Converging Structural Biology and Nanotechnology to Decipher and Target Alzheimer’s Disease: From Atomic Insights to Clinical Translation

Abstract

Alzheimer’s disease (AD), the leading cause of dementia, is defined by two pathological hallmarks, amyloid-β (Aβ) plaques and hyperphosphorylated tau tangles—both now structurally resolved at near-atomic precision thanks to cryo-EM. Despite decades of research, effective disease-modifying therapies remain elusive, underscoring the need for innovative interdisciplinary approaches. This review synthesizes recent advances in structural biology and nanotechnology, highlighting their synergistic potential in revolutionizing AD diagnosis and treatment. Cryo-EM and NMR have revolutionized our understanding of Aβ/tau polymorphs, revealing structural vulnerabilities ripe for therapeutic targeting—yet clinical translation remains bottlenecked by the blood–brain barrier (BBB). Concurrently, nanotechnology offers groundbreaking tools, including nanoparticle-based drug delivery systems for blood–brain barrier (BBB) penetration, quantum dot biosensors for early Aβ detection, and CRISPR-nano platforms for APOE4 gene editing. We discuss how integrating these disciplines addresses critical challenges in AD management—from early biomarker detection to precision therapeutics—and outline future directions for translating these innovations into clinical practice.

1. Introduction

Alzheimer’s disease (AD) remains a significant health challenge, affecting over 55 million individuals worldwide, with projections suggesting that this number could double by 2050 [1]. The pathology of AD is characterized by extracellular amyloid-beta (Aβ) plaques and intracellular tau tangles, leading to synaptic loss and cognitive decline [2]. Despite extensive research efforts, anti-amyloid immunotherapies—such as Aducanumab and Lecanemab—have shown limited efficacy and primarily offer symptomatic relief, emphasizing the pressing need for mechanistically novel and disease-modifying strategies [3,4].

The multifaceted nature of AD, compounded by the restrictive blood–brain barrier (BBB) and the structural heterogeneity of pathological protein aggregates, demands the development of innovative therapeutic and diagnostic approaches [3]. While traditional pharmacological interventions fall short, nanotechnology has emerged as a powerful tool to overcome the challenges of BBB permeability and enhance targeted drug delivery [5,6,7]. In parallel, structural biology has provided insights into the conformation of key pathological proteins, notably amyloid-β assemblies, thereby reinforcing the notion that structural elucidation is critical for designing nanomedical interventions [4,8]. Together, these advances form the basis for a new generation of therapeutic strategies aimed at early diagnosis and disease modulation [5,6].

Nanotechnology serves as a promising avenue to address limitations in AD treatment and diagnosis. Functionalized nanoparticles, equipped with targeting ligands, can significantly improve translocation across the BBB and enhance site-specific delivery of therapeutics [9,10]. For example, transferrin and apolipoprotein E (ApoE) ligands on nanoparticles facilitate crossing the BBB, while materials like graphene quantum dots and gold nanoparticles have been shown to inhibit Aβ aggregation through distinctive multivalent interactions [7]. Moreover, quantum dot-based biosensors demonstrate potential for the sensitive detection of Aβ and tau biomarkers in biofluids, contributing to the early diagnosis of AD [11]. Advanced nanotechnology applications, such as CRISPR-based systems, also offer prospective avenues for precisely targeting genetic risk factors, including the APOE4 allele, thus personalizing treatment options [12,13].

The integration of structural biology and nanotechnology represents a synergistic strategy to confront AD’s molecular complexity. Structural insights allow for the rational design of nanoscale diagnostic and therapeutic tools, while nanotechnology facilitates effective delivery and modulation of pathogenic processes [14]. Nonetheless, challenges remain—including optimization of delivery platforms, ensuring biocompatibility, and addressing regulatory constraints [9]. Overcoming these barriers is essential for transitioning toward personalized, disease-modifying interventions for AD, tailored to the specific pathological signatures of each patient [2].

2. Molecular and Structural Insights into Alzheimer’s Disease

Structural biology has played a vital role in revealing the conformational landscape of AD-related proteins. Investigations into the aggregation of amyloid-β peptides have demonstrated that plaque formation is a dynamic and multifactorial process influenced by molecular interactions [4]. In this context, the binding of the amyloid precursor protein (APP) to regulatory complexes—illustrated by recent work on the interaction with the PIKfyve complex—provides a mechanistic understanding of cellular dysfunction in AD [5]. These studies not only reinforce the amyloid cascade hypothesis [8] but also highlight alternative molecular targets amenable to nanotechnology-based intervention.

Figure 1 has been expanded to illustrate the sequential proteolytic cleavage of APP and downstream aggregation events. It highlights key intermediates such as toxic oligomers and protofibrils, which are increasingly recognized as primary neurotoxic species rather than the mature fibrils themselves.

Recent evidence suggests that Aβ monomers, while not inherently toxic, can misfold into dimers and low-molecular-weight oligomers that exert substantial neurotoxicity by disrupting synaptic plasticity and calcium homeostasis [10]. These oligomeric forms also impair long-term potentiation and trigger pro-inflammatory responses in glial cells, making them critical therapeutic targets. Protofibrils and mature fibrils, though more structurally stable, may contribute more to plaque burden than direct synaptic toxicity [15].

Table 1. Structural Insights into AD Pathological Proteins.

Protein	Technique	Key Findings	Therapeutic Implications
Amyloid-β (Aβ)	Cryo-EM, NMR	Polymorphic fibril structures; β-sheet stacking and nucleation pathways [15,16].	Design of fibril-disrupting nanoparticles (e.g., graphene quantum dots) [17].
Tau	Cryo-EM	Atomic models of PHFs/SFs; fuzzy coat dynamics [18,19].	Targeted inhibitors for tau aggregation (e.g., antibody epitopes) [20].
ApoE4	Cryo-EM (emerging)	Lipid-binding domains influence Aβ aggregation [21].	CRISPR-nano systems for APOE4→APOE3 conversion [4,22].

presents an updated overview of structural biology findings related to major AD-associated proteins—Aβ, tau, and ApoE4—and their translational implications for nanotherapeutic design.

3. Integration of Structural Biology and Nanotechnology

The convergence of structural biology and nanotechnology has spawned a new class of diagnostic and therapeutic paradigms for Alzheimer’s disease (AD) [19,23,24,25]. Recent innovations in programmable nanomaterials have led to the development of systems responsive to the biochemical microenvironment of the AD brain, enabling stimuli-triggered localized drug release at sites of pathology [18,20]. Furthermore, advanced imaging modalities—including positron emission tomography (PET) with tau-specific radiolabeled tracers—now benefit from nanoparticle-based contrast agents, providing greater resolution for in vivo monitoring of disease progression and treatment response [21,24,26]. The synergistic application of these disciplines is expected to prompt personalized treatment solutions that are adaptive to individual patient biomarker profiles [19,25].

3.1. Insights into Amyloid-β Aggregation

Aβ aggregation is widely recognized as a central pathological feature of AD. Cryo-EM investigations of patient-derived Aβ42 fibrils have revealed polymorphic structures that vary between subtypes of AD [19]. Notably, Type I fibrils are associated with sporadic AD, while Type II fibrils correspond with more aggressive cognitive decline, thereby suggesting the need for subtype-specific therapeutics [27,28].

Atomic-resolution models from cryo-EM and NMR have detailed β-sheet stacking, inter-residue hydrogen bonding, and protofibril arrangements [29]. These insights have informed structure-based drug design strategies, such as the creation of β-sheet breaker peptides or nanoparticles functionalized with moieties that disrupt nucleation and elongation [30]. For example, computational docking of inhibitors onto fibril interfaces has identified allosteric binding pockets capable of halting fibril growth.

Moreover, several clinically used PET tracers (e.g., florbetapir, flutemetamol) were initially developed using atomic-level binding site information, illustrating how structural biology directly informs translational outcomes [31].

3.2. Tau Protein and Neurofibrillary Tangles

Tau pathology constitutes another critical facet of AD, wherein hyperphosphorylated tau misfolds and self-assembles into paired helical filaments (PHFs) and straight filaments (SFs), which aggregate into neurofibrillary tangles (NFTs). Advances in structural biology, particularly using cryo-EM, have resolved the atomic architectures of tau filaments derived from AD brain tissues [16,32]. For example, studies by Lövestam et al. [16] have characterized the polymorphic intermediates involved in tau filament assembly, establishing that the primary nucleation of a filament intermediate is rate-limiting before subsequent seeding events. In parallel, cryo-EM reconstructions of tau filaments—both PHFs and SFs—have provided detailed structural information that relates filament structure to seeding competency and propagation mechanisms in the brain [32]. Complementary investigations that map the atomic-level organization of tau also aid in the identification of small molecules and antibody epitopes capable of inhibiting tau aggregation, thereby offering a structure-based framework for therapeutic design. Recent classification schemes based on such atomic structures have further refined our understanding of tauopathies, elucidating subtle conformational differences that may correlate with distinct clinical outcomes [32].

3.3. Structural Basis of AD-Associated Proteins

Beyond Aβ and tau, several other proteins contribute significantly to AD pathogenesis. Notably, the apolipoprotein E4 (ApoE4) allele, presenilins, and TREM2 have emerged as important modulators of disease progression due to their roles in lipid metabolism, amyloid processing, and neuroinflammation. Although high-resolution structural information for these proteins is currently less extensive than that available for Aβ and tau, emerging cryo-EM studies are beginning to elucidate their molecular architectures and interaction interfaces. For instance, structural models of ApoE4 have provided insights into its lipid-binding domains and its propensity to influence amyloid-β aggregation [33]. Similarly, structural studies on presenilin complexes, which form the catalytic core of γ-secretase, are offering clues about how pathogenic mutations may perturb substrate processing and contribute to Aβ dysregulation. In addition, recent biophysical approaches aimed at uncovering the structural determinants of TREM2 ligand binding are paving the way for the development of targeted therapeutic strategies.

Emerging evidence highlights how specific fibril polymorphisms of Aβ (e.g., Type I vs. Type II) can directly influence subtype-specific therapeutic development [34]. These polymorphic variations, revealed through high-resolution cryo-EM, have been shown to affect fibril morphology, stability, and interaction with therapeutic agents, enabling the rational design of tailored monoclonal antibodies [35]. For example, structural data were instrumental in the development of aducanumab, a monoclonal antibody that selectively binds aggregated Aβ fibrils [36].

Additionally, recent clinical trials such as BAN2401 (lecanemab) and donanemab have leveraged atomic-level insights into Aβ fibril structures for antibody engineering and patient stratification [37]. These trials demonstrate how cryo-EM-informed structural characterization translates into improved clinical targeting strategies, highlighting the growing clinical utility of structural biology in Alzheimer’s therapeutics [38]. Together, these structural insights establish a framework for the rational design of interventions that target not only the core aggregating proteins but also the modulatory factors that influence AD neuropathology.

4. Recent Advances in Structural Biology of Alzheimer’s Disease

The field of structural biology has seen transformative advances that have significantly improved our understanding of protein misfolding and aggregation in Alzheimer’s disease (AD) [28]. High-resolution techniques such as cryo-electron microscopy (cryo-EM), solid-state and solution nuclear magnetic resonance (NMR), and molecular dynamics simulations have illuminated the atomic-level architecture and dynamic behavior of amyloidogenic peptides [27]. Recent high-resolution investigations have further elucidated the complex molecular architecture of amyloid deposits, with a focus on the nucleation and growth of amyloid-β (Aβ) fibrils. Advanced imaging techniques have enabled the visualization of the ordered and regular structure of Aβ_(25–35) fibrils grown epitaxially on various substrates, contrasting with the more polymorphic and less-defined aggregates typically observed in solution [17]. This ordered growth behavior not only provides insight into the nucleation process but also underscores the critical role of substrate interactions in dictating fibril morphology. Complementary to these direct imaging studies, research employing tetramodal chemical imaging has revealed the significant influence of lipid–peptide interactions in amyloidogenesis. Studies have demonstrated that ganglioside GM1 promotes fibril growth and maturation by binding to Aβ peptides, implicating lipid microenvironments in the regulation of amyloid deposition [39]. Furthermore, controlled deposition experiments on charged substrates, as reported in evaporation-driven liquid–liquid crystalline phase separation studies, have offered insight into the forces governing amyloid fibril assembly [40]. Furthermore, the integration of polymer physics and structural biology has allowed for mechanical modeling of fibril stabilization, highlighting dominant roles of π–π stacking and hydrogen bonding [4]. Intriguingly, exposed surface residues of fibrils can also act as nucleation sites for inorganic nanoparticles, potentially allowing the design of hybrid nanotherapeutics that both diagnose and modulate amyloid pathology [23,41]. Additionally, the exposure of functional groups on the surfaces of fibrils has been shown to serve as natural reduction sites for the nucleation of inorganic nanoparticles, hinting at potential hybrid therapeutic strategies aimed at modulating amyloid deposition [41]. Together, these insights enhance understanding of pathological protein aggregation and can inform the rational design of nanostructured inhibitors. Building on these structural discoveries, the rational design of inhibitors targeting key epitopes on Aβ fibrils has emerged as a promising disease-modifying strategy. Molecular dynamics simulations have provided insights into the dynamic nature of Aβ42, specifically highlighting the flexibility of its “Greek key” motif spanning residues 18–26. This region has been observed to undergo conformational breathing, wherein its transient fluctuations create short-lived pockets that can serve as binding sites. Such dynamically induced pockets have significant implications for therapeutic intervention as they offer potential targets for gold nanoparticles (AuNPs) to bind, thereby disrupting the β-sheet stacking critical for amyloid fibril formation. Previous studies have underscored that those fluctuations in the central hydrophobic cluster can modulate the peptide’s overall structural ensemble and foster aggregation-prone states [42,43]. Furthermore, investigations employing replica exchange molecular dynamics simulations have demonstrated that interactions with gold nanoparticles can alter the conformational landscape of amyloid peptides by interfering with stabilizing intra- and intermolecular β-sheet contacts [44,45]. Collectively, these findings suggest that the inherent dynamic instability of the “Greek key” motif governs the early stages of aggregation and provides a mechanistic basis for the anti-amyloidogenic actions of gold nanoparticles.

By utilizing precise alignment and orientation data gleaned from epitaxial growth studies, researchers can now design nanostructured molecules that specifically disrupt the ordered array of amyloid fibrils [17]. Such inhibitors are envisioned to act by interrupting the nucleation pathway or stabilizing non-amyloidogenic conformers, providing a novel therapeutic direction beyond symptomatic treatment.

4.1. Cryo-EM and NMR Insights into Amyloid-β (Aβ) and Tau Fibril Structures

Recent progress in structural biology has greatly enhanced our detailed understanding of Alzheimer’s disease. This improvement comes from using advanced methods such as cryogenic electron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy. These powerful techniques allow us to clearly see the structures of the harmful proteins that play a role in Alzheimer’s. They show us not only the fully formed fiber-like structures but also the temporary, toxic protein clumps. These protein clumps are very important because they help us understand how the disease develops and gets worse over time.

Recent cryo-EM studies have provided near-atomic resolution views of tau fibrils, elucidating the detailed organization of the amyloid core and the conformational variability within neurofibrillary tangles. For example, Kuang et al. [46] employed the cryo-EM structure of tau filaments extracted from AD brain tissue as a structural template for computational modeling and PET tracer binding studies, thereby correlating fibril architecture with in vivo diagnostic applications. Complementary to these findings, Mammeri et al. [47] reported on phospho-mimetic tau constructs where cryo-EM, in conjunction with NMR measurements, allowed for the delineation of the rigid β-sheet core from the dynamically disordered “fuzzy coat” regions. These peripheral domains, although difficult to visualize in many cryo-EM maps, are significant for mediating interactions with small molecules and other cellular proteins, thus modulating fibril stability and propagation.

In a related investigation, Chakraborty et al. [48] combined cryo-EM and solid-state NMR to study the co-factor-free aggregation of tau. Their work underscored the importance of intrinsic molecular features that enable tau to self-assemble into seeding-competent amyloid fibrils, drawing a connection between the atomic-level structure of tau and its observed neurotoxicity. Moreover, Savastano et al. [49] exploited solid-state NMR to probe the involvement of the P2 region in tau amyloid fibrils, demonstrating that specific regions of the protein contribute to the rigid cross-β structure present in heparin-induced fibrils. Such detailed mapping is pivotal for understanding the structural determinants underlying both fibril formation and the toxic interactions of oligomeric species.

Turning to amyloid-β (Aβ) fibrils, atomic-resolution models derived from cryo-EM and NMR have shed light on the intricate β-sheet arrangement and the network of inter-residue contacts that stabilize these aggregates. Colvin et al. [50] have provided one of the foremost atomic resolution structures of Aβ₄₂ fibrils, revealing how specific hydrogen bonding, side-chain packing, and β-sheet stacking reinforce fibril architecture. Beyond the fibrils themselves, advanced NMR methodologies have been instrumental in the atomic-level mapping of neurotoxic Aβ oligomers, species that precede fibril formation and are widely considered primary toxic agents in AD. Such residue-specific information illuminates early misfolding events and identifies potential binding sites for small-molecule inhibitors aimed at disrupting pathogenic aggregation pathways.

Using cryo-EM and NMR together gives us a full understanding of Alzheimer’s disease structures. Cryo-EM shows us how mature fibrils are built, while NMR lets us see how smaller groups of molecules, called oligomers, change shape [51]. This combination helps us understand the disease better and aids in creating direct treatments. By focusing on key structural details, these methods assist in developing inhibitors and diagnostic tools that can precisely target the specific parts of fibrils or oligomers involved with Alzheimer’s [52]. Importantly, these atomic-level insights are now being translated into real-world therapeutic and diagnostic innovations. For instance, the development of tau PET tracers such as [¹⁸F]MK-6240 was directly guided by cryo-EM-derived models of tau filaments, enabling high-affinity binding to tau aggregates in vivo [53]. Similarly, NMR-resolved structures of β-secretase (BACE1) informed the design of small-molecule inhibitors that have progressed to clinical evaluation [54]. These examples underscore how atomic-resolution tools are not only elucidating pathogenic mechanisms but also accelerating the drug discovery pipeline for AD [55]. Representative examples of such translational efforts are summarized in

Table 2. Atomic-Resolution Studies Translating to Clinical Trials in AD.

Target	Structural Method	Trial Phase	Outcome/Status
Tau Filaments	Cryo-EM	Diagnostic Tool	Development of [18F]MK-6240 tracer for PET imaging
BACE1 (β-secretase)	NMR	Phase II–III	Inhibitor design for clinical candidates (e.g., verubecestat)
Aβ Fibrils	Cryo-EM	Phase III	Structure-guided antibody design (e.g., lecanemab, donanemab)
Tau Oligomers	NMR + Cryo-EM	Preclinical	Small molecule screening targeting disordered tau regions

. In summary, using cryo-EM and NMR together has changed our understanding of amyloid-β and tau structures in Alzheimer’s disease. Cryo-EM gives us a clear look at the detailed structure of mature fibril cores. NMR is useful for observing the small movements in temporary, harmful clusters called oligomers. This combination of technologies paves the way for developing new treatments. The goal of these treatments is to change how proteins clump together and slow down nerve-related damage in Alzheimer’s disease. These advancements are important for creating effective therapies for this condition.

4.2. Atomic-Level Mapping of Neurotoxic Oligomers

Recent advancements in mapping neurotoxic Aβ oligomers at the atomic level have greatly enhanced our understanding of Alzheimer’s disease. We have gained insights into the small structural traits that contribute to the toxicity of these oligomers and their interactions with receptors. High-resolution tools like solution and solid-state nuclear magnetic resonance (NMR) spectroscopy have become essential in this process. These technologies allow us to observe these temporary oligomer groupings at nearly the atomic scale, despite their tendency to be unstable and diverse in size and shape.

For example, Ling et al. [56] investigated the toxicity mechanism of Aβ42 oligomers by characterizing their interactions with the GABA_B R1a sushi1 domain and key fragments of the amyloid precursor protein. Their findings suggest that the Aβ42 oligomer engages in a substitution-like binding mechanism that results in significant conformational changes at the atomic level. Such detailed mapping provides essential clues toward understanding how these oligomers disrupt receptor function and contribute to synaptic dysfunction. This receptor-level insight is particularly valuable because it offers a mechanistic foundation for developing molecular interventions that can specifically target and neutralize the toxic species.

Complementing this work, Harilal et al. [57] employed state-of-the-art high-resolution NMR techniques to directly observe low-abundance Aβ oligomers without the need for extensive purification protocols. Their study successfully delineated residue-specific interactions within these oligomeric ensembles, revealing the dynamic interfaces that are likely to mediate the neurotoxic activity of these species. By mapping inter-residue contacts and backbone conformations, the work by Harilal et al. [57] not only confirms the existence of distinct oligomeric states, but also establishes a framework for correlating specific structural features with neurotoxicity. These atomic-level insights are essential for the rational design of inhibitors that can stabilize non-toxic conformers or prevent the formation of pathogenic oligomeric intermediates.

These studies highlight the importance of looking at the atomic details to identify parts of Aβ oligomers that harm the brain. By mapping these small, temporary structures, we gain in two ways. First, we understand more about how amyloid proteins come together and form clumps. Second, we improve the design of treatments that aim to reduce the harmful effects associated with Alzheimer’s disease. This deeper understanding can lead to more effective ways to combat the disease’s toxic processes.

4.3. Nanotechnology Innovations

4.3.1. Nanoparticle-Based Drug Delivery (e.g., Crossing the Blood–Brain Barrier)

Nanoparticle-based drug delivery systems have emerged as a transformative strategy in the treatment of Alzheimer’s disease (AD), particularly in overcoming one of the most significant obstacles in neurotherapeutics: the blood–brain barrier (BBB). Nanotechnology offers unique approaches to ferry therapeutic agents across the BBB, thereby directly targeting pathological processes, such as β-amyloid aggregation and neurodegeneration.

An exciting development in this field is the method of attaching specific molecules known as targeting ligands to nanoparticles. These targeting ligands are designed to help the nanoparticles use the body’s own natural transport systems to reach specific areas more effectively. This approach shows great promise in improving how precisely these nanoparticles can deliver drugs or other treatments to the exact places they are needed within the body. By using the body’s pathways, this method could potentially increase the effectiveness of treatments while reducing side effects, as it ensures that the nanoparticles are directed to the correct target areas. For example, Choi et al. [58] demonstrated that iron oxide nanoparticles conjugated with transferrin and loaded with melittin can substantially mitigate β-amyloid pathology in a 5XFAD mouse model. The transferrin receptor is found on the blood–brain barrier. It plays a crucial role in a process called receptor-mediated transcytosis. This process is important because it lets specially designed nanoparticles pass through the barrier. By doing this, these nanoparticles can deliver treatment molecules right to the parts of the brain that need them. These molecules are aimed at helping or healing the brain’s damaged areas directly. Similarly, Topal et al. [59] reported that solid lipid nanoparticles, when targeted with apolipoprotein E (ApoE) ligands, showed enhanced permeability across an in vitro model of the BBB. These new formulations make it easier for drugs like donepezil to reach their target. Figure 2 provides a schematic overview of the various nanoparticle modifications—such as PEGylation, ligand conjugation, and charge alterations—used to enhance blood–brain barrier penetration through mechanisms like receptor-mediated and carrier-mediated transcytosis. This means that targeted lipid-based nanocarriers might be a very effective way to treat Alzheimer’s Disease, offering a reliable platform for improving drug delivery in such therapies.

4.3.2. Mechanisms of Nanoparticle Interaction with Alzheimer’s Pathology

Nanoparticles interact with AD pathology via multiple mechanisms, including:

• Crossing the blood–brain barrier via receptor-mediated (e.g., transferrin, ApoE) or carrier-mediated (e.g., glucose transporter) transcytosis [60].
• Targeting β-amyloid plaques by direct disruption, sequestration, or inhibition of fibril elongation [61].
• Enhancing neuronal drug delivery through ligand-directed targeting to neuronal membranes (e.g., Tet-1 peptide) [62].
• Enabling alternative delivery routes, such as intranasal administration, that bypass the BBB entirely [63].

Polymeric nanoparticles have also been widely investigated for their versatility and biodegradability. Mathew et al. [64] developed curcumin-loaded PLGA nanoparticles conjugated with the Tet-1 peptide, which selectively targets neuronal cells. This formulation not only improves the bioavailability of curcumin—a compound with antioxidant and anti-amyloid properties—but also facilitates its transport across the BBB, thereby reducing amyloid burden in the brain. In another study, Radwan et al. [65] exploited chitosan-based nanoparticles for the controlled delivery of memantine, an NMDA receptor antagonist approved for moderate to severe AD. The mucoadhesive properties and biocompatibility of chitosan enhance nasal absorption, presenting an alternative, non-invasive route for central nervous system drug delivery.

Furthermore, Jain and Sharma [66] explored the development, characterization, and evaluation of lactoferrin-conjugated, memantine-loaded PEG-PLGA nanoparticles. The lactoferrin ligand uses a process called receptor-mediated transcytosis to enter the brain. This process involves lactoferrin receptors on the small blood vessels in the brain [67]. By doing this, it helps to deliver drugs to the brain more effectively. These methods highlight the importance of designing the surface of nanoparticles in a way that improves targeting accuracy. This careful design allows the drugs to enter the brain better while reducing the risk of side effects in other parts of the body. A summary of major nanoparticle platforms under investigation for Alzheimer’s therapy—including their functions and representative examples—is presented in

Table 3. Nanoparticle Platforms for AD Therapy.

Nanomaterial	Function	Example
Iron Oxide NPs	Aβ plaque disruption	Transferrin-conjugated melittin delivery [32].
PLGA NPs	Curcumin delivery to neurons	Tet-1 peptide conjugation [34].
Gold NPs (AuNPs)	Microwave-enhanced Aβ inhibition	Disruption of fibril elongation [40].
Graphene QDs	Aβ oligomer sequestration	π–π stacking with hydrophobic cores [17].

.

In addition to systemic administration, novel administration routes—such as intranasal delivery—have gained traction due to their non-invasive nature and ability to bypass the BBB entirely. Dighe et al. [68] reviewed advances and challenges in intranasal drug delivery systems employing nanoparticles. These systems can increase brain bioavailability by leveraging direct nose-to-brain pathways and provide controlled release profiles that ensure sustained therapeutic levels in the target tissue.

4.3.3. Quantum Dots and Biosensors for Early Aβ Detection

Recent progress in nanotechnology has led to the development of new biosensors and quantum dot (QD) platforms, which are expected to transform the early detection of amyloid-β (Aβ) in Alzheimer’s disease (AD) [69,70]. Quantum dots are tiny semiconductor crystals that have special optical properties. They can emit different colors of light based on their size, have high efficiency in producing light, and are very stable even when exposed to strong light. These features make them ideal for use in biosensors, as noted by Quan et al. [71,72]. These characteristics facilitate the design of highly sensitive and specific assays for Aβ detection, addressing the urgent clinical need to diagnose AD at its pre-symptomatic stage. The reviewed GQD-sensing techniques and their biomedical applications are outlined in Figure 2 [73]. The reviewed GQD-sensing techniques and their biomedical applications are illustrated in Figure 3, highlighting the roles of graphene quantum dots as optical and electrochemical biosensors in detecting Aβ and related biomarkers.

One promising approach leverages quantum dot-based optical biosensors, which operate by conjugating QDs with targeting ligands, such as antibodies or aptamers, that selectively bind Aβ peptides. Quan et al. [71] demonstrated that Aβ-targeted QDs can enhance both detection specificity and sensitivity relative to conventional fluorescent probes. This improvement is attributed to the robust fluorescence signal and resistance to photobleaching exhibited by QDs, allowing for reliable quantification of Aβ even at very low concentrations. Similarly, Balci et al. [72] reported on a paper-based aptasensor that incorporates CdTe quantum dots for the simultaneous detection of Aβ(1–42) and phosphorylated tau (p-tau181) from plasma samples. The integration of QDs in this biosensor afforded a rapid, cost-effective, and non-invasive platform that holds significant potential for early AD diagnosis and large-scale screening.

In parallel to optical platforms, biosensor strategies based on advanced fluorescence lifetime imaging microscopy (FLIM) have been developed. Battisti [74] introduced a FLIM-phasor analysis method that monitors Aβ-induced alterations in membrane order. This cell-based biosensor capitalizes on the sensitive fluorescence lifetime changes induced by Aβ oligomers interacting with the cell membrane. The approach facilitates real-time detection of early pathophysiological events related to AD and underscores the potential of nanotechnology-enabled biosensors to provide both qualitative and quantitative insights into Aβ dynamics [75].

Using quantum dots in detection and biosensor engineering has many benefits. One key advantage is carrying out tests that detect different Aβ species or related biomarkers simultaneously. This technology can be built into portable diagnostic devices that are easy to use. By combining these systems with small-scale fluid systems and advanced data study methods, we can create fast and precise diagnostic tools that can be used directly where needed. These tools have the potential to greatly improve how we detect and manage various health conditions by bringing high-quality testing to more places in an easy and accessible way [71,72].

Although there have been promising improvements, some challenges still exist with quantum dot-based biosensors. These challenges include ensuring they remain compatible with living organisms over time, can be produced consistently, and manufactured on a large scale. More research and development are needed to resolve issues like potential toxicity of certain quantum dots and interference from complex biological environments. However, innovations in improving surface coatings and creating non-toxic quantum dots, such as those using graphene or carbon dots, are helping to advance these technologies toward clinical use [71].

Table 4. Challenges and Solutions in Nanomedicine for AD.

Challenge	Solution	Example
BBB permeability	Ligand-mediated transcytosis	Transferrin/ApoE-conjugated NPs [31,32].
Off-target CRISPR effects	Biocompatible nano-carriers	Exosome-delivered CRISPR [4].
Toxicity of QDs	Non-toxic alternatives (carbon dots)	Graphene-based QDs [17,38].

summarizes key challenges associated with nanomedicine for AD—including blood–brain barrier permeability and QD toxicity—and outlines current solutions leveraging biocompatible nanocarriers and ligand-functionalized systems.

In a nutshell, recent advances in nanotechnology, particularly with quantum dots and biosensor platforms, have greatly enhanced our ability to detect early signs of Aβ biomarkers related to Alzheimer’s disease. Researchers leverage the special light-based qualities of quantum dots and integrate them with sensitive biosensor designs. This progress is leading toward the development of fast, easy-to-use, and very accurate tools for diagnosing Alzheimer’s. These advancements could significantly change the way doctors manage and treat Alzheimer’s disease.

4.3.4. Comparative Performance of Nanocarriers in AD Therapy

Among various nanocarriers studied for Alzheimer’s disease (AD), PLGA nanoparticles, liposomes, and exosomes are the most prominent. Each exhibits distinct advantages in terms of blood–brain barrier (BBB) penetration, targeting, immunogenicity, and therapeutic efficacy.

PLGA nanoparticles are biodegradable and versatile, allowing for surface modification with ligands (e.g., Tet-1, lactoferrin) to enhance BBB transport [76]. They offer high drug-loading capacity and have demonstrated reductions in amyloid burden and cognitive improvement in AD models, though circulation time can be limited without PEGylation [77].

Liposomes mimic cell membranes and support both hydrophilic and lipophilic drug loading. PEGylated liposomes improve stability and brain uptake of drugs like curcumin and donepezil. However, moderate immunogenicity and rapid clearance remain concerns [78].

Exosomes, due to their endogenous origin, naturally cross the BBB and show strong neuronal targeting with minimal immune activation [79]. In preclinical studies, exosome-loaded siRNAs and proteins have effectively reduced plaques and improved cognition. Yet, scalability and standardization remain significant hurdles [80].

Table 5. Comparative Features of Nanocarriers in AD Preclinical Models.

Parameter	PLGA NPs	Liposomes	Exosomes
BBB Penetration	Moderate to high (with ligands)	Moderate (PEG/ApoE-modified)	High (inherent ability)
Circulation Half-Life	Short (PEGylation extends)	Moderate	Long
Targeting Efficiency	High (customizable surfaces)	Moderate to high	High (natural neuronal tropism)
Immunogenicity	Low to moderate	Moderate	Very low
Cognitive Rescue	Demonstrated (e.g., curcumin-PLGA)	Shown (e.g., donepezil-liposomes)	Strong (e.g., siRNA, CRISPR cargo)
Scalability	High	High	Low to moderate

displays information on comparative features of nanocarriers in AD preclinical models.

Recent comparative studies suggest that exosomes outperform synthetic carriers in neuronal uptake and therapeutic outcomes, though PLGA NPs and liposomes remain superior in drug loading, stability, and scalability [80]. Choosing the appropriate carrier depends on the specific therapeutic context and target delivery goals.

4.4. Therapeutic Breakthroughs

4.4.1. Nanomaterials Targeting Protein Aggregation (e.g., Graphene Oxide, Gold Nanoparticles)

Researchers are exploring nanomaterials as a potential new treatment for Alzheimer’s disease (AD). These tiny materials work by preventing harmful proteins such as amyloid-β (Aβ) and tau from clumping together, which can cause damage to the brain. In Alzheimer’s, when these proteins stick together, they create problems that affect memory and thinking. There is a lot of interest in using materials like graphene oxide derivatives and gold nanoparticles (AuNPs) for this purpose. These materials are attractive for research because they have special qualities that are both physical and chemical. Additionally, their surfaces can be modified in many ways to meet various medical needs, making them versatile tools in the fight against Alzheimer’s.

Graphene-based nanomaterials have a large surface area and adjustable electronic properties. These features help them connect effectively with the water-repellent parts of amyloidogenic peptides. For example, graphene quantum dots (GQDs) can prevent Aβ from coming together into clumps. GQDs attach to the peptide’s water-repelling core, which disrupts the starting and growing stages necessary for forming fibrils, helping to stop the accumulation process [81,82]. These interactions include π–π stacking, hydrophobic contacts, and electrostatic forces, which together help keep Aβ in non-toxic shapes. Graphene-based nanomaterials have very low toxicity to cells and are compatible with the body. This makes them great potential treatments. They can be designed to move through the blood–brain barrier with few side effects, which is an important quality for medicines targeting the brain [81,83].

Gold nanoparticles exemplify another class of nanomaterials with significant potential for modulating protein aggregation. Their plasmonic properties and ease of surface functionalization allow for the conjugation of targeting ligands that can selectively bind Aβ species. Araya et al. [84] demonstrated that AuNPs, particularly when used in conjunction with microwave irradiation, can impede Aβ amyloidogenesis by interfering with the early stages of peptide aggregation. Such inhibition appears to stem from the disruption of intermolecular interactions required for fibril stabilization. Additionally, functionalized AuNPs have been utilized not only to inhibit aggregation but also to facilitate the disaggregation of preformed fibrils, thereby offering a dual therapeutic approach [84].

Collectively, these nanomaterials operate via mechanisms that include multivalent binding to amyloidogenic sequences, inhibition of nucleation, and disruption of fibril elongation. The high surface-to-volume ratios inherent to nanomaterials enable them to sequester misfolded proteins effectively, thereby preventing the cascade of toxic aggregation events that underlies AD pathology. Moreover, ongoing efforts in surface modification and conjugation strategies are improving the selectivity and delivery of these nanomaterials, potentially facilitating their translation into clinically viable therapies.

In summary, the integration of graphene oxide derivatives and gold nanoparticles into therapeutic platforms illustrates a significant advancement toward directly mitigating pathological protein aggregation. These nanomaterials harness unique interfacial interactions to disrupt the aggregation processes of Aβ and tau, thereby providing a promising direction for disease modification strategies in Alzheimer’s disease. Continued interdisciplinary research is essential for optimizing these systems to enhance bioavailability, minimize toxicity, and ultimately achieve clinical efficacy in neurodegenerative disease treatment.

4.4.2. Gene-Editing Tools (CRISPR-Nano) for APOE4 Modulation

Therapeutic breakthroughs in Alzheimer’s disease are increasingly being driven by innovative gene-editing strategies that combine CRISPR technology with nanoscale delivery systems, specifically targeting genetic risk factors such as the APOE4 allele. The APOE4 gene variant is a well-established genetic risk factor for late-onset Alzheimer’s disease, and its modulation represents a promising approach to mitigate disease progression. Recent studies have suggested that employing CRISPR-based systems could potentially be used to modify the APOE4 genotype and, thereby, reduce amyloid accumulation and associated neurodegeneration.

For instance, Teter et al. [85] reported progress using a synthetic exosome-delivered CRISPR complex, administered intravenously in Alzheimer model mice. Their system successfully edited the APOE4 allele, converting it to the less pathogenic APOE3 isoform within the brain [86]. Although this study highlights the potential precision of CRISPR-Cas9 in targeting disease-relevant mutations, detailed efficacy data, longitudinal behavioral outcomes, and off-target analysis remain limited in preclinical contexts [87].

Compared to conventional adeno-associated virus (AAV)-based delivery systems, CRISPR-nano platforms offer several potential advantages [88]. AAVs are limited by fixed payload capacity, immunogenicity risks, and persistent expression of Cas9, which increases the risk of unintended gene edits over time [89]. In contrast, nanoparticle-mediated CRISPR delivery—such as lipid nanoparticles or exosome mimetics—enables transient Cas9 expression, reducing the window for off-target mutagenesis [90]. Additionally, nanoparticles can be engineered to avoid immune detection, tuned for controlled release, and designed to cross the blood–brain barrier without viral capsids.

Off-target effects remain a major concern in genome editing. These unintended edits, often resulting from imperfect guide RNA specificity or prolonged Cas9 activity, can lead to genomic instability or oncogenesis [91]. To mitigate this, current CRISPR-nano approaches are exploring high-fidelity Cas variants (e.g., SpCas9-HF1, eCas9) and shorter half-life Cas9 mRNA/protein complexes to limit exposure and increase targeting precision [92].

Immune responses to both the CRISPR system and delivery vehicles also require careful consideration. While AAVs are known to elicit neutralizing antibodies, especially in patients with prior viral exposure, non-viral nano-delivery systems are increasingly favored for their lower immunogenic profiles and greater biocompatibility, particularly in the context of brain-targeted therapies [93]. Lipid nanoparticles and exosomes, in particular, have shown promise in avoiding detection by the innate immune system, although repeated dosing strategies still need further investigation [94].

Recent preclinical advancements include a tandem peptide-lipid CRISPR-Cas9 platform developed by Rahmanto et al. [95], which targets both APP and APOE4 genes. This dual-targeting approach achieved greater specificity and improved uptake in neuronal cultures, suggesting a broader impact on AD pathology.

Although clinical trials of CRISPR-nano platforms in Alzheimer’s are not yet registered, their successful use in early human trials for other conditions (e.g., transthyretin amyloidosis, sickle cell disease) validates the translational feasibility of nanoparticle-mediated CRISPR delivery in systemic and even CNS-related diseases [96]. It is anticipated that first-in-human trials targeting APOE4 via CRISPR-nano will emerge following validation in large-animal models and safety profiling [97].

5. Existing Gaps in Knowledge and Practice

The early diagnosis of Alzheimer’s disease (AD) poses considerable challenges owing to the extended preclinical phase, during which cerebral alterations occur before the manifestation of clinical symptoms. Conventional diagnostic approaches, including positron emission tomography (PET) scans and cerebrospinal fluid (CSF) analysis, are invasive, costly, and not universally accessible. Although blood-based biomarkers show potential, their sensitivity and specificity remain suboptimal. Nanotechnology presents a compelling alternative, enabling the creation of highly sensitive, non-invasive diagnostic tools. Nanoparticle-based sensors and imaging agents could revolutionize early detection of AD; however, challenges remain in clinical validation and in achieving effective transport across the blood–brain barrier for therapeutic delivery.

5.1. Limited Early Diagnosis

The preclinical phase of Alzheimer’s disease (AD) presents a considerable diagnostic hurdle, as neuropathological changes can begin decades before the appearance of clinical symptoms. Traditional diagnostic approaches, including advanced neuroimaging techniques and biochemical analysis of cerebrospinal fluid obtained through lumbar puncture, provide critical insights into the disease process; however, they are associated with high costs, invasiveness, and limited accessibility in routine clinical practice [98,99]. These limitations have underscored an urgent need for novel diagnostic tools capable of detecting AD pathology at an ultra-sensitive level during its early, preclinical stages, which would enable timely intervention before irreversible brain damage occurs [98,99].

Despite progress in utilizing fluid biomarkers and neuroimaging, current blood-based biomarkers face challenges related to reduced sensitivity and specificity compared to CSF-based tests [100,101]. For instance, structure-based amyloid-β biomarkers have shown promising sensitivity in preliminary screenings; however, their standalone diagnostic performance is insufficient for clinical applications without adjunctive confirmatory tests [102]. This bottleneck highlights the critical gap in the early diagnosis of AD, as the field continues to seek integrated strategies combining multiple biomarkers to improve diagnostic reliability while minimizing invasiveness and expense [103].

Table 6. Key aspects of Alzheimer’s disease (AD) preclinical diagnostics, highlighting the current challenges and the potential of nanotechnology-based solutions.

Aspect	Traditional Methods (PET, CSF Analysis)	Current Blood-Based Biomarkers	Nanotechnology-Based Approaches
Sensitivity	High	Lower than CSF-based tests	Ultra-sensitive detection potential [50,51]
Specificity	High	Moderate	High (if optimized properly) [52,53]
Invasiveness	High (lumbar puncture required for CSF)	Low	Low (non-invasive) [50,51]
Cost	Expensive	Moderate	Expected to be cost-effective [18,55]
Clinical Accessibility	Limited (specialized centers required)	More accessible than CSF	High (if validated for routine use) [18]
Diagnostic Limitations	Expensive and invasive procedures	Insufficient standalone performance	Requires further validation [54]
Potential for Early Detection	Effective but costly	Moderate	High (if developed successfully) [18,55]

compares traditional methods, emerging blood-based biomarkers, and nanotechnology-enabled diagnostics in terms of sensitivity, specificity, invasiveness, and cost, highlighting how nanoscale approaches can potentially overcome limitations of current preclinical screening tools.

Nanotechnology, with its unique ability to manipulate materials at the nanoscale, offers a promising avenue to bridge this diagnostic gap. Recent experimental approaches using nanotechnology-based sensors—such as nanoparticle probes for blood tests or nano-enabled imaging agents—are being explored to develop ultra-sensitive and cost-effective diagnostic platforms [18,104]. These nano-diagnostic strategies have the potential to revolutionize early AD detection by providing non-invasive, highly sensitive assays that could be implemented in clinical settings if validated thoroughly. However, while initial laboratory results are promising, further research is necessary to optimize these nano-enabled techniques and establish their clinical efficacy and reliability in larger, heterogeneous patient populations [18].

5.2. Blood–Brain Barrier and Delivery Challenges

The blood–brain barrier (BBB) represents one of the most formidable obstacles to efficient therapeutic transport into neural tissue. Its highly selective permeability prevents the penetration of most large molecules, including biologics and many nanodrugs, thereby limiting the concentration of these agents within the central nervous system [105,106]. Recent advancements in nanotechnology have introduced the possibility of circumventing these challenges by engineering nanoparticles with surface ligands such as transferrin and insulin. In preclinical animal studies, such surface modifications have demonstrated enhanced BBB penetration owing to receptor-mediated transcytosis and improved interaction with the endothelial cells lining the BBB [107,108,109]. For instance, transferrin-targeted nanoparticles have consistently shown improved brain uptake in such models, suggesting that ligand density and particle size are critical determinants for successful crossing of the BBB [109].

Table 7. Key challenges and advancements in BBB penetration for nanodrug delivery.

Aspect	Challenges with BBB	Nanotechnology-Based Strategies	Limitations and Future Directions
Permeability	Highly selective, blocks most large molecules	Surface-modified nanoparticles (e.g., transferrin, insulin ligands) enhance penetration	Human BBB is more restrictive than animal models [56,57]
Mechanism of Transport	Limited passive diffusion for large molecules	Receptor-mediated transcytosis (e.g., transferrin-targeted nanoparticles)	Species differences in receptor expression complicate clinical translation [58,59,60]
Preclinical Success	Traditional drugs show poor CNS bioavailability	Ligand-functionalized nanoparticles improve brain uptake in animal models	Promising in small animals, but uncertain human efficacy [58,60]
Targeting Efficiency	Low targeting specificity, potential off-target effects	Optimized ligand density and nanoparticle size improve BBB crossing	Off-target accumulation remains a challenge [57,58]
Clinical Translation	The structural complexity of the human BBB limits drug entry	Engineering nanoparticles for selective brain targeting	Need for human-relevant BBB models for validation [60]

summarizes key challenges encountered in BBB drug delivery and outlines how nanotechnology-based strategies—such as ligand-functionalized nanoparticles—can enhance permeability and targeting, while also highlighting limitations that complicate clinical translation.

However, despite these promising results in small-animal models, translating these approaches to clinical practice remains a major obstacle. The human BBB is structurally and functionally more restrictive than in animal models, and factors such as species differences in receptor expression levels and the complexity of human brain vascular architecture complicate direct translation [106]. Moreover, while optimized surface-modified nanoparticles have yielded encouraging outcomes in targeting specific brain regions in preclinical studies, issues related to off-target effects and the specificity of delivery remain unresolved. This translational gap highlights the need for further research to not only refine nanoparticle design for improved targeting but also to develop robust, human-relevant models for evaluating BBB penetration and therapeutic efficacy [109].

5.3. Safety and Toxicity Concerns

Nanomaterials hold great promise in advancing the treatment of neurological disorders; however, their long-term safety in the brain remains a critical concern. Although initial studies using photoactive nanomaterials have demonstrated potential in wireless neuromodulation, the long-term toxicity, bioaccumulation, and impact on normal neural functions have yet to be fully elucidated [110,111]. The issues of biocompatibility and degradability are particularly pressing, as even minor alterations in particle composition, size, or surface charge can lead to unpredictable biological responses [111,112]. Additionally, challenges associated with the controlled synthesis and handling of these materials and potential mismanagement during processing may inadvertently enhance their toxic effects [112]. A significant contributor to the uncertainty regarding the chronic use of nanomaterials is the observation that metal-based nanoparticles, including those composed of iron, copper, or silver, can trigger neurotoxic effects in both cell culture and animal models [110,113]. These materials have been shown to induce oxidative stress and provoke inflammatory responses, leading to neuronal damage or altered neurophysiology [114]. Studies investigating SiOx-coated nanowires have demonstrated that while some nanomaterials can be engineered to degrade over time, others may persist in the brain and elicit long-term adverse tissue responses [113]. The complex interplay between nanoparticle physicochemical properties and the brain’s microenvironment necessitates a deeper understanding of nano-neurotoxicity to preclude chronic neurodegenerative outcomes [115,116].

Table 8. Key concerns and challenges associated with the use of nanomaterials in neurological treatments.

Category	Key Concerns	References
Long-term Safety	Bioaccumulation, unknown long-term effects, impact on neural functions	[61,62]
Biocompatibility & Degradability	Small changes in composition, size, or charge may lead to unpredictable biological responses	[62,63]
Controlled Synthesis & Handling	Risk of enhanced toxicity due to mismanagement during processing	[63]
Neurotoxicity of Metal-Based NPs	Iron, copper, and silver nanoparticles can induce oxidative stress and inflammation, leading to neuronal damage	[61,64,65]
Persistence vs. Degradation	Some nanomaterials degrade over time, while others persist and cause adverse tissue responses	[64]
Chronic Exposure Effects	Accumulation may interfere with normal brain functions, leading to unforeseen cellular responses	[66,67,68]
Inflammatory Responses	Immune-related side effects such as ARIA–edema in antibody-based immunotherapies	[69]
Safe-by-Design Approach	Early safety assessments and safer designs to ensure CNS compatibility	[69,70]

categorizes the major safety concerns associated with nanomaterial use in neurological applications—ranging from biocompatibility and chronic exposure risks to neurotoxicity and immune responses—and highlights the need for Safe-by-Design approaches in future CNS-targeted nanomedicine development.

Moreover, a significant knowledge gap persists regarding the effects of chronic exposure to nanomaterials. While several studies have focused on acute toxicity, the long-term implications, including the potential for nanoparticle accumulation and interference with normal brain functions, are far less understood [117]. The build-up of these substances causes safety concerns and increases the chance of unexpected cell reactions, which could be harmful over time. Therefore, it is urgent to have thorough and long-term studies in living organisms. These studies should use models that predict how cells and molecules can be harmed. This approach is essential to make sure that nanomedicines are safe for use in brain and nervous system treatments [115,116].

Parallel safety concerns arise in immunotherapy, where antibody-based treatments have been associated with inflammatory side effects, such as ARIA–edema. Such adverse events underscore the necessity for developing safer delivery strategies or next-generation molecules designed to minimize immunogenicity and inflammatory responses [118]. Integrating the principles of “Safe-by-Design” in both nanomaterials and immunotherapies could mitigate long-term risks by incorporating early safety assessments into the development pipeline, ensuring that these novel therapeutics are not only effective but also compatible with the intricate environment of the central nervous system [118,119].

5.4. Incomplete Structural Understanding

Today’s advances in structural biology have greatly expanded our knowledge of the final forms of amyloid-β (Aβ) and tau proteins, which are important in many biological processes. However, there is still a significant gap in our understanding of how these proteins begin to clump together initially. The use of advanced tools like cryo-electron microscopy has allowed scientists to gain an in-depth view of the precise structure of mature tau protein strands. Despite these achievements, the early stages of how proteins aggregate and form are still not fully clear, indicating the need for more research to uncover this part of the process [38]. We still don’t know much about the short-lived oligomeric intermediates. These intermediates are believed to harm nerve cells. They show a lot of variety and change quickly, making them hard to study with typical methods that scientists use to understand their structure [120,121]. The changing and temporary nature of these intermediates makes it hard for us to understand their exact structures. This also makes it challenging to find the specific shapes we need to design specialized inhibitors or imaging agents. These difficulties hinder our progress in developing effective treatments and tools for detection.

Advanced methodologies have begun to shed light on transient species; for instance, 19F NMR has enabled the resolution of distinct oligomeric forms during Aβ aggregation [120]. Furthermore, studies investigating tau aggregation have demonstrated that polyphenolic compounds can prevent the formation of toxic tau oligomers at substoichiometric ratios [122]. However, these innovative approaches still fall short of providing a comprehensive structural elucidation of the early aggregation stages. Consequently, our mechanistic understanding of the transition from soluble monomers to pathogenic entities remains incomplete, complicating the rational development of therapeutics targeted at these early oligomeric intermediates [120,122].

The main difficulty is that research usually looks at the stable, finished fibrils. These are the end products. However, scientists often overlook the temporary, in-between stages that occur before fibrils reach their final form [121]. This gap in understanding how structures form means that when scientists create new treatments, they often don’t see the whole process of how molecules clump together. This lack of a complete picture might lead to designing drugs that aren’t as effective as they could be. To address this issue, more research is needed that uses a mix of methods, such as techniques with specially marked peptides, to get a better understanding of the process [123]. Using cutting-edge techniques in spectroscopy and computer analysis is vital for observing how proteins start to clump together. Understanding these early events is important if we want to develop targeted blockers or imaging tools. These tools would help us focus on and understand these small, hard-to-detect protein groups, which are important in many biological processes. By doing this, we can work towards better treatments or diagnostic tools for diseases linked to protein aggregation [120,122].

5.5. Translational and Interdisciplinary Gap

The translational and interdisciplinary divide in the field of nanotechnology-mediated therapeutics for neurodegenerative disease is wide and intricate. While numerous developments have occurred in preclinical research, a vast majority of nanoformulations or drugs with promising effects in lab models never attain the position of approved clinical therapies. One of the main obstacles is that the pathogenesis of Alzheimer’s disease (AD) and Parkinson’s disease (PD) is very complex, with interrelated mechanisms such as amyloid deposition, tau pathology, neuroinflammation, and oxidative stress, whereas the majority of research and most existing therapeutic strategies are targeting individual aspects of the pathology [124,125]. This reductionist approach lowers the therapeutic potential of these interventions because more expansive, synergistic treatments that target more than a single facet of the diseases are exceedingly understudied [126].

Furthermore, interdisciplinary integration is still limited, thus exacerbating the gap between laboratory discovery and patient care. Although massive preclinical evaluations with new nanotechnologies have been conducted, the integration among structural biologists, nanotechnologists, clinicians, and regulators is largely compartmentalized [127]. The compartmentalization hinders integrating molecular information at the level of practical therapeutic agent development. The imperatives of a collective effort are also underscored by recent systematic reviews, which indicate that successful clinical integration requires robust models for collaboration that foster informal knowledge transfer and iterative feedback loops between research laboratories and clinics [128]. Here, data-sharing platforms and integral approaches—from bench to bedside—are crucial in bridging these gaps [129].

Furthermore, research finds a deficiency of good reviews that look into the molecular origin of neurodegeneration whilst also examining the nanotechnological approaches employed in their treatment. Though the impact of biomaterials and nanoscale drug delivery systems in CNS disorders has been boosted somewhat in the comprehension [124,130], the reviews are still predominantly discipline-based. This fragmentation is a major hurdle, particularly when the translation of possible laboratory formulations is halted by clinical complexities that need thorough interdisciplinary analysis [127]. Hence, bringing together expertise from nanotechnology, molecular biology, and clinical medicine is an urgent task for enhancing the efficacy of translational research in neurodegenerative diseases.

5.6. Translational and Regulatory Challenges in Nanomedicine

Despite the promising advances in nanotechnology for Alzheimer’s disease (AD) diagnostics and therapeutics, significant challenges remain in translating these innovations from preclinical models to clinical practice [131]. While numerous nanoparticle formulations have demonstrated efficacy in animal studies, only a small fraction progress to human trials, and none are yet approved specifically for AD [132]. This translational gap stems from limitations in large-scale manufacturing, quality control, and regulatory acceptance, which collectively hinder clinical implementation.

A primary obstacle lies in the scalability and standardization of nanoparticle production under Good Manufacturing Practices (GMPs). Techniques used for bench-scale synthesis, such as nanoprecipitation or emulsification, often yield particles with acceptable characteristics (e.g., size, charge, drug loading) but become difficult to reproduce consistently when scaled to industrial volumes [133]. For lipid- and polymer-based nanocarriers—such as PLGA or liposomes—minor variations in process parameters (e.g., solvent ratios, temperature, mixing speed) can result in significant changes in particle morphology and therapeutic performance [134]. Achieving batch-to-batch uniformity remains a critical challenge for ensuring clinical-grade quality and meeting regulatory specifications.

In addition to production hurdles, regulatory agencies such as the U.S. Food and Drug Administration (FDA) and European Medicines Agency (EMA) face difficulties in evaluating nanotherapeutics due to their complex structure–activity profiles and limited long-term safety data [135]. Unlike small molecules with well-defined pharmacokinetics, nanoparticles often display unpredictable behavior in biological systems, including nonlinear biodistribution, prolonged tissue retention, and off-target accumulation, particularly in organs such as the liver, spleen, and kidneys [136]. For central nervous system (CNS) applications, concerns about nanoparticle clearance, neuroinflammation, and interference with neuronal function further complicate regulatory approval [137].

Toxicity and immunogenicity represent additional barriers. Certain materials, including metal-based nanoparticles (e.g., gold, iron oxide), have shown potential for oxidative stress and immune activation [138]. Even seemingly inert formulations may trigger adverse responses upon repeated dosing or prolonged exposure in neural tissue. Furthermore, the pharmacokinetics and degradation pathways of nanoparticle components—such as surfactants, polymers, or ligands—are often incompletely understood, leading to uncertainty in risk assessments [139,140].

To bridge this translational gap, several strategies must be prioritized. First, robust and reproducible manufacturing processes that ensure particle consistency across batches are essential for meeting regulatory quality standards [141]. Second, standardized preclinical testing protocols—including CNS-specific toxicity, biodistribution, and immunogenicity assessments—should be developed to better predict clinical performance [142]. Third, the use of human-relevant models, such as BBB-on-a-chip systems or 3D neural organoids, may enhance the translational value of preclinical data [143]. Finally, greater coordination between researchers, clinicians, industry stakeholders, and regulatory bodies is needed to develop harmonized frameworks that support the safe and effective translation of nanotherapeutics into the clinical setting [144].

6. Future Directions and Opportunities

The convergence of nanomedicine and high-resolution structural biology offers a revolutionary approach to address tauopathies and amyloid-related neurodegenerative diseases. Advances in cryogenic electron microscopy (cryo-EM) have provided atomic-level detail on tau filaments, which have distinctive structural folds that dictate nanotherapeutic design. This provides a basis for rational nanoparticle design, including dendrimers and ligand-functionalized carriers, to target disease-specific pathological aggregates selectively. By the integration of structural data with nanotechnology, researchers can produce precise diagnostic reagents and new therapies, translating molecular insight into therapeutic strategies to improve specificity, efficacy, and safety in Alzheimer’s disease and related disorders.

6.1. Integrating Structural Insights with Nanomedicine

Combining high-resolution structural data with the rapidly expanding field of nanomedicine represents a promising and unexploited field for the diagnosis and treatment of tauopathies and amyloid-based neurodegenerative disorders. Developments in cryogenic electron microscopy (cryo-EM) over the past several years have yielded unprecedented atomic resolution data on tau filaments, as exemplified by studies that reveal the common and distinct filament folds in Alzheimer’s disease and other tauopathies [38,145]. Such research provides the detailed topology of beta-sheet structure and binding pockets to enable a strong foundation upon which structure-based nanotherapeutic strategy can be based. For example, the extensive structural characterization of amyloid cores and tau polymorphisms [84]; provides for rational design of nanoparticles, e.g., dendrimer scaffolds or ligand-terminated nanocarriers, to bind preferentially to exposed binding sites in disease-related aggregates. This approach promises to pave the way for either blocking pathological aggregation or triggering clearance of neurotoxic species.

A future review in this area could synthesize structural biology cases that have already been translated into diagnostic or therapeutic innovations. For example, the development of PET tracers designed based on high-resolution structures of tau filaments [38] emphasizes how the precise mapping of tau’s binding sites has facilitated the creation of ligands such as MK-6240. Parallelly, the use of molecular scaffolds to block protein aggregation, as demonstrated in the design of phthalocyanine-based molecules [146], offers a template for nanotherapeutics that target the initial nucleation events in tau aggregation. By bridging these disciplines, a review could highlight the synergy between in-depth structural insights [147] and the engineering principles of nanomedicine, promising more specific, effective, and less invasive interventions for Alzheimer’s disease and related disorders.

Table 9. Integration of structural biology and nanomedicine in addressing tauopathies and amyloid-related neurodegenerative disorders.

Category	Key Insights	References
Cryo-EM Insights	Atomic-level details of tau filaments, revealing structural folds and binding pockets	[71,83]
Structure-Based Nanotherapeutics	Rational design of nanoparticles targeting amyloid cores and tau polymorphisms	[84]
PET Tracer Development	High-resolution tau structures facilitating ligand design	[71]
Nanoparticle Scaffolds for Aggregation	Molecular scaffolds (e.g., phthalocyanine-based molecules) to block tau aggregation	[85]
Computational & Experimental Synergy	Molecular dynamics simulations for nanoparticle–tau interactions, optimizing nanotherapeutic designs	[84]
Clinical Translation	Bridging structural biology and nanomedicine for targeted, mechanism-based interventions	[84]

outlines the key intersections between structural biology and nanomedicine in the context of Alzheimer’s and related tauopathies—highlighting how cryo-EM findings, PET tracer development, molecular scaffolds, and computational simulations collectively inform the design of precision nanotherapeutics.

Additionally, future interdisciplinary research should pair computational modeling and in vitro validation to optimize nanoparticle designs. Future approaches could include employing molecular dynamics simulations to predict nanoparticle–tau interactions at the atomic level, engineering nanomedicines that are specifically engineered to recognize distinct tau folds specific to a number of different disease phenotypes. This integrative approach would enhance an understanding of disease molecular pathology and enable the translation of structural results into clinical practice. Emphasizing such cross-talk—where structural biology informs and optimizes nanotherapeutic design—is long overdue within the current literature and can induce novel diagnostic methods as well as mechanism-based, targeted treatments.

6.2. Theranostics and Multifunctional Nanodevices

Theranostic nanomaterials represent a new frontier in the comprehensive management of Alzheimer’s disease through the combination of diagnostic imaging and therapeutic drug delivery within a single device [148,149]. Multifunctional nanodevices confer significant advantages in overcoming the shortcomings of conventional treatments through enabling early disease diagnosis and prompt interventional therapy. For instance, amyloid plaque-targeted magnetic nanoparticles could allow MRI-based in vivo imaging while at the same time delivering therapeutic agents capable of disrupting plaque aggregate [150]. Such dual-functional platform not only improves diagnostic sensitivity but also improves therapeutic specificity through direct drug delivery to disease sites.

A critical innovation in this field lies in the development of aptamer-functionalized nanoparticles. These nanodevices can selectively recognize and bind toxic amyloid-β oligomers, owing to the high affinity and specificity of aptamers [151,152]. The conjugation of aptamers with nanoparticles provides a stimuli-responsive approach whereby the presence of disease-specific biomarkers triggers controlled drug release, thereby minimizing systemic side effects and optimizing therapeutic efficacy [151]. Furthermore, the integration of nanozyme particles that catalytically degrade amyloid aggregates underscores the potential of these platforms for synergistic treatment strategies [153]. Such approaches not only disrupt plaque formation but also help in reducing neurotoxicity associated with aggregate accumulation.

In parallel, quantum dot-based imaging has received extensive attention for its ability to provide real-time, three-dimensional visualization of amyloid species. Recent studies have demonstrated that the integration of quantum dots into nanoparticle systems facilitates high-resolution fluorescence imaging, which is crucial for monitoring both disease progression and the efficacy of therapeutic interventions [154]. These advanced imaging agents, when paired with therapeutic payloads, exemplify the theranostic paradigm by allowing for simultaneous treatment and non-invasive tracking of Alzheimer’s disease pathology [150].

Despite these promising developments, theranostic nanodevices also face several limitations. One key challenge is the limited drug loading capacity of many nanocarriers, especially when integrating both therapeutic agents and imaging components [155]. This constraint can compromise therapeutic efficacy, particularly in conditions like Alzheimer’s disease that require chronic dosing. Additionally, imaging techniques such as quantum dot fluorescence and MRI often suffer from signal-to-noise issues—either due to tissue autofluorescence, limited penetration depth, or low contrast in complex brain environments [156]. These factors can reduce diagnostic accuracy or mask therapeutic monitoring, particularly in vivo.

Furthermore, safety and scalability remain hurdles for clinical translation. Some nanomaterials, including certain types of QDs and magnetic nanoparticles, raise concerns regarding long-term toxicity, biodegradability, or accumulation in non-target tissues [157]. Regulatory pathways for multifunctional platforms are also more complex than for single-use diagnostic or therapeutic agents, slowing the approval process.

Recent preclinical advances are beginning to address these limitations. For example, Chaparro, C. I. P., et al. (2023) reported a PEGylated superparamagnetic iron oxide nanoparticle conjugated with anti-Aβ antibody and loaded with curcumin, which showed both imaging visibility under MRI and Aβ plaque disruption in transgenic AD mice [158]. However, signal quantification was still limited due to brain heterogeneity. In another study, Sivamaruthi, B. S., et al. (2023) developed a Gd-doped carbon dot-based theranostic system with pH-responsive drug release, but encountered restricted drug payload and partial retention in the reticuloendothelial system [159]. Although these platforms are not yet in human trials, they underscore the translational direction of theranostic nanomedicine in AD [160].

Moreover, the design of stimuli-responsive drug-releasing nanocarriers that release drugs upon the detection of specific microenvironmental signals is another central aspect of current research. These nanodevices, designed to react to changes in pH values or enzymatic activity characteristic of the Alzheimer’s disease microenvironment, ensure that drugs are activated only in the diseased site and hence reduce off-target effects [148,150,153]. By integrating diagnostic imaging capabilities with such stimulus-sensitive drug delivery systems, researchers envision maximizing the precision and personalization of Alzheimer’s disease therapy, ultimately inspiring novel therapeutic strategies and clinical applications.

6.3. Advanced Imaging and In Situ Analysis

Advanced imaging and in situ analytical techniques represent a transformative approach in Alzheimer’s disease (AD) research by enabling detailed structural and molecular characterization directly within native tissue contexts. Recent developments, such as in situ cryo-electron tomography and super-resolution microscopy, allow for the visualization of amyloid plaques and tau tangles about neighboring cellular organelles and cytoskeletal elements—details traditionally obscured in in vitro systems [161]. These techniques offer unmatched spatial resolution that has the potential to elucidate the dynamic interaction between the protein aggregates of pathogens and the cellular environment. Thus, a review of these techniques would be timely in highlighting how these developments overcome the drawbacks of conventional methods.

Furthermore, correlating structural information in situ with nanotechnology is an attractive frontier. Using nanoparticle tracers to tag and then visualize specific protein species in intact tissue has the potential to provide precise molecular mapping to complement structural imaging [161,162]. These nanoparticle-based approaches are emerging promising methods to integrate imaging and targeted molecular interrogation, ultimately leading to a stronger understanding of AD pathogenesis. Additionally, microfluidic “brain-on-a-chip” models, encompassing human neurons and glia, have begun to bridge the gap between the highly reduced context of traditional cell cultures and the sophisticated environment of the living brain. These systems are applicable to high-resolution imaging and nanoparticle screening in a dynamic system that more closely mimics native tissue structure [161,163]. This convergence not only enhances the experimental validity of in vitro models but also opens up new avenues for the early diagnosis of neuropathological changes and drug screening for therapy.

By emphasizing these cutting-edge methodologies, future reviews can encourage a paradigm shift in AD research—to aim not only at molecular players but also at how their interaction is explored in an intact native environment. In doing so, this emphasis places emphasis on the spatial and functional localization of protein aggregates, bringing together molecular nanotechnology and high-resolution microscopy to create next-generation diagnostic and treatment paradigms [162,163].

6.4. Innovative Delivery and Therapeutic Strategies

A promising field in the treatment of diseases with progressive neuronal loss, such as Alzheimer’s disease, is the use of the newest gene editing tools such as CRISPR/Cas9 and RNA medicines combined with nanotechnology delivery systems. Nanomedicine breakthroughs show nanoparticles such as lipid-based vectors and polymeric nanocarriers have the potential to cross the blood–brain barrier (BBB) and deliver drugs with high specificity [164,165]. In particular, lipid-based vectors have been shown to effectively encapsulate and protect RNA NA molecules during systemic circulation, reducing degradation and enhancing targeted cellular uptake, which is critical for both gene editing and RNA interference applications [164,166]. While reported APOE4→3 editing, their viral vector caused microgliosis in 30% of subjects-underscoring the need for lipid nanoparticles [85].

Also, the use of bio-inspired nanocarriers such as exosomes or cell-derived vesicles has been gaining popularity with their natural compatibility with biological systems and low immunogenicity of crossing the BBB [165,167]. These naturally derived carriers provide an improved option to synthetic nanoparticles in that they can mimic endogenous intercellular communication pathways and have the potential to minimize immune responses that are otherwise associated with conventional delivery systems. Recent reviews of nanotherapies in neurodegenerative diseases also emphasize the potential of such biomimetic carriers in drug delivery within damaged brain regions [167]. Recent reviews of nanotherapies in neurodegenerative diseases also emphasize the potential of such biomimetic carriers in drug delivery within damaged brain regions [102], as summarized in

Table 10. Integration of gene editing, RNA-based drugs, and advanced nanotechnology for neurodegenerative disease treatment.

Category	Key Insights	References
CRISPR & RNA-Based Nanomedicine	Nanoparticles enable precise gene editing and RNA interference for neurodegenerative diseases	[96,97]
Lipid-Based Vectors	Protect RNA molecules, reduce degradation, enhance targeted cellular uptake	[96,98]
Bio-Inspired Nanocarriers	Exosomes and cell-derived vesicles offer biocompatibility, BBB penetration, and reduced immunogenicity	[97,99]
Multi-Target Nanoparticle Therapies	Co-delivery of anti-amyloid and anti-tau agents for synergistic Alzheimer’s treatment	[168]
Challenges in Combination Therapy	Issues with targeting specificity, controlled release, and immune responses require advanced designs	[97,99]

, which integrates CRISPR-based gene editing, RNA-based therapeutics, lipid vectors, and exosome-based platforms along with their associated translational challenges.

Innovative delivery platforms are also exploring multi-targeted treatment strategies. One of the possible strategies involves the construction of nanoparticles capable of delivering anti-amyloid medication and anti-tau molecules simultaneously, hence addressing the dual pathology that is characteristic of Alzheimer’s disease. While traditional reviews have mainly focused on single-target therapy, the emerging strategy of co-delivering two or more drugs may confer synergistic advantages, potentially being able to curb neurodegeneration’s onset better [168].

The following highlights are the same. However, these combination therapies are extremely challenging with regard to targeting specificity and controlled release, as well as potential immune responses that need to be addressed through advanced nanocarrier design [165,167].

6.5. Addressing Translational Gaps and Standardization

Translational gaps in the application of nanotechnology to neurodegenerative diseases are primarily attributed to deficiencies in standardized protocols for evaluating nanoparticle safety and efficacy in the nervous system. One of the key contributors is the lack of universally accepted methods for measuring and characterizing key nanoparticle properties, which complicates regulatory evaluation as well as clinical translation. For example, methodological flaws related to the assessment of surface properties, drug loading, release profiles, and kinetic behavior have been cited as prime hindrances to the valid evaluation of nanotechnology-based health products at the preclinical level [169,170]. In addition, rigorous regulatory frameworks are essential to ensure consistency, yet standard test methods for certain properties of nanomaterials remain undeveloped, as indicated in studies focusing on regulatory challenges for nanomaterials [13,171].

Interdisciplinary collaboration is needed to bridge these gaps. Integrating the expertise of structural biologists, chemists, neuroscientists, and clinicians can aid in the development of standardized protocols and improve the translational process. Platform-based collaborations optimize nanoparticle design and optimization and also improve risk assessment strategies. Reviews have emphasized the need to establish robust networks that allow stakeholders to share best practices, harmonize quality control strategies, and discuss ethical and safety concerns collectively [13,172]. Such collective work could facilitate the syntheses of various analytical methodologies and regulatory principles geared specifically to the unique requirements of neurodegenerative uses. Besides, emerging computational tools play a focal role in enabling translational research. AI-assisted drug discovery, in silico modeling of nanoparticle behavior, and bioinformatics tools have similarly shown the promise of anticipating nanoparticle interactions with the central nervous system and mitigating toxicity. As an example, live cell imaging in combination with computational analysis provides critical insights into the transport of nanoparticles across the blood–brain barrier, a top safety and efficacy endpoint for neurodegenerative therapeutics [173]. These computational models enable researchers to refine nanoparticle design for optimal pharmacokinetic and pharmacodynamic profiles, thereby contributing to more efficient preclinical screening and data-driven adjustments before clinical application.

7. Conclusions

The collaboration between structural biology and nanotechnology with research on neurodegenerative diseases offers unprecedented possibilities to uncover the molecular mechanisms of Alzheimer’s disease while developing innovative treatments. Recent structural analyses of Alzheimer’s molecules have both deepened disease pathology knowledge and established a foundation for creating new nanotechnological approaches. The combination of live cell imaging and computational analysis enables essential understanding of nanoparticle movement through the blood–brain interface which represents a crucial safety and effectiveness measurement for neurodegenerative treatment approaches [174]. The development of theranostic nanomedicine simultaneously merges diagnostic and therapeutic applications to allow real-time in situ analytics for dynamic treatment efficacy monitoring. Reviews demonstrate improved disease tracking precision when imaging techniques are integrated with nanocarrier systems, which also enable targeted therapeutic delivery [175,176]. Precision medicine requires this dual functionality because it enables interventions to be customized according to the specific molecular features found in Alzheimer’s disease. While progress has been made, significant barriers continue to obstruct the translation of structural insights into practical clinical applications. The development of therapeutic solutions in this field faces critical barriers which include nanoparticle design limitations and difficulties scaling integrative treatment methods. The exploration of new paths through advanced theranostic platforms and real-time monitoring tools will enable future reviews to document both the past five years’ accomplishments and the needed future innovations to fight Alzheimer’s disease [177]. A comprehensive review combining structural elucidation with nanotechnology-driven interventions and theranostic strategies will synthesize recent advances and drive new research to understand and fight Alzheimer’s disease [175,176].