids, conferring distinct functionalities, and molecular affinity characteristics. However, whereas interest in the biological potency of bioactive peptides has grown, cost-effective techniques for monitoring the structural changes in these peptides and how these changes affect the biological properties have not grown at the same rate. Due to the high binding affinity of aptamers for other biomolecules, they have a huge potential for use in tracking the structural, conformational, and compositional changes in bioactive peptides. This review provides an overview of bioactive peptides and their essential structure-activity relationship. The review further highlights on the types and methods of synthesis of aptamers before the discussion of the prospects, merits, and challenges in the use of aptamers for bioaffinity interactions with bioactive peptides.
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Affiliation(s)
- Caleb Acquah
- Department of Chemical Engineering, Curtin University, Sarawak, Malaysia.,School of Nutrition Sciences, Faculty of Health Sciences, Curtin University, Sarawak, Malaysia
| | - Dominic Agyei
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Eugene Marfo Obeng
- Bioengineering Laboratory, Department of Chemical Engineering, Monash University, Victoria, Australia
| | - Sharadwata Pan
- School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Kei Xian Tan
- Department of Chemical Engineering, Curtin University, Sarawak, Malaysia
| | - Michael Kobina Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga, Tennessee, USA
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Cai S, Yan J, Xiong H, Liu Y, Peng D, Liu Z. Investigations on the interface of nucleic acid aptamers and binding targets. Analyst 2019; 143:5317-5338. [PMID: 30357118 DOI: 10.1039/c8an01467a] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA of 20-100 nucleotides in length that have attracted substantial scientific interest due to their ability to specifically bind to target molecules via the formation of three-dimensional structures. Compared to traditional protein antibodies, aptamers have several advantages, such as their small size, high binding affinity, specificity, flexible structure, being chemical synthesizable and modifiable, good biocompatibility, high stability and low immunogenicity, which all contribute to their widely applications in the biomedical field. To date, much progress has been made in the study and applications of aptamers, however, detailed information on how aptamers bind to their targets is still scarce. Over the past few decades, many methods have been introduced to investigate the aptamer-target binding process, such as measuring the main kinetic or thermodynamic parameters, detecting the structural changes of the binding complexes, etc. Apart from traditional physicochemical methods, various types of molecular docking programs have been applied to simulate the aptamer-target interactions, while these simulations also have limitations. To facilitate the further research on the interactions, herein, we provide a brief review to illustrate the recent advances in the study of aptamer-target interactions. We summarize the binding targets of aptamers, such as small molecules, macromolecules, and even cells. Their binding constants (KD) are also summarized. Methods to probe the aptamer-target binding process, such as surface plasmon resonance (SPR), circular dichroism spectroscopy (CD), isothermal titration calorimetry (ITC), footprinting assay, truncation and mutation assay, nuclear magnetic resonance spectroscopy (NMR), X-ray crystallography and molecular docking simulation are indicated. The binding forces mediating the aptamer-target interactions, such as hydrogen bonding, electrostatic interaction, the hydrophobic effect, π-π stacking and van der Waals forces are summarized. The challenges and future perspectives are also discussed.
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Affiliation(s)
- Shundong Cai
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, PR China.
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Non canonical genetic material. Curr Opin Biotechnol 2018; 57:25-33. [PMID: 30554069 DOI: 10.1016/j.copbio.2018.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 11/13/2018] [Accepted: 12/03/2018] [Indexed: 01/20/2023]
Abstract
To increase the scope of natural biosystem, nucleic acids have been intensively modified. One direction includes the development of a synthetic alternative to the native DNA and RNA, denoted Xenobiotic nucleic acids (XNAs) that are able to store and transfer genetic information either by base-modification or backbone-modification. Another line of research aims to develop alternative third base pair additional to natural A:T and G:C. These unnatural base pairs (UBPs) can store increased information content encoded in three base pairs. This review outlines the recent progress made towards XNA and UBP applications as new components of the genomic DNA as well as biostable aptamers. New achievements in the replacement of a bacterial genome by unnatural non-canonical nucleotides are also described.
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Kovacevic KD, Gilbert JC, Jilma B. Pharmacokinetics, pharmacodynamics and safety of aptamers. Adv Drug Deliv Rev 2018; 134:36-50. [PMID: 30321620 DOI: 10.1016/j.addr.2018.10.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 12/15/2022]
Abstract
Aptamers are synthetic molecules structured as single-stranded DNA or RNA oligonucleotides that can be designed to mimic the functional properties of monoclonal antibodies. They bind to the target molecules (typically soluble or cell-bound proteins) with high affinity (with picomolar to low nanomolar range) and specificity, and therefore can be an alternative to therapeutic antibodies or peptide ligands. This paper reviews published data regarding pharmacokinetics, pharmacodynamics and safety of aptamers from preclinical and clinical studies. Aptamers have been developed for the treatment of a variety of diseases, including cancer, macular degeneration,g cardiovascular disease, diabetes and anaemia of chronic diseases. There are several preclinical studies with unmodified aptamers, but the vast majority of aptamer trials in humans have been conducted with modified aptamers, because unmodified aptamers demonstrate metabolic instability, as well as rapid renal filtration and elimination. Various strategies have been developed to improve the pharmacokinetic profile of aptamers. Aside from chemical modification of nucleotides in order to stabilize them against nuclease degradation, the main modification to extend the half-life is pegylation. Therefore, the process of pegylation as well as its benefits and possible shortcomings will briefly be discussed.
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Fernández G, Moraga A, Cuartero MI, García-Culebras A, Peña-Martínez C, Pradillo JM, Hernández-Jiménez M, Sacristán S, Ayuso MI, Gonzalo-Gobernado R, Fernández-López D, Martín ME, Moro MA, González VM, Lizasoain I. TLR4-Binding DNA Aptamers Show a Protective Effect against Acute Stroke in Animal Models. Mol Ther 2018; 26:2047-2059. [PMID: 29910175 PMCID: PMC6094477 DOI: 10.1016/j.ymthe.2018.05.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 05/18/2018] [Accepted: 05/21/2018] [Indexed: 02/08/2023] Open
Abstract
Since Toll-like receptor 4 (TLR4) mediates brain damage after stroke, development of TLR4 antagonists is a promising therapeutic strategy for this disease. Our aim was to generate TLR4-blocking DNA aptamers to be used for stroke treatment. From a random oligonucleotide pool, we identified two aptamers (ApTLR#1R, ApTLR#4F) with high affinity for human TLR4 by systematic evolution of ligands by exponential enrichment (SELEX). Optimized truncated forms (ApTLR#1RT, ApTLR#4FT) were obtained. Our data demonstrate specific binding of both aptamers to human TLR4 as well as a TLR4 antagonistic effect. ApTLR#4F and ApTLR#4FT showed a long-lasting protective effect against brain injury induced by middle cerebral artery occlusion (MCAO), an effect that was absent in TLR4-deficient mice. Similar effects were obtained in other MCAO models, including in rat. Additionally, efficacy of ApTLR#4FT in a model of brain ischemia-reperfusion in rat supports the use of this aptamer in patients undergoing artery recanalization induced by pharmacological or mechanical interventions. The absence of major toxicology aspects and the good safety profile of the aptamers further encourage their future clinical positioning for stroke therapy and possibly other diseases in which TLR4 plays a deleterious role.
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Affiliation(s)
| | - Ana Moraga
- Unidad de Investigación Neurovascular, Departamento de Farmacología y Toxicología, Facultad de Medicina, Instituto Universitario de Investigación en Neuroquímica, Universidad Complutense de Madrid, 28040 Madrid, Spain; Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - María I Cuartero
- Unidad de Investigación Neurovascular, Departamento de Farmacología y Toxicología, Facultad de Medicina, Instituto Universitario de Investigación en Neuroquímica, Universidad Complutense de Madrid, 28040 Madrid, Spain; Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Alicia García-Culebras
- Unidad de Investigación Neurovascular, Departamento de Farmacología y Toxicología, Facultad de Medicina, Instituto Universitario de Investigación en Neuroquímica, Universidad Complutense de Madrid, 28040 Madrid, Spain; Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Carolina Peña-Martínez
- Unidad de Investigación Neurovascular, Departamento de Farmacología y Toxicología, Facultad de Medicina, Instituto Universitario de Investigación en Neuroquímica, Universidad Complutense de Madrid, 28040 Madrid, Spain; Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Jesús M Pradillo
- Unidad de Investigación Neurovascular, Departamento de Farmacología y Toxicología, Facultad de Medicina, Instituto Universitario de Investigación en Neuroquímica, Universidad Complutense de Madrid, 28040 Madrid, Spain; Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | | | - Silvia Sacristán
- Laboratorio de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, 28034 Madrid, Spain
| | - M Irene Ayuso
- Grupo de Investigación Neurovascular, Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot s/n, 41013 Sevilla, Spain
| | - Rafael Gonzalo-Gobernado
- Grupo de Investigación Neurovascular, Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot s/n, 41013 Sevilla, Spain
| | - David Fernández-López
- Unidad de Investigación Neurovascular, Departamento de Farmacología y Toxicología, Facultad de Medicina, Instituto Universitario de Investigación en Neuroquímica, Universidad Complutense de Madrid, 28040 Madrid, Spain; Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - M Elena Martín
- Laboratorio de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, 28034 Madrid, Spain
| | - María A Moro
- Unidad de Investigación Neurovascular, Departamento de Farmacología y Toxicología, Facultad de Medicina, Instituto Universitario de Investigación en Neuroquímica, Universidad Complutense de Madrid, 28040 Madrid, Spain; Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain
| | - Victor M González
- Laboratorio de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, 28034 Madrid, Spain.
| | - Ignacio Lizasoain
- Unidad de Investigación Neurovascular, Departamento de Farmacología y Toxicología, Facultad de Medicina, Instituto Universitario de Investigación en Neuroquímica, Universidad Complutense de Madrid, 28040 Madrid, Spain; Instituto de Investigación Hospital 12 de Octubre (i+12), 28041 Madrid, Spain.
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Yan AC, Levy M. Aptamer-Mediated Delivery and Cell-Targeting Aptamers: Room for Improvement. Nucleic Acid Ther 2018; 28:194-199. [PMID: 29883295 PMCID: PMC5994660 DOI: 10.1089/nat.2018.0732] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/25/2018] [Indexed: 01/01/2023] Open
Abstract
Targeting cells with aptamers for the delivery of therapeutic cargoes, in particular oligonucleotides, represents one of the most exciting applications of the aptamer field. Perhaps nowhere has there been more excitement in the field than around the targeted delivery of siRNA or miRNA. However, when industry leaders in the field of siRNA delivery have tried to recapitulate aptamer-siRNA delivery results, they have failed. This problem stems from more than just the age-old problem of delivery to the cytoplasm, a challenge that has stymied the targeted delivery of therapeutic oligonucleotides since its inception. With aptamers, the problem is compounded further by the fact that many aptamers simply do not function as reported. This is distressing, as clearly, all published aptamers should be able to function as described. However, it is often challenging to recognize the details that might flag an unreliable aptamer from a viable one. As such, unreliable aptamers continue to be peer reviewed and published. We need to raise the bar and level of rigor in the field. Only then can we think about taking advantage of the unique attributes of these molecules and address the issues associated with their use as agents for targeted delivery.
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Affiliation(s)
- Amy C. Yan
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York
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Tunable cytotoxic aptamer-drug conjugates for the treatment of prostate cancer. Proc Natl Acad Sci U S A 2018; 115:4761-4766. [PMID: 29666232 DOI: 10.1073/pnas.1717705115] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Therapies that can eliminate both local and metastatic prostate tumor lesions while sparing normal organ tissue are desperately needed. With the goal of developing an improved drug-targeting strategy, we turned to a new class of targeted anticancer therapeutics: aptamers conjugated to highly toxic chemotherapeutics. Cell selection for aptamers with prostate cancer specificity yielded the E3 aptamer, which internalizes into prostate cancer cells without targeting normal prostate cells. Chemical conjugation of E3 to the drugs monomethyl auristatin E (MMAE) and monomethyl auristatin F (MMAF) yields a potent cytotoxic agent that efficiently kills prostate cancer cells in vitro but does not affect normal prostate epithelial cells. Importantly, the E3 aptamer targets tumors in vivo and treatment with the MMAF-E3 conjugate significantly inhibits prostate cancer growth in mice, demonstrating the in vivo utility of aptamer-drug conjugates. Additionally, we report the use of antidotes to block E3 aptamer-drug conjugate cytotoxicity, providing a safety switch in the unexpected event of normal cell killing in vivo.
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Zeninskaya NA, Kolesnikov AV, Ryabko AK, Shemyakin IG, Dyatlov IA, Kozyr AV. [Aptamers in the Treatment of Bacterial Infections: Problems and Prospects]. ACTA ACUST UNITED AC 2018; 71:350-8. [PMID: 29297663 DOI: 10.15690/vramn591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Aptamers are short single-stranded oligonucleotides which are selected via targeted chemical evolution in vitro to bind a molecular target of interest. The aptamer selection technology is designated as SELEX (Systematic evolution of ligands by exponential enrichment). SELEX enables isolation of oligonucleotide aptamers binding a wide range of targets of interest with little respect for their nature and molecular weight. A number of applications of aptamer selection were developed ranging from biosensor technologies to antitumor drug discovery. First aptamer-based pharmaceutical (Macugen) was approved by FDA for clinical use in 2004, and since then more than ten aptamer-based drugs undergo various phases of clinical trials. From the medicinal chemist’s point of view, aptamers represent a new class of molecules suitable for the development of new therapeutics. Due to the stability, relative synthesis simplicity, and development of advanced strategies of target specific molecular selection, aptamers attract increased attention of drug discovery community. Difficulties of the development of next-generation antibiotics basing on the conventional basis of combinatorial chemistry and high-throughput screening have also amplified the interest to aptamer-based therapeutic candidates. The present article reviews the investigations focused on the development of antibacterial aptamers and discusses the potential and current limitations of the use of this type of therapeutic molecules.
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Fluorescence Sensing Using DNA Aptamers in Cancer Research and Clinical Diagnostics. Cancers (Basel) 2017; 9:cancers9120174. [PMID: 29261171 PMCID: PMC5742822 DOI: 10.3390/cancers9120174] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 12/12/2022] Open
Abstract
Among the various advantages of aptamers over antibodies, remarkable is their ability to tolerate a large number of chemical modifications within their backbone or at the termini without losing significant activity. Indeed, aptamers can be easily equipped with a wide variety of reporter groups or coupled to different carriers, nanoparticles, or other biomolecules, thus producing valuable molecular recognition tools effective for diagnostic and therapeutic purposes. This review reports an updated overview on fluorescent DNA aptamers, designed to recognize significant cancer biomarkers both in soluble or membrane-bound form. In many examples, the aptamer secondary structure switches induced by target recognition are suitably translated in a detectable fluorescent signal using either fluorescently-labelled or label-free aptamers. The fluorescence emission changes, producing an enhancement (“signal-on”) or a quenching (“signal-off”) effect, directly reflect the extent of the binding, thereby allowing for quantitative determination of the target in bioanalytical assays. Furthermore, several aptamers conjugated to fluorescent probes proved to be effective for applications in tumour diagnosis and intraoperative surgery, producing tumour-type specific, non-invasive in vivo imaging tools for cancer pre- and post-treatment assessment.
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Russo Krauss I, Napolitano V, Petraccone L, Troisi R, Spiridonova V, Mattia CA, Sica F. Duplex/quadruplex oligonucleotides: Role of the duplex domain in the stabilization of a new generation of highly effective anti-thrombin aptamers. Int J Biol Macromol 2017; 107:1697-1705. [PMID: 29024684 DOI: 10.1016/j.ijbiomac.2017.10.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 12/19/2022]
Abstract
Recently, mixed duplex/quadruplex oligonucleotides have attracted great interest for use as biomedical aptamers. In the case of anti-thrombin aptamers, the addition of duplex-forming sequences to a G-quadruplex module identical or very similar to the best-known G-quadruplex of the Thrombin Binding Aptamer (HD1) results in new or improved biological properties, such as higher activity or different recognition properties with respect to HD1. Remarkably, this bimodular fold was hypothesized, based on its sequence, for the only anti-thrombin aptamer in advanced clinical trial, NU172. Whereas cation modulation of G-quadruplex conformation and stability is well characterized, only few data from similar analysis on duplex/quadruplex oligonucleotides exist. Here we have performed a characterization of structure and stability of four different duplex/quadruplex anti-thrombin aptamers, including NU172, in the presence of different cations and in physiological-mimicking conditions in comparison to HD1, by means of spectroscopic techniques (UV and circular dichroism) and differential scanning calorimetry. Our data show a strong reciprocal influence of each domain on the stability of the other and in particular suggest a stabilizing effect of the duplex region in the presence of solutions mimicking the physiological conditions, strengthening the idea that bimodular aptamers present better therapeutic potentialities than those containing a single G-quadruplex domain.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Via della Lastruccia 3, I-50019, Sesto Fiorentino, FI, Italy
| | - Valeria Napolitano
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy
| | - Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy
| | - Vera Spiridonova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Carlo Andrea Mattia
- Department of Pharmacy, University of Salerno, Via Ponte Don Melillo, I-84084, Fisciano, SA, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Naples, Italy.
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Kratschmer C, Levy M. Effect of Chemical Modifications on Aptamer Stability in Serum. Nucleic Acid Ther 2017; 27:335-344. [PMID: 28945147 DOI: 10.1089/nat.2017.0680] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
There is increasing interest in the use of aptamers for the development of therapeutics. However, as oligonucleotides, aptamers are susceptible to nuclease degradation; poor serum stability is likely to negatively affect in vivo function. Modified nucleotides have been used to thwart nuclease degradation. However, few studies report the serum stability of selected aptamers. In this study, we examined the effect of various chemical modifications (2'-deoxy, 2'-hydroxyl, 2'-fluoro, and 2'-O-methyl) on the stability of a control oligonucleotide sequence following incubation in frozen human, fresh mouse, and fresh human serum. We also assessed the effect of the 3' inverted dT cap on stability. Surprisingly, we found that fYrR (2'-fluoro RNA) is only roughly as stable as DNA (2'-deoxy). Interestingly, the inclusion of a 3' inverted dT cap had only a modest effect on serum stability, if any. In one instance, the addition of a 3' inverted dT cap rendered a molecule composed of DNA more stable than its fYrR counterpart. By far, fully modified oligonucleotides (100% 2-O-Methyl or 2'-O-methyl A, C, and U in combination with 2'-fluoro G, termed fGmH) had the longest half-lives. These compositions demonstrated little degradation in human serum even after prolonged incubation. Together these results support the need for using fully modified aptamers for in vivo applications and should encourage those in the field to exploit newer polymerase variants capable of directly generating such polymers.
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Affiliation(s)
- Christina Kratschmer
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York
| | - Matthew Levy
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York
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Tawiah KD, Porciani D, Burke DH. Toward the Selection of Cell Targeting Aptamers with Extended Biological Functionalities to Facilitate Endosomal Escape of Cargoes. Biomedicines 2017; 5:biomedicines5030051. [PMID: 28837119 PMCID: PMC5618309 DOI: 10.3390/biomedicines5030051] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 08/19/2017] [Accepted: 08/19/2017] [Indexed: 12/26/2022] Open
Abstract
Over the past decades there have been exciting and rapid developments of highly specific molecules to bind cancer antigens that are overexpressed on the surfaces of malignant cells. Nanomedicine aims to exploit these ligands to generate nanoscale platforms for targeted cancer therapy, and to do so with negligible off-target effects. Aptamers are structured nucleic acids that bind to defined molecular targets ranging from small molecules and proteins to whole cells or viruses. They are selected through an iterative process of amplification and enrichment called SELEX (systematic evolution of ligands by exponential enrichment), in which a combinatorial oligonucleotide library is exposed to the target of interest for several repetitive rounds. Nucleic acid ligands able to bind and internalize into malignant cells have been extensively used as tools for targeted delivery of therapeutic payloads both in vitro and in vivo. However, current cell targeting aptamer platforms suffer from limitations that have slowed their translation to the clinic. This is especially true for applications in which the cargo must reach the cytosol to exert its biological activity, as only a small percentage of the endocytosed cargo is typically able to translocate into the cytosol. Innovative technologies and selection strategies are required to enhance cytoplasmic delivery. In this review, we describe current selection methods used to generate aptamers that target cancer cells, and we highlight some of the factors that affect productive endosomal escape of cargoes. We also give an overview of the most promising strategies utilized to improve and monitor endosomal escape of therapeutic cargoes. The methods we highlight exploit tools and technologies that can potentially be incorporated in the SELEX process. Innovative selection protocols may identify aptamers with extended biological functionalities that allow effective cytosolic translocation of therapeutics. This in turn may facilitate successful translation of these platforms into clinical applications.
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Affiliation(s)
- Kwaku D Tawiah
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - David Porciani
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
- Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65212, USA.
| | - Donald H Burke
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
- Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65212, USA.
- Department of Bioengineering, University of Missouri, Columbia, MO 65211, USA.
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Duncan R. Polymer therapeutics at a crossroads? Finding the path for improved translation in the twenty-first century. J Drug Target 2017; 25:759-780. [PMID: 28783978 DOI: 10.1080/1061186x.2017.1358729] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Despite the relatively small early investment, first generation 'polymer therapeutics' have been remarkably successful with more than 25 products licenced for human use as polymeric drugs, sequestrants, conjugates, and as an imaging agent. Many exhibit both clinical and commercial success with new concepts already in clinical trials. Nevertheless after four decades of evolution, this field is arriving at an important crossroads. Over the last decade, the landscape has changed rapidly. There are an increasing number of failed clinical trials, the number of 'copy' and 'generic' products is growing (danger of ignoring the biological rationale for design and suppression of innovation), potential drawbacks of PEG are becoming more evident, and the 'nanomedicine' boom has brought danger of loss of scientific focus/hype. Grasping opportunities provided by advances in understanding of the patho-physiology and molecular basis of diseases, new polymer/conjugate synthetic and analytical methods, as well as the large database of clinical experience will surely ensure a successful future for innovative polymer therapeutics. Progress will, however, be in jeopardy if polymer safety is overlooked in respect of the specific route of administration/clinical use, poorly characterised materials/formulations are used to define biological or early clinical properties, and if clinical trial protocols fail to select patients most likely to benefit from these macromolecular therapeutics. Opportunities to improve clinical trial design for polymer-anticancer drug conjugates are discussed. This short personal perspective summarises some of the important challenges facing polymer therapeutics in R&D today, and future opportunities to improve successful translation.
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Affiliation(s)
- Ruth Duncan
- a Polymer Therapeutics Laboratory , Centro de Investigación Príncipe Felipe , Valencia , Spain.,b Intracellular Delivery Solutions Laboratory, Faculty of Engineering and Science , University of Greenwich , Kent , UK
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Chemical Modifications of Nucleic Acid Aptamers for Therapeutic Purposes. Int J Mol Sci 2017; 18:ijms18081683. [PMID: 28767098 PMCID: PMC5578073 DOI: 10.3390/ijms18081683] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 01/16/2023] Open
Abstract
Nucleic acid aptamers have minimal immunogenicity, high chemical synthesis production, low cost and high chemical stability when compared with antibodies. However, the susceptibility to nuclease degradation, rapid excretion through renal filtration and insufficient binding affinity hindered their development as drug candidates for therapeutic applications. In this review, we will discuss methods to conquer these challenges and highlight recent developments of chemical modifications and technological advances that may enable early aptamers to be translated into clinical therapeutics.
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50
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Eremeeva E, Abramov M, Margamuljana L, Herdewijn P. Base-Modified Nucleic Acids as a Powerful Tool for Synthetic Biology and Biotechnology. Chemistry 2017; 23:9560-9576. [PMID: 28513881 DOI: 10.1002/chem.201700679] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 11/10/2022]
Abstract
The ability of various nucleoside triphosphate analogues of deoxyguanosine and deoxycytidine with 7-deazadeoxyadenosine (A1 ) and 5-chlorodeoxyuridine (T1 ) to serve as substrates for Taq DNA polymerase was evaluated. The triphosphate set composed of A1 , T1 , and 7-deazadeoxyguanosine with either 5-methyldeoxycytidine or 5-fluorodeoxycytidine was successfully employed in the polymerase chain reaction (PCR) of 1.5 kb fragments as well as random oligonucleotide libraries. Another effective combination of triphosphates for the synthesis of a 1 kb PCR product was A1 , T1 , deoxyinosine, and 5-bromodeoxycytidine. In vivo experiments using an antibiotic-resistant gene containing the latter set demonstrated that the bacterial machinery accepts fully modified sequences as genetic templates. Moreover, the ability of the base-modified segments to selectively protect DNA from cleavage by restriction endonucleases was shown. This approach can be used to regulate the endonuclease cleavage pattern.
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Affiliation(s)
- Elena Eremeeva
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium
| | - Michail Abramov
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium
| | - Lia Margamuljana
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium.,Université d'évry, CNRS-UMR8030/ Laboratoire iSSB, CEA, DRF, IG, Genoscope, Université Paris-Saclay, évry, 91000, Paris, France
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