Nanotechnology‐Enabled Targeted Protein Degradation: Strategies, Opportunities, and Challenges

ABSTRACT

Targeted protein degradation (TPD) has redefined the therapeutic landscape by shifting the focus from merely inhibiting protein function to actively eliminating disease‐causing proteins. However, the clinical translation of TPD agents remains hampered by their inherent physicochemical limitations, including poor solubility, membrane impermeability, and lack of tissue selectivity. Nanotechnology offers a strategic pathway to overcome these barriers. This review examines the convergence of TPD and nanotechnology, highlighting how diverse nanoplatforms—ranging from lipid and polymeric nanoparticles to inorganic carriers and biomimetic systems—can address fundamental delivery challenges. We discuss key design strategies such as physical encapsulation, chemical conjugation, and carrier‐free self‐assembly between nanocarrier‐assisted TPD—where nanoparticles improve degrader pharmacokinetics—and nanostructure‐integrated TPD—where the nanoscaffold directly participates in ternary complex formation, and explore how engineering the nano‐bio interface enables precise control over cellular uptake, intracellular trafficking, and ternary complex formation. We also critically assess current translational hurdles, including manufacturing complexity, biosafety concerns, and tumor heterogeneity, while offering perspectives on how rational design and interdisciplinary collaboration can accelerate clinical adoption. By reimagining protein degraders as components of intelligent nano‐systems, nano‐TPD holds the potential to transform undruggable targets into actionable therapeutic opportunities.

The convergence of nanotechnology and targeted protein degradation transforms therapeutic protein elimination from a molecule‐centric endeavor into a systems‐based discipline. This review explores how nanoplatforms overcome delivery barriers, enabling spatiotemporally controlled degradation through intelligent design at the nano‐bio interface.

1. Introduction

1.1. Paradigm Shift From Inhibition to Degradation

The therapeutic modulation of protein function has historically been dominated by occupancy‐based inhibitors—small molecules or biologics that bind to active sites or allosteric pockets to block protein activity. While this approach has yielded numerous successful drugs, it is fundamentally constrained by several inherent limitations: 1) High‐affinity dependence: Sustained therapeutic efficacy requires continuous high‐affinity binding to functional sites; 2) Sustained exposure requirement: Effective target suppression necessitates maintaining adequate drug concentrations; 3) Targeting of “undruggable protein”: Inability to address proteins lacking conventional druggable pockets, such as transcription factors, scaffolding proteins, and non‐enzymatic components; 4) Susceptibility to resistance: Target mutation or upregulation readily leading to drug resistance [1, 2]. It is estimated that approximately 85% of human proteins are implicated in disease pathogenesis, yet conventional drugs target fewer than 400 proteins, predominantly enzymes and receptors with well‐defined binding sites [3, 4]. The remaining vast “undruggable” proteome represents both a formidable challenge and an immense opportunity for therapeutic innovation.

The emergence of targeted protein degradation (TPD) has fundamentally reshaped this therapeutic paradigm. Rather than merely inhibiting protein function, TPD agents actively eliminate target proteins by harnessing the cell's endogenous degradation machinery (such as the ubiquitin‐proteasome system or lysosomes). This “event‐driven” pharmacology offers several distinctive advantages: 1) Catalytic activity: A single degrader molecule can induce the destruction of multiple target proteins, theoretically enabling efficacy at substantially lower doses; 2) Expansion of the “druggable” space: The ability to target proteins regardless of enzymatic function makes targeting of scaffolding and structural proteins possible; 3) Sustained pharmacodynamic effects: Degradation effects persist until new protein synthesis occurs, potentially allowing for reduced dosing frequency; 4) Potential to overcome resistance: Capability to target resistant mutants or circumvent traditional resistance through mechanisms distinct from inhibition [5, 6, 7]. Since the conceptualization of proteolysis‐targeting chimeras (PROTACs) in 2001 [8], the TPD field has experienced explosive growth, with numerous degraders advancing into clinical trials and the first agents receiving regulatory designations for accelerated approval [9].

1.2. Delivery Conundrum of TPD

Despite the mechanistic elegance and therapeutic promise of TPD, its clinical translation has been profoundly hindered by biopharmaceutical challenges rooted in the molecular properties of degraders. First‐generation PROTACs, as heterobifunctional molecules comprising two ligand domains connected by a linker, typically exhibit molecular weights exceeding 700–1000 Da, highly polar surface areas, and poor aqueous solubility, thus frequently violating multiple rules of drug qualities. These physicochemical characteristics severely compromise membrane permeability, oral bioavailability, and pharmacokinetic profiles, resulting in rapid systemic clearance and limited tumor accumulation [10, 11]. Moreover, the absence of intrinsic tissue selectivity leads to widespread non‐specific biodistribution, potentially causing significant “on‐target off‐tumor” toxicity, particularly concerning for degraders targeting proteins essential for normal cellular function [12]. The “hook effect”—wherein supraphysiological degrader concentrations favor the formation of inactive binary complexes over functional ternary complexes, paradoxically reducing degradation efficacy—further complicates dose optimization [13, 14]. These challenges are magnified for emerging TPD modalities targeting extracellular proteins (LYTACs), autophagy substrates (AUTACs), or requiring cell‐type‐specific engagement [15, 16].

1.3. Nanotechnology as a Strategic Enabler

Nanotechnology offers a compelling strategic framework to address the delivery challenges confronting TPD therapeutics. Nanoparticle‐based delivery systems—encompassing a diverse array of materials including lipids, polymers, inorganic compounds, and biomimetic vesicles—provide versatile platforms for modulating the pharmacokinetic and pharmacodynamic properties of protein degraders [17, 18, 19, 20]. Through encapsulation or conjugation, nanocarriers can: 1) Protect and solubilize: Shield degraders from premature degradation and enhance their solubility [21]; 2) Prolong circulation and enable targeted accumulation: Extend blood circulation half‐life and promote specific accumulation at pathological sites via passive targeting (enhanced permeability and retention effect) or active targeting (ligand‐receptor interaction) mechanisms [22]; 3) Achieve spatiotemporally controlled release: This represents a core advantage of nanotechnology. By responding to characteristic signals of the pathological microenvironment (such as pH, redox potential, specific enzyme activities) or externally applied precise triggers (such as light, ultrasound, magnetic fields), drugs can be released with remarkable spatial and temporal precision [23, 24]. This programmable delivery paradigm transforms systemically distributed protein degraders into precision therapeutics capable of executing degradation selectively in diseased tissues while sparing healthy counterparts [25].

1.4. Scope and Perspective of This Review

The convergence of nanotechnology with TPD—termed nano‐enabled protein degradation (Nano‐TPD)—represents more than incremental improvement; it constitutes a fundamental reconceptualization of how protein degraders interact with biological systems. To provide a clear conceptual framework, it is crucial to distinguish between two distinct paradigms within this field: “nanocarrier‐assisted TPD” and “nanostructure‐integrated TPD”. The former primarily utilizes nanoplatforms (such as lipid or polymeric encapsulation) for the passive or active delivery of PROTACs to overcome pharmacokinetic barriers. The latter, however, represents a more advanced integration where the nanoscaffold itself (such as DNA‐origami or self‐assembled structures) acts as a functional entity that directly participates in and catalyzes ternary complex formation. By engineering the nano‐bio interface, researchers can orchestrate cellular uptake pathways, facilitate endosomal escape, and direct intracellular trafficking to optimize engagement with the degradation machinery. As the TPD field matures, its deep integration with nanotechnology illuminates a clear path forward for overcoming current clinical bottlenecks and realizing the full therapeutic potential of protein degradation. This review aims to deeply explore the cutting‐edge developments at the dynamic interface of TPD and nanotechnology. We critically examine the burgeoning field of nano‐TPD, highlighting the key design principles, mechanistic insights, and therapeutic applications across a diverse spectrum of nanoplatforms—from inorganic and polymeric nanoparticles to lipid‐based systems and bio‐inspired carriers. By analyzing recent pioneering studies, we elucidate how different nanocarrier architectures address specific TPD delivery challenges. Finally, we critically address the current translational hurdles, from manufacturing complexities and biocompatibility concerns to the gap between preclinical models and clinical reality, and envision the future trajectories of this rapidly evolving interdisciplinary field as it navigates the path from laboratory innovation to clinical impact.

2. Fundamentals of TPD

2.1. Mechanisms of Proteostasis and Degradation Pathways

Cellular protein homeostasis (proteostasis) is maintained through an intricate network of quality control mechanisms that regulate protein synthesis, folding, trafficking, and degradation [26, 27]. The two principal degradation pathways exploited for therapeutic TPD are the ubiquitin‐proteasome system (UPS) and the autophagy‐lysosome pathway, each with distinct substrate preferences, mechanistic features, and therapeutic opportunities [28, 29].

The UPS mediates the degradation of short‐lived, misfolded, or damaged intracellular proteins through a highly regulated cascade of enzymatic reactions [30]. Ubiquitination is accomplished through the sequential action of three enzyme classes: E1 ubiquitin‐activating enzymes, E2 ubiquitin‐conjugating enzymes, and E3 ubiquitin ligases that confer substrate specificity by recognizing and binding to target proteins, thereby determining degradation specificity [31]. The human genome encodes approximately 600–700 E3 ligases, each with distinct substrate preferences and tissue expression patterns, providing a rich “toolbox” for therapeutic exploitation [32]. Polyubiquitination through lysine‐48 linkages serves as the canonical signal for proteasomal recognition and degradation, although alternative linkage types modulate diverse cellular processes [33]. The 26S proteasome, a multisubunit protease complex, recognizes ubiquitinated substrates, removes the ubiquitin chain, and gradually degrades the protein into small peptides [34].

The autophagy‐lysosome pathway governs the degradation of longer‐lived proteins, protein aggregates, organelles, and extracellular materials [35]. involves the sequestration of cytoplasmic cargo within double‐membrane autophagosomes that subsequently fuse with lysosomes for degradation by acidic hydrolases [36]. Chaperone‐mediated autophagy selectively targets proteins containing KFERQ‐like motifs for direct translocation across the lysosomal membrane [37]. Lysosomal degradation is essential for clearing aggregate‐prone proteins, maintaining organellar homeostasis, and regulating cellular responses to stress and nutrient availability. The recent expansion of TPD to encompass autophagy‐targeting modalities reflects recognition of the therapeutic potential inherent in this pathway, particularly for eliminating protein aggregates and organelles implicated in neurodegenerative disorders and metabolic diseases [38, 39] (Figure 1).

FIGURE 1.

Schematic illustration of the mechanism of protein degradation mediated by PROTAC, LYTAC, and AUTAC.

2.2. PROTACs: Architecture, Mechanism, and Evolution

Proteolysis‐targeting chimeras (PROTACs) represent the most extensively developed TPD modality and serve as the foundation for construction of many nano‐enabled strategies [12]. A PROTAC molecule is a heterobifunctional entity comprising three essential components: 1) A ligand that binds the protein of interest (POI): Responsible for recognizing and binding the target protein; 2) A ligand that recruits an E3 ubiquitin ligase: Responsible for recruiting a specific E3 ligase; 3) A chemical linker: Connecting the two aforementioned “warheads”. The mechanism of action involves the simultaneous engagement of both target and E3 ligase, inducing formation of a stable ternary complex that positions the target for ubiquitination by the E2 enzyme recruited to the ligase complex. Polyubiquitinated targets are subsequently recognized and degraded by the proteasome, while the PROTAC molecule is released to engage additional substrate molecules, enabling its catalytic, sub‐stoichiometric activity [40, 41].

The first PROTAC reported in 2001 by Sakamoto et al. utilized a peptide derived from IκBα to recruit the SCFβ‐TRCP E3 ligase for degradation of methionine aminopeptidase‐2, providing the initial proof‐of‐concept [8]. However, peptide‐based PROTACs suffered from poor cellular permeability and metabolic instability. The development of fully small‐molecule PROTACs in 2008, exemplified by ARV‐645 targeting the androgen receptor, marked a pivotal advancement enabling drug‐like properties and in vivo efficacy [42]. Subsequent refinements have expanded the E3 ligase repertoire beyond the initial CRBN and VHL ligases to include MDM2, IAP, DCAF15, RNF114, and others, each offering distinct tissue expression profiles and substrate preferences [43, 44, 45, 46]. Linker optimization has emerged as a critical design consideration, with length, composition, and attachment geometry profoundly influencing ternary complex formation, degradation kinetics, and physicochemical properties.

The clinical advance of PROTACs has been remarkable, with multiple candidates advancing into human trials. Bavdegalutamide (ARV‐110, targeting androgen receptor) and vepdegestrant (ARV‐471, targeting estrogen receptor) have demonstrated proof‐of‐mechanism in patients with prostate and breast cancer, respectively. Notably, ARV‐471, as the world's first PROTAC drug approved by the FDA, and also the first approved heterologous bifunctional protein degrader, marks the transition of TPD technology from the proof‐of‐concept stage to clinical application. Additional PROTACs targeting BTK, STAT3, IRAK4, and other therapeutic species are advancing through preclinical and early clinical development [9, 47, 48]. Despite this progress, persistent challenges, including oral bioavailability limitations, tissue selectivity deficits, and potential resistance mechanisms, underscore the need for advanced delivery strategies.

2.3. Expanding the TPD Toolbox: Molecular Glues, LYTACs, AUTACs, and Beyond

The success of PROTACs has catalyzed the development of diverse TPD modalities that significantly expand the degradable proteome and exploit alternative degradation pathways.

Molecular glues represent an elegant minimalist approach to targeted degradation, functioning as single small molecules that stabilize otherwise weak interactions between an E3 ligase and a target protein [49]. Unlike bifunctional PROTACs, molecular glues do not contain separate target‐binding and E3‐binding domains, but instead bind to the ligase and create a neo‐surface that recruits the target. The immunomodulatory imide drugs (IMiDs)—thalidomide, lenalidomide, and pomalidomide—exemplify this mechanism, binding to CRBN and recruiting neosubstrates including IKZF1 and IKZF3 for degradation [50, 51]. Despite their clinical success in multiple myeloma, rational design of molecular glues remains challenging, with most identified serendipitously.

Lysosome‐targeting chimeras (LYTACs) address the limitation of PROTACs to intracellular targets by enabling degradation of extracellular and membrane‐associated proteins through lysosomal trafficking [52]. First reported by the Bertozzi group in 2020 [15], LYTACs are bifunctional molecules comprising an antibody or small molecule targeting the extracellular POI and conjugated to a glycopeptide ligand for the cation‐independent mannose‐6‐phosphate receptor (CI‐M6PR). Engagement of CI‐M6PR directs the ternary complex to the endolysosomal pathway for degradation. Subsequent iterations have expanded the repertoire of lysosome‐targeting receptors to include ASGPR for liver‐specific degradation, sortilin, and the transferrin receptor [53, 54, 55]. Related strategies include MoDE‐A (molecular degrader of extracellular proteins) using small molecule ASGPR ligands, KineTACs exploiting cytokine receptors, and TransTACs utilizing transferrin receptor engagement [55, 56, 57].

Autophagy‐targeting chimeras (AUTACs) harness the autophagy‐lysosome pathway for degradation of intracellular targets, including protein aggregates and organelles inaccessible to proteasomal degradation [16]. AUTACs contain a target‐binding ligand linked to a degradation tag, such as a guanine derivative that mimics autophagy signals, directing tagged cargo to autophagosomes for subsequent lysosomal degradation [58, 59]. AUTOTACs (autophagy‐targeting chimeras) employ a similar principle using p62‐mediated recognition, while ATTECs (autophagy‐tethering compounds) induce proximity between LC3 on autophagosomal membranes and target proteins [60, 61]. These autophagy‐based modalities expand TPD beyond soluble proteins to encompass aggregated species and organelles implicated in neurodegenerative diseases and metabolic disorders.

Antibody‐based degraders exploit the specificity and pharmacological properties of biologics to achieve targeted degradation. AbTACs (antibody‐based PROTACs) are bispecific antibodies with one arm binding a transmembrane E3 ligase (RNF43 or ZNRF3) and the other binding a membrane‐associated POI, thereby inducing proximity and subsequent lysosomal degradation [62]. PROTABs (proteolysis‐targeting antibodies) similarly recruit membrane‐associated E3 ligases for target elimination, while REULR (receptor elimination by E3 recruitment) employs a similar strategy for receptor degradation [63, 64]. These approaches combine the favorable pharmacokinetics and manufacturability of antibodies with the catalytic mechanism of induced degradation.

Nucleic acid‐based degraders represent an emerging frontier, employing aptamers or oligonucleotides as recognition elements for targets lacking small molecule ligands. Aptamer‐based PROTACs have been developed for degrading transcription factors and other challenging targets, while siRNA‐mediated degradation through RNA interference remains a complementary but mechanistically distinct approach to protein knockdown [65, 66].

2.4. Clinical Landscape and Persistent Challenges

The TPD field has witnessed remarkable translational progress, with over 20 degraders entering clinical trials across diverse indications [9]. Currently, ARV‐110 and ARV‐471 remain the most advanced, with phase II data demonstrating target engagement and preliminary antitumor activity in heavily pretreated patients [47, 48]. KT‐474 (Kymera Therapeutics) targeting IRAK4 has shown promise in inflammatory diseases, while NX‐2127 (Nurix Therapeutics) degrades BTK and IKZF3 in B‐cell malignancies [67, 68]. CFT1946 (C4 Therapeutics) targeting BRAF V600E and DT2216 targeting BCL‐XL exemplify the expanding scope of degradable oncology targets [69, 70].

Despite this clinical validation, persistent challenges continue to limit the full therapeutic potential of TPD agents. Physicochemical liabilities—high molecular weight, poor aqueous solubility, and limited membrane permeability—compromise oral bioavailability and require formulation strategies for clinical administration. Pharmacokinetic limitations include rapid systemic clearance, extensive non‐specific tissue distribution, and inadequate tumor penetration [10, 11]. “On‐target off‐tumor” toxicity arises from degradation of proteins essential for normal tissue function, particularly concerning for targets with broad expression patterns [12]. The “hook effect” complicates dose optimization, as supraphysiological concentrations may reduce rather than enhance degradation efficacy [13, 14]. Resistance mechanisms are emerging, including mutations in degrader binding sites, E3 ligase downregulation, and proteasome alterations. Expanding target scope requires development of ligands for “undruggable” proteins and engagement of additional E3 ligases with tissue‐restricted expression [71].

These challenges create a compelling rationale for nanotechnology‐enabled delivery strategies that can modulate pharmacokinetics, enhance tissue selectivity, and enable controlled degradation while mitigating systemic toxicity [25].

3. Nano‐Arsenal for TPD

Nanotechnology overcomes the limitations in the clinical application of traditional small‐molecule degraders, such as unfavorable pharmacokinetics, insufficient tumor accumulation, and off‐target toxicity. The core of a rationally designed nano‐degradation platform lies in the holistic control over material composition, surface chemistry, response mechanisms, and the biological microenvironment. Based on material properties and functional configurations, this chapter systematically dissects the current diverse nano‐platforms used for TPD, delving into their design logic and mechanisms of action. Each platform type offers distinct advantages: inorganic nanoparticles provide precise size control and versatile surface functionalization but face long‐term retention concerns; polymeric nanoparticles offer tunable degradation kinetics and ease of modification yet may suffer from inconsistent release; lipid‐based systems excel in biocompatibility and clinical translatability though limited by endosomal escape; self‐assembled platforms enable unparalleled spatial precision but require enhanced in vivo stability; and bio‐inspired systems leverage natural homing capabilities yet encounter manufacturing complexity. Evolving beyond mere delivery vehicles, a new generation of nanoplatforms has emerged as intelligent tools capable of sensing the microenvironment, executing multifunctional synergistic tasks, and enabling self‐tracking (Table 1).

TABLE 1.

Comparison of different nano‐TPD systems.

Nanocarrier Type	Inorganic NPs	Polymeric NPs	Lipid‐Based NPs	Self‐Assembled NPs	Bio‐Inspired NPs
Material Examples	Gold nanoparticles, [72, 73] mesoporous silica, [74] quantum dots, [75] MOFs [76]	PLGA, [77] PEG‐PLA [78, 79]	Liposomes [80, 81, 82]	DNA origami, [83, 84, 85, 86] peptides [87]	Cell membrane‐coated NPs, [88, 89] exosomes [90]
Targeting Mechanism	Passive or ligand‐mediated targeting; stimuli‐responsive release	Passive targeting; surface functionalization with ligands	Passive targeting; surface modification with ligands	Programmable organization; multivalent ligand display	Homotypic targeting; immune evasion
Loading Efficiency or Encapsulation Efficiency	54.05% and 77.25%; [72] >99%; [74] 82.4% and 91.6%; [76]	85.3%; [91] >50% [92]	95% [81]	Such systems are usually directly incorporated as part of the TPD molecule	86.2%±2.1%; [88] 67.8±5.1% [89]
Degradation Efficiency of Target Protein	HER2: >95%; [72] BRD4: 74.1%; [74] PD‐L1: >90% [75]	EGFR: >60%; [78] AR: 70% [79]	PTKT: >90%; [81] ERα: >90% [82]	CDK9: 75.2%; [83] STAT3: >90%; [84] EGFR: 90% [86]	HER2: 47%; [90] PD‐L1: >75% [93]
Tumor Inhibition Efficiency	85.35%; [72] 58.7%; [74] >80% [75]	>70%; [78] >60% [79]	>65% [81]	95.79%; [84] 80% [86]	>80% [93]
Advantages	Precise size control, high surface area, stimuli responsiveness	Tunable composition, biodegradability, ease of functionalization	High biocompatibility, capacity for hydrophilic/hydrophobic drugs	Unparalleled spatial control, high drug loading, modularity	Biomimetic properties, enhanced targeting, low immunogenicity
Limitations	Potential long‐term accumulation, metallic toxicity concerns	Acidic degradation products, inconsistent release profiles	Limited loading efficiency, endosomal escape issues, batch variability	Limited mechanical strength, circulation stability concerns	Complex preparation, scalability issues

3.1. Inorganic Nanoparticles

Inorganic nanocarriers, such as gold nanoparticles (AuNPs), mesoporous silica nanoparticles (MSNs), metal‐organic frameworks (MOFs), and quantum dots, provide highly controllable platforms for the precise delivery of TPD agents. The core of their design lies in utilizing their high specific surface areas to achieve covalent or non‐covalent modification of multiple functional modules, thereby constructing multifunctional nano‐chimeras.

For instance, Wang et al. ingeniously utilized gold nanoclusters (GNCs) covalently conjugated with HER2‐targeting peptides and CRBN E3 ligase ligands to construct GNCTACs (Figure 2A) [72]. This design extends the traditional “bifunctional molecule” concept to the nano‐interface, achieving catalytic degradation of the membrane protein HER2 and fully demonstrating the unique advantages of inorganic nano‐nuclei in enriching local ligand concentrations and promoting ternary complex formation. To achieve active seeking of target proteins, Ning et al. went a step further by integrating gold nano‐cups with molecular motors to develop MotorTACs [73]. These nanomachines can move autonomously, actively capturing and degrading extracellular proteins, and providing a novel strategy for addressing the challenge of degrading low‐abundance or soluble proteins.

FIGURE 2.

(A) Schematic illustration of Persistent Degradation of HER2 Protein by GNCTACs for Programmed Cell Death. Reproduced with permission [72]. Copyright 2023, American Chemical Society. (B) Schematic illustration of HA coating MOF‐based nano platform (ZMCH). Reproduced with permission [76]. Copyright 2024, Elsevier. (C) Synthesis of CDs and CDTACs. Reproduced with permission [75]. Copyright 2023, Wiley‐VCH GmbH. (D) Schematic Illustration of Synthesis and NIR Photoactivation Mechanism of NAP. Reproduced with permission [94]. Copyright 2023, American Chemical Society.

The high porosity of inorganic carriers makes them ideal platforms for co‐loading cargos, facilitating the synergy of degradation therapy with other treatments. For example, Zhu et al. designed a zeolitic imidazolate framework‐8 (ZIF‐8)‐based nanoplatform (ZMCH) co‐loaded with a BRD4‐targeting PROTAC and a photosensitizer (Figure 2B) [76]. This design utilized the pH‐responsive release of ZIF‐8 to release the PROTAC for target degradation in the acidic tumor microenvironment, while simultaneously inducing immunogenic cell death through photodynamic therapy (PDT) to activate anti‐tumor immunity, thus achieving synergistic enhancement of protein degradation and immunotherapy. Similarly, Su et al. utilized carbon dots to develop a CDTACs platform, which not only efficiently degraded the immune checkpoint protein PD‐L1 but also unexpectedly activated the STING pathway, revealing the potential immunomodulatory functions of the nanomaterial itself and offering a new strategy for cancer immunotherapy (Figure 2C) [75].

Inorganic nanoplatforms exhibit significant potential in achieving intelligent functionalities. Their inherent physicochemical properties can be ingeniously transformed into therapeutic functions. For instance, Wang et al. reported a near‐infrared (NIR) light‐activatable nano‐PROTAC (Figure 2D) [94]. Irradiation of the tumor site with NIR light, which allows deep tissue penetration, prompts an embedded photosensitizer to generate singlet oxygen. This action both releases the PROTAC by cleaving a linker and concurrently executes photodynamic therapy. To achieve more precise imaging‐guided therapy, Ning et al. also described a tetrahedral framework LYTAC, capable of degrading PDGF. Importantly, this construct incorporates a fluorescent signal that simultaneously reveals how intracellular ATP levels correlate with degradation efficiency. Such a system holds promise for monitoring cellular parameters in parallel with therapeutic intervention [95]. These studies fully demonstrate the advanced capabilities of inorganic platforms in achieving light‐controlled drug release and theragnostic integration.

Although inorganic nano‐platforms are powerful, their long‐term retention in vivo, potential toxicity of metallic elements, and lack of clear metabolic pathways are major obstacles to clinical translation. Future research should focus on developing biodegradable inorganic materials and reducing their immunogenicity and toxicity through more sophisticated surface modifications (e.g., biomimetic membrane coating) to ensure their clinical translatability.

3.2. Polymeric Nanoparticles

Polymeric nanoparticles exhibit remarkable versatility in the TPD field due to their exceptional structural designability and functional tunability. By selecting polymers with different chemical compositions (e.g., PLGA, PEG, peptides), molecular weights, and chain architectures, one can precisely control the nanoparticle degradation rate, drug release kinetics, and surface properties, thereby significantly enhancing the stability and targeting of TPD molecules and reducing off‐target effects.

One design strategy leverages their easily modifiable surfaces to construct modular degradation platforms. Yao et al. developed a plug‐and‐play platform named MONOTAB, based on antibody‐conjugated polystyrene nanoparticles, which achieved potent degradation of PD‐L1 without compromising lysosomal function (Figure 3A) [96]. Liu et al. constructed TPD‐NPs utilizing poly (lactic‐co‐glycolic acid) (PLGA) nanoparticles functionalized with POI ligands via DSPE‐PEG linkers [77]. This platform enables the degradation of membrane and extracellular proteins without the need to synthesize complex bifunctional molecules for specific targets, significantly simplifying degradation development.

FIGURE 3.

(A) Schematic illustration of targeted degradation of extracellular proteins or vesicles mediated by MONOTABs. Reproduced with permission [96]. Copyright 2024, Springer Nature. (B) Schematic illustration of antibody‐based TPD‐NP structure generated by self‐assembly of hybrid NPs. Reproduced with permission [78]. Copyright 2024, Springer Nature. (C) Schematic Illustration of ARL‐PLA‐SS‐PEG micelle composition and the functional mechanism for targeted protein degradation via dual proteolytic pathways. Reproduced with permission [79]. Copyright 2025, American Chemical Society. (D) Schematic illustration of the sequential activation of POLY‐PROTAC. Reproduced with permission [92]. Copyright 2022, Springer Nature.

The versatility of polymers is also reflected in their ability to manipulate intracellular degradation pathways. Beyond the classical lysosomal targeting pathway, polymer systems can also recruit the autophagy pathway. Huang et al. designed nano‐receptors self‐assembled from maleimide‐polyethylene glycol‐polylactic acid (Mal‐PEG‐PLA) nanoparticles and DOTAP liposomes, which enhanced autophagic flux and promoted the degradation of mutant p53 (Figure 3B) [78]. Lee et al. also integrated an androgen receptor ligand with hydrophobic polylactic acid (PLA) to form micelles that simultaneously activate proteasomal and lysosomal degradation pathways (Figure 3C) [79].

Introducing stimuli‐responsive polymers is another effective means to enhance the specificity of TPD delivery. Liu et al. encapsulated a BRD4 degrader with glutathione (GSH)‐sensitive poly (disulfide amide) (PDSA) polymers to construct a system capable of specific drug release in the high‐GSH tumor environment [91]. This design not only achieved tumor‐specific protein degradation but also allowed the released polymer backbone to induce ferroptosis, producing a synergistic anti‐tumor effect. The POLY‐PROTAC system developed by Gao et al. is even more sophisticated, capable of sequentially responding to matrix metalloproteinase‐2 (MMP‐2) in the tumor microenvironment, the acidic environment of endosomes, and the high GSH concentration in the cytoplasm (Figure 3D) [92]. This enables cascade amplification and spatiotemporal control of BRD4 degradation, as well as combination with photodynamic therapy.

The main challenges facing polymeric nano‐platforms include potential inflammation caused by acidic degradation products of some polymers, unpredictable drug release kinetics (e.g., “burst release” or “no release”), and potential long‐term tissue residues after repeated administration. Future directions involve developing fully biodegradable polymers based on endogenous monomers (e.g., amino acids, sugars) and establishing standardized, scalable manufacturing processes to facilitate clinical translation.

3.3. Lipid Nanoparticles (LNPs)

Lipid nanoparticles (LNPs), which comprise one of the most successfully translated platforms in the fields of mRNA vaccine and small‐molecule drug delivery, are now actively explored for TPD.

The clinical potential of LNPs was first demonstrated in their ability to intervene in difficult‐to‐drug targets. For instance, Luo et al. used reactive oxygen species (ROS)‐degradable LNPs (dGPX4@401‐TK‐12) to deliver a GPX4‐targeting PROTAC [97]. This system disassembles in the high‐ROS tumor environment, releasing the PROTAC to selectively induce ferroptosis in cancer cells. It shows significant tumor inhibition in vivo and provides an effective strategy for targeting the non‐enzymatic ferroptosis key protein. Chan et al. extended the application of LNPs to deliver protein‐based degraders (bioPROTACs), achieving rapid >95% target protein degradation within hours in cells (Figure 4A) [80]. To achieve a more sustained pharmacodynamic effect, Chang et al. innovatively used LNPs to encapsulate mRNA encoding a lysosome‐targeting chimera (MedTAC) (Figure 4B) [81]. A single low‐dose injection enabled sustained de novo synthesis and degradation of the target protein in vivo, avoiding the need for repeated dosing and offering a novel “genetic medicine” paradigm for protein degradation therapy.

FIGURE 4.

(A) Schematic illustration of lipid‐mediated exogenous bioPROTAC delivery system. Reproduced with permission [80]. Copyright 2024, Springer Nature. (B) Schematic illustration of the MedTAC Platform. Reproduced with permission [81]. Copyright 2025, Wiley‐VCH GmbH. (C) Preparation of biGEXs. Reproduced with permission [90]. Copyright 2023, American Chemical Society.

To overcome challenges like low endosomal escape efficiency and batch‐to‐batch variability, researchers have developed various innovative formulations. Li et al., for example, constructed a split‐and‐mix PROTAC system (LipoSM‐PROTAC) via liposomal self‐assembly [82]. This system allows for the tunable surface display of E3 ligase and POI recruiting ligands on the liposome surface. Through multivalent effects, it significantly enhances degradation efficiency and targeting specificity, cleverly circumventing the complexity of traditional covalent conjugation. Furthermore, the genetically engineered exosomes LYTEXs proposed by Wang et al. serve as initial examples of naturally derived lipid nano‐platforms (Figure 4C) [90]. By expressing LYTAC fusion proteins in donor cells and displaying them on exosome surfaces, LYTEXs inherit the low immunogenicity and efficient targeted delivery capabilities of natural exosomes, achieving effective degradation of membrane proteins in recipient cells.

Despite their promise, traditional LNPs still face challenges such as short blood circulation half‐life, susceptibility to liver accumulation, and complex formulation processes. Future optimization strategies will focus on: (1) improving pharmacokinetic properties through sophisticated surface modifications (e.g., PEGylation, targeting ligands); (2) development of libraries of ionizable lipids to screen for components that more efficiently promote endosomal escape; and (3) exploration of hybrid nanoparticles combined with materials like polymers to balance delivery efficiency and safety.

3.4. Self‐Assembled Nanoparticles

Self‐assembled nanocarriers, particularly those based on DNA origami and peptides, represent the frontier of exploration in the TPD field towards “programmable” intelligent responsiveness. These platforms leverage specific recognition between biomolecules to achieve precise control over ligand spatial arrangement, molecular stoichiometry, and dynamic conformation.

Due to their programmability, DNA‐based platforms offer ideal frameworks for constructing structurally defined degraders. Zhou et al. developed DbTACs using a rigid DNA tetrahedral scaffold to precisely assemble E3 ligase and target protein ligands (Figure 5A) [83]. This rigid structure and precise spacing mimic the formation of natural ternary complexes, significantly enhancing the ubiquitination and degradation efficiency of intracellular proteins. Similarly, Li, Zhu et al. demonstrated that multivalent display of ligands on DNA nanostructures can dramatically enhance degradation efficiency through increased binding avidity and can simultaneously target multiple different proteins (Figure 5B) [84, 85]. To endow the system with environmental responsiveness, Cui et al. designed an IMTAC system based on circular DNA origami (Figure 5C) [86]. They ingeniously incorporated pH‐responsive elements (e.g., i‐motif structures) into the DNA strands, resulting in conformational changes in the acidic tumor microenvironment to expose or activate recruiting ligands and achieving conditional activation and degradation of multiple target proteins. Huang et al. constructed nucleic acid hydrogels integrating VEGFR‐binding peptides, M6P lysosomal sorting signals, and siRNA, achieving simultaneous degradation of membrane proteins and gene silencing and demonstrating the potential for multifunctional synergistic therapy [98].

FIGURE 5.

(A) Design of the DbTACs platform. Reproduced with permission [83]. Copyright 2023, Springer Nature. (B) Schematic illustration of the DNA tetrahedron‐driven multivalent proteolysis‐targeting chimera strategy. Reproduced with permission [84]. Copyright 2025, American Chemical Society. (C) Design principles and degradation mechanisms of IMTACs. Reproduced with permission [86]. Copyright 2024, American Chemical Society. (D) Schematic illustration of SR‐A‐mediated lysosomal degradation of IL‐17A in macrophage. Reproduced with permission [87]. Copyright 2024, Springer Nature.

Peptide‐based self‐assembled systems, on the other hand, show potential for in vivo applications due to their inherent biocompatibility and ease of functionalization. Wang et al. co‐assembled bispecific peptides into nanoparticles capable of promoting macrophage‐mediated degradation of IL‐17A (Figure 5D) [87]. This strategy not only showed therapeutic efficacy in a mouse model of psoriasis but, more importantly, the multivalent interactions within the nanoparticles amplified the biological effect of the monomer, offering a novel approach for treating inflammatory diseases. Additionally, the hydrophobic core inside peptide self‐assemblies can serve as an excellent “molecular pocket” for loading other therapeutic agents to achieve combination therapy. Wang et al. ingeniously designed nanospheres self‐assembled from polypeptide‐modified N‐acetyl galactosamine, which actively target liver cancer cells via the ASGPR receptor [99]. Subsequently, they conjugated a CD24 antibody onto the nanosphere surface via crosslinking to construct a nanoplatform targeting CD24 degradation. In addition, they efficiently loaded glucose oxidase (GOx) into the hydrophobic nanosphere interior. Upon targeted delivery, release of GOx depletes glucose in hepatocellular carcinoma cells, synergizing with CD24 degradation to achieve combined protein degradation and starvation therapy.

While these systems benefit from straightforward preparation and high modularity, they may suffer from insufficient mechanical strength, poor in vivo circulation stability, and sensitivity to nucleases/proteases. Future research must focus on enhancing their durability in physiological environments through chemical crosslinking, ligand optimization, and hybrid material design (e.g., combination with polymers) to propel these precisely designed structures from concept to application.

3.5. Bio‐Inspired Nanoparticles

The core concept of biomimetic nanoparticles is the utilization of the natural cell membrane camouflage to endow synthetic cores with “biomimetic” properties, such as immune evasion, homotypic targeting, and inflammatory chemotaxis. This strategy offers an elegant solution to overcome multiple biological barriers in TPD drug delivery, particularly crossing the blood‐brain barrier and targeting the complex tumor microenvironment.

Xu et al. coated nanoparticles loaded with PROTACs with membranes from drug‐resistant glioblastoma (GBM) cells to prepare biomimetic nanoparticles (Figure 6A) [88]. This design leveraged “homotypic targeting” mediated by adhesion molecules on the cancer cell membrane, enabling effective traversal of the blood‐brain barrier (BBB) and precise homing and accumulation at intracranial GBM tumor sites, significantly enhancing the therapeutic effect of PROTACs against brain tumors. In a similar vein, Gao et al. mimicked the clearance mechanism of senescent erythrocytes to construct liposome‐based biomimetic nanodegraders (Figure 6B) [89]. By precisely controlling the density of CD47 on the liposome surface to simulate the “eat‐me” signal of senescent red blood cells, they enabled receptor‐mediated endocytosis, directing SIRPα into lysosomes for degradation. This effectively relieves the CD47‐SIRPα immune checkpoint inhibition and activates the anti‐tumor activity of macrophages.

FIGURE 6.

(A) Schematic illustration of the design of the biomimetic hybrid liposome system (M@TP). Reproduced with permission [88]. Copyright 2025, Wiley‐VCH GmbH. (B) Schematic Illustration of aRLP fabrication, which served as a nano‐degrader to block the CD47‐SIRPα axis and promote macrophage efferocytosis. Reproduced with permission [89]. Copyright 2024, Wiley‐VCH GmbH.

Extracellular vehicles (EVs), including exosomes and microvesicles, are cell‐derived nanoparticles that mediate intercellular communication through the transfer of proteins, lipids, and nucleic acids. Their endogenous origin confers excellent biocompatibility, low immunogenicity, and the capacity to cross biological barriers, including the blood‐brain barrier. EVs can be loaded with protein degraders through electroporation, sonication, or co‐incubation of producer cells with degrader molecules, yielding “engineered exosomes” for targeted delivery [100]. He et al. employed a novel microfluidic droplet‐based EV electro‐transfection system (μDES) to integrate PROTAC into EVs for in vivo delivery [101, 102]. This strategy retains the optimal integrity of drug loaded EVs with improved loading efficiency, and significantly enhances the therapeutic function of PROTAC in vivo in TNBC mouse models. Surface display of targeting ligands can be achieved through genetic engineering of parental cells to express fusion proteins incorporating targeting moieties.

The challenges for biomimetic nano‐platforms lie in the complexity of preparation, maintaining the activity of membrane proteins, and batch‐to‐batch consistency. Future directions involve establishing cell membrane banks, development of modern membrane extrusion or microfluidic technologies, and integration with synthetic biology to produce “engineered” cell membranes with customized functions.

In general, nanotechnology provides a diverse and powerful “arsenal” for the TPD field. From the precision of inorganics, the tailor‐ability of polymers, the efficiency of lipid nanoparticles, and the accuracy of self‐assembly, to the intelligence of biomimetics, each platform expands the boundaries of protein degradation therapy in its unique way. Current development trends clearly indicate that the next generation of nano‐TPD platforms will no longer be merely passive carriers addressing solubility and stability issues, but will evolve into active intelligent systems capable of sensing the microenvironment, executing multifunctional synergistic tasks, and enabling self‐reporting.

4. Functionalization Design in Nano‐TPD Systems

The diverse nanoplatforms described above provide the basic building blocks—the “hardware”—for Nano‐TPD. The real therapeutic sophistication, however, comes from precisely engineering how these platforms interact with target cells and release their payloads. This chapter delves into the core design strategies and mechanistic engineering principles that govern the performance of nano‐TPD systems. We move beyond mere material classification to explore the “software” that dictates functionality: how degraders are loaded, how they are released, and how the system is programmed to interact with complex biological environments to achieve precise protein degradation. Based on our refined conceptual framework, these strategies align with either nanocarrier‐assisted TPD (primarily involving physical encapsulation) or nanostructure‐integrated TPD (which encompasses chemical conjugation, carrier‐free self‐assembly, and innovative “split‐and‐mix” platforms, where the nanoscale architecture is indispensable for the degradation mechanism itself) (Figure 7).

FIGURE 7.

Schematic illustration of functionalization design in nano‐TPD systems.

4.1. Physical Encapsulation

Physical encapsulation represents the most direct and widely adopted approach for constructing Nano‐TPD systems. In this strategy, degraders are noncovalently loaded into preformed nanocarriers through hydrophobic interactions, electrostatic attraction, hydrogen bonding, or other weak intermolecular forces [103, 104, 105, 106]. This approach is particularly attractive for classical small‐molecule degraders, especially PROTACs, whose clinical translation is frequently limited by poor aqueous solubility, low membrane permeability, rapid systemic clearance, and suboptimal tumor accumulation.

The primary strength of physical encapsulation lies in its simplicity and versatility. Because it does not require chemical modification of the degrader, this method preserves the original molecular structure and minimizes the risk of impairing binding affinity or degradation activity. At the same time, encapsulation can markedly improve apparent solubility, prolong circulation time, reduce premature systemic exposure, and enhance local accumulation at diseased tissues. For this reason, lipid nanoparticles [97, 107], polymeric micelles [91], liposomes [81], and related nanocarriers have become common entry points for adapting existing degraders into more pharmaceutically tractable formulations.

However, the advantages of physical encapsulation come with important limitations. Since the degrader is only loosely associated with the carrier, loading stability may be compromised in complex biological environments, leading to premature leakage, burst release, or inconsistent intracellular bioavailability. In addition, because the drug and the nanocarrier remain structurally independent, this strategy often improves exposure more effectively than it improves mechanistic precision. In other words, physical encapsulation can facilitate delivery to cells or tissues, but it does not inherently solve deeper issues such as controlled ligand presentation, multivalent receptor engagement, or programmed intracellular routing [108, 109].

Therefore, in the context of Nano‐TPD, physical encapsulation should be regarded as a foundational but relatively low‐integration strategy. It is most useful when the goal is to rescue unfavorable pharmaceutical properties of existing degraders without substantially altering their chemical identity. Yet, as the field moves toward more complex and selective degradation paradigms, the limitations of this approach have motivated the development of more structurally integrated functionalization strategies.

4.2. Chemical Conjugation

Chemical conjugation introduces a higher level of structural control by covalently linking the degrader, targeting ligand, responsive linker, or other functional motifs to the nanoplatform. Compared with physical encapsulation, this strategy provides a more stable and predictable molecular relationship between the active payload and the carrier, thereby enabling finer control over stoichiometry, release behavior, and biological presentation.

A major advantage of chemical conjugation is the ability to arrange functional modules in a predesigned manner. For example, degraders may be tethered to nanoparticle surfaces or polymer backbones through cleavable linkers that respond to pH, redox conditions, reactive oxygen species, enzymes, or other disease‐associated cues [110, 111]. This permits the system to remain stable during circulation while releasing or exposing its active components only after reaching the intended biological milieu. In this way, chemical conjugation can enhance both pharmacokinetic robustness and spatial selectivity, helping to reduce off‐target degradation and systemic toxicity [112, 113].

Beyond simple controlled release, covalent integration also enables the nanoplatform to participate more actively in the degradation process. By fixing the orientation or density of ligands on the particle surface [114, 115], conjugation can improve target accessibility, promote receptor clustering [116], or support cooperative interactions that are difficult to achieve through free molecular diffusion alone. This feature is especially relevant for lysosome‐directed degradation strategies, in which the nanoscale display of target‐binding and receptor‐recruiting elements can strongly influence endocytic efficiency and downstream trafficking.

Nevertheless, chemical conjugation is not without trade‐offs. Covalent modification increases synthetic complexity and may alter the steric or electronic properties of the degrader, potentially weakening its activity if the linkage site is not carefully chosen. Moreover, highly integrated constructs can become harder to characterize, optimize, and manufacture reproducibly. Thus, although conjugation expands the functional capabilities of Nano‐TPD systems, its design must balance structural sophistication with synthetic practicality and translational scalability.

4.3. Carrier‐Free Self‐Assembly

Carrier‐free self‐assembly represents a more conceptually advanced strategy, in which the degrader or its functional components directly participate in the formation of the nanostructure. Rather than being passively loaded into an external carrier, the active molecules themselves act as building blocks that spontaneously organize into nanoscale assemblies through hydrophobic interactions, π–π stacking, hydrogen bonding, metal coordination, host–guest recognition, or other noncovalent forces [117, 118, 119, 120].

This design philosophy offers several important advantages. First, because the nanostructure is composed largely or entirely of active components, drug‐loading efficiency can be maximized while minimizing the burden of pharmacologically inert carrier materials. Second, self‐assembly often enables a higher degree of functional density, which may strengthen target engagement or improve local effective concentration at the cell surface or within intracellular compartments. Third, the reversible and dynamic nature of noncovalent assembly can introduce environmentally responsive behavior, allowing the system to reorganize, disassemble, or activate under specific biological conditions [121, 122].

In the context of Nano‐TPD, carrier‐free systems are particularly appealing because they blur the boundary between “drug” and “delivery vehicle.” The assembled architecture is not merely a container; it becomes an active structural state that influences how degradation is initiated and propagated. This is especially valuable for systems that benefit from multivalent presentation, cooperative receptor recruitment, or tunable assembly/disassembly behavior. Supramolecular and host–guest systems exemplify this principle by showing that degradation activity can emerge from the reversible organization of functional modules at the nanoscale [120, 123].

At the same time, the high sensitivity of self‐assembled systems to local physicochemical conditions can present challenges. Their stability may be compromised by serum proteins, ionic strength, enzymatic degradation, or competitive molecular interactions in vivo. In addition, minor changes in component ratio or assembly conditions may lead to significant differences in particle morphology and biological performance. Accordingly, while carrier‐free self‐assembly offers elegant opportunities for maximizing functional integration, its successful implementation requires especially careful control of assembly thermodynamics, kinetic stability, and batch reproducibility.

4.4. “Split‐and‐Mix” Platforms

Among current strategies, split‐and‐mix modular assembly most clearly illustrates the conceptual shift introduced by nanotechnology into the TPD field. Conventional degrader design generally relies on a pre‐synthesized, covalently linked molecule in which the target ligand and degradation‐recruiting ligand are fixed within a single architecture. Although powerful, this paradigm is often constrained by synthetic complexity, difficult linker optimization, and limited modularity. Split‐and‐mix platforms circumvent these problems by separating functional elements into distinct modules and reconstituting degrader activity through nanoscale co‐assembly [82, 124, 125].

The significance of this strategy lies in its modularity. Target‐recognition ligands, degradation‐inducing ligands, and auxiliary functional units can be independently optimized and then recombined within a nanostructured system. This not only reduces synthetic burden, but also allows more flexible tuning of stoichiometry, spatial organization, and multifunctionality. In this way, degradative function is no longer confined to a single covalent molecule, but emerges from the controlled organization of multiple components at the nanoscale.

Such modular assembly is particularly attractive because it expands the design space of induced‐proximity therapeutics. By leveraging nanoscale co‐localization, split‐and‐mix systems can generate multivalent interfaces, improve effective local concentration, and integrate targeting or responsive elements that would be difficult to encode into a single small‐molecule degrader. Moreover, this design logic is not limited to classical PROTAC‐like systems, but can be extended to lysosome‐targeting constructs, RNA‐targeting strategies, and multifunctional hybrid therapeutics [126, 127, 128]. Its main challenges remain formulation heterogeneity, batch reproducibility, and the difficulty of maintaining precise module organization in complex biological settings.

However, the main technical bottleneck of this strategy lies in the accurate characterization and quality control of the ligand co‐loading state at the nanoscale. Significant variations in ligand density and spatial distribution may exist among different nanoparticles. Therefore, for such systems, conventional characterization methods based solely on particle size analysis and morphology observation are clearly insufficient. More systematic multiscale analytical approaches are required to verify whether functional co‐loading is truly achieved at the single nanoparticle level. For example, techniques such as energy‐dispersive spectroscopy (EDS) [124] and fluorescence resonance energy transfer (FRET) [129, 130, 131] analysis could be employed to confirm whether the two functional ligands coexist on the same nanoparticle, rather than forming a heterogeneous mixture of single‐function particles. In particular, FRET enables nanoscale evaluation of the spatial proximity between the target ligand and the E3 ligand, making it highly valuable for validating the “functional cooperative assembly” mechanism underlying the split‐and‐mix strategy. Furthermore, the influence of ligand surface density on degradation efficiency should also be carefully considered. Since E3 recruitment generally depends on transient yet precise spatial conformations [132], a random distribution of target‐binding ligands and E3 ligands on the nanoparticle surface may result in insufficient local concentration or increased steric hindrance, thereby reducing the probability of effective ternary complex formation. Accordingly, techniques such as microscale thermophoresis (MST) [133, 134] and biolayer interferometry (BLI) [135, 136] could be further introduced to investigate the multivalent binding kinetics between nanoparticle and POI/E3 complexes. Even so, split‐and‐mix assembly represents one of the clearest examples of how Nano‐TPD moves beyond “nanocarrier‐assisted delivery” toward the construction of functionally orchestrated degradation systems.

5. Engineering the Nano‐Bio Interface for Enhanced Degradation Efficiency

While the choice of platform is foundational, the ultimate therapeutic success of a Nano‐TPD system is determined by a more complex and nuanced series of events: its interaction with the biological milieu. This chapter delves into the critical principles of engineering the nano‐bio interface to overcome key biological barriers and maximize the efficiency of TPD. We explore how nanocarrier design dictates cellular uptake and the subsequent intracellular trafficking and ternary complex formation, all of which are paramount for catalytic degradation.

5.1. The Protein Corona and Targeted Delivery

Upon systemic administration, a nanocarrier is instantly confronted with a complex biological fluid rich in proteins, lipids, and other biomolecules. This leads to the spontaneous formation of a “protein corona” on the nanoparticle surface, a dynamic layer that fundamentally alters its identity, size, surface charge, and aggregation state. This corona, rather than the pristine nanomaterial, is what the body's cells “see” and interact with, thereby dictating the biological fate of the Nano‐TPD system [137].

The composition of the protein corona is a double‐edged sword. On one hand, the adsorption of opsonin (e.g., immunoglobulins, complement proteins) can flag the nanoparticle for rapid clearance by the mononuclear phagocyte system (MPS), primarily in the liver and spleen, drastically reducing its circulation half‐life and preventing it from reaching its intended target [138, 139]. This is a major hurdle for all nanomedicines, including Nano‐TPD. On the other hand, the corona can be strategically engineered. By pre‐coating nanoparticles with “dysopsonins” such as albumin, or by grafting stealth polymers like polyethylene glycol (PEG), we can create a hydration shell that sterically hinders protein adsorption [140]. This “stealth” effect minimizes MPS uptake, prolongs circulation time, and enhances the probability of passive accumulation at diseased sites via the enhanced permeability and retention (EPR) effect.

However, the corona also poses a significant challenge for active targeting. Targeting ligands (e.g., antibodies, peptides) displayed on the nanoparticle surface can become buried or denatured within the corona, rendering them ineffective [141]. This phenomenon, known as “targeting moiety shielding,” can abolish receptor‐mediated recognition and uptake. Therefore, future Nano‐TPD designs must move beyond simple PEGylation. Advanced strategies include the use of “sheddable” coatings, in which the stealth layer is designed to detach upon exposure to the target microenvironment (e.g., low pH, specific enzymes), revealing the targeting ligands precisely where they are needed. Alternatively, the architecture of the targeting moiety itself can be optimized to project beyond the predicted corona thickness, ensuring its continuous accessibility. Understanding and predicting corona formation through techniques like liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) and integrating this knowledge into the design process are no longer optional but are prerequisite for rational Nano‐TPD engineering [142, 143].

5.2. Cellular Uptake

Once a Nano‐TPD system successfully arrives at the target tissue, its next critical task is to gain entry into the specific diseased cells. Cellular internalization is not a singular event but a complex process involving multiple, often competing, pathways. These pathways can be broadly categorized into phagocytosis (typically for specialized immune cells) and pinocytosis, which includes macropinocytosis, clathrin‐mediated endocytosis (CME), caveolae‐mediated endocytosis, and clathrin‐ and caveolae‐independent pathways [144, 145, 146, 147]. The route of entry profoundly influences the subsequent intracellular trafficking and, ultimately, the fate of the TPD payload.

For most non‐phagocytic cells, CME is the predominant uptake mechanism. Nanoparticles entering via CME are typically directed to early endosomes, then to late endosomes, and finally to lysosomes for degradation [145, 148]. This is a favorable pathway for Nano‐LYTACs or other systems designed to degrade targets within the endolysosomal pathway [52]. However, for Nano‐PROTACs that need to reach cytosolic targets, CME can be a dead end, leading to payload degradation before it can exert its function. In contrast, caveolae‐mediated endocytosis, which involves small, flask‐shaped invaginations rich in caveolin proteins, can bypass lysosomal degradation. Caveolar vesicles often traffic to caveosomes or the endoplasmic reticulum (ER), providing a potential route for cytosolic delivery [149, 150]. Similarly, macropinocytosis, a non‐specific form of uptake involving large membrane ruffles, can also lead to less degradative intracellular compartments.

Therefore, the rational design of a nano‑based TPD system hinges on steering its cellular uptake toward the desired endocytic pathway. This is achieved by fine‑tuning three key physicochemical and biological parameters: size and shape, surface charge, and targeting ligand selection. Particles with specific dimensions (e.g., approximately 50 nm for caveolae‑mediated uptake) or distinct morphologies (such as rod‑like versus spherical) can preferentially engage one internalization route over another. Surface characteristics further modulate this interaction. While cationic surfaces often promote uptake through multiple pathways including macropinocytosis, they may also trigger toxicity and immune activation. In contrast, zwitterionic or slightly anionic surfaces tend to favor more specific receptor‑mediated processes. Ultimately, the choice of targeting ligand is paramount—selecting receptors known to internalize via caveolae (e.g., certain GPI‑anchored proteins) can enhance cytosolic delivery for applications such as PROTACs [151], whereas ligands for receptors that undergo rapid clathrin‑mediated endocytosis (like the transferrin receptor) are ideally suited for LYTACs destined for lysosomal trafficking [54, 55].

5.3. Intracellular Trafficking and Ternary Complex Optimization

Once in the cytosol, the journey is not over. The released PROTAC molecule must now successfully locate and engage both its intended target protein and the E3 ubiquitin ligase to form a functional ternary complex. The crowded, dynamic intracellular environment presents a new set of challenges. For Nano‐TPD systems, the nanocarrier itself can influence this process. For example, the site of payload release (e.g., near the nucleus vs. near the plasma membrane) can affect the local concentration of the degrader and its access to target pools.

This is where the unique properties of nanocarriers can be harnessed for more than just delivery. The multivalent display of POI and E3 ligase ligands on a nanoparticle surface, as seen in platforms like MONOTAB or LipoSM‐PROTAC [82, 96], can fundamentally alter the kinetics of ternary complex formation. The high local concentration of ligands on the nanoparticle can increase the probability of simultaneous engagement of both target and ligase through avidity effects. This can lower the effective concentration of the degrader needed and potentially overcome the “hook effect,” as the scaffold prevents the formation of inactive binary complexes at high local ligand densities by tethering the components together [13, 14].

Furthermore, the nanocarrier can be engineered to direct the payload to specific subcellular compartments where the target is most abundant [152, 153, 154]. For instance, a nanocarrier could be decorated with a mitochondrial targeting element to deliver an AUTAC to clear damaged mitochondria. Pan et al. employed gold nanoparticles co‐modified with a mitochondria‐binding peptide and an LC3‐targeting peptide to successfully induce the specific degradation of mitochondria within autophagosomes of cancer cells [152]. This intervention remodeled the metabolic characteristics of the tumor cells, thereby enhancing the specific killing efficacy of CD8+ T cells. In addition, by using endoplasmic reticulum (ER)‐associated degradation (ERDA), Song et al. constructed ERAD‐engaging chimeras (ERADECs), which can simultaneously bind transmembrane (TM) proteins and E3 ligase on the ER membrane, and then induce the degradation of TM proteins that fold in the ER through the ERAD pathway [154]. Whereas PROTACs rely primarily on E3 ligases in the cytoplasm, ERADECs hijack the ER system for the first time. This paradigm shift has brought previously inaccessible membrane protein targets into the realm of degradability. This subcellular precision adds another layer of control, ensuring that the degradation machinery is activated precisely where it is needed most, thereby enhancing efficacy and minimizing off‐target effects [155]. Ultimately, the design of a truly intelligent Nano‐TPD system must consider the entire journey of the nanocarrier and its payload—from the moment of injection to the moment of target degradation—and engineer each step for optimal performance.

5.4. Monitoring Methods for the Transport and Fate of Nano‐Degraders

A deeper understanding of the nano–bio interface requires precise characterization of intracellular trafficking pathways and tissue‐level biodistribution of Nano‐TPD systems after administration. At the cellular level, fluorescence‐based imaging techniques remain among the most widely used approaches for tracking intracellular trafficking. Confocal laser scanning microscopy (CLSM) enables visualization of nanoparticle uptake and subcellular localization by co‐staining with organelle‐specific markers, such as lysosomes, endosomes, mitochondria, or the endoplasmic reticulum. Cryogenic transmission electron microscope (cryo‐TEM) can directly visualize nanoparticle localization within cells and assess structural integrity after cellular internalization [156, 157]. At the tissue level, in vivo imaging techniques are essential for evaluating biodistribution and tissue targeting efficiency. Fluorescence imaging and near‐infrared (NIR) imaging are commonly employed for small‐animal tracking of labeled nanocarriers due to their high sensitivity and real‐time capability [158]. Positron emission tomography (PET) and single‐photon emission computed tomography (SPECT), typically combined with radiolabeled nanoparticles, enable quantitative whole‐body pharmacokinetic analysis with high tissue penetration depth [159, 160]. Additionally, magnetic resonance imaging (MRI) has been explored to characterize nanoparticle accumulation within tumors or specific organs with improved anatomical resolution [161, 162].

These analytical platforms provide critical insights into the dynamic interactions occurring at the nano–bio interface, including cellular uptake pathways, intracellular trafficking behavior, endosomal escape efficiency, and tissue‐specific accumulation. Such mechanistic understanding is essential for rationally optimizing Nano‐TPD systems with improved targeting specificity, therapeutic efficacy, and biosafety profiles.

6. Critical Hurdles and Opportunities in Nano‐TPD

6.1. Manufacturing and Quality Control

While numerous studies have demonstrated the feasibility of Nano‐TPD platforms, the primary challenge in transitioning these complex systems from the laboratory to the clinic lies in manufacturing. Unlike the well‐defined chemical synthesis pathways of small‐molecule PROTACs, nano‐formulations—especially structurally defined nanocarriers—often involve multi‐step processes of self‐assembly, surface modification, and drug loading. Batch‐to‐batch reproducibility, the safety of excipients, the feasibility of sterilization processes, and long‐term storage stability are critical parameters that determine whether a formulation can be translated into a viable pharmaceutical product [163]. For instance, the particle size distribution of lipid nanoparticles, the drug release kinetics of polymeric nanoparticles, and the integrity of membrane proteins on biomimetic vesicles all require precise control during scale‐up. Therefore, development of robust and scalable platforms is the foremost task in advancing nano‐TPD technologies toward clinical translation.

6.2. Deep Understanding of Biosafety and In vivo Fate

Upon entering the human body, the complicated in vivo fate of nanomaterials is far more unpredictable than that of small‐molecule drugs. The first concern is biocompatibility: although many carrier materials, such as lipids and biodegradable polymers are generally considered safe, their long‐term accumulation in vivo, immunogenicity, and the potential toxicity of their metabolites still require systematic evaluation [164, 165]. Secondly, the unique “protein corona” phenomenon can alter the biological identity of nanocarriers, rendering intended targeting functions ineffective or leading to rapid clearance by the immune system [166, 167]. Gaining a deep understanding of the in vivo distribution, metabolic pathways, and clearance mechanisms of different nanomaterials under various pathological conditions, and the construction of predictive models of their in vivo fate, comprise the theoretical foundation for designing safe and effective Nano‐TPD systems. The long‐term safety concerns are particularly pronounced for non‐degradable carriers, such as those based on metallic or inorganic materials, posing a major hurdle for clinical translation.

6.3. Tumor Heterogeneity and the Limitations of Active Targeting

The Enhanced Permeability and Retention (EPR) effect has been a central tenet for passive targeting of nanomedicines, but its actual involvement in human tumors has recently become a subject of intense debate. The leakiness of tumor vasculature, the level of interstitial pressure, and the density of the extracellular matrix vary greatly, not only between patients but also between different lesions within the same patient. This heterogeneity makes it challenging for nanomedicines relying solely on passive targeting to achieve consistent therapeutic efficacy across a variety of patient populations [168]. While active targeting strategies (e.g., modification with antibodies or peptides) aim to address this issue, the in vivo stability of these targeting ligands, their ability to penetrate dense tumor tissue, and their shielding by the protein corona often limit their theoretical advantages [169, 170, 171]. Consequently, future Nano‐TPD designs must move beyond sole reliance on the EPR effect and include intelligent delivery strategies based on active penetration and in situ activation.

6.4. The Trade‐off Between Degradation Efficiency and Off‐Target Effects

While nanocarriers can reduce the distribution of PROTACs in normal tissues through passive or active targeting, thereby mitigating “on‐target off‐tumor” toxicity, they themselves can introduce new off‐target effects. For example, cationic carrier materials may interact non‐specifically with cell membranes and cause toxicity; certain targeting ligands may cross‐react with proteins other than their intended receptors [172, 173]. Furthermore, the efficiency of cargo release and subsequent degradation within the target cell is critical. If the nanocarrier fails to facilitate efficient endosomal/lysosomal escape, the engulfed PROTAC will be degraded, leading to therapeutic failure. Thus, a fine balance must be struck: enhancing cellular uptake while simultaneously ensuring that the drug can reach its site of action (cytosol or lysosome) and be released at the right time [174]. This is a core contradiction that must be carefully addressed in nano‐TPD design.

6.5. Regulatory Considerations for Clinical Translation of Nano‐TPD Systems

Despite the rapid development of Nano‐TPD platforms, their clinical translation remains strongly influenced by regulatory considerations associated with both nanomedicine products and heterobifunctional degraders. In many cases, Nano‐TPD systems may be regarded as combination products because they integrate a pharmacologically active degrader with a nanoparticle‐based delivery carrier. Regulatory agencies such as the U.S. Food and Drug Administration (FDA) and the European Medicines Agency (EMA) generally evaluate such products using a multidisciplinary framework that considers both drug substance and delivery carrier attributes. For formulations containing targeting ligands, imaging moieties, or stimuli‐responsive materials, additional regulatory scrutiny may be required to demonstrate manufacturing consistency and biological safety. Another critical consideration is nanoparticle characterization. Regulatory agencies increasingly emphasize comprehensive physicochemical characterization for nanomedicines during IND submission. For Nano‐TPD systems, key parameters typically include particle size distribution, polydispersity index, encapsulation efficiency, degrader loading, aggregation behavior, release profiles, and batch‐to‐batch reproducibility. Therefore, early integration of regulatory science, standardized characterization protocols, and scalable manufacturing strategies will be essential for accelerating the clinical translation of Nano‐TPD therapeutics.

7. Conclusion and Perspectives

Over the past two decades, TPD has evolved from a clever concept in chemical biology into a revolutionary force reshaping the paradigm of drug discovery. However, the clinical translation of TPD, particularly its ambition to conquer the “undruggable” proteome, is increasingly constrained by the “undruggable” nature of the degraders themselves—their high molecular weight, poor permeability, and non‐specific distribution become obstacles hindering their clinical translation [10, 11, 12].

The intervention of nanotechnology is not merely an incremental improvement but a fundamental reconceptualization of how to address this dilemma. As this review has illustrated, a diverse arsenal of nanoplatforms—from inorganic, polymeric, and lipid‐based systems to self‐assembled and biomimetic carriers—is providing protein degraders with an “intelligent suit” capable of crossing biological barriers, recognizing pathological signals, and controlling release behavior. We have witnessed how nano‐TPD enhances degradation efficiency through multivalency, achieves spatiotemporal precision with stimuli‐responsive mechanisms, and even subverts the traditional design philosophy through “split‐and‐mix” strategies [82, 84]. Critically, as the field transitions from nanocarrier‐assisted delivery to nanostructure‐integrated degradation, the nanocarrier is no longer a passive delivery vehicle; it is actively reshaping the degradation process itself—from guiding cellular uptake pathways and facilitating endosomal escape to acting as a synthetic scaffold that catalyzes the formation of degradation complexes.

Looking ahead, the future of nano‐TPD will depend on a coordinated effort across three dimensions. First, deepening our fundamental understanding of the nano‐bio interface is foundational. We must systematically investigate how the physicochemical properties of nanoparticles quantitatively dictate protein corona formation, cellular uptake mechanisms, intracellular trafficking routes, and ultimately, degradation kinetics. Only by establishing clear structure‐activity relationships can we move from empirical design to rational engineering.

Second, driving the integrated innovation of platform technologies is the core objective. The next generation of nano‐TPD systems will be defined by intelligence. We foresee the advent of smart nano‐systems capable of sensing and integrating multiple pathological signals (“logic‐gated” activation) [175, 176], enabling them to distinguish between diseased and healthy cells with high fidelity before initiating degradation. Concurrently, the integration of diagnostic and therapeutic functions into theragnostic nano‐TPD will enable real‐time monitoring of drug delivery and therapeutic response [95].

Finally, overcoming clinical translation hurdles is the ultimate test. This requires close collaboration between academia and industry to develop scalable, stable, and biocompatible nano‐formulations. We must leverage more physiologically relevant disease models, such as patient‐derived xenografts, organoids, and organs‐on‐chips, to rigorously evaluate the efficacy and safety of nano‐TPD, bridging the chasm between preclinical promise and clinical reality.

In conclusion, nano‐TPD represents the inevitable evolution of protein degradation therapy. By endowing degraders with intelligence, it is transforming TPD from a molecule‐centric area of study into a systems‐based discipline. While the path to the clinic is fraught with challenges, the vibrant energy of this emerging interdisciplinary field gives us confidence that we can ultimately convert the once “undruggable” targets into therapeutic opportunities that can be modulated with precision, efficiency, and safety. This quest, which began with a profound inquiry into the regulation of proteins, will ultimately find its answer in ingenious designs at the nanoscale, reshaping the landscape of disease treatment.

Conflicts of Interest

The authors declare no conflicts of interest.

Data Availability Statement

The data that support the findings of this study are available from the corresponding author upon reasonable request.