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Special Issue "Aptamers: Biomedical Interest and Applications"

A special issue of Pharmaceuticals (ISSN 1424-8247).

Deadline for manuscript submissions: closed (30 September 2016)

Special Issue Editors

Guest Editor
Dr. Alfredo Berzal-Herranz

Department of Molecular Biology, Instituto de Parasitología y Biomedicina López-Neyra, (IPBLN-CSIC), PTS Granada, Av del Conocimiento 17, 18016 Granada, Spain
Website | E-Mail
Interests: structure-function of RNA; aptamers; antisense; ribozymes; viral RNA genomes; RNA as tool; therapeutic RNAs
Co-Guest Editor
Dr. Cristina Romero-López

Department of Molecular Biology, Instituto de Parasitología y Biomedicina López-Neyra (IPBLN-CSIC), PTS Granada, Av. Conocimiento, 18016 Armilla, Granada, Spain
E-Mail
Interests: RNA structural biology; Aptamers; Viral RNA genomes; Functional RNA

Special Issue Information

Dear Colleagues,

Aptamers are emerging as powerful tools in the biomedical field, with a great potential for developing specific therapeutics, diagnostics, or biosensor detection platforms. They also represent an excellent alternative to antibodies.

Aptamers have been obtained against a great variety of molecules, covering a wide range of molecular sizes and complexities, from ions to full cells, including small molecules (such as amino acids, nucleotides, antibiotics, or metabolites), peptides, proteins, nucleic acids, macromolecular complexes, viruses, or cell organelles. In all cases they have been selected following a general scheme known as SELEX (Systematic Evolution of Ligands by Exponential Enrichment). The latest modifications of this general scheme, the identification of aptamers against malignant cells, as well as the progresses made in nucleic acids chemistry, have greatly contributed to the reinforcing of the potential of aptamers as biomedical tools.

This Special Issue intends to summarize the current state-of-the-art in this interesting field; therefore, we invite you to contribute review or original research articles covering different aspects of this technology and describing recent and novel results.

Dr. Alfredo Berzal-Herranz
Dr. Cristina Romero-López
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Pharmaceuticals is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 850 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Aptamers
  • RNA aptamer
  • DNA aptamer
  • Therapeutic Nucleic Acids
  • SELEX
  • In vitro selection
  • oligonucleotides
  • Modified nucleotides
  • Nucleotide analogs
  • Spiegelmers
  • Biosensor
  • Diagnostic

Related Special Issue

Published Papers (7 papers)

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Editorial

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Open AccessEditorial Aptamers: Biomedical Interest and Applications
Pharmaceuticals 2017, 10(1), 32; https://doi.org/10.3390/ph10010032
Received: 13 March 2017 / Accepted: 14 March 2017 / Published: 16 March 2017
Cited by 2 | PDF Full-text (186 KB) | HTML Full-text | XML Full-text
Abstract
Aptamers are short DNA or RNA oligonucleotides specialized in the specific and efficient binding to a target molecule. They are obtained by in vitro selection or evolution processes. It was in 1990 that two independent research groups described the bases of a new
[...] Read more.
Aptamers are short DNA or RNA oligonucleotides specialized in the specific and efficient binding to a target molecule. They are obtained by in vitro selection or evolution processes. It was in 1990 that two independent research groups described the bases of a new in vitro technology for the identification of RNA molecules able to specifically bind to a target [1,2]. Tuerk and Gold established the principals of the in vitro selection process that was named SELEX (Systematic Evolution of Ligands by Exponential enrichment), which is based on iterative cycles of binding, partitioning, and amplification of oligonucleotides from a pool of variant sequences [2]. Ellington and Szostak coined the term aptamer to define the selected molecules by the application of this method [1]. To date, numerous reports have described the isolation of aptamers directed against a great variety of targets covering a wide diversity of molecules varying in nature, size, and complexity ranging from ions to whole cells, including small molecules (e.g., aminoacids, nucleotides, antibiotics), peptides, proteins, nucleic acids, and viruses, among others (for example, see [3–6]). Modifications and optimization of the SELEX procedure aimed to get newly modified aptamers has also attracted much interest (examples can be found in [7,8]). These advances along with the parallel progresses in the nucleic acids chemistry and cellular delivery fields have allowed for the rise of a new hope in developing aptamers as efficient molecular tools for diagnostics and therapeutics (for recent comprehensive reviews, see [9–11]).
Full article
(This article belongs to the Special Issue Aptamers: Biomedical Interest and Applications)

Research

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Open AccessArticle Improved Aptamers for the Diagnosis and Potential Treatment of HER2-Positive Cancer
Pharmaceuticals 2016, 9(2), 29; https://doi.org/10.3390/ph9020029
Received: 20 February 2016 / Revised: 9 May 2016 / Accepted: 10 May 2016 / Published: 19 May 2016
Cited by 9 | PDF Full-text (4066 KB) | HTML Full-text | XML Full-text
Abstract
Aptamers provide a potential source of alternative targeting molecules for existing antibody diagnostics and therapeutics. In this work, we selected novel DNA aptamers targeting the HER2 receptor by an adherent whole-cell SELEX approach. Individual aptamers were identified by next generation sequencing and bioinformatics
[...] Read more.
Aptamers provide a potential source of alternative targeting molecules for existing antibody diagnostics and therapeutics. In this work, we selected novel DNA aptamers targeting the HER2 receptor by an adherent whole-cell SELEX approach. Individual aptamers were identified by next generation sequencing and bioinformatics analysis. Two aptamers, HeA2_1 and HeA2_3, were shown to bind the HER2 protein with affinities in the nanomolar range. In addition, both aptamers were able to bind with high specificity to HER2-overexpressing cells and HER2-positive tumor tissue samples. Furthermore, we demonstrated that aptamer HeA2_3 is being internalized into cancer cells and has an inhibitory effect on cancer cell growth and viability. In the end, we selected novel DNA aptamers with great potential for the diagnosis and possible treatment of HER2-positive cancer. Full article
(This article belongs to the Special Issue Aptamers: Biomedical Interest and Applications)
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Review

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Open AccessReview Use of Aptamers as Diagnostics Tools and Antiviral Agents for Human Viruses
Pharmaceuticals 2016, 9(4), 78; https://doi.org/10.3390/ph9040078
Received: 13 October 2016 / Revised: 12 December 2016 / Accepted: 13 December 2016 / Published: 16 December 2016
Cited by 10 | PDF Full-text (2053 KB) | HTML Full-text | XML Full-text
Abstract
Appropriate diagnosis is the key factor for treatment of viral diseases. Time is the most important factor in rapidly developing and epidemiologically dangerous diseases, such as influenza, Ebola and SARS. Chronic viral diseases such as HIV-1 or HCV are asymptomatic or oligosymptomatic and
[...] Read more.
Appropriate diagnosis is the key factor for treatment of viral diseases. Time is the most important factor in rapidly developing and epidemiologically dangerous diseases, such as influenza, Ebola and SARS. Chronic viral diseases such as HIV-1 or HCV are asymptomatic or oligosymptomatic and the therapeutic success mainly depends on early detection of the infective agent. Over the last years, aptamer technology has been used in a wide range of diagnostic and therapeutic applications and, concretely, several strategies are currently being explored using aptamers against virus proteins. From a diagnostics point of view, aptamers are being designed as a bio-recognition element in diagnostic systems to detect viral proteins either in the blood (serum or plasma) or into infected cells. Another potential use of aptamers is for therapeutics of viral infections, interfering in the interaction between the virus and the host using aptamers targeting host-cell matrix receptors, or attacking the virus intracellularly, targeting proteins implicated in the viral replication cycle. In this paper, we review how aptamers working against viral proteins are discovered, with a focus on recent advances that improve the aptamers’ properties as a real tool for viral infection detection and treatment. Full article
(This article belongs to the Special Issue Aptamers: Biomedical Interest and Applications)
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Open AccessReview Applications of High-Throughput Sequencing for In Vitro Selection and Characterization of Aptamers
Pharmaceuticals 2016, 9(4), 76; https://doi.org/10.3390/ph9040076
Received: 15 November 2016 / Revised: 6 December 2016 / Accepted: 7 December 2016 / Published: 10 December 2016
Cited by 18 | PDF Full-text (571 KB) | HTML Full-text | XML Full-text
Abstract
Aptamers are identified through an iterative process of evolutionary selection starting from a random pool containing billions of sequences. Simultaneously to the amplification of high-affinity candidates, the diversity in the pool is exponentially reduced after several rounds of in vitro selection. Until now,
[...] Read more.
Aptamers are identified through an iterative process of evolutionary selection starting from a random pool containing billions of sequences. Simultaneously to the amplification of high-affinity candidates, the diversity in the pool is exponentially reduced after several rounds of in vitro selection. Until now, cloning and Sanger sequencing of about 100 sequences was usually used to identify the enriched candidates. However, High-Throughput Sequencing (HTS) is now extensively used to replace such low throughput sequencing approaches. Providing a deeper analysis of the library, HTS is expected to accelerate the identification of aptamers as well as to identify aptamers with higher affinity. It is also expected that it can provide important information on the binding site of the aptamers. Nevertheless, HTS requires handling a large amount of data that is only possible through the development of new in silico methods. Here, this review presents these different strategies that have been recently developed to improve the identification and characterization of aptamers using HTS. Full article
(This article belongs to the Special Issue Aptamers: Biomedical Interest and Applications)
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Open AccessFeature PaperReview Aptamer-Mediated Targeted Delivery of Therapeutics: An Update
Pharmaceuticals 2016, 9(4), 69; https://doi.org/10.3390/ph9040069
Received: 5 October 2016 / Revised: 27 October 2016 / Accepted: 28 October 2016 / Published: 3 November 2016
Cited by 26 | PDF Full-text (2133 KB) | HTML Full-text | XML Full-text
Abstract
The selective delivery of drugs in a cell- or tissue-specific manner represents the main challenge for medical research; in order to reduce the occurrence of unwanted off-target effects. In this regard, nucleic acid aptamers have emerged as an attractive class of carrier molecules
[...] Read more.
The selective delivery of drugs in a cell- or tissue-specific manner represents the main challenge for medical research; in order to reduce the occurrence of unwanted off-target effects. In this regard, nucleic acid aptamers have emerged as an attractive class of carrier molecules due to their ability to bind with high affinity to specific ligands; their high chemical flexibility; as well as tissue penetration capability. To date, different aptamer-drug systems and aptamer–nanoparticles systems, in which nanoparticles function together with aptamers for the targeted delivery, have been successfully developed for a wide range of therapeutics, including toxins; peptides; chemotherapeutics and oligonucleotides. Therefore, aptamer-mediated drug delivery represents a powerful tool for the safe and effective treatment of different human pathologies, including cancer; neurological diseases; immunological diseases and so on. In this review, we will summarize recent progress in the field of aptamer-mediated drug delivery and we will discuss the advantages, the achieved objectives and the challenges to be still addressed in the near future, in order to improve the effectiveness of therapies. Full article
(This article belongs to the Special Issue Aptamers: Biomedical Interest and Applications)
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Open AccessReview Aptamers: A New Technological Platform in Cancer Immunotherapy
Pharmaceuticals 2016, 9(4), 64; https://doi.org/10.3390/ph9040064
Received: 29 August 2016 / Revised: 29 September 2016 / Accepted: 19 October 2016 / Published: 24 October 2016
Cited by 9 | PDF Full-text (757 KB) | HTML Full-text | XML Full-text
Abstract
The renaissance of cancer immunotherapy is, nowadays, a reality. In the near future, it will be very likely among the first-line treatments for cancer patients. There are several different approaches to modulate the immune system to fight against tumor maladies but, so far,
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The renaissance of cancer immunotherapy is, nowadays, a reality. In the near future, it will be very likely among the first-line treatments for cancer patients. There are several different approaches to modulate the immune system to fight against tumor maladies but, so far, monoclonal antibodies may currently be the most successful immuno-tools used to that end. The number of ongoing clinical trials with monoclonal antibodies has been increasing exponentially over the last few years upon the Food and Drug Administration (FDA) approval of the first immune-checkpoint blockade antibodies. In spite of the proved antitumor effect of these reagents, the unleashing of the immune system to fight cancer cells has a cost, namely auto-inflammatory toxicity. Additionally, only a small fraction of all patients treated with immune-checkpoint antibodies have a clinical benefit. Taking into account all this, it is urgent new therapeutic reagents are developed with a contained toxicity that could facilitate the combination of different immune-modulating pathways to broaden the antitumor effect in most cancer patients. Based on preclinical data, oligonucleotide aptamers could fulfill this need. Aptamers have not only been successfully used as antagonists of immune-checkpoint receptors, but also as agonists of immunostimulatory receptors in cancer immunotherapy. The simplicity of aptamers to be engineered for the specific delivery of different types of cargos to tumor cells and immune cells so as to harvest an efficient antitumor immune response gives aptamers a significant advantage over antibodies. In this review all of the recent applications of aptamers in cancer immunotherapy will be described. Full article
(This article belongs to the Special Issue Aptamers: Biomedical Interest and Applications)
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Other

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Open AccessMeeting Report Aptamers in Bordeaux, 24–25 June 2016
Pharmaceuticals 2017, 10(1), 14; https://doi.org/10.3390/ph10010014
Received: 16 November 2016 / Revised: 12 January 2017 / Accepted: 13 January 2017 / Published: 20 January 2017
Cited by 1 | PDF Full-text (193 KB) | HTML Full-text | XML Full-text
Abstract
The symposium covered the many different aspects of the selection and the characterization of aptamers as well as their application in analytical, diagnostic and therapeutic areas. Natural and artificial riboswitches were discussed. Recent advances for the design of mutated polymerases and of chemically
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The symposium covered the many different aspects of the selection and the characterization of aptamers as well as their application in analytical, diagnostic and therapeutic areas. Natural and artificial riboswitches were discussed. Recent advances for the design of mutated polymerases and of chemically modified nucleic acid bases that provide aptamers with new properties were presented. The power of aptamer platforms for multiplex analysis of biomarkers of major human diseases was described. The potential of aptamers for the treatment of cancer or cardiovascular diseases was also presented. Brief summaries of the lectures presented during the symposium are given in this report. A second edition of “Aptamers in Bordeaux” will take place on September 2017 (http://www.aptamers-in-bordeaux.com/). Full article
(This article belongs to the Special Issue Aptamers: Biomedical Interest and Applications)
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