Water soluble RNA based antagonist of AMPA receptors

TLR4-Binding DNA Aptamers Show a Protective Effect against Acute Stroke in Animal Models

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.

Chemically Modified, α-Amino-3-hydroxy-5-methyl-4-isoxazole (AMPA) Receptor RNA Aptamers Designed for in Vivo Use

Glutamate ion channels have three subtypes, that is, α-amino-3-hydroxy-5-methyl-4-isoxazole (AMPA), kainate, and N-methyl-d-aspartate (NMDA) receptors. Excessive activity of these receptor subtypes either individually or collectively is involved in various neurological disorders. RNA aptamers as antagonists of these receptors are potential therapeutics. For developing aptamer therapeutics, the RNA aptamers must be chemically modified to become ribonuclease-resistant or stable in biological fluids. Using systematic evolution of ligands by exponential enrichment (SELEX) and a chemically modified library, prepared enzymatically (i.e., the library contains RNAs with 2'-fluoro modified nucleoside triphosphates or ATPs, CTPs and UTPs, but regular GTPs), we have isolated an aptamer. The short aptamer (69 nucleotides) FN1040s selectively inhibits the GluA1 and GluA2Q_flip AMPA receptor subunits, whereas the full-length aptamer (101 nucleotides) FN1040 additionally inhibits GluK1, but not GluK2, kainate receptor, and GluN1a/2A and GluN1a/2B, the two major native NMDA receptors. The two aptamers show similar potency (2-4 μM) and are stable with a half-life of at least 2 days in serum-containing medium or cerebrospinal fluid. Therefore, these two aptamers are amenable for in vivo use.

Aptamers as promising molecular recognition elements for diagnostics and therapeutics in the central nervous system

Oligonucleotide aptamers are short, synthetic, single-stranded DNA or RNA able to recognize and bind to a multitude of targets ranging from small molecules to cells. Aptamers have emerged as valuable tools for fundamental research, clinical diagnosis, and therapy. Due to their small size, strong target affinity, lack of immunogenicity, and ease of chemical modification, aptamers are an attractive alternative to other molecular recognition elements, such as antibodies. Although it is a challenging environment, the central nervous system and related molecular targets present an exciting potential area for aptamer research. Aptamers hold promise for targeted drug delivery, diagnostics, and therapeutics. Here we review recent advances in aptamer research for neurotransmitter and neurotoxin targets, demyelinating disease and spinal cord injury, cerebrovascular disorders, pathologies related to protein aggregation (Alzheimer's, Parkinson's, and prions), brain cancer (glioblastomas and gliomas), and regulation of receptor function. Challenges and limitations posed by the blood brain barrier are described. Future perspectives for the application of aptamers to the central nervous system are also discussed.

RNA based antagonist of NMDA receptors

The N-methyl d-aspartate (NMDA) class of ionotropic glutamate receptors plays important roles in learning and memory as well as in a number of neurological disorders including Huntington's disease and cerebral ischemia. Here, we describe the isolation and characterization of a 2' F-modified RNA aptamers directed against GluN2A-containing NMDA receptors. By adding a negative selection step toward the closely related AMPA and kainate receptors, the RNA aptamers specifically recognize NMDA receptors with dissociation constants in the nanomolar range. Electrophysiological characterization of these aptamers using rapid perfusion in outside-out patches reveals that they selectively inhibit the GluN2A containing subtype of NMDA receptors with little effect on the AMPA and kainate receptor subtypes. We also demonstrate that this RNA aptamer significantly reduces neurotoxicity in an in vitro model of cerebral ischemia. Given that the RNA based antagonist can be readily modified, it can be used as a tool in targeted drug delivery or for imaging purposes in addition to having the potential use as a therapeutic intervention in disorders involving glutamate receptors.

Identification of aptamers as specific binders and modulators of cell-surface receptor activity

In recent years, the SELEX (Systematic Evolution of Ligands by EXponential enrichment) technology has established itself as a powerful tool in basic research with promising applications in diagnostics and therapeutics. Oligonucleotides with high-affinities to their targets, denominated as aptamers, are obtained from partially random oligonucleotide pools by reiterative in vitro selection cycles and screening for binding activity. The original technique allowing the identification of aptamers binding to soluble targets, has recently been extended in order to produce aptamers binding to complex targets including receptors and ion channels embedded in the plasma membrane as well as whole cell surfaces or parasite organisms. In addition to discussing the most recent developments with focus on possible diagnostic and therapeutic application, we provide a simple protocol which has been successfully used to select for RNA aptamers as allosteric modulators of nicotinic receptor activity.

Methods To Identify Aptamers against Cell Surface Biomarkers

Aptamers are nucleic acid-based ligands identified through a process of molecular evolution named SELEX (Systematic Evolution of Ligands by Exponential enrichment). During the last 10-15 years, numerous aptamers have been developed specifically against targets present on or associated with the surface of human cells or infectious pathogens such as viruses, bacteria, fungi or parasites. Several of the aptamers have been described as potent probes, rivalling antibodies, for use in flow cytometry or microscopy. Some have also been used as drugs by inhibiting or activating functions of their targets in a manner similar to neutralizing or agonistic antibodies. Additionally, it is straightforward to conjugate aptamers to other agents without losing their affinity and they have successfully been used in vitro and in vivo to deliver drugs, siRNA, nanoparticles or contrast agents to target cells. Hence, aptamers identified against cell surface biomarkers represent a promising class of ligands. This review presents the different strategies of SELEX that have been developed to identify aptamers for cell surface-associated proteins as well as some of the methods that are used to study their binding on living cells.

Nucleic acid aptamers targeting cell-surface proteins

Aptamers are chemical antibodies that bind to their targets with high affinity and specificity. These short stretches of nucleic acids are identified using a repetitive in vitro selection and partitioning technology called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since the emergence of this technology, many modifications and variations have been introduced to enable the selection of specific ligands, even for implausible targets. For membrane protein, the selection scheme can be chosen depending upon the availability of the system, the protein characteristics and the application required. Aptamers have been generated for a significant number of disease-associated membrane proteins and have been shown to have considerable diagnostic and therapeutic importance. In this article, we review the SELEX process used for identification of aptamers that target cell-surface proteins and recapitulate their use as therapeutic and diagnostic reagents.

Searching for interesting channels: pairing selection and molecular evolution methods to study ion channel structure and function

The pairing of selection and screening methods with randomly mutated libraries can be an exceptionally powerful means for probing the functions of biological molecules and for developing novel regents from random libraries of peptides and oligonucleotides. The use of such approaches is beginning to permeate the ion channel field where they are being deployed to uncover fundamental aspects about ion channel structure and gating, small molecule-channel interactions, and the development of novel agents to control channel activity.