In vivo properties of an anti-GnRH Spiegelmer: an example of an oligonucleotide-based therapeutic substance class

[18F]fluoropyridines: From conventional radiotracers to the labeling of macromolecules such as proteins and oligonucleotides

Molecular in vivo imaging with the high-resolution and sensitive positron emission tomography (PET) technique requires the preparation of a positron-emitting radiolabeled probe or radiotracer. For this purpose, fluorine-18 is becoming increasingly the radionuclide of choice due to its adequate physical and nuclear characteristics, and also because of the successful use in clinical oncology of 2-[18F]fluoro-2-deoxy-D-glucose ([18F]FDG), which is currently the most widely used PET-radiopharmaceutical and probably the driving force behind the growing availability and interest for this positron-emitter in radiopharmaceutical chemistry. With a few exceptions, radiofluorinations involving fluorine-18 of high specific radioactivity (e.g. > 185 GBq/micromole) had, until recently, been limited to nucleophilic substitutions in homoaromatic and aliphatic series with [18F]fluoride. Considering chemical structures showing a fluoropyridinyl moiety, nucleophilic heteroaromatic substitution at the ortho-position with no-carrier-added [l8F]fluoride, as its K[18F]F-K222 complex, appears today as a highly efficient method for the radiosynthesis of radiotracers and radiopharmaceuticals. This chapter summarizes the recent applications of this methodology and highlights its potential in the design and preparation of, often drug-based, fluorine-18-labeled probes of high specific radioactivity for PET imaging, including macromolecules of biological interest such as peptides, proteins and oligonucleotides.

Chiral stationary phase based on a biostable L-RNA aptamer

An immobilized anti-L-arginine d-RNA aptamer, used as a target-specific chiral stationary phase (CSP), was found to be very quickly degraded by RNases under usual chromatographic utilization and storage. To overcome this severe limitation for a practical use, a CSP based on the L-RNA aptamer, that is, the mirror image of the D-RNA aptamer, was created. It was shown that this mirror-image approach was a very simple and powerful strategy to develop a highly stable stationary phase due to the intrinsic insensitivity of l-RNA to the RNase degradation. In addition, such an approach allowed one to reverse the enantiomer elution order relative to that obtained with the corresponding d-RNA CSP.

Anti-ghrelin Spiegelmer NOX-B11 inhibits neurostimulatory and orexigenic effects of peripheral ghrelin in rats

BACKGROUND AND AIMS

Ghrelin, the natural ligand of the growth hormone secretagogue receptor 1a, is the most powerful peripherally active orexigenic agent known. In rodents, ghrelin administration stimulates growth hormone release, food intake, and adiposity. Because of these effects, blocking of ghrelin has been widely discussed as a potential treatment for obesity. Spiegelmer NOX-B11 is a synthetic l-oligonucleotide, which was previously shown to bind ghrelin. We examined the effects of NOX-B11 on ghrelin induced neuronal activation and food intake in non-fasted rats.

METHODS

Animals received various doses of NOX-B11, inactive control Spiegelmer, or vehicle intravenously. Ghrelin or vehicle was administered intraperitoneally 12 hours later and food intake was measured over four hours. Neuronal activation was assessed as c-Fos-like immunoreactivity in the arcuate nucleus.

RESULTS

Treatment with NOX-B11 30 nmol suppressed ghrelin induced c-Fos-like immunoreactivity in the arcuate nucleus and blocked the ghrelin induced increase in food intake within the first half hour after ghrelin injection (mean 1.13 (SEM 0.59) g/kg body weight; 4.94 (0.63) g/kg body weight versus 0.58 (0.58) g/kg body weight; p<0.0001). Treatment with NOX-B11 1 nmol or control Spiegelmer had no effect whereas treatment with NOX-B11 10 nmol showed an intermediate effect on ghrelin induced food intake.

CONCLUSIONS

Spiegelmer NOX-B11 suppresses ghrelin induced food intake and c-Fos induction in the arcuate nucleus in rats. The use of an anti-ghrelin Spiegelmer could be an innovative new approach to inhibit the biological action of circulating ghrelin. This may be of particular relevance to conditions associated with elevated plasma ghrelin, such as the Prader-Willi syndrome.

Inhibition of stimulated meningeal blood flow by a calcitonin gene-related peptide binding mirror-image RNA oligonucleotide

Calcitonin gene-related peptide (CGRP) released from trigeminal afferents is known to play an important role in the control of intracranial blood flow. In a rat preparation with exposed cranial dura mater, periods of electrical stimulation induce increases in meningeal blood flow. These responses are due to arterial vasodilatation mediated in part by the release of CGRP. In this preparation, the effect of a CGRP-binding mirror-image oligonucleotide (Spiegelmer NOX-C89) was examined. Spiegelmer NOX-C89 applied topically at concentrations between 10(-7) and 10(-5) M to the exposed dura mater led to a dose-dependent inhibition of the electrically evoked blood flow increases. The highest dose reduced the mean increases in flow to 56% of the respective control levels. A nonfunctional control Spiegelmer (not binding to CGRP) was ineffective in changing blood flow increases. Intravenous injection of NOX-C89 (5 mg kg(-1)) reduced the evoked blood flow increases to an average of 65.5% of the control. The basal blood flow was not changed by any of the applied substances. In addition, an ex vivo preparation of the hemisected rat skull was used to determine CGRP release from the cranial dura mater caused by antidromic activation of meningeal afferents. In this model, 10(-6) M of NOX-C89 reduced the evoked CGRP release by about 50%. We conclude that increases in meningeal blood flow due to afferent activation can be reduced by sequestering the released CGRP and thus preventing it from activating vascular CGRP receptors. Moreover, the Spiegelmer NOX-C89 may inhibit CGRP release from meningeal afferents. Therefore, the approach to interfere with the CGRP/CGRP receptor system by binding the CGRP may open a new opportunity for the therapy of diseases that are linked to excessive CGRP release such as some forms of primary headaches.

An L-RNA-based aquaretic agent that inhibits vasopressin in vivo

A class of diuretic/aquaretic agents based on mirror-image oligonucleotides (so-called Spiegelmers) has been identified. These molecules directly bind and inhibit the neuropeptide vasopressin (AVP). AVP is the major regulatory component of body fluid homeostasis mediated through binding to the renal V(2) receptor. Elevated plasma levels of AVP are implicated in several pathological conditions, mainly cardiovascular diseases. In congestive heart failure, AVP is part of a neuroendocrine imbalance that is responsible for progressive worsening of the disease. Employing in vitro selection techniques, RNA aptamers that bind to the unnatural d-configuration of AVP were isolated. The best aptamer displayed an affinity to d-AVP of approximately 560 pM at 37 degrees C. The corresponding Spiegelmer, a 38-mer mirror-image oligonucleotide (l-RNA) termed NOX-F37, inhibits vasopressin-dependent activation of V(1a) as well as V(2) receptors with IC(50) values of 6.1 nM and 1 nM, respectively. NOX-F37 administered to healthy rats effectively neutralized AVP and increased diuresis dose-dependently for 24 h. The mode of action was strictly aquaretic, i.e., the increase in urine volume was not accompanied by an increase in electrolytes. These results clearly prove the in vivo efficacy of NOX-F37 and points out its potential as a drug in the treatment of diseases that are associated with body fluid overload.

Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease

Aptamers are oligonucleotide ligands that are selected for high-affinity binding to molecular targets. Pegaptanib sodium (Macugen; Eyetech Pharmaceuticals/Pfizer) is an RNA aptamer directed against vascular endothelial growth factor (VEGF)-165, the VEGF isoform primarily responsible for pathological ocular neovascularization and vascular permeability. After nearly a decade of preclinical development to optimize and characterize its biological effects, pegaptanib was shown in clinical trials to be effective in treating choroidal neovascularization associated with age-related macular degeneration. Pegaptanib therefore has the notable distinction of being the first aptamer therapeutic approved for use in humans, paving the way for future aptamer applications.

Aptamers against extracellular targets for in vivo applications

Oligonucleotides are multifunctional molecules which can interfere with gene expression by different mechanism such as antisense, RNA interference, ribozymes, etc. For most in vivo diagnostic and therapeutic applications, oligonucleotides need to be delivered to the intracellular compartment of a specific organ, a difficult task which limits considerably their use. However, aptamer oligonucleotides which target extracellular markers obviate this problem. Aptamers are short oligonucleotides (<100 bases) selected from large combinatorial pools of sequences for their capacity to bind to many types of different targets, ranging from small molecules (amino acids, antibiotics...) to proteins or nucleic acid structures. Aptamers present the same high specificity and affinity for their targets as antibodies. In addition to efficient binding, aptamers have been shown in many cases to display an inhibitory activity on their targets. Moreover, they seem to lack immunogenicity and can be chemically modified in order to improve their stability against nucleases or extend their blood circulation time, two properties which are particularly useful for in vivo applications. Recently, aptamers have been selected against whole living cells, opening a new avenue which presents three major advantages 1) direct selection without prior purification of the targets; 2) conservation of membrane proteins in their native conformation similar to the in vivo conditions and 3) identification of (new) targets for a specific phenotype. Many aptamers are now being developed against biomedical relevant extracellular targets: membrane receptor proteins, hormones, neuropeptides, coagulation factors... Among them, one aptamer that inhibits the human VEGF165 has recently been approved by FDA for the treatment of age-related macular degeneration. Here we discuss the recent developments of aptamers against extracellular targets for in vivo therapy and as tools for diagnosis using molecular imaging.

Deconvolution of a complex target using DNA aptamers

In vitro selection of single-stranded nucleic acid aptamers from large random sequence libraries is now a straightforward process particularly when screening with a single target molecule. These libraries contain considerable shape diversity as evident by the successful isolation of aptamers that bind with high affinity and specificity to chemically diverse targets. We propose that aptamer libraries contain sufficient shape diversity to allow deconvolution of a complex mixture of targets. Using unfractionated human plasma as our experimental model, we aim to develop methods to obtain aptamers against as many proteins as possible. To begin, it is critical that we understand how aptamer populations change with increasing rounds of in vitro selection when using complex mixtures. Our results show that sequence representation in the selected population changes dramatically with increasing rounds of selection. Certain aptamer families were apparent after only three selection rounds. Two additional cycles saw a decline in the relative abundance of these families and the emergence of yet another family that accounted for more than 60% of sequences in the pool. To overcome this population convergence, an aptamer-based target depletion method was developed, and the library screen was repeated. The previous dominant family effectively disappeared from the selected populations but was replaced by other aptamer families. Insights gained from these initial experiments are now being applied in the creation of second generation plasma protein screens and also to the analysis of other complex biological targets.

Pharmacokinetics and biodistribution of novel aptamer compositions

PURPOSE

Aptamers are highly selective nucleic acid-based drugs that are currently being developed for numerous therapeutic indications. Here, we determine plasma pharmacokinetics and tissue distribution in rat of several novel aptamer compositions, including fully 2'-O-methylated oligonucleotides and conjugates bearing high-molecular weight polyethylene glycol (PEG) polymers, cell-permeating peptides, and cholesterol.

METHODS

Levels of aptamer conjugates in biological samples were quantified radiometrically and by a hybridization-based dual probe capture assay with enzyme-linked fluorescent readout. Intact aptamer in urine was detected by capillary gel electrophoresis and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF).

RESULTS

Aptamer compositions examined exhibited a wide range of mean residence times in circulation (0.6-16 h) and significant variation in distribution levels among organs and tissues. Among the conjugates tested, in vivo properties of aptamers were altered most profoundly by conjugation with PEG groups. Complexation with a 20 kDa PEG polymer proved nearly as effective as a 40 kDa PEG polymer in preventing renal clearance of aptamers. Conjugation with 20 kDa PEG prolonged aptamer circulatory half-life, while reducing both the extent of aptamer distribution to the kidneys and the rate of urinary elimination. In contrast, the fully 2'-O-Me aptamer composition showed rapid clearance from circulation, and elimination with intact aptamer detectable in urine at 48 h post-administration.

CONCLUSIONS

We find that conjugation and chemical composition can alter fundamental aspects of aptamer residence in circulation and distribution to tissues. Though the primary effect of PEGylation was on aptamer clearance, the prolonged systemic exposure afforded by presence of the 20 kDa moiety appeared to facilitate distribution of aptamer to tissues, particularly those of highly perfused organs.

Aptamers in research and drug development

Aptamers are short single-stranded oligonucleotides that fold into well defined three-dimensional shapes allowing them to bind to and inhibit their targets with high affinity and specificity. Aptamers can be considered truly multifunctional tools, because they can be generated rapidly and applied for specific detection, inhibition, and characterization of proteins. Recent publications impressively confirm that aptamers can be used either as surrogate inhibitors for the identification of small molecule lead compounds or as biopharmaceuticals.

In vivo biodistribution and pharmacokinetics of 18F-labelled Spiegelmers: a new class of oligonucleotidic radiopharmaceuticals

PURPOSE

Single-stranded mirror-image oligonucleotides (Spiegelmers) are highly resistant to nuclease degradation and are capable of tightly and specifically binding to protein targets. Here we explored the potential of Spiegelmers as in vivo imaging probes for positron emission tomography (PET).

METHODS

We investigated the biodistribution and pharmacokinetics of [18F]-L-DNA and [18F]-L-RNA Spiegelmers by dynamic quantitative whole-body PET imaging after intravenous administration in non-human primates. Their metabolic profile was explored in primates and rats, and ex vivo autoradiography of [(125)I]-L-RNA was performed in rat kidneys, the major organ for Spiegelmer uptake.

RESULTS

Both [18F]-L-DNA and [18F]-L-RNA Spiegelmers were metabolically stable in plasma during 2 h after injection. No evidence of non-specific binding was found with either type of Spiegelmer in any tissue.

CONCLUSION

The biodistribution and metabolic profiles of [18F]-L-DNA and [18F]-L-RNA Spiegelmers highlight their potential as radiotracers for in vivo imaging applications.

Nucleic acid aptamers as tools and drugs: recent developments

Nucleic acid aptamers are molecules that bind to their ligands with high affinity and specificity. Unlike other functional nucleic acids such as antisense oligonucleotides, ribozymes, or siRNAs, aptamers almost never exert their effects on the genetic level. They manipulate their target molecules such as gene products or epitopes directly and site specifically, leaving nontargeted protein functions intact. In a similar way to antibodies, aptamers bind to many different kinds of target molecules with high specificity and can be made to order, but as a result of their different biochemical nature and size they can also be used complementary to antibodies. In some cases, aptamers might be more suitable or more specific than antibody approaches or small molecules, both as scientific and biotechnological tools and as therapeutic agents. Recent examples of characterization of aptamers as tools for scientific research to study regulatory circuits, as tools in diagnostic or biosensor development, and as therapeutic agents are discussed.

A survey of the year 2002 commercial optical biosensor literature

We have compiled 819 articles published in the year 2002 that involved commercial optical biosensor technology. The literature demonstrates that the technology's application continues to increase as biosensors are contributing to diverse scientific fields and are used to examine interactions ranging in size from small molecules to whole cells. Also, the variety of available commercial biosensor platforms is increasing and the expertise of users is improving. In this review, we use the literature to focus on the basic types of biosensor experiments, including kinetics, equilibrium analysis, solution competition, active concentration determination and screening. In addition, using examples of particularly well-performed analyses, we illustrate the high information content available in the primary response data and emphasize the impact of including figures in publications to support the results of biosensor analyses.

Bottom-up Assembly of RNA Arrays and Superstructures as Potential Parts in Nanotechnology

DNA and protein have been extensively scrutinized for feasibility as parts in nanotechnology, but another natural building block, RNA, has been largely ignored. RNA can be manipulated to form versatile shapes, thus providing an element of adaptability to DNA nanotechnology, which is predominantly based upon a double-helical structure. The DNA-packaging motor of bacterial virus phi29 contains six DNA-packaging RNAs (pRNA), which together form a hexameric ring via loop/loop interaction. Here we report that this pRNA can be redesigned to form a variety of structures and shapes, including twins, tetramers, rods, triangles, and 3D arrays several microns in size via interaction of programmed helical regions and loops. Three dimensional RNA array formation required a defined nucleotide number for twisting of the interactive helix and a palindromic sequence. Such arrays are unusually stable and resistant to a wide range of temperatures, salt concentrations, and pH.

Inhibition of ghrelin action in vitro and in vivo by an RNA-Spiegelmer

Employing in vitro selection techniques, we have generated biostable RNA-based compounds, so-called Spiegelmers, that specifically bind n-octanoyl ghrelin, the recently discovered endogenous ligand for the type 1a growth hormone secretagogue (GHS) receptor. Ghrelin is a potent stimulant of growth hormone release, food intake, and adiposity. We demonstrate that our lead compound, L-NOX-B11, binds ghrelin with low-nanomolar affinity and inhibits ghrelin-mediated GHS-receptor activation in cell culture with an IC(50) of 5 nM. l-NOX-B11 is highly specific for the bioactive, n-octanoylated form of ghrelin. Like the GHS receptor, it does not recognize the inactive unmodified peptide and requires only the N-terminal five amino acids for the interaction. The i.v. administration of polyethylene glycol modified l-NOX-B11 efficiently suppresses ghrelin-induced growth hormone release in rats. These results demonstrate that the neutralization of circulating bioactive ghrelin leads to inhibition of ghrelin's secretory effects in the CNS.

Short bioactive Spiegelmers to migraine-associated calcitonin gene-related peptide rapidly identified by a novel approach: tailored-SELEX

We developed an integrated method to identify aptamers with only 10 fixed nucleotides through ligation and removal of primer binding sites within the systematic evolution of ligands by exponential enrichment (SELEX) process. This Tailored-SELEX approach was validated by identifying a Spiegelmer ('mirror-image aptamer') that inhibits the action of the migraine-associated target calcitonin gene-related peptide 1 (alpha-CGRP) with an IC50 of 3 nM at 37 degrees C in cell culture. Aptamers are oligonucleotide ligands that can be generated to bind to targets with high affinity and specificity. Stabilized aptamers and Spiegelmers have shown activity in vivo and may be used as therapeutics. Aptamers are isolated by in vitro selection from combinatorial nucleic acid libraries that are composed of a central randomized region and additional fixed primer binding sites with approximately 30-40 nt. The identified sequences are usually not short enough for efficient chemical Spiegelmer synthesis, post-SELEX stabilization of aptamers and economical production. If the terminal primer binding sites are part of the target recognizing domain, truncation of aptamers has proven difficult and laborious. Tailored-SELEX results in short sequences that can be tested more rapidly in biological systems. Currently, our identified CGRP binding Spiegelmer serves as a lead compound for in vivo studies.

A DNA Spiegelmer to staphylococcal enterotoxin B

Bacterial staphylococcal enterotoxin B is involved in several severe disease patterns and it was therefore used as a target for the generation of biologically stable mirror-image oligonucleotide ligands, so called Spiegelmers. The toxin is a 28 kDa protein consisting of 239 amino acids. Since the full-length protein is not accessible to chemical peptide synthesis, a stable domain of 25 amino acids was identified as a suitable selection target. DNA in vitro selection experiments were carried out against the equivalent mirror-image D-peptide domain resulting in high affinity D-DNA aptamers. As expected, the corresponding enantiomeric L-DNA Spiegelmer showed comparable binding characteristics to the L-peptide domain. Moreover, the Spiegelmer bound the whole protein target with only slightly reduced affinity. Dissociation constants of both peptide-oligonucleotide complexes were measured in the range of 200 nM, whereas the Spiegelmer binding to the full-length protein was determined at approximately 420 nM. These data demonstrate the possibility to identify Spiegelmers against large protein targets by a domain approach.

In vivo imaging with oligonucleotides for diagnosis and drug development

Molecular imaging, the science that combines non-invasive in vivo imaging and molecular biology, has begun to use labelled oligonucleotides as radiotracers. Antisense oligonucleotides target gene expression at the RNA level, while aptamer oligonucleotides are designed to hit proteins of interest. Oligonucleotides for imaging cover a large range of applications, from the invention of new contrast agents for diagnosis to exquisite research tools for the development of new drugs.

Internal 32P-labeling of L-deoxyoligonucleotides

A general two step procedure for the internal labeling of L-deoxyoligonucleotides, Spiegelmers, has been developed. Through radioactive labeling oligonucleotides can easily be detected and monitored in biological samples. T4 polynucleotide kinase is shown to efficiently phosphorylate strands of L-nucleic acids which allows the labeling with phosphorous isotopes such as (32)P. In order to protect the terminal phosphate label against unspecific phosphatases, one of two fragments of a Spiegelmer is enzymatically phosphorylated with [gamma-(32)P]ATP. In a second step we used a template- directed chemical ligation reaction in order to attach the labeled oligonucleotide to the other fragment to yield the full-length Spiegelmer with an internal [(32)P]phosphodiester bond. It has been shown that the functionality of a chemically ligated Spiegelmer is still retained.

Aptamers as tools for target prioritization and lead identification

The increasing number of potential drug target candidates has driven the development of novel technologies designed to identify functionally important targets and enhance the subsequent lead discovery process. Highly specific synthetic nucleic acid ligands--also known as aptamers--offer a new exciting route in the drug discovery process by linking target validation directly with HTS. Recently, aptamers have proven to be valuable tools for modulating the function of endogenous cellular proteins in their natural environment. A set of technologies has been developed to use these sophisticated ligands for the validation of potential drug targets in disease models. Moreover, aptamers that are specific antagonists of protein function can act as substitute interaction partners in HTS assays to facilitate the identification of small-molecule lead compounds.

Nucleic acid aptamers in cancer medicine

Many signalling proteins involved in diverse functions such as cell growth and differentiation can act as oncogenes and cause cellular transformation. These molecules represent attractive targets for cancer diagnosis or therapy and are therefore subject to intensive investigation. Aptamers are small nucleic acid molecules, isolated from combinatorial libraries by a procedure termed SELEX, that bind to a target molecule by providing a limited number of specific contact points embedded in a larger, defined three-dimensional structure. In some cases aptamers have the potential to inhibit the biological function of the molecule resulting in useful reagents for target validation in a variety of disease models.

Reflections on a novel therapeutic candidate

Aptamers composed of L-nucleic acids, Spiegelmers, were selected to specifically bind GnRH. Spiegelmer inhibition of GnRH activity was demonstrated in both cellular and animal models. Rabbit studies showed minimal immunogenic response to the agents.