Advances on aptamers targeting Plasmodium and trypanosomatids

Aptamers are single-stranded oligonucleotides (ssDNA or RNA) selected from combinatorial libraries by an in vitro process and possess a specific three-dimensional structure depending on its sequence. These molecules are able to recognize and, eventually, alter the activity of their targets by binding directly in a similar way to antibodies. 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 Plasmodium and trypanosomatid proteins associated with parasitic diseases which affect hundreds of millions people. One approach tries to block the interaction between the parasite and the host using aptamers targeting host-cell matrix receptors. A second strategy consists in attack the parasite intracellularly targeting heme group or interfering in the intracellular RNA transport. In another strategy, aptamers targeting invariant polypeptides could be used as a specific drug delivery system into the parasite. Finally, aptamers addressed to re-direct the immune response of the infected host are being studied. Other potential use of the aptamers is as biorecognition element in diagnostic systems for parasitic diseases. In this paper, we briefly review how aptamers against Plasmodium and trypanosomatids are discovered, with a focus on recent advances that improve the aptamers properties as a real tool for parasite fighting.     

Aptamers: from bench side research towards patented molecules with therapeutic applications

Background: RNA and DNA aptamers recognize their targets with high specificity and affinity. These aptamers can be developed against almost any target protein through iterative cycles of in vitro screening of a combinatorial oligonucleotide library for target binding. Aptamer sequences from the final pool of in vitro selection are screened for pharmacological activity and possible medical applications. Methods: Chemical modifications and improvements of the identification of aptamer selection procedures made aptamers rival antibodies in diagnostic and therapeutic applications. This article reviews recent literature and patents and discusses the properties of aptamers as high-affinity and specificity target binders as well as their stability in biological fluids that turns them into therapeutic agents. Conclusion: The development of aptamers into compounds with therapeutic and diagnostic compounds has resulted in patents protecting the sequences and the use of these oligonucleotides. Several of these patented aptamers are currently being tested in Phase I or II clinical trials. Moreover, an anti-VEGF aptamer has already been approved by the FDA for treatment of age-related macular degeneration in humans.     

G-quadruplex DNA aptamers and their ligands: structure, function and application

Highly specific and tight-binding nucleic acid aptamers have been selected against a variety of molecular targets for over 20 years. A significant proportion of these oligonucleotides display G-quadruplex structures, particularly for DNA aptamers, that enable molecular recognition of their ligands. G-quadruplex structures couple a common scaffold to varying loop motifs that act in target recognition. Here, we review DNA G-quadruplex aptamers and their ligands from a structural and functional perspective. We compare the diversity of DNA G-quadruplex aptamers selected against multiple ligand targets, and consider structure with a particular focus on dissecting the thrombin binding aptamer - thrombin interaction. Therapeutic and analytical applications of DNA G-quadruplex aptamers are also discussed. Understanding DNA G-quadruplex aptamers carries implications not only for therapeutics and diagnostics, but also in the natural biochemistry of guanine-rich nucleic acids.     

Aptamers: potential applications to pancreatic cancer therapy

There is an unquestionable need for more effective therapies for pancreatic cancer. Aptamers are single-stranded DNA or RNA oligonucleotide ligands whose 3-dimensional structures are dictated by their sequences. Aptamers have been generated against numerous purified protein targets using an iterative in vitro selection technique known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Several biochemical properties make them attractive tools for use in an array of biological research applications and as potential pharmacologic agents. Isolated aptamers may directly affect target protein function, or they may also be modified for use as delivery agents for other therapeutic cargo or as imaging agents. More complex selections, using whole cancer cells or tumor tissue, may simultaneously identify novel or unexpected targets and aptamers to inhibit them. This review summarizes recent advances in the field of aptamers and discusses aptamer targets that have relevance to pancreatic cancer.     

Improving the stability of aptamers by chemical modification

Ever since the invention of SELEX (systematic evolution of ligands by exponential enrichment), there has been rapid development for aptamers over the last two decades, making them a promising approach in therapeutic applications as either drug candidates or diagnostic tools. For therapeutic purposes, a durable performance of aptamers in biofluids is required, which is, however, hampered by the lack of stability of most aptamers. Not only are the nucleic acid aptamers susceptible to nucleases, the peptide aptamers are also subjective to degradation by proteases. With the advancement of chemical biology, numerous attempts have been made to overcome this obstacle, many resulting in significant improvements in stability. In this review, chemical modifications to increase the stability of three main types of aptamers, DNA, RNA and peptide are comprehensively summarized. For nucleic acid aptamers, development of modified SELEX coupled with mutated polymerase is discussed, which is adaptive to a number of modifications in aptamers and in a large extent facilitates the research of aptamer-modifications. For peptide aptamers, approaches in molecular biology with introduction of stabilizing protein as well as the switch of scaffold protein are included, which may represent a future direction of chemical conjugations to aptamers.     

Aptamers against cell surface receptors: selection, modification and application

Aptamers are synthetic oligonucleotides selected from pools of random-sequence oligonucleotides which bind to a wide range of biomolecular targets with high affinity and specificity. Compared with antibodies, aptamers exhibit significant advantages including small size, easy synthesis and modification, as well as low immunogenicity. Many of the aptamers also show inhibition of their targets, making them potential therapeutic and targeting reagents in clinical applications. Compared with aptamers against intracellular proteins and molecules, however, the identification of aptamers against cell-surface receptors and receptor-related antigens is more difficult, due to the complex cellular environment in which receptors are located, and also the unique conformations and compositions of receptors to keep their activity. In this review, we will introduce the identification, modification and working mechanism of aptamers against cell-surface receptors. Based on the different characteristics of target receptors and selection strategies used, the identified aptamers show distinct binding affinity with recombinant targets or specific cell lines which express receptors on the surface in vitro. Some of the in vivo experiments also indicate that aptamers have the capability of inhibiting the overexpressing receptor-related tumor growth, working as potential anti-tumor therapeutic drugs. Despite of the difficulties during the selection of receptor aptamers and the study of their working mechanism during the present time, it is possible that in the future aptamers will increasingly exhibit therapeutic and diagnostic utility.     

Nucleic acid aptamers: clinical applications and promising new horizons

Aptamers are a special class of nucleic acid molecules that are beginning to be investigated for clinical use. These small RNA/DNA molecules can form secondary and tertiary structures capable of specifically binding proteins or other cellular targets; they are essentially a chemical equivalent of antibodies. Aptamers have the advantage of being highly specific, relatively small in size, and non-immunogenic. Since the discovery of aptamers in the early 1990s, great efforts have been made to make them clinically relevant for diseases like cancer, HIV, and macular degeneration. In the last two decades, many aptamers have been clinically developed as inhibitors for targets such as vascular endothelial growth factor (VEGF) and thrombin. The first aptamer based therapeutic was FDA approved in 2004 for the treatment of age-related macular degeneration and several other aptamers are currently being evaluated in clinical trials. With advances in targeted-therapy, imaging, and nanotechnology, aptamers are readily considered as potential targeting ligands because of their chemical synthesis and ease of modification for conjugation. Preclinical studies using aptamer-siRNA chimeras and aptamer targeted nanoparticle therapeutics have been very successful in mouse models of cancer and HIV. In summary aptamers are in several stages of development, from pre-clinical studies to clinical trials and even as FDA approved therapeutics. In this review, we will discuss the current state of aptamers in clinical trials as well as some promising aptamers in pre-clinical development.     

Potential use of aptamers for diagnosis and treatment of pancreatic cancer

Abstract

Pancreatic cancer (PC) is highly malignant with a low 5-year survival rate. PC currently does not have good early diagnostic markers and responses poorly to chemotherapeutic drugs. The search for better biomarkers and developing more effective chemotherapy are important ways to improve the healthcare of PC patients. Aptamers are single-stranded nucleic acids with high binding affinity and specificity to target molecules. Many aptamers against different forms of cancer including PC have been selected for both diagnostic and therapeutic use. Aptamers can work as ligands to distinguish tumour cells from normal cells. Using cells as selection targets, the obtained aptamers have been used to discover new cancer biomarkers after identification of the binding target. Aptamers have been shown to have antagonists effect on cancer cell proliferation, apoptosis, and metastasis. In addition, aptamers have been used as carriers to deliver therapeutic agents to selectively kill PC cells. This review summarises the potential use of aptamers in the diagnosis and treatment of PC.     

Aptamers as inhibitors of target proteins

Background: Aptamers as inhibitors of proteins in therapeutic applications offer great advantages over their antibody counterparts and the promise to be developed into the next generation therapeutic agents. However, the control of aptamer intellectual property (IP) by two major players has made aptamers an area difficult to operate and often off-putting for academic and commercial organisations. Yet, their great potential is keeping aptamers at the research forefront, with one aptamer in the clinic and various at different stages of clinical trials. Objective: To provide a comprehensive review of the aptamer IP landscape and the issues associated with aptamer therapeutics against protein targets. Methods: Extensive review of the scientific and patent literature. Conclusions: Following our experience in developing, patenting and commercialising our aptamers against MUC1 and an extensive review of the literature, we have identified a variety of issues pertaining to the development of aptamers against protein targets for therapeutic applications, their patenting and granting of patents, the original IP holders and their policy, as well as the current market and traits. Despite a slow start, aptamers have been developed against various therapeutic proteins and offer the promise of providing a novel generation of therapeutic entities with a variety of applications.     

Multifunctional magnetic nanoparticles for targeted imaging and therapy

Magnetic nanoparticles have become important tools for the imaging of prevalent diseases, such as cancer, atherosclerosis, diabetes, and others. While first generation nanoparticles were fairly nonspecific, newer generations have been targeted to specific cell types and molecular targets via affinity ligands. Commonly, these ligands emerge from phage or small molecule screens, or are based on antibodies or aptamers. Secondary reporters and combined therapeutic molecules have further opened potential clinical applications of these materials. This review summarizes some of the recent biomedical applications of these newer magnetic nanomaterials.     

Entropic fragment-based approach to aptamer design

Aptamers are short RNA/DNA sequences that are identified through the process of systematic evolution of ligands by exponential enrichment and that bind to diverse biomolecular targets. Aptamers have strong and specific binding through molecular recognition and are promising tools in studying molecular biology. They are recognized as having potential therapeutic and diagnostic clinical applications. The success of the systematic evolution of ligands by exponential enrichment process requires that the RNA/DNA pools used in the process have a sufficient level of sequence diversity and structural complexity. While the systematic evolution of ligands by exponential enrichment technology is well developed, it remains a challenge in the efficient identification of correct aptamers. In this article, we propose a novel information-driven approach to a theoretical design of aptamer templates based solely on the knowledge regarding the biomolecular target structures. We have investigated both theoretically and experimentally the applicability of the proposed approach by considering two specific targets: the serum protein thrombin and the cell membrane phospholipid phosphatidylserine. Both of these case studies support our method and indicate a promising advancement in theoretical aptamer design. In unfavorable cases where the designed sequences show weak binding affinity, these template sequences can be still modified to enhance their affinities without going through the systematic evolution of ligands by exponential enrichment process.     

RNA aptamers: from basic science towards therapy

The SELEX technique (systematic evolution of ligands by exponential enrichment) provides a powerful tool for the in vitro selection of nucleic acid ligands (aptamers) from combinatorial oligonucleotide libraries against a target molecule. In the beginning of the technique's use, RNA molecules were identified that bind to proteins that naturally interact with nucleic acids or to small organic molecules. In the following years, the use of the SELEX technique was extended to isolate oligonucleotide ligands (aptamers) for a wide range of proteins of importance for therapy and diagnostics, such as growth factors and cell surface antigens. These oligonucleotides bind their targets with similar affinities and specificities as antibodies do. The in vitro selection of oligonucleotides with enzymatic activity, denominated aptazymes, allows the direct transduction of molecular recognition to catalysis. Recently, the use of in vitro selection methods to isolate protein inhibitors has been extended to complex targets, such as membrane-bound receptors, and even entire cells. RNA aptamers have also been expressed in living cells. These aptamers, also called intramers, can be used to dissect intracellular signal transduction pathways. The utility of RNA aptamers for in vivo experiments, as well as for diagnostic and therapeutic purposes, is considerably enhanced by chemical modifications, such as substitutions of the 2'-OH groups of the ribose backbone in order to provide resistance against enzymatic degradation in biological fluids. In an alternative approach, Spiegelmers are identified through in vitro selection of an unmodified D-RNA molecule against a mirror-image (i.e. a D-peptide) of a selection target, followed by synthesis of the unnatural nuclease-resistant L-configuration of the RNA aptamer that recognizes the natural configuration of its selection target (i.e. a L-peptide). Recently, nuclease-resistant inhibitory RNA aptamers have been developed against a great variety of targets implicated in disease. Some results have already been obtained in animal models and in clinical trials.     

Emerging developments in RNA therapeutics

Exciting developments have recently emerged in the field of RNA therapeutics, with potential applications in the treatment of human diseases. The second International Conference on RNA in drug development was held to highlight several novel RNA-based technologies, including different approaches to silence gene expression, the broad range of diagnostic and therapeutic applications for aptamers, and the targeting of RNA with small molecules. Highlights of the meeting included the utilisation of RNA interference to silence genes, with applications for the treatment of both cancer and viral infections, and for systemic silencing of gene expression. Novel approaches to safer drug design using aptamers were presented, which would enable control of their therapeutic activity to be achieved with antidote oligonucleotides. Updates were also presented on the clinical and preclinical development of ribozymes and aptamers, including good progress in increasing the half-life of these molecules in serum.     

Emerging Developments in RNA Therapeutics

Exciting developments have recently emerged in the field of RNA therapeutics, with potential applications in the treatment of human diseases. The second International Conference on RNA in drug development was held to highlight several novel RNA-based technologies, including different approaches to silence gene expression, the broad range of diagnostic and therapeutic applications for aptamers, and the targeting of RNA with small molecules. Highlights of the meeting included the utilisation of RNA interference to silence genes, with applications for the treatment of both cancer and viral infections, and for systemic silencing of gene expression. Novel approaches to safer drug design using aptamers were presented, which would enable control of their therapeutic activity to be achieved with antidote oligonucleotides. Updates were also presented on the clinical and preclinical development of ribozymes and aptamers, including good progress in increasing the half-life of these molecules in serum.     

Nucleic acid aptamers against protein kinases

Deregulation of kinase function has been implicated in several important diseases, including cancer, neurological and metabolic disorders. Because of their key role in causing disease, kinases have become one of the most intensively pursued classes of drug targets. To date, several monoclonal antibodies (mAbs) and small-molecule inhibitors have been approved for the treatment of cancer. Aptamers are short structured single stranded RNA or DNA ligands that bind at high affinity to their target molecules and are now emerging as promising molecules to target specific cancer epitopes in clinical diagnosis and therapy. Further, because of their high specificity and low toxicity aptamers will likely reveal among the most promising molecules for in vivo targeted recognition as therapeutics or delivery agents for nanoparticles, small interfering RNAs bioconjugates, chemotherapeutic cargos and molecular imaging probes. In this article, we discuss recent advances in the development of aptamers targeting kinase proteins.     

Aptamers: new arrows to target dendritic cells

Aptamers, as a novel class of molecular probes for diagnosis, imaging and targeting therapy, have attracted increasing attention in recent years. Aptamers are generated from libraries of single-stranded nucleic acids against different molecules via the “systematic evolution of ligands by exponential enrichment” (SELEX) method. SELEX is a repetitive process of a sequential selection procedure in which a DNA or RNA library pool is incubated separately with target and control molecules to select specific oligonucleotide aptamers with high affinities and specificities. Cell-SELEX is a modified version of the SELEX process in which whole living cells are used as targets for the aptamers. Dendritic cell (DC) targeting, as a new therapeutic approach, can improve the efficiency of immunotherapy in the treatment of allergies and cancers. DCs use various receptors to continuously induce adaptive immunity via capture and presentation of antigens to naïve T cells. DCs are considered as the best targets in modulating immune responses against cancer, autoimmunity, allergy and transplantation. Aptamers, as a new agent, can be applied in DC targeting. The purpose of this review is to present some general concepts of aptamer production and DC targeting by aptamer molecules.     

The use of synthetic oligonucleotides as protein inhibitors and anticode drugs in cancer therapy: accomplishments and limitations

The function of gene products can be altered at many levels, including the mutation of gene sequence and the change in steady state levels of mRNA and/or protein by various mechanisms. The cumulative malfunction of specific gene products underlies many pathological conditions such as the multi-step and multi-cause acquisition of cancer. Here we discuss two oligonucleotide-based strategies in which these compounds target defective gene products acting either as antiprotein or anticode agents. The SELEX technique (systematic evolution of ligands by exponential enrichment) is an antiprotein approach in which nuclease-resistant DNA or RNA aptamers are selected by their ability to bind their protein targets with high affinity and specificity of the same range as antibodies. Such inhibitors were previously evolved against a great variety of targets, including receptors, growth factors and adhesion molecules implicated in the genesis of some kinds of cancer. Moreover, some results have already been obtained in animal models. The antigene technology interferes with earlier steps in the information flow leading from gene to protein. In this approach selective gene silencing is provided by the formation of stable and specific complexes between triplex forming molecules and their DNA targets. The feasibility of this strategy as well as a molecular mechanism for the action of antigene oligonucleotides has been demonstrated in cellular systems and in vivo. The use of oligonucleotide drugs (of either the antiprotein or the anticode type) as a viable approach to cancer therapy is limited by some common problems that will be discussed.     

Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis

RNAs are involved in the crucial processes of disease progression and have emerged as powerful therapeutic targets and diagnostic biomarkers. However, efficient delivery of therapeutic RNA to the targeted location and precise detection of RNA markers remains challenging. Recently, more and more attention has been paid to applying nucleic acid nanoassemblies in diagnosing and treating. Due to the flexibility and deformability of nucleic acids, the nanoassemblies could be fabricated with different shapes and structures. With hybridization, nucleic acid nanoassemblies, including DNA and RNA nanostructures, can be applied to enhance RNA therapeutics and diagnosis. This review briefly introduces the construction and properties of different nucleic acid nanoassemblies and their applications for RNA therapy and diagnosis and makes further prospects for their development.     

Molecular diagnostic and drug delivery agents based on aptamer-nanomaterial conjugates

Recent progress in an emerging area of designing aptamer and nanomaterial conjugates as molecular diagnostic and drug delivery agents in biomedical applications is summarized. Aptamers specific for a wide range of targets are first introduced and compared to antibodies. Methods of integrating these aptamers with a variety of nanomaterials, such as gold nanoparticles, quantum dots, carbon nanotubes, and superparamagnetic iron oxide nanoparticles, each with unique optical, magnetic, and electrochemical properties, are reviewed. Applications of these systems as fluorescent, colorimetric, magnetic resonance imaging, and electrochemical sensors in medical diagnostics are given, along with new applications as smart drug delivery agents.