Development of DNA Aptamer as a β-Amyloid Aggregation Inhibitor

Aptamer Technologies in Neuroscience, Neuro-Diagnostics and Neuro-Medicine Development

Aptamers developed using in vitro Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology are single-stranded nucleic acids 10-100 nucleotides in length. Their targets, often with specificity and high affinity, range from ions and small molecules to proteins and other biological molecules as well as larger systems, including cells, tissues, and animals. Aptamers often rival conventional antibodies with improved performance, due to aptamers' unique biophysical and biochemical properties, including small size, synthetic accessibility, facile modification, low production cost, and low immunogenicity. Therefore, there is sustained interest in engineering and adapting aptamers for many applications, including diagnostics and therapeutics. Recently, aptamers have shown promise as early diagnostic biomarkers and in precision medicine for neurodegenerative and neurological diseases. Here, we critically review neuro-targeting aptamers and their potential applications in neuroscience research, neuro-diagnostics, and neuro-medicine. We also discuss challenges that must be overcome, including delivery across the blood-brain barrier, increased affinity, and improved in vivo stability and in vivo pharmacokinetic properties.

CRISPR-Powered Aptasensor for Diagnostics of Alzheimer's Disease

Alzheimer's disease (AD) is a neurodegenerative disorder and the most common cause of dementia, characterized by the accumulation of amyloid beta (Aβ) peptides in the brain. Here, we present a simple, rapid, and affordable CRISPR-powered aptasensor for the quantitative detection of Aβ40 and Aβ42 biomarkers in cerebrospinal fluid (CSF) samples, enabling early and accurate diagnostics of AD patients. The aptasensor couples the high specificity of aptamers for Aβ biomarkers with CRISPR-Cas12a-based fluorescence detection. The CRISPR-powered aptasensor enables us to detect Aβ40 and Aβ42 in CSF samples within 60 min, achieving a detection sensitivity of 1 pg/mL and 0.1 pg/mL, respectively. To validate its clinical utility, we quantitatively detected Aβ40 and Aβ42 biomarkers in clinical CSF samples. Furthermore, by combining CSF Aβ42 levels with the c(Aβ42)/c(Aβ40) ratio, we achieved an accurate diagnostic classification of AD patients and healthy individuals, showing superior performance over the conventional ELISA method. We believe that our innovative aptasensor approach holds promise for the early diagnostic classification of AD patients.

Combining iontronic, chromatography and nanopipette for Aβ42 aggregates detection and separation

In this work, we aim to capture, detect and analysis at single molecule level Aβ42 aggregates. To this end, two strategies of track-etched nanopore membranes functionalization were investigated. The first one uses an aptamer and requires only three steps, whereas the second strategy uses Lecanemab antibodies and requires six steps. Out of the two presented strategies, the second one was found to be the most suitable to detect Aβ42 aggregates using a quick current-voltage readout. The resulting single nanopore was then upscale to multipore membranes to capture the Aβ42 aggregates before analysis through them through a single-molecule approach. By comparing the species present in the retentate and filtrate, we confirmed the membrane's affinity for the larger Aβ42 aggregates present in the sample. We found that chromatographic membranes combined with an ionic diode for binary on/off readout are powerful tools for detecting rare biomarkers before single molecule analysis.

A label-free dually-amplified aptamer sensor for the specific detection of amyloid-beta peptide oligomers in cerebrospinal fluids

Amyloid-beta peptide oligomer (Aβo) is widely acknowledged to be associated with Alzheimer's disease (AD). The immediate and accurate detection of Aβo may provide the index for tracking the progress of the state of the disease, as well as some useful information for investigating the pathology of AD. In this work, based on a triple helix DNA which triggers a series of circular amplified reactions in the presence of Aβo, we designed a simple and label-free colorimetric biosensor with dually-amplified signal for the specific detection of Aβo. The sensor displays some advantages including high specificity, high sensitivity, low detection limit down to 0.23 pM, and wide detection range with three orders of magnitude from 0.3472 to 694.44 pM. Furthermore, the proposed sensor was successfully applied for detecting Aβo in artificial and real cerebrospinal fluids with satisfactory results, suggesting the potential application of the proposed sensor for state-monitoring and pathological studies of AD.

A critical review on the role of nanotheranostics mediated approaches for targeting β amyloid in Alzheimer's

Alzheimer's is one of the most common neurodegenerative illnesses that affect brain cellular function. In this disease, the neurons in the brain are considered to be decaying steadily but consistently by the accumulation of amyloid mass, particularly the β-amyloids, amyloid proteins, and Tau proteins. The most responsible amyloid-proteins are amyloid-40 and amyloid-42, which have a high probability of accumulating in excess over the brain cell, interfering with normal brain cell function and triggering brain cell death. The advancement of pharmaceutical sciences leads to the development of Nanotheranostics technology, which may be used to diagnose and treat Alzheimer's. They are the colloidal nanoparticles functionalised with the therapeutic moiety as well as a diagnostic moiety. This article discusses the prognosis of Alzheimer's, various nanotheranostics approaches (nanoparticles, quantum dots, aptamers, dendrimers, etc), and their recent advancement in managing Alzheimer's. Also, various in-vitro and in-vivo diagnostic methodologies were discussed with respect to nanotheranostics.

A liposome-based aptasensor integrated with competitive reaction enabling portable and electrochemical detection of Aβ oligomer

Aggregation of β-amyloid (Aβ) were considered as a typical pathological feature of Alzheimer's disease (AD). Extensive studies have verified that soluble Aβ oligomers (AβO) were more toxic to neurons than plaques. Herein, in this work, a glucose entrapped liposome-based portable aptasensor was fabricated for recognizing and interacting with AβO by specific aptamer on liposome (G-Lip-Apt). Then, a single strand DNA, designed to be partially complementary to AβO aptamer, was modified on amino-functionalized Fe₃O₄@SiO₂ to obtain a magnetic nanocomposite (Fe₃O₄@SiO₂/NH₂-DNA). In the presence of AβO, the specific recognition between AβO and its aptamer on G-Lip-Apt made AβO bounded with G-Lip-Apt. With subsequent introduction of Fe₃O₄@SiO₂/NH₂-DNA, the unreacted G-Lip-Apt was further linked with Fe₃O₄@SiO₂/NH₂-DNA by double stranded complementary pairing interaction. Along with the addition of TritonX-100 into the formed G-Lip-Apt/Fe₃O₄@SiO₂/NH₂-DNA complex, the encapsulated glucose was released from liposome and then measured by a personal glucose meter (PGM). Good linear correlation was acquired over concentration of 5.0-1000 nM and the limit of detection (LOD) was calculated to be 2.27 nM for AβO. The developed portable electrochemical strategy integrated magnetic separation, competitive reaction and point of care test (POCT) to achieve high sensitivity, selectivity and accuracy, therefore enabled it successfully applied to the analysis of AβO in the hippocampus and cortex of APP/PS1 transgenic AD mice.

Nanoparticle Scanners for the Identification of Key Sequences Involved in the Assembly and Disassembly of β-Amyloid Peptides

The aggregation of β-amyloid peptides (Aβ), implied in the development and progression of Alzheimer's disease, is driven by a complex set of intramolecular and intermolecular interactions involving both hydrophobic and polar residues. The key residues responsible for the forward assembling process may be different from those that should be targeted to disassemble already formed aggregates. Molecularly imprinted nanoparticle (MINP) receptors are reported in this work to strongly and selectively bind specific segments of Aβ₄₀. Combined fluorescence spectroscopy, atomic force microscopy (AFM) imaging, and circular dichroism (CD) spectroscopy indicate that binding residues 21-30 near the loop region is most effective at inhibiting the aggregation of monomeric Aβ₄₀, but residues 11-20 that include the internal β strand closer to the N-terminal represent the best target for disaggregating already formed aggregates in the polymerization phase. Once the aggregation proceeds to the saturation phase, binding residues 1-10 has the largest effect on the disaggregation, likely because of the accessibility of these amino acids relative to others to the MINP receptors.

Construction of a DNA Nanoassembly Based on Spatially Ordered Recognition Elements for Inhibiting β-Amyloid Aggregation

A β-amyloid (Aβ) aggregation process is a spontaneous process where the original random coil or helical structure changes into a regularly arranged β-sheet structure. The development of inhibitors with the features of low cost, high efficiency, and biosafety by targeting Aβ self-aggregation is significant for Alzheimer's disease treatment. However, the issues of low inhibition efficiency under low concentrations of inhibitors and biological toxicity are currently to be addressed. To resolve the above problems, a DNA nanoassembly (HCR-Apt) based on spatially ordered recognition elements was constructed by targeted disruption of Aβ ordered arrangement. It was discovered that HCR-Apt could inhibit effectively the fibrillation of Aβ₄₀ monomers and oligomers at substoichiometric ratios. This may be due to orderly arrangement of aptamers in rigid nanoskeletons for enhancing the recognition interaction between aptamers and Aβ₄₀. The strong interaction between HCR-Apt and Aβ₄₀ limited the flexible conformational conversion of Aβ₄₀ molecules, thereby inhibiting their self-assembly. Computational simulations and experimental analysis revealed the interactions of Apt₄₂ with Aβ₄₀, which explained different inhibition effects on the fibrillation of Aβ₄₀ monomers and oligomers. Furthermore, the analysis of tyrosine intrinsic fluorescence spectra and surface plasmon resonance imaging showed that the interaction of HCR-Apt and Aβ₄₀ was stronger than that of Apt₄₂ and Aβ₄₀. These findings contributed to establishing a promising method of boosting the recognition interaction by orderly arrangement of recognition elements. Taken together, this work is expected to provide a simple and efficient strategy for inhibiting Aβ aggregation, expanding aptamer's application potential in neurodegenerative diseases.

bioTCIs: Middle-to-Macro Biomolecular Targeted Covalent Inhibitors Possessing Both Semi-Permanent Drug Action and Stringent Target Specificity as Potential Antibody Replacements

Monoclonal antibody therapies targeting immuno-modulatory targets such as checkpoint proteins, chemokines, and cytokines have made significant impact in several areas, including cancer, inflammatory disease, and infection. However, antibodies are complex biologics with well-known limitations, including high cost for development and production, immunogenicity, a limited shelf-life because of aggregation, denaturation, and fragmentation of the large protein. Drug modalities such as peptides and nucleic acid aptamers showing high-affinity and highly selective interaction with the target protein have been proposed alternatives to therapeutic antibodies. The fundamental limitation of short in vivo half-life has prevented the wide acceptance of these alternatives. Covalent drugs, also known as targeted covalent inhibitors (TCIs), form permanent bonds to target proteins and, in theory, eternally exert the drug action, circumventing the pharmacokinetic limitation of other antibody alternatives. The TCI drug platform, too, has been slow in gaining acceptance because of its potential prolonged side-effect from off-target covalent binding. To avoid the potential risks of irreversible adverse drug effects from off-target conjugation, the TCI modality is broadening from the conventional small molecules to larger biomolecules possessing desirable properties (e.g., hydrolysis resistance, drug-action reversal, unique pharmacokinetics, stringent target specificity, and inhibition of protein-protein interactions). Here, we review the historical development of the TCI made of bio-oligomers/polymers (i.e., peptide-, protein-, or nucleic-acid-type) obtained by rational design and combinatorial screening. The structural optimization of the reactive warheads and incorporation into the targeted biomolecules enabling a highly selective covalent interaction between the TCI and the target protein is discussed. Through this review, we hope to highlight the middle to macro-molecular TCI platform as a realistic replacement for the antibody.

Modulation of beta-amyloid aggregation using ascorbic acid

Studies have shown that the level of ascorbic acid (AA) is reduced in the brain of Alzheimer's disease (AD) patients. However, its effect on amyloid-β 1-42 (Aβ₄₂) aggregation has not yet been elucidated. Here we investigated for the first time the effect of AA on Aβ₄₂ aggregation using fluorescence assay, circular dichroism, atomic force microscopy, isothermal titration calorimetry, ligand docking, and molecular dynamics. Our results showed that the fibril content decreases in the growth phase when the peptides are co-incubated with AA. AA molecules bind to Aβ₄₂ peptides with high binding affinity and a binding site for AA between the β-strands of Aβ₄₂ oligomers prevents the stack of adjacent strands. We demonstrate the inhibitory effect of AA on the aggregation of Aβ₄₂ and its molecular interactions, which can contribute to the development of an accessible therapy for AD and also to the design of novel drugs for other amyloidogenic diseases.

Aptamers targeting amyloidogenic proteins and their emerging role in neurodegenerative diseases

Aptamers are oligonucleotides selected from large pools of random sequences based on their affinity for bioactive molecules and are used in similar ways to antibodies. Aptamers provide several advantages over antibodies, including their small size, facile, large-scale chemical synthesis, high stability, and low immunogenicity. Amyloidogenic proteins, whose aggregation is relevant to neurodegenerative diseases, such as Alzheimer's, Parkinson's, and prion diseases, are among the most challenging targets for aptamer development due to their conformational instability and heterogeneity, the same characteristics that make drug development against amyloidogenic proteins difficult. Recently, chemical tethering of aptagens (equivalent to antigens) and advances in high-throughput sequencing-based analysis have been used to overcome some of these challenges. In addition, internalization technologies using fusion to cellular receptors and extracellular vesicles have facilitated central nervous system (CNS) aptamer delivery. In view of the development of these techniques and resources, here we review antiamyloid aptamers, highlighting preclinical application to CNS therapy.

Coassembled Chitosan-Hyaluronic Acid Nanoparticles as a Theranostic Agent Targeting Alzheimer's β-Amyloid

β-Amyloid (Aβ) fibrillogenesis is closely associated with the pathogenesis of Alzheimer's disease (AD), so detection and inhibition of Aβ aggregation are of significance for the theranostics of AD. In this work, the coassembled nanoparticles of chitosan and hyaluronic acid cross-linked with glutaraldehyde (CHG NPs) were found to work as a theranostic agent for imaging/probing and inhibition of Aβ fibrillization both in vitro and in vivo. The biomass-based CHG NPs of high stability exhibited a wide range of excitation/emission wavelengths and showed binding affinity toward Aβ aggregates, especially for soluble Aβ oligomers. CHG NPs displayed weak emission in the monodispersed state, while they remarkably emitted increased red fluorescence upon interacting with Aβ oligomers and fibrils, showing high sensitivity with a detection limit of 0.1 nM. By comparing the different fluorescence responses of CHG NPs and Thioflavin T to Aβ aggregation, the Aβ oligomerization rate during nucleation can be determined. Moreover, the fluorescence recognition behavior of CHG NPs was selective. CHG NPs specifically bind to negatively charged amyloid aggregates but not to positively charged amyloids and negatively charged soluble proteins. Such enhancement in fluorescence emission is attributed to the clustering-triggered emission effect of CHG NPs after interaction with Aβ aggregates via various electronic conjugations and hydrogen bonding, electrostatic, and hydrophobic interactions. Besides fluorescent imaging/probing, CHG NPs over 360 μg/mL could almost completely inhibit the formation of Aβ fibrils, exhibiting the capability of regulating Aβ aggregation. In-vivo assays with Caenorhabditis elegans CL2006 demonstrated the potency of CHG NPs as an effective theranostic nanoagent for imaging Aβ plaques and inhibiting Aβ deposition. The findings proved the potential of CHG NPs for development as a potent agent for the diagnosis and treatment of AD.

Oligonucleotide aptamers: Recent advances in their screening, molecular conformation and therapeutic applications

Aptamers are single stranded oligonucleotides with specific recognition and binding ability to target molecules, which can be obtained by Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Aptamers have the advantages of low molecular weight, low immunogenicity, easy modification and high stability. They play promising role in promoting food safety, monitoring the environment and basic research, especially in clinical diagnosis and therapeutic drugs. To date, great achievements regarding the selection, modifications and application of aptamers have been made. However, since it is still a challenge to obtain aptamers with high affinity in a more effective way, few aptamer-based products have already successfully entered into clinical use. This review aims to provide a thorough overview of the latest advances in this rapidly developing field, focusing on aptamer screening methods for different targets, the structure of the interaction between aptamers and target substances, and the challenges and potential of current therapeutic aptamers.

Current Strategies for Modulating Aβ Aggregation with Multifunctional Agents

Alzheimer's disease (AD), as the primary cause of dementia, has seriously affected millions of people worldwide and brought a very heavy financial and social burden. With the growth of population and aging, the situation will worsen unless efficacious drugs are found to reverse, stop, or even slow down disease progression. More and more evidence has demonstrated that amyloid-β (Aβ) aggregation is an upstream causative factor in AD pathogenesis and then triggers a slew of pathological events. Furthermore, the concentrated redox metal ions in the AD brain, especially Cu(II), can significantly exacerbate Aβ aggregation and contribute to the formation of neurotoxic reactive oxygen species (ROS). Therefore, the inhibition of Aβ aggregation and relief of amyloidosis-initiated neurotoxicity play a critical role in AD treatment. Until now, several methods have been proposed to modulate Aβ aggregation, such as developing aggregation inhibitors to interfere with Aβ assembly via noncovalent interactions, copper chelators to cut off metal-accelerated Aβ aggregation and concomitant cytotoxicity, photooxidation to reduce the hydrophobicity and aggregation tendency of Aβ, thermal dissociation to disrupt amyloid aggregates susceptible to temperature, degradation with artificial protease to fracture the Aβ peptide into small fragments, and the clearance of peripheral Aβ to bypass the obstruction of the BBB and reduce the Aβ burden.In this Account, we focus on our contributions to the development of Aβ-targeted multifunctional molecules and nanoparticles, emphasizing the diversified strategies and synergistic therapeutic effects. These therapeutic agents possess the following multifunctionalities: (1) compared with frequently used aggregation inhibitors restricted by intrinsically feeble and sensitive noncovalent interactions, multifunctional agents can efficiently block Aβ aggregation by exploiting two or more Aβ-specific inhibition strategies simultaneously; (2) apart from regulating Aβ aggregation, multipronged agents can also target and modulate other pathological factors in AD pathogenesis, such as increased oxidative stress, abnormal copper accumulation, and irreversible neuron loss; (3) multifunctional platforms with both diagnostic and therapeutic modalities through integrating in situ imaging, real-time diagnostics, a multitarget direction, stimuli-responsive drug release, and the blood-brain barrier (BBB) translocation features are instrumental in improving drug levels at trouble sites, diminishing off-target adverse reactions, evaluating therapeutic effects, and averting overtreatment.Given the fact that amyloid aggregation, local inflammation, and metal dyshomeostasis are universal biomarkers shared by various neurodegenerative disorders, this Account provides a perspective for the evolution of customized therapeutic agents with multiple reactivities for other neurodegenerative diseases. In addition, recent studies have indicated that Aβ aggregates can enter the nucleus and induce DNA damage and anomalous conformational transition. We also explore the influences of DNA on the biological effects of Aβ aggregates.