Covalently Engineered Nanobody Chimeras for Targeted Membrane Protein Degradation

Recent advances in degraders engaging lysosomal pathways and related nanomedicine

The advent of targeted protein degradation (TPD) strategies presents unparalleled opportunities for innovating and expediting the development of new drugs. As the most mature TPD technology to date, proteolysis targeting chimeras (PROTACs) reliant on the ubiquitin proteasome system (UPS) have successfully transitioned from the laboratory to phase III clinical trials after nearly two decades of development. In recent years, the gradually emerging degraders engaging lysosomal pathways have further broadened the range of degradation mechanisms and substantially increased the diversity of potential targets and indications, ushering in a new era for the TPD field. Despite their significant advantages, the limited permeability, adverse pharmacokinetic properties, and off-target side effects caused by non-specific distribution still pose significant challenges to the clinical translation of these degraders. Currently, researchers are exploring the use of nanotechnology to surmount these obstacles and have achieved notable progress. This paper systematically summarizes the fundamental design principles, research status, challenges and future prospects of degraders engaging lysosomal pathways, and highlights the efforts and latest advances in related nanomedicine to optimize these degraders. The aim of this review is to deepen our comprehension of this emerging field and offer guidance for future exploration, development, and further utilization of new TPD techniques.

Identification and characterization of Bufalin as a novel EGFR degrader

Esophageal squamous cell carcinoma (ESCC) stands out as a common cancer type worldwide, characterized by its notably high rates of occurrence and mortality. The epidermal growth factor receptor (EGFR) is one of the main targets for cancer treatment as it is one of the genes whose expression is often altered by overexpression, amplification, and mutation in a variety of solid tumors. Substantial efforts have been made to develop EGFR-targeted therapeutic agents, including monoclonal antibodies and tyrosine kinase inhibitors (TKIs). However, these agents exhibited limited efficacy due to the emergence of acquired resistance. Therefore, novel treatment strategies targeting EGFR are urgently needed. Recent studies have identified a few natural compounds that can efficiently inhibit EGFR, indicating that natural products may be potential sources for the development of new EGFR inhibitors. Here, using the Drug Affinity Responsive Target Stability (DARTS) assay combined with liquid chromatography/tandem mass spectrometry analysis, co-crystal method, we discovered that Bufalin directly interacts with EGFR and causes EGFR endocytosis and degradation in the lysosome. Moreover, Bufalin exhibits superior anti-tumor activity compared with another EGFR TKIs. Our study identified Bufalin as the first natural small-molecule EGFR degrader, which suppresses EGFR signaling by inducing the degradation of EGFR via the endosome-lysosome pathway.

Membrane-Bounded Intracellular E3 Ubiquitin Ligase-Targeting Chimeras (MembTACs) for Targeted Membrane Protein Degradation

Targeted protein degradation (TPD) represents a potent therapeutic strategy aimed at dismantling disease-associated target proteins. PROTAC is the most widely developed technique for intracellular protein degradation, while its degradation ability on membrane proteins has been hindered by the need for complex synthetic processes and limited permeability. In this study, we developed the membrane-bounded intracellular E3 ubiquitin ligase-targeting chimeras (MembTACs) that simultaneously recruit intracellular E3 ubiquitin ligase and bind to the desired membrane proteins for targeted degradation of membrane proteins. We demonstrate that the MembTACs can effectively utilize intracellular E3 ubiquitin ligase to degrade the therapeutically relevant membrane proteins of EpCAM and Met via the proteasome pathway. We anticipate that the new platform will expand the range of PROTAC applications and provide a new dimension for targeted membrane protein degradation.

Highly Specific Cytokine Receptor-Targeting Chimeras for Targeted Membrane Protein Degradation and Sensitization of Osimertinib in EGFR-Mutated Non-Small-Cell Lung Cancer

The ability of cytokine receptors to mediate the internalization of targets in lysosomes positions them as specific and effective effectors for protein degradation strategies. However, challenges remain, including the potential unintended activation of cell-proliferation-related cytokine receptors, as well as limitations in programmability and structural flexibility of protein degradators. In this work, a CXCR7-targeting chimera (AP-CRTAC) that functions as a CXCR7 inducer by covalently linking a membrane protein-targeting aptamer with a mutant-CXCL12 mimic peptide is developed. This peptide selectively binds to CXCR7 without activating CXCR4. The AP-CRTAC, which incorporates various aptamer forms from DNA, RNA, or even bispecific aptamers, has shown significant efficacy in degrading one or more proteins or protein mutants on the cell surface. Moreover, the AP-CRTAC constructed with a 2' F-pyrimidine-modified RNA aptamer targeting EGFR effectively degrades various EGFR activating mutations. Notably, AP-CRTAC enhances the sensitivity of the L858R/T790M/C797S triple mutant lung cancer cells, which are resistant to current EGFR-targeted therapies, to the third-generation EGFR inhibitor osimertinib in both in vitro and in vivo settings. This research introduces an engineered CXCR7 inducer with high specificity and programmability for the targeted degradation of cell surface proteins, while minimizing unwanted side effects.

A Self-Assembling LYTAC Mediates CTGF Degradation and Remodels Inflammatory Tumor Microenvironment for Triple-Negative Breast Cancer Therapy

As a multifunctional extracellular protein, connective tissue growth factor (CTGF/CCN2) is significantly associated with the progression and prognosis of triple-negative breast cancer (TNBC). However, current blockade therapies targeting CTGF's multiple domains are limited, creating substantial challenges in treatment. Lysosome-targeting chimeras (LYTACs) have emerged as a promising approach for achieving complete protein degradation and inhibiting CTGF's various bioactivities. In this study, a self-assembling LYTAC nanoplatform, NanoCLY, designed to tumor microenvironment (TME)-responsively degrade CTGF is presented. The complete degradation of CTGF downregulates the TGF-β signaling pathway and disrupts the CTGF-IL-6 cell crosstalk within the TME, which further inhibits the activation of inflammatory cancer-associated fibroblasts (CAFs) and alleviates the inflammatory TME. Notably, the anti-TNBC effect of LYTAC-based CTGF degradation therapy surpasses that of antibody-based blockade therapy in both in vitro and in vivo models. The findings provide a proof of concept for CTGF degradation in TNBC and introduce the first CTGF-LYTAC nanoplatform aimed at TME-directed therapy.

Research trends in the use of nanobodies for cancer therapy

Although there are many challenges in using nanobodies for treating various complex tumor diseases, including rapid renal clearance and the complex blood-brain barrier environment, nanobodies have shown great potential due to their high antigen affinity, excellent tumor penetration ability, and favorable safety profile. Since the discovery of the variable domain (VHH) of camelid heavy-chain antibodies in 1993, nanobodies have been progressively applied to various cancer therapy platforms, such as antagonistic drugs and targeting agents for effector domains. In recent years, several nanobody-based drugs, including Caplacizumab, KN-035, and Ozoralizumab, have been approved for clinical use. Among them, KN-035 is used for treating advanced solid tumors, and these advancements have propelled nanobody development to new heights. Currently, nanobodies are being rapidly applied to the treatment of a wide range of diseases, from viral infections to cancer, demonstrating strong advantages in areas such as targeted protein degradation, bioimaging, nanobody-drug conjugation, bispecific T-cell engagers, and vaccine applications. Bibliometric tools, including CiteSpace, HisCite Pro, and Alluvial Generator, were employed to trace the historical development of nanobodies in cancer research. The contributions of authors, countries, and institutions in this field were analyzed, and research hotspots and emerging trends were identified through keyword analysis and influential articles. Future trends were also predicted. This study provides a unique, comprehensive, and objective perspective on the use of nanobodies in tumor research, laying a foundation for future research directions and offering valuable insights for researchers in the field.

Advances in sulfonyl exchange chemical biology: expanding druggable target space

Targeted covalent inhibitors possess advantages over reversible binding drugs, that include higher potency, enhanced selectivity and prolonged pharmacodynamic duration. The standard paradigm for covalent inhibitor discovery relies on the use of α,β-unsaturated carbonyl electrophiles to engage the nucleophilic cysteine thiol, but due to its rarity in binding sites, the amino acid is often not available for targeting. 10 years ago we highlighted the emerging potential of sulfonyl fluoride chemical probes that were initially found to serendipitously modify residues beyond cysteine, including tyrosine, lysine, histidine, serine and threonine. Since then, the rational application of sulfonyl fluorides and related sulfonyl exchange warheads to site-specifically target diverse amino acid residues in proteins using small molecules, oligonucleotides, peptides and proteins, has made considerable progress, which has significantly advanced covalent therapeutic discovery. Additionally, sulfonyl exchange chemistry has recently shown utility in the labeling of RNA and carbohydrates, further expanding the biomolecular diversity of addressable targets. This Perspective provides not only a timely update regarding this exciting area of research, thus serving as a useful resource to scientists working in the field, but areas of challenge and opportunity are highlighted that may stimulate new research at the chemistry-biology interface.

Proximity-induced membrane protein degradation for cancer therapies

The selective modulation of membrane proteins presents a significant challenge in drug development, particularly in cancer therapies. However, conventional small molecules and biologics often face significant hurdles in effectively targeting membrane-bound proteins, largely due to the structural complexity of these proteins and their involvement in intricate cellular processes. In light of these limitations, proximity-induced protein modulation has recently emerged as a transformative approach. It leverages molecule-induced proximity strategies to commandeer endogenous cellular machinery for precise protein manipulation. One of these modulatory strategies is protein degradation, wherein membrane-targeting degraders derived from proximity-induction approaches offer a unique therapeutic avenue by inducing the irreversible removal of key oncogenic and immune-regulatory proteins to combat cancer. This review explores the fundamental principles underlying proximity-driven membrane protein degradation, highlighting key strategies such as LYTACs, PROTABs, TransTACs, and IFLD that are reshaping targeted cancer therapy. We discuss recent technological advancements in the application of proximity-induced degraders across breast cancer, lung cancer, immunotherapy, and other malignancies, underscoring how these innovative approaches have demonstrated significant therapeutic potential. Lastly, while these emerging technologies offer significant promise, they still face substantial limitations, including drug delivery, selectivity, and resistance mechanisms that need to be addressed to achieve successful clinical translation.

Structure-Guided Development of Chemically Tailored Peptide Binders of RNF43/ZNRF3 to Enable Versatile Design of Membrane Protein-Targeting PROTACs

Targeted membrane protein degradation using cell surface E3 ligases RNF43/ZNRF3 via proteolysis targeting chimeras (PROTACs) represents an effective strategy for treating membrane drug targets that cannot be fully inhibited using traditional inhibitors. Several ingenious chimeras have been developed to tether RNF43/ZNRF3 to target membrane proteins, resulting in the degradation of targets at sub-nanomolar concentrations both in vitro and in vivo. However, currently available RNF43/ZNRF3 binders are genetically encoded and have poor plasticity, which limits the design and promotion of such PROTACs. Here, we exploited the AlphaFold-predicted complex structures of ligand-bound RNF43/ZNRF3 and developed a class of chemically tailored peptide binders for ZNRF3/RNF43. With these peptide binders that can be conveniently prepared by de novo peptide synthesis, we established a new membrane protein degradation platform that allows versatile modular design and targeted degradation of clinically relevant membrane proteins, i.e., PD-L1 and EGFR. This study presents a new subtype within the PROTAC field to develop therapeutic peptides targeting membrane proteins.

Targeted degradation of extracellular proteins: state of the art and diversity of degrader designs

Selective elimination of proteins associated with the pathogenesis of diseases is an emerging therapeutic modality with distinct advantages over traditional inhibitor-based approaches. This strategy, called targeted protein degradation (TPD), is based on hijacking the cellular proteolytic machinery using chimeric degrader molecules that physically link the target protein of interest with the degradation effectors. The TPD era began with the development of PROteolysis TAtrgeting Chimeras (PROTACs) in 2001, with various methods and applications currently available. Classical PROTAC molecules are heterobifunctional chimeras linking target proteins with E3 ubiquitin ligases. This induced interaction leads to the ubiquitylation of the target protein, which is needed for its recognition and subsequent degradation by the cellular proteasomes. However, this technology is limited to intracellular proteins since the effectors involved (E3 ubiquitin ligases and proteasomes) are located in the cytosol. The related methods for selective destruction of proteins present in the extracellular space have only emerged recently and are collectively termed extracellular TPD (eTPD). The prototypic eTPD technology utilizes LYsosomal TArgeting Chimeras (LYTACs) that link extracellular target proteins (secreted or membrane-associated) to lysosome-targeting receptors (LTRs) on the cell surface. The resulting complex is then internalized by endocytosis and trafficked to lysosomes, where the target protein is degraded. The successful elimination of various extracellular proteins via LYTACs and related approaches has been reported, including several important targets in oncology that drive tumor growth and dissemination. This review summarizes current progress in the eTPD field and focuses primarily on the respective technological developments. It discusses the design principles and diversity of degrader molecules and the landscape of available targets and effectors that can be employed for eTPD. Finally, it emphasizes current open questions, challenges, and perspectives of this technological platform to promote the expansion of the eTPD toolkit and further development of its therapeutic applications.

Bifunctional compounds for targeted degradation of carbonic anhydrase IX through integrin-facilitated lysosome degradation

As an important therapeutic target, carbonic anhydrase IX (CAIX) is crucial in the pH regulation of hypoxic solid tumors, thus keeping the survival of them in acidic microenvironment and promoting their proliferation, invasion, and metastasis. To degrade endogenous CAIX, three bifunctional compounds were designed according to the integrin-facilitated lysosomal degradation strategy. These compounds are composed of a CAIX-binding ligand, an integrin-recognizing ligand, connected via a linker, which could induce CAIX degradation in an integrin- and lysosome-dependent manner. Among them, Sul-L1-RGD showed the highest degradation efficacy and could inhibit the proliferation of tumor cells under hypoxic conditions, thus it has great potential to be applied in cancer drug discovery.

Sortilin-Mediated Rapid, Precise and Sustained Degradation of Membrane Proteins via mRNA-Encoded Lysosome-Targeting Chimera

Recent advances in lysosome-targeting degradation technologies have introduced strategies to regulate therapeutic membrane proteins (MPs), potentially transforming treatment paradigms. However, challenges persist, including limited degradation precision due to the broad distribution of lysosome-targeting receptors (LTRs), as well as the high cost and complexity of recombinant protein production or chemical synthesis. Herein, it identifies sortilin as a promising LTR, highly expressed in malignancies but minimally present in healthy tissues outside the nervous system. Using AlphaFold-Multimer, it screened for a specific non-endogenous protein binder to sortilin and developed a modular, mRNA-encoded lysosomal targeting chimera (MedTAC) strategy, enabling rapid design and precise degradation of oncogenic MPs. In a breast cancer-bearing mouse model, a single low dose of MedTACPTK7 (0.5 mg kg-1) reduced protein tyrosine kinase-7 (PTK7) levels by up to 80% within 24 h, with sustained degradation of 44% at 72 h, demonstrating excellent pharmacokinetics. MedTACPTK7 significantly extended survival to over 50 days without systemic toxicity, compared to 20-30 days in controls. This MedTAC strategy establishes sortilin as a selective and efficient shuttle for targeted protein degradation, offering a scalable, rapidly producible platform for biochemical research and precise therapeutic applications.

Targeted protein degradation for cancer therapy

Targeted protein degradation (TPD) aims at reprogramming the target specificity of the ubiquitin-proteasome system, the major cellular protein disposal machinery, to induce selective ubiquitination and degradation of therapeutically relevant proteins. Since its conception over 20 years ago, TPD has gained a lot of attention mainly due to improvements in the design of bifunctional proteolysis targeting chimeras (PROTACs) and understanding the mechanisms underlying molecular glue degraders. Today, PROTACs are on the verge of a first clinical approval and recent structural and mechanistic insights combined with technological leaps promise to unlock the rational design of protein degraders, following the lead of lenalidomide and related clinically approved analogues. At the same time, the TPD universe is expanding at a record speed with the discovery of novel modalities beyond molecular glue degraders and PROTACs. Here we review the recent progress in the field, focusing on newly discovered degrader modalities, the current state of clinical degrader candidates for cancer therapy and upcoming design approaches.

De Novo Design of Structure-Tunable Multivalent Targeting Chimeras for Tumor-Targeted PD-L1 Degradation and Potentiated Cancer Immunotherapy

Targeted protein degradation (TPD) technology holds significant potential for modulating protein homeostasis and treating diseases. However, current methods for degrading membrane proteins highly depend on the lysosome-targeting ligands or membrane receptors. In this study, we present a set of multivalent targeting chimeras (multi-TACs) for tumor-specific degradation of programmed death ligand 1 (PD-L1) on the surface of the tumor cell membrane. The multi-TACs are synthesized by copolymerization of small-molecule PD-L1 inhibitor BMS-1 with acid-responsive monomers. The chemical structures of the multi-TACs are optimized by investigating the correlation between PD-L1 degradation efficacy and the key parameters, including acid-sensitive moieties, BMS-1 valency, and spacer length. Mechanistic study reveals that the multi-TACs highly efficiently degrade PD-L1 on the surface of tumor cells via the adsorption-mediated endocytosis and lysosomal degradation pathways, which differ from the reported strategies for membrane protein degradation. The outperformed multi-TAC GG56 with tumor extracellular acidity and enzyme-sensitivity dramatically reduces PD-L1 levels and suppresses tumor growth in mouse models of B16-F10 melanoma and 4T1 breast tumors. Furthermore, GG56 serves as a versatile nanoplatform for combinatory chemo-immunotherapy and radio-immunotherapy of 4T1 breast tumor by co-delivery of chemotherapeutic and radio-sensitizer, respectively.

Engineering Covalent Aptamer Chimeras for Enhanced Autophagic Degradation of Membrane Proteins

Targeted degradation of membrane proteins represents an attractive strategy for eliminating pathogenesis-related proteins. Aptamer-based chimeras hold great promise as membrane protein degraders, however, their degradation efficacy is often hindered by the limited structural stability and the risk of off-target effects due to the non-covalent interaction with target proteins. We here report the first design of a covalent aptamer-based autophagosome-tethering chimera (CApTEC) for the enhanced autophagic degradation of cell-surface proteins, including transferrin receptor 1 (TfR1) and nucleolin (NCL). This strategy relies on the site-specific incorporation of sulfonyl fluoride groups onto aptamers to enable the cross-linking with target proteins, coupled with the conjugation of an LC3 ligand to hijack the autophagy-lysosomal pathway for targeted protein degradation. The chemically engineered CApTECs exhibit enhanced on-target retention and improved structural stability. Our results also demonstrate that CApTECs achieve remarkably enhanced and prolonged degradation of membrane proteins compared to the non-covalent designs. Furthermore, the CApTEC targeting TfR1 is combined with 5-fluorouracil (5-FU) for synergistic tumor therapy in a mouse model, leading to substantial suppression of tumor growth. Our strategy may provide deep insights into the LC3-mdiated autophagic degradation, affording a modular and effective strategy for membrane protein degradation and precise therapeutic applications.

Post-translational modifications of immune checkpoints: unlocking new potentials in cancer immunotherapy

Immunotherapy targeting immune checkpoints has gained traction across various cancer types in clinical settings due to its notable advantages. Despite this, the overall response rates among patients remain modest, alongside issues of drug resistance and adverse effects. Hence, there is a pressing need to enhance immune checkpoint blockade (ICB) therapies. Post-translational modifications (PTMs) are crucial for protein functionality. Recent research emphasizes their pivotal role in immune checkpoint regulation, directly impacting the expression and function of these key proteins. This review delves into the influence of significant PTMs-ubiquitination, phosphorylation, and glycosylation-on immune checkpoint signaling. By targeting these modifications, novel immunotherapeutic strategies have emerged, paving the way for advancements in optimizing immune checkpoint blockade therapies in the future.

Multivalent RGD Peptide-Mediated Nanochimera for Lysosomal Degradation of PDL1 Protein

The development of immune checkpoint inhibitors, especially PDL1 antibodies, has revolutionized cancer therapy, but the posttherapy recycling of PDL1 proteins poses a significant challenge by inducing resistance and reducing treatment efficacy. To address this, we introduce an integrin-driven, lysosome-targeted nanochimera, composed of poly(glutamic acid), RGD peptides, and PDL1 antibodies, is designed to engage the target PDL1 protein, with the αvβ3 integrin binding to the multivalent RGD peptides to direct the complex through the endocytosomal pathway to the lysosome, ensuring PDL1 degradation and blocking its recycling. Our in vitro and in vivo experiments demonstrate that these nanochimeras potently activate T-cell antitumor immunity by downregulating PDL1 expression within tumor cells and tissues, significantly enhancing the efficacy of PDL1 antibodies. A key discovery of our study is the pivotal role of multivalent RGD peptides in facilitating target protein degradation, providing valuable insights for the development of more efficacious and sophisticated immunotherapies.

Recent advances in targeted degradation in the RAS pathway

RAS (rat sarcoma) is one of the most frequently mutated gene families in cancer, encoding proteins classified as small GTPases. Mutations in RAS proteins result in abnormal activation of the RAS signaling pathway, a key driver in the initiation and progression of various malignancies. Consequently, targeting RAS proteins and the RAS signaling pathway has become a critical strategy in anticancer therapy. While RAS was historically considered an "undruggable" target, recent breakthroughs have yielded inhibitors specifically targeting KRASG12C and KRASG12D mutations, which have shown clinical efficacy in patients. However, these inhibitors face limitations due to rapid acquired resistance and the toxic effects of combination therapies in clinical settings. Targeted protein degradation (TPD) strategies, such as PROTACs and molecular glues, provide a novel approach by selectively degrading RAS proteins, or their upstream and downstream regulatory factors, to block aberrant signaling pathways. These degraders offer a promising alternative to traditional inhibitors by potentially circumventing resistance and enhancing therapeutic precision. This review discusses recent advancements in RAS pathway degraders, with an emphasis on targeting RAS mutations as well as their upstream regulators and downstream effectors for potential cancer treatments.

Engineering IGF2 for Lysosome-targeting chimeras development to target drug-resistant membrane proteins in tumor therapy

Lysosome-targeting chimeras (LYTACs) represent a promising approach for the targeted degradation of membrane proteins. Currently, two primary methods for LYTAC development involve chemically modified antibodies and wild-type insulin-like growth factor 2 (IGF2) fusion proteins (iLYTACs). However, LYTACs necessitate intricate chemical modification processes, while wild-type IGF2 in iLYTAC technology binds to IGF1R, potentially triggering carcinogenesis. To tackle this challenge, we introduce specific IGF2R-binding lysosomal targeting chimeras (sLYTACs), a novel technology utilizing engineered IGF2 mutant fusion antibodies for the degradation of endogenous membrane proteins. Diverging from iLYTACs, sLYTACs exhibit selective binding to IGF2R with increased affinity, significantly bolstering the anti-proliferative impact on drug-resistant tumor cells both in vitro and in vivo. By effectively degrading third-generation tyrosine kinase inhibitor-resistant EGFR mutants, masking binding epitope HER2, and concurrently targeting compensatory receptors interacting with these proteins, sLYTACs show great promise in drug development to overcome bypass signaling and combat drug resistance in tumors.

Covalent Affibody-Molecular Glue Drug Conjugate Nanoagent for Proximity-Enabled Reactive Therapeutics

Sulfur-fluoride exchange (SuFEx) reaction is an emerging class of click chemistry reaction. Owing to its efficient reactivity under physiological conditions, SuFEx reaction is used to construct covalent protein drugs. Herein, a covalent affibody-molecular glue drug conjugate nanoagent is reported, which can irreversibly bind with its target protein through proximity-enabled SuFEx reaction. As a proof of concept, a latent bioreactive unnatural amino acid fluorosulfate-L-tyrosine (FSY) is first introduced at site 36 of the affibody with cysteine mutation (ZHER2:342-Cys) to produce ZHER2:342-36FSY-Cys. Subsequently, ZHER2:342-36FSY-Cys is coupled with a molecular glue drug (CR8) to yield an amphiphilic conjugate of ZHER2:342-36FSY-CR8, which can self-assemble into affibody-drug conjugate nanoagent (ZHER2:342-36FSY-CR8 ADCN) in PBS. When ZHER2:342-36FSY-CR8 ADCN specific binds to human epidermal growth factor receptor 2 (HER2) on cancer cells, the FSY36 of ZHER2:342 approaches to the His490 of HER2 and ultimately reacts with each other to form a covalent bond via SuFEx reaction. Such a covalent binding mode endows ZHER2:342-36FSY-CR8 ADCN with permanent binding ability to effectively increase the concentration of drugs in tumor. Eventually, the covalent ZHER2:342-36FSY-CR8 ADCN exhibits an outstanding tumor inhibition ratio of 90.03 ± 4.29% in HER2-positive ovary tumor models, strikingly higher than that of the noncovalent one (64.25 ± 7.71%).

Protein-Based Degraders: From Chemical Biology Tools to Neo-Therapeutics

The nascent field of targeted protein degradation (TPD) could revolutionize biomedicine due to the ability of degrader molecules to selectively modulate disease-relevant proteins. A key limitation to the broad application of TPD is its dependence on small-molecule ligands to target proteins of interest. This leaves unstructured proteins or those lacking defined cavities for small-molecule binding out of the scope of many TPD technologies. The use of proteins, peptides, and nucleic acids (otherwise known as "biologics") as the protein-targeting moieties in degraders addresses this limitation. In the following sections, we provide a comprehensive and critical review of studies that have used proteins and peptides to mediate the degradation and hence the functional control of otherwise challenging disease-relevant protein targets. We describe existing platforms for protein/peptide-based ligand identification and the drug delivery systems that might be exploited for the delivery of biologic-based degraders. Throughout the Review, we underscore the successes, challenges, and opportunities of using protein-based degraders as chemical biology tools to spur discoveries, elucidate mechanisms, and act as a new therapeutic modality.

A covalent peptide-based lysosome-targeting protein degradation platform for cancer immunotherapy

The lysosome-targeting chimera (LYTAC) strategy provided a very powerful tool for the degradation of membrane proteins. However, the synthesis of LYTACs, antibody-small molecule conjugates, is challenging. The ability of antibody-based LYTACs to penetrate solid tumor is limited as well, especially to cross the blood-brain barrier (BBB). Here, we propose a covalent chimeric peptide-based targeted degradation platform (Pep-TACs) by introducing a long flexible aryl sulfonyl fluoride group, which allows proximity-enabled cross-linking upon binding with the protein of interest. The Pep-TACs platform facilitates the degradation of target proteins through the mechanism of recycling transferrin receptor (TFRC)-mediated lysosomal targeted endocytosis. Biological experiments demonstrate that covalent Pep-TACs can significantly degrade the expression of PD-L1 on tumor cells, dendritic cells and macrophages, especially under acidic conditions, and markedly enhance the function of T cells and tumor phagocytosis by macrophages. Furthermore, both in anti-PD-1-responsive and -resistant tumor models, the Pep-TACs exert significant anti-tumor immune response. It is noteworthy that Pep-TACs can cross the BBB and prolong the survival of mice with in situ brain tumor. As a proof-of-concept, this study introduces a modular TFRC-based covalent peptide degradation platform for the degradation of membrane protein, and especially for the immunotherapy of brain tumors.

Designed endocytosis-inducing proteins degrade targets and amplify signals

Endocytosis and lysosomal trafficking of cell surface receptors can be triggered by endogenous ligands. Therapeutic approaches such as lysosome-targeting chimaeras1,2 (LYTACs) and cytokine receptor-targeting chimeras3 (KineTACs) have used this to target specific proteins for degradation by fusing modified native ligands to target binding proteins. Although powerful, these approaches can be limited by competition with native ligands and requirements for chemical modification that limit genetic encodability and can complicate manufacturing, and, more generally, there may be no native ligands that stimulate endocytosis through a given receptor. Here we describe computational design approaches for endocytosis-triggering binding proteins (EndoTags) that overcome these challenges. We present EndoTags for insulin-like growth factor 2 receptor (IGF2R) and asialoglycoprotein receptor (ASGPR), sortilin and transferrin receptors, and show that fusing these tags to soluble or transmembrane target protein binders leads to lysosomal trafficking and target degradation. As these receptors have different tissue distributions, the different EndoTags could enable targeting of degradation to different tissues. EndoTag fusion to a PD-L1 antibody considerably increases efficacy in a mouse tumour model compared to antibody alone. The modularity and genetic encodability of EndoTags enables AND gate control for higher-specificity targeted degradation, and the localized secretion of degraders from engineered cells. By promoting endocytosis, EndoTag fusion increases signalling through an engineered ligand-receptor system by nearly 100-fold. EndoTags have considerable therapeutic potential as targeted degradation inducers, signalling activators for endocytosis-dependent pathways, and cellular uptake inducers for targeted antibody-drug and antibody-RNA conjugates.

Targeting intracellular cancer proteins with tumor-microenvironment-responsive bispecific nanobody-PROTACs for enhanced therapeutic efficacy

Proteolysis targeting chimeras (PROTACs) are pivotal in cancer therapy for their ability to degrade specific proteins. However, their non-specificity can lead to systemic toxicity due to protein degradation in normal cells. To address this, we have integrated a nanobody into the PROTACs framework and leveraged the tumor microenvironment to enhance drug specificity. In this study, we engineered BumPeD, a novel bispecific nanobody-targeted PROTACs-like platform, by fusing two nanobodies with a Furin protease cleavage site (RVRR) and a degron sequence (ALAPYIP or KIGLGRQKPPKATK), enabling the tumor microenvironment to direct the degradation of intracellular proteins. We utilized KN035 and Nb4A to target PD-L1 (programmed death ligand 1) on the cell surface and intracellular Survivin, respectively. In vitro experiments showed that BumPeD triggers Survivin degradation via the ubiquitin-proteasome pathway, inducing tumor apoptosis and suppressing bladder tumor cell proliferation and migration. In vivo experiments further confirmed BumPeD's robust anti-tumor efficacy, underscoring its potential as a precise protein degradation strategy for cancer therapy. Our platform provides a systematic approach to developing effective and practical protein degraders, offering a targeted theoretical basis and experimental support for the development of novel degradative drugs, as well as new directions for cancer therapy.

Staudinger Reaction-Responsive Coacervates for Cytosolic Antibody Delivery and TRIM21-Mediated Protein Degradation

A low-molecular-weight compound whose structure strikes a fine balance between hydrophobicity and hydrophilicity may form coacervates via liquid-liquid phase separation in an aqueous solution. These coacervates may encapsulate and convoy proteins across the plasma membrane into the cell. However, releasing the cargo from the vehicle to the cytosol is challenging. Here, we address this issue by designing phase-separating coacervates, which are disassembled by the bioorthogonal Staudinger reaction. We constructed and selected triphenylphosphine-based compounds that formed phase-separated coacervates in an aqueous solution. Reacting the coacervates with azides resulted in microdroplet dissolution, so they received the name Staudinger Reaction-Responsive Coacervates, SR-Coa. SR-Coa could encapsulate proteins, including antibodies, and translocate them across the plasma membrane into the cell. Further treatment of the cell with ethyl azidoacetate induced the cargo dispersion from the puncta to the cytosolic distribution. We showcased an application of the SR-Coa/ethyl azidoacetate system in facilitating the translocation of the EGFR/antibody complex into the cell, which induced EGFR degradation via the TRIM21-dependent pathway both in vitro and in vivo. Besides the membrane protein EGFR, this system could also degrade endogenous protein EZH2. Taken together, here we report a strategy of controlling molecular coacervates by a bioorthogonal reaction in the cell for cytosolic protein delivery and demonstrate its use in promoting targeted protein degradation via the proteasome-dependent pathway.

Microenvironment-confined kinetic elucidation and implementation of a DNA nano-phage with a shielded internal computing layer

Multiple receptor analysis-based DNA molecular computation has been developed to mitigate the off-target effect caused by nonspecific expression of cell membrane receptors. However, it is quite difficult to involve nanobodies into molecular computation with programmed recognition order because of the "always-on" response mode and the inconvenient molecular programming. Here we propose a spatial segregation-based molecular computing strategy with a shielded internal computing layer termed DNA nano-phage (DNP) to program nanobody into DNA molecular computation and build a series of kinetic models to elucidate the mechanism of microenvironment-confinement. We explain the contradiction between fast molecular diffusion and effective DNA computation using a "diffusion trap" theory and comprehensively overcome the kinetic bottleneck of DNP by determining the rate-limiting step. We predict and verify that identifying trace amount of target cells in complex cell mixtures is an intrinsic merit of microenvironment-confined DNA computation. Finally, we show that DNP can efficiently work in complex human blood samples by shielding the interference of erythrocytes and enhance phagocytosis of macrophages toward target cells by blocking CD47-SIRPα pathway.

Applications of cell penetrating peptide-based drug delivery system in immunotherapy

Cell penetrating peptides (CPPs) are usually positive charged peptides and have good cell membrane permeability. Meanwhile, CPPs are facile to synthesize, and can be functionalized to satisfy different demands, such as cyclization, incorporating unnatural amino acids, and lipid conjugation. These properties have made them as efficient drug-delivery tools to deliver therapeutic molecules to cells and tissues in a nontoxic manner, including small molecules, DNA, siRNA, therapeutic proteins and other various nanoparticles. However, the poor serum stability and low tumor targeting ability also hindered their broad application. Besides, inappropriate chemical modification can lead to membrane disruption and nonspecific toxicity. In this paper, we first reviewed recent advances in the CPP applications for cancer therapy via covalent or non-covalent manners. We carefully analyzed the advantages and disadvantages of each CPP modifications for drug delivery. Then, we concluded the recent progress of their clinical trials for different diseases. Finally, we discussed the challenges and opportunities CPPs met to translate into clinical applications. This review presented a new insight into CPPs for drug delivery, which could provide advice on the design of clinically effective systemic delivery systems using CPPs.

Unleashing the Power of Covalent Drugs for Protein Degradation

Targeted protein degradation (TPD) has emerged as a significant therapeutic approach for a variety of diseases, including cancer. Advances in TPD techniques, such as molecular glue (MG) and lysosome-dependent strategies, have shown substantial progress since the inception of the first PROTAC in 2001. The PROTAC methodology represents the forefront of TPD technology, with ongoing evaluation in more than 20 clinical trials for the treatment of diverse medical conditions. Two prominent PROTACs, ARV-471 and ARV-110, are currently undergoing phase III and II clinical trials, respectively. Traditional PROTACs are encountering obstacles such as limited binding affinity and a restricted range of E3 ligase ligands for facilitating the protein of interest (POI) degradation. Covalent medicines offer the potential to enhance PROTAC efficacy by enabling the targeting of previously considered "undruggable" shallow binding sites. Strategic alterations allow PROTAC to establish covalent connections with particular target proteins, including Kirsten rat sarcoma viral oncogene homolog (KRAS), Bruton's tyrosine kinase (BTK), epidermal growth factor receptor (EGFR), as well as E3 ligases such as DDB1 and CUL4 associated factor 16 (DCAF16) and Kelch-like ECH-associated protein 1 (Keap1). The concept of covalent degradation has also been utilized in various new forms of degraders, including covalent molecule glue (MG), in-cell click-formed proteolysis targeting chimera (CLIPTAC), HaloPROTAC, lysosome-targeting chimera (LYTAC) and GlueTAC. This review focuses on recent advancements in covalent degraders beyond covalent PROTACs and examines obstacles and future directions pertinent to this field.

Lysosomal Trafficking and Degradation of Extracellular Proteins via Multivalent Small Molecule Ligand Display on Dextran Scaffolds

Targeted protein degradation (TPD) marks a shift in drug development from conventional inhibition to the complete removal of pathological proteins. Traditional TPD technologies target intracellular proteins of interest (POIs) for degradation but are ineffective against extracellular cell surface and soluble proteins, a significant portion of the human proteome. Recent advances involve the formation of ternary complexes between a POI and a cell surface lysosomal trafficking receptor, directing POIs to lysosomes for degradation. We report on DEXtran TRAfficking Chimeras (DEXTRACs) comprising multiple copies of synthetic small molecule ligands for a model POI and the cation-independent mannose-6-phosphate receptor (CI-M6PR) lysosomal trafficking receptor. These ligands are arranged along the dextran backbones. We demonstrate that DEXTRACs leverage multivalency with their efficacy dependent on the dextran chain length and ligand density to form high-avidity ternary complexes. Our in vitro studies confirmed that DEXTRACs traffic the target POI to lysosomes and facilitate its degradation.

Chemically engineered antibodies for autophagy-based receptor degradation

Cell surface receptor-targeted protein degraders hold promise for drug discovery. However, their application is restricted because of the complexity of creating bifunctional degraders and the reliance on specific lysosome-shuttling receptors or E3 ubiquitin ligases. To address these limitations, we developed an autophagy-based plasma membrane protein degradation platform, which we term AUTABs (autophagy-inducing antibodies). Through covalent conjugation with polyethylenimine (PEI), the engineered antibodies acquire the capacity to degrade target receptors through autophagy. The degradation activities of AUTABs are self-sufficient, without necessitating the participation of lysosome-shuttling receptors or E3 ubiquitin ligases. The broad applicability of this platform was then illustrated by targeting various clinically important receptors. Notably, combining specific primary antibodies with a PEI-tagged secondary nanobody also demonstrated effective degradation of target receptors. Thus, our study outlines a strategy for directing plasma membrane proteins for autophagic degradation, which possesses desirable attributes such as ease of generation, independence from cell type and broad applicability.

Programmable Circular Multivalent Nanobody-Targeting Chimeras (mNbTACs) for Multireceptor-Mediated Protein Degradation and Targeted Drug Delivery

Multispecific therapeutics hold significant promise in drug delivery, protein degradation, and cell recruitment to address clinical issues of tumor heterogeneity, resistance, and immune evasion. However, their modular engineering remains challenging. We developed a targeted degradation platform, termed multivalent nanobody-targeting chimeras (mNbTACs), by encoding diverse nanobody codons on a circular template using DNA printing technology. The homo- or hetero- mNbTACs specifically recognized membrane targets in a multivalent manner and simultaneously recruited scavenger receptors to favor clathrin-/caveolae-dependent endocytosis and lysosomal degradation of multiple proteins with high efficiency and selectivity. We demonstrated that a bispecific doxorubicin-loaded mNbTAC, named Doxo-mvNbsPPH, passively accumulated at tumor sites, specifically interacted with PD-L1 and HER2 targets, and was rapidly transported into lysosome, inducing potent immunogenic cell death and alleviating immune checkpoint evasion. The synergistic boosting of innate and adaptive immunity promoted the infiltration and proliferation of CD8+ T cells in tumor microenvironment (an 11-fold increase) with high toxicity and low exhaustion, eventually enhancing antitumor efficacy. Our mNbTAC platform provides multispecific therapeutics with variable valences and programmed species, whereas it induces targeted protein degradation through multireceptor-mediated endocytosis and lysosomal degradation without the need for lysosome-targeting receptors, representing a general and modular tool to harness extracellular proteome for disease treatment.

Aptamer and N-Degron Ensemble (AptaGron) as a Target Protein Degradation Strategy

Target protein degradation (TPD) is a promising strategy for catalytic downregulation of target proteins through various cellular proteolytic pathways. Despite numerous reports on novel TPD mechanisms, the discovery of target-specific ligands remains a major challenge. Unlike small-molecule ligands, aptamers offer significant advantages, owing to their SELEX-based systematic screening method. To fully utilize aptamers for TPD, we designed an aptamer and N-degron ensemble system (AptaGron) that circumvents the need for synthetic conjugations between aptamers and proteolysis-recruiting units. In our AptaGron system, a peptide nucleic acid containing an N-degron peptide and a sequence complementary to the aptamer was designed. Using this system, we successfully degraded three target proteins, tau, nucleolin, and eukaryotic initiation factor 4E (eIF4E), which lack specific small-molecule ligands. Our results highlight the potential of the AptaGron approach as a robust platform for targeted protein degradation.

Nanomotor-Driven Targeting Chimeras as Accelerators for the Degradation of Extracellular Proteins

Targeted protein degradation (TPD) is emerging as a therapeutic paradigm and a serviceable research tool in chemical biology and disease treatment. However, without driving sources, most targeting chimeras (TACs) lack the capability of self-diffusion and active searching in biological environments, which significantly impedes degradation efficiency. Herein, nanomotor-driven targeting chimeras (MotorTACs) are ingeniously designed to achieve effective internalization and degradation of extracellular platelet-derived growth factor (PDGF), a driver to cancer invasion and metastasis. Catalyzed by endogenous H2O2, MotorTACs diffused rapidly and searched actively in living cells, as visualized at the single-particle level under the dark-field mode. Hydrolysis efficiency is significantly enhanced as target protein degradation is complete in only 4 h. Furthermore, MotorTACs-mediated degradation of PDGF is found to be via the lysosome and ubiquitin-proteasome dual-degradation pathways. Taking advantage of the properties, it is anticipated that MotorTACs provide a unique strategy against extracellular undruggable proteins, thus advancing the development of therapeutic interventions in chemical biology and disease treatment.

How to target membrane proteins for degradation: Bringing GPCRs into the TPD fold

We are now in the middle of a so-called "fourth wave" of drug innovation: multispecific medicines aimed at diseases and targets previously thought to be "undruggable"; by inducing proximity between two or more proteins, for example, a target and an effector that do not naturally interact, such modalities have potential far beyond the scope of conventional drugs. In particular, targeted protein degradation (TPD) strategies to destroy disease-associated proteins have emerged as an exciting pipeline in drug discovery. Most efforts are focused on intracellular proteins, whereas membrane proteins have been less thoroughly explored despite the fact that they comprise roughly a quarter of the human proteome with G-protein coupled receptors (GPCRs) notably dysregulated in many diseases. Here, we discuss the opportunities and challenges of developing degraders for membrane proteins with a focus on GPCRs. We provide an overview of different TPD platforms in the context of membrane-tethered targets, and we present recent degradation technologies highlighting their potential application to GPCRs.

Targeted protein degradation: expanding the technology to facilitate the clearance of neurotoxic proteins in neurodegenerative diseases

In neurodegenerative diseases (NDDs), disruptions in protein homeostasis hinder the clearance of misfolded proteins, causing the formation of misfolded protein oligomers and multimers. The accumulation of these abnormal proteins results in the onset and progression of NDDs. Removal of non-native protein is essential for cell to maintain proteostasis. In recent years, targeted protein degradation (TPD) technologies have become a novel means of treating NDDs by removing misfolded proteins through the intracellular protein quality control system. The TPD strategy includes the participation of two primary pathways, namely the ubiquitin-proteasome pathway (for instance, PROTAC, molecular glue and hydrophobic tag), and the autophagy-lysosome pathway (such as LYTAC, AUTAC and ATTEC). In this review, we systematically present the mechanisms of various TPD strategies employed for neurotoxic protein degradation in NDDs. The article provides an overview of the design, in vitro and in vivo anti-NDD activities and pharmacokinetic properties of these small-molecular degraders. Finally, the advantages, challenges and perspectives of these TPD technologies in NDDs therapy are discussed, providing ideas for further development of small molecule degraders in the realm of NDDs.

Conditionally Activatable Chimeras for Tumor-Specific Membrane Protein Degradation

The recent advancements on membrane protein degraders (MPDs) have broadened the applicability of proteolysis-targeting chimeras (PROTACs) beyond intracellular proteins to include the previously "undruggable" cell-surface targets. However, the potential toxicity of MPDs caused by undesired off-target degradation poses a significant challenge to clinical deployment, mirroring concerns associated with PROTACs. Here, we introduce a conditionally activatable membrane protein degrader (Pro-MPD), which leverages the specificity and high affinity of biparatopic nanobodies combined with a tumor microenvironment-activated cell-penetrating peptide (Pro-CPP) to achieve on-target activated internalization and degradation of PD-L1 within tumor sites. This modularly designed Pro-MPD demonstrated a high target degradation efficiency and T cell reactivation, as well as sustained inhibition of tumor growth in xenograft models, highlighting its potential as a safer and highly efficient MPD for in vivo applications. Our work provides a general strategy for the development of conditionally activatable MPDs, which offers a new avenue for reducing the undesired systemic toxicity of MPDs due to the off-tumor degradation.

Targeted protein degradation: current molecular targets, localization, and strategies

Targeted protein degradation (TPD) has revolutionized drug discovery by selectively eliminating specific proteins within and outside the cellular context. Over the past two decades, TPD has expanded its focus beyond well-established targets, exploring diverse proteins beyond cancer-related ones. This evolution extends the potential of TPD to various diseases. Notably, TPD can target proteins at demanding locations, such as the extracellular matrix (ECM) and cellular membranes, presenting both opportunities and challenges for future research. In this review, we comprehensively examine the exciting opportunities in the burgeoning field of TPD, highlighting different targets, their cellular environment, and innovative strategies for modern drug discovery.

Nanotechnology-Enabled Targeted Protein Degradation for Cancer Therapeutics

Targeted protein degradation (TPD) represents an innovative therapeutic strategy that has garnered considerable attention from both academic and industrial sectors due to its promising developmental prospects. Approximately 85% of human proteins are implicated in disease pathogenesis, and the FDA has approved around 400 drugs targeting these disease-related proteins, predominantly enzymes, transcription factors, and non-enzymatic proteins. However, existing therapeutic modalities fail to address certain "high-value" targets, such as c-Myc and Ras. The emergence of proteolysis-targeting chimeras (PROTAC) technology has introduced TPD into a new realm. The capability to target non-druggable sites has expanded the therapeutic horizon of protein-based drugs, although challenges related to bioavailability, safety, and adverse side effects have constrained their clinical progression. Nano-delivery systems and emerging TPD modalities, such as molecular glues, lysosome-targeted chimeras (LYTACs), autophagy system compounds (ATTEC), and antibody PROTAC (AbTACs), have mitigated some of these limitations. This paper reviews the latest advancements in TPD, highlighting their applications and benefits in cancer therapy, and concludes with a forward-looking perspective on the future development of this field.

Recent breakthroughs in innovative elements, multidimensional enhancements, derived technologies, and novel applications of PROTACs

Proteolysis Targeting Chimera (PROTAC) is an emerging and evolving technology based on targeted protein degradation (TPD). Small molecule PROTACs have shown great efficacy in degrading disease-specific proteins in preclinical and clinical studies, but also showed various limitations. In recent years, new technologies and advances in TPD have provided additional optimized strategies based on conventional PROTACs that can overcome the shortcomings of conventional PROTACs in terms of undruggable targets, bioavailability, tissue-specificity, spatiotemporal control, and degradation scope. In addition, some designs of special targeting chimeras and applications based on multidisciplinary science have shed light on novel therapeutic modalities and drug design. However, each improvement has its own advantages, disadvantages and application conditions. In this review, we summarize the exploration of PROTAC elements, depict a landscape of improvements and derived concepts of PROTACs, and expect to provide perspectives for technological innovations, combinations and applications in future targeting chimera design.

Intelligent Modular DNA Lysosome-Targeting Chimera Nanodevice for Precision Tumor Therapy

Lysosome targeting chimeras (LYTACs) have emerged as a powerful modality that can eliminate traditionally undruggable extracellular tumor-related pathogenic proteins, but their low bioavailability and nonspecific distribution significantly restrict their efficacy in precision tumor therapy. Developing a LYTAC system that can selectively target tumor tissues and enable a modular design is crucial but challenging. We here report a programmable nanoplatform for tumor-specific degradation of multipathogenic proteins using an intelligent modular DNA LYTAC (IMTAC) nanodevice. We employ circular DNA origami to integrate predesigned modular multitarget protein binding sites and pH-responsive protein degradation promoters that specifically recognize cell-surface lysosome-shuttling receptors in tumor tissues. By precisely manipulating the stoichiometry and modularity of promoters and ligands targeting diverse proteins, the IMTAC nanodevice enables accurate localization and delivery into tumor tissues, where the acidic tumor microenvironment triggers degradation switch activation, multivalent binding, and efficient degradation of various prespecified proteins. The tissue-specificity and multiple ligands in IMTACs significantly improve the drug utilization rate while reducing off-target effects. Importantly, this system demonstrates the capability of collabo-rative degradation of EGFR and PDL1 in tumor tissue for combined targeting and immunity therapy of hepatocellular carcinoma (HCC), resulting in obvious tumor necrosis and inhibition of tumor growth in vivo even at low concentrations. This study presents a unique strategy for building a general, intelligent, modular, and simple encoded nanoplatform for designing precision medicine degraders and developing proprietary antitumor drugs.

Glucose Transporter-Targeting Chimeras Enabling Tumor-Selective Degradation of Secreted and Membrane Proteins

Tumor-selective degradation of target proteins has the potential to offer superior therapeutic benefits with maximized therapeutic windows and minimized off-target effects. However, the development of effective lysosome-targeted degradation platforms for achieving selective protein degradation in tumors remains a substantial challenge. Cancer cells depend on certain solute carrier (SLC) transporters to acquire extracellular nutrients to sustain their metabolism and growth. This current study exploits facilitative glucose transporters (GLUTs), a group of SLC transporters widely overexpressed in numerous types of cancer, to drive the endocytosis and lysosomal degradation of target proteins in tumor cells. GLUT-targeting chimeras (GTACs) were generated by conjugating multiple glucose ligands to an antibody specific for the target protein. We demonstrate that the constructed GTACs can induce the internalization and lysosomal degradation of the extracellular and membrane proteins streptavidin, tumor necrosis factor-alpha (TNF-α), and human epidermal growth factor receptor 2 (HER2). Compared with the parent antibody, the GTAC exhibited higher potency in inhibiting the growth of tumor cells in vitro and enhanced tumor-targeting capacity in a tumor-bearing mouse model. Thus, the GTAC platform represents a novel degradation strategy that harnesses an SLC transporter for tumor-selective depletion of secreted and membrane proteins of interest.

Autophagy modulation in cancer therapy: Challenges coexist with opportunities

Autophagy, a crucial intracellular degradation process facilitated by lysosomes, plays a pivotal role in maintaining cellular homeostasis. The elucidation of autophagy key genes and signaling pathways has significantly advanced our understanding of this process and has led to the exploration of autophagy as a promising therapeutic approach. This review comprehensively assesses the latest developments in small molecule modulators targeting autophagy. Moreover, the review delves into the most recent strategies for drug discovery, specifically focusing on selective agents that exploit autophagosomes and lysosomes for targeted protein degradation. Additionally, this article highlights the prevailing challenges and outlines potential future advancements in the field. By amalgamating the cutting-edge knowledge in the field, we aim to offer valuable insights and references for the anti-cancer drug development of autophagy-targeted therapies, thus contributing to the advancement of novel therapeutic interventions.

Lysosome-targeting chimeras containing an endocytic signaling motif trigger endocytosis and lysosomal degradation of cell-surface proteins

Lysosome-targeting degradation technologies have emerged as a promising therapeutic strategy for the selective depletion of target extracellular and cell-surface proteins by harnessing a cell-surface effector protein such as lysosome-targeting receptors (LTRs) or transmembrane E3 ligases that direct lysosomal degradation. We recently developed a lysosome-targeting degradation platform termed signal-mediated lysosome-targeting chimeras (SignalTACs) that functions independently of an LTR or E3 ligase; these are engineered fusion proteins comprising a target binder, a cell-penetrating peptide (CPP), and a lysosomal sorting signal motif (P1). Herein, we present the next-generation SignalTACs containing a single endocytic signal that bypasses the need for a CPP. We demonstrate that the fusion with a 10-amino acid endocytic signaling peptide (P3) derived from the cation-independent mannose-6-phosphate receptor (CI-M6PR) induces robust internalization and lysosomal degradation of the target protein. The P3-based SignalTAC exhibited enhanced antitumor efficacy compared to the parent antibody. We envision that the fusion of the endocytic signaling peptide P3 to a target binder may allow the construction of an effective degrader for membrane-associated targets. Furthermore, mechanistic studies identified different drivers for the activities of the P3- and P1-based SignalTACs, which is expected to provide crucial insights toward the harnessing of the intrinsic signaling pathways to direct protein trafficking and degradation.

Functionalized Protein Binders in Developmental Biology

Developmental biology has greatly profited from genetic and reverse genetic approaches to indirectly studying protein function. More recently, nanobodies and other protein binders derived from different synthetic scaffolds have been used to directly dissect protein function. Protein binders have been fused to functional domains, such as to lead to protein degradation, relocalization, visualization, or posttranslational modification of the target protein upon binding. The use of such functionalized protein binders has allowed the study of the proteome during development in an unprecedented manner. In the coming years, the advent of the computational design of protein binders, together with further advances in scaffold engineering and synthetic biology, will fuel the development of novel protein binder-based technologies. Studying the proteome with increased precision will contribute to a better understanding of the immense molecular complexities hidden in each step along the way to generate form and function during development.

To homeostasis and beyond! Recent advances in the medicinal chemistry of heterobifunctional derivatives

The field of induced proximity therapeutics has expanded dramatically over the past 3 years, and heterobifunctional derivatives continue to form a significant component of the activities in this field. Here, we review recent advances in the field from the perspective of the medicinal chemist, with a particular focus upon informative case studies, alongside a review of emerging topics such as Direct-To-Biology (D2B) methodology and utilities for heterobifunctional compounds beyond E3 ligase mediated degradation. We also include a critical evaluation of the latest thinking around the optimisation of physicochemical and pharmacokinetic attributes of these beyond Role of Five molecules, to deliver appropriate therapeutic exposure in vivo.

Peptide-Mediated Small Molecule Lysosome-Targeting Chimeras for Targeted Degradation of Membrane and Intracellular Proteins

Targeted protein degradation through the lysosomal pathway has attracted increasing attention and expanded the scope of degradable proteins. However, the endogenous lysosomal degradation strategies are mainly based on antibodies or nanobodies. Effective small molecule lysosomal degraders are still rather rare. Herein, a new lysosomal degradation approach, termed peptide-mediated small molecule lysosome-targeting chimeras (PSMLTACs), was developed by the incorporation of small molecule ligands with a lysosome-sorting NPGY motif containing the cell-penetrating peptide. PSMLTACs were successfully applied to degrade both membrane and intracellular targets. In particular, the PSMLTAC strategy demonstrated higher degradation efficiency on membrane target PD-L1 and intracellular target PDEδ than corresponding PROTAC degraders. Taken together, this proof-of-concept provides a convenient and effective strategy for targeted protein degradation.

Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion

Over 20 years ago, the pyrrolysine encoding translation system was discovered in specific archaea. Our Review provides an overview of how the once obscure pyrrolysyl-tRNA synthetase (PylRS) tRNA pair, originally responsible for accurately translating enzymes crucial in methanogenic metabolic pathways, laid the foundation for the burgeoning field of genetic code expansion. Our primary focus is the discussion of how to successfully engineer the PylRS to recognize new substrates and exhibit higher in vivo activity. We have compiled a comprehensive list of ncAAs incorporable with the PylRS system. Additionally, we also summarize recent successful applications of the PylRS system in creating innovative therapeutic solutions, such as new antibody-drug conjugates, advancements in vaccine modalities, and the potential production of new antimicrobials.

An Aptamer Glue Enables Hyperefficient Targeted Membrane Protein Degradation

Targeted membrane protein degradation (TMPD) offers significant therapeutic potential by enabling the removal of harmful membrane-anchored proteins and facilitating detailed studies of complex biological pathways. However, existing TMPD methodologies face challenges such as complex molecular architectures, scarce availability, and cumbersome construction requirements. To address these issues, this study presents a highly efficient TMPD system (TMPDS) that integrates an optimized bivalent aptamer glue with a potent protein transport shuttle. Utilizing this approach, we successfully degraded both the highly expressed protein tyrosine kinase 7 in CCRF-CEM cells and the poorly expressed PTK7 in MV-411 cells. This system represents significant advancement in the field of molecular medicine, offering a new avenue for targeted therapeutic interventions and the exploration of cellular mechanisms.

Targeted protein degradation in hematologic malignancies: clinical progression towards novel therapeutics

Targeted therapies, such as small molecule kinase inhibitors, have made significant progress in the treatment of hematologic malignancies by directly modulating protein activity. However, issues such as drug toxicity, drug resistance due to target mutations, and the absence of key active sites limit the therapeutic efficacy of these drugs. Targeted protein degradation (TPD) presents an emergent and rapidly evolving therapeutic approach that selectively targets proteins of interest (POI) based on endogenous degradation processes. With an event-driven pharmacology of action, TPD achieves efficacy with catalytic amounts, avoiding drug-related toxicity. Furthermore, TPD has the unique mode of degrading the entire POI, such that resistance derived from mutations in the targeted protein has less impact on its degradation function. Proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) are the most maturely developed TPD techniques. In this review, we focus on both preclinical experiments and clinical trials to provide a comprehensive summary of the safety and clinical effectiveness of PROTACs and MGDs in hematologic malignancies over the past two decades. In addition, we also delineate the challenges and opportunities associated with these burgeoning degradation techniques. TPD, as an approach to the precise degradation of specific proteins, provides an important impetus for its future application in the treatment of patients with hematologic malignancies.

Progress of proteolysis-targeting chimeras (PROTACs) delivery system in tumor treatment

Proteolysis targeting chimeras (PROTACs) can use the intrinsic protein degradation system in cells to degrade pathogenic target proteins, and are currently a revolutionary frontier of development strategy for tumor treatment with small molecules. However, the poor water solubility, low cellular permeability, and off-target side effects of most PROTACs have prevented them from passing the preclinical research stage of drug development. This requires the use of appropriate delivery systems to overcome these challenging hurdles and ensure precise delivery of PROTACs towards the tumor site. Therefore, the combination of PROTACs and multifunctional delivery systems will open up new research directions for targeted degradation of tumor proteins. In this review, we systematically reviewed the design principles and the most recent advances of various PROTACs delivery systems. Moreover, the constructive strategies for developing multifunctional PROTACs delivery systems were proposed comprehensively. This review aims to deepen the understanding of PROTACs drugs and promote the further development of PROTACs delivery system.