Recent Developments in PROTAC-Mediated Protein Degradation: From Bench to Clinic

Proteolysis-targeting chimeras (PROTACs), an emerging paradigm-shifting technology, hijacks the ubiquitin-proteasome system for targeted protein degradation. PROTACs induce ternary complexes between an E3 ligase and POI, and this induced proximity leads to polyUb chain formation on substrates and eventual proteasomal-mediated POI degradation. PROTACs have shown great therapeutic potential by degrading many disease-causing proteins, such as the androgen receptor and BRD4. The PROTAC technology has advanced significantly in the last two decades, with the repertoire of PROTAC targets increased tremendously. Herein, we describe recent developments of PROTAC technology, focusing on mechanistic and kinetic studies, pharmacokinetic study, spatiotemporal control of PROTACs, covalent PROTACs, resistance to PROTACs, and new E3 ligands.     

Jostling for Position: Optimizing Linker Location in the Design of Estrogen Receptor‐Targeting PROTACs

Estrogen receptor‐α (ER) antagonists have been widely used for breast cancer therapy. Despite initial responsiveness, hormone‐sensitive ER‐positive cancer cells eventually develop resistance to ER antagonists. It has been shown that in most of these resistant tumor cells, the ER is expressed and continues to regulate tumor growth. Recent studies indicate that tamoxifen initially acts as an antagonist, but later functions as an ER agonist, promoting tumor growth. This suggests that targeted ER degradation may provide an effective therapeutic approach for breast cancers, even those that are resistant to conventional therapies. With this in mind, we previously demonstrated that proteolysis targeting chimeras (PROTACs) effectively induce degradation of the ER as a proof‐of‐concept experiment. Herein we further refined the PROTAC approach to target the ER for degradation. The ER‐targeting PROTACs are composed of an estradiol on one end and a hypoxia‐inducing factor 1α (HIF‐1α)‐derived synthetic pentapeptide on the other. The pentapeptide is recognized by an E3 ubiquitin ligase called the von Hippel Lindau tumor suppressor protein (pVHL), thereby recruiting the ER to this E3 ligase for ubiquitination and degradation. Specifically, the pentapeptide is attached at three different locations on estradiol to generate three different PROTAC types. With the pentapeptide linked through the C7α position of estradiol, the resulting PROTAC shows the most effective ER degradation and highest affinity for the estrogen receptor. This result provides an opportunity to develop a novel type of ER antagonist that may overcome the resistance of breast tumors to conventional drugs such as tamoxifen and fulvestrant (Faslodex).     

HaloTag-Targeted Sirtuin-Rearranging Ligand (SirReal) for the Development of Proteolysis-Targeting Chimeras (PROTACs) against the Lysine Deacetylase Sirtuin 2 (Sirt2)**

We have discovered the sirtuin-rearranging ligands (SirReals) as a novel class of highly potent and selective inhibitors of the NAD⁺-dependent lysine deacetylase sirtuin 2 (Sirt2). In previous studies, conjugation of a SirReal with a ligand for the E3 ubiquitin ligase cereblon to form a so-called proteolysis-targeting chimera (PROTAC) enabled small-molecule-induced degradation of Sirt2. Herein, we report the structure-based development of a chloroalkylated SirReal that induces the degradation of Sirt2 mediated by Halo-tagged E3 ubiquitin ligases. Using this orthogonal approach for Sirt2 degradation, we show that other E3 ligases than cereblon, such as the E3 ubiquitin ligase parkin, can also be harnessed for small-molecule-induced Sirt2 degradation, thereby emphasizing the great potential of parkin to be used as an E3 ligase for new PROTACs approaches. Thus, our study provides new insights into targeted protein degradation in general and Sirt2 degradation in particular.     

A Modular Chemistry Platform for the Development of a Cereblon E3 Ligase-Based Partial PROTAC Library

Pr oteolysis ta rgeting c himeras (PROTACs) are a promising therapeutic strategy to selectively promote the degradation of protein targets by exploiting the ubiquitin-proteasome system. Among the limited number of E3 ligase ligands discovered for the PROTAC technology, ligands of cereblon (CRBN) E3 ligase, such as pomalidomide, thalidomide, or lenalidomide, are the most frequently used for the development of PROTACs. Our group previously reported that a phenyl group could be tolerated on the C4-position of lenalidomide as the ligand of CRBN to develop PROTACs. Herein, we report a modular chemistry platform for the efficient attachment of various ortho-, meta-, and para-substituted phenyls to the C4-position of the lenalidomide via Suzuki cross-coupling reaction, which allows the systematic investigation of the linker effect for the development of PROTACs against any target. We examined the substrate scope by preparing twelve lenalidomide-derived CRBN E3 ligase ligands with different linkers.     

A Degron Blocking Strategy Towards Improved CRL4CRBN Recruiting PROTAC Selectivity**

Small molecules inducing protein degradation are important pharmacological tools to interrogate complex biology and are rapidly translating into clinical agents. However, to fully realise the potential of these molecules, selectivity remains a limiting challenge. Herein, we addressed the issue of selectivity in the design of CRL4^CRBN recruiting PROteolysis TArgeting Chimeras (PROTACs). Thalidomide derivatives used to generate CRL4^CRBN recruiting PROTACs have well described intrinsic monovalent degradation profiles by inducing the recruitment of neo-substrates, such as GSPT1, Ikaros and Aiolos. We leveraged structural insights from known CRL4^CRBN neo-substrates to attenuate and indeed remove this monovalent degradation function in well-known CRL4^CRBN molecular glues degraders, namely CC-885 and Pomalidomide. We then applied these design principles on a previously published BRD9 PROTAC (dBRD9-A) and generated an analogue with improved selectivity profile. Finally, we implemented a computational modelling pipeline to show that our degron blocking design does not impact PROTAC-induced ternary complex formation. We believe that the tools and principles presented in this work will be valuable to support the development of targeted protein degradation.     

The separate effects of E60Q in Lactobacillus casei thymidylate synthase delineate between mechanisms for formation of intermediates in catalysis

X-Ray crystal structures of Lactobacillus casei thymidylate synthase (TS) mutant complexes of E60D with dUMP, and E60Q with dUMP or FdUMP, as well as ternary complexes with folate analog inhibitor CB3717, are described. The structures we report address the decrease in rate of formation of ternary complexes in the E60 mutants. Structures of ternary complexes of L.casei TS mimic ligand-bound TS just prior to covalent bond formation between ligands and protein. Ternary complex structures of L.casei TS E60Q show the ligands are not optimally aligned for making the necessary covalent bonds. Since CB3717 is an analog of the open, activated form of the cofactor, these structures suggest that the slow rate of ternary complex formation in E60 mutants is at least partly the result of impaired alignment of ligands in the active site after binding and activation of the cofactor. Binary complexes of TS E60Q and TS E60D with substrate (dUMP) show no change in dUMP position or occupancy. These results are consistent with the fact that Kd(dUMP) and Km(dUMP) are almost the same, and the rates of folate-independent debromination of 5-bromo-dUMP are even higher than for wild type TS.      

The tale of proteolysis targeting chimeras (PROTACs) for Leucine-Rich Repeat Kinase 2 (LRRK2)

Here we present the rational design and synthetic methodologies towards proteolysis-targeting chimeras (PROTACs) for the recently-emerged target leucine-rich repeat kinase 2 (LRRK2). Two highly potent, selective, brain-penetrating kinase inhibitors were selected, and their structure was appropriately modified to assemble a cereblon-targeting PROTAC. Biological data show strong kinase inhibition and the ability of the synthesized compounds to enter the cells. However, data regarding the degradation of the target protein are inconclusive. The reasons for the inefficient degradation of the target are further discussed.     

Biophysical and Computational Approaches to Study Ternary Complexes: A ‘Cooperative Relationship’ to Rationalize Targeted Protein Degradation

Degraders have illustrated that compound-induced proximity to E3 ubiquitin ligases can prompt the ubiquitination and degradation of disease-relevant proteins. Hence, this pharmacology is becoming a promising alternative and complement to available therapeutic interventions (e. g., inhibitors). Degraders rely on protein binding instead of inhibition and, hence, they hold the promise to broaden the druggable proteome. Biophysical and structural biology approaches have been the cornerstone of understanding and rationalizing degrader-induced ternary complex formation. Computational models have now started to harness the experimental data from these approaches with the aim to identify and rationally help design new degraders. This review outlines the current experimental and computational strategies used to study ternary complex formation and degradation and highlights the importance of effective crosstalk between these approaches in the advancement of the targeted protein degradation (TPD) field. As our understanding of the molecular features that govern drug-induced interactions grows, faster optimizations and superior therapeutic innovations for TPD and other proximity-inducing modalities are sure to follow.     

Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology

A protein complex consists of two or more proteins that are linked together through protein–protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.     

稀土钐二元、三元配合物的合成、表征及其生物活性研究

以氯化钐、2-氨基嘧啶和钼酸钠为原料,制备了两种新型稀土钐二元、三元配合物,通过元素分析、紫外光谱、红外光谱等手段对其进行了表征,确定了二元配合物的化学组成为Sm2(AP)(H2O)2Cl3(AP=2-氨基嘧啶),三元配合物的化学组成为:Sm3(AP)(MoO4)2(CH3OH)4Cl5。抗菌结果表明,二元配合物对大肠杆菌和金黄色葡萄球菌的抑菌圈直径分别为13 mm和15 mm,三元配合物分别为13 mm和13 mm,两种配合物对大肠杆菌、金黄色葡萄球菌都有一定的抑制作用。采用MTT法对两种配合物诱导癌细胞凋亡能力做了初步研究,两种配合物的半数抑制浓度IC50在0.001~0.01 mg/mL之间,证明其具有诱导癌细胞凋亡的作用。     

Synthesis, Characterization and Thermal Studies of Zn(II), Cd(II) and Hg(II) Complexes of N-Methyl-N-Phenyldithiocarbamate: The Single Crystal Structure of [(C(6)H(5))(CH(3))NCS(2)](4)Hg(2)

Zn(II), Cd(II) and Hg(II) complexes of N-methyl-N-phenyl dithiocarbamate have been synthesized and characterized by elemental analysis and spectral studies (IR, (1)H and (13)C-NMR). The single crystal X-ray structure of the mercury complex revealed that the complex contains a Hg centre with a distorted tetrahedral coordination sphere in which the dinuclear Hg complex resides on a crystallographic inversion centre and each Hg atom is coordinated to four S atoms from the dithiocarbamate moiety. One dithiocarbamate ligand acts as chelating ligand while the other acts as chelating bridging ligand between two Hg atoms, resulting in a dinuclear eight-member ring. The course of the thermal degradation of the complexes has been investigated using thermogravimetric and differential thermal analyses techniques. Thermogravimetric analysis of the complexes show a single weight loss to give MS (M = Zn, Cd, Hg) indicating that they might be useful as single source precursors for the synthesis of MS nanoparticles and thin films.     

Solution NMR studies of an intrinsically unstructured protein within a dilute, 75 kDa eukaryotic protein assembly; probing the practical limits for efficiently assigning polypeptide backbone resonances

This paper describes an efficient NMR strategy for assigning the backbone resonances of an intrinsically unstructured protein (IUP), p21-KID, bound to its biological target, Cdk2/cyclin A. In order to overcome the challenges associated with the high molecular weight (75 kDa) and low solubility of the ternary complex (0.2 mM), we used perdeuteration, TROSY, and high-sensitivity cryogenic NMR probes at high magnetic-field strengths (i.e. 16.4, 18.8 and 21.1 Tesla). p21-KID was also prepared by using specific amino acid isotope labels. Most importantly, we studied binary, subcomplexes that allowed resonance assignments to be made in stages. We show that subdomains of p21-KID folded within binary complexes into the same conformations as observed in the ternary, Cdk2/cyclin A complex. This is a general feature of IUPs, which often adopt highly extended conformations when bound to other proteins. This strategy is suitable for studies of IUPs within considerably larger biomolecular assemblies as long as the IUP can be uniformly and selectively isotope labeled.     

dSTORM-Based Single-Cell Protein Quantitative Analysis Can Effectively Evaluate the Degradation Ability of PROTACs

As an emerging therapeutic strategy, proteolysis-targeting chimeras (PROTACs) have been proven to be superior to traditional drugs in many aspects. However, due to their unique mechanism of action, existing methods for evaluating the degradation still have many limitations, which seriously restricts the development of PROTACs. In this methodological study, using direct stochastic optical reconstruction microscopy (dSTORM)-based single-cell protein quantitative analysis, we systematically investigated the dynamic degradation characteristics of FLT3 protein during PROTACs treatment. We found that the distribution of FLT3 varies between FLT3-ITD mutation and FLT3-WT cells. PROTACs had an obvious time-course effect on protein degradation and present two distinct phases; this provided a basis for deciding when to evaluate protein degradation. High concentrations of PROTACs were more effective than long-time administration because a higher D_max was achieved. Two-color dSTORM-based colocalization analysis efficiently detected the proportion of ternary complexes, making it very useful in screening PROTACs. Taken together, our findings show that the dSTORM method is an ideal tool for evaluating PROTACs and will accelerate the development of new PROTACs.     

铜(Ⅱ)-氨基葡萄糖-α-氨基酸三元配合物的稳定性

为研究铜(Ⅱ)-氨基葡萄糖-α-氨基酸三元配合物的稳定性,用pH电位滴定法测定了298±0.1 K,I=0.10 mol/L KNO3条件下铜(Ⅱ)-氨基葡萄糖-α-氨基酸三元配合物的稳定常数。结果表明,在铜(Ⅱ)-氨基葡萄糖-α-氨基酸三元体系中,生物配体氨基葡萄糖和α-氨基酸具有良好的相容性,三元配合物的稳定性与α-氨基酸的碱性及二元配合物稳定性之间存在直线自由能关系。     

Synthesis and Evaluation of Cereblon-Recruiting HaloPROTACs

Target validation is key to the development of protein degrading molecules such as proteolysis-targeting chimeras (PROTACs) to identify cellular proteins amenable for induced degradation by the ubiquitin-proteasome system (UPS). Previously the HaloPROTAC system was developed to screen targets of PROTACs by linking the chlorohexyl group with the ligands of E3 ubiquitin ligases VHL and cIAP1 to recruit target proteins fused to the HaloTag for E3-catalyzed ubiquitination. Reported here are HaloPROTACs that engage the cereblon (CRBN) E3 to ubiquitinate and degrade HaloTagged proteins. A focused library of CRBN-pairing HaloPROTACs was synthesized and screened to identify efficient degraders of EGFP-HaloTag fusion with higher activities than VHL-engaging HaloPROTACs at sub-micromolar concentrations of the compound. The CRBN-engaging HaloPROTACs broadens the scope of the E3 ubiquitin ligases that can be utilized to screen suitable targets for induced protein degradation in the cell.     

镧-磺基水杨酸-8-羟基喹啉三元配合物合成、表征及其抑菌性

合成了一种镧-磺基水杨酸-8-羟基喹啉三元配合物,采用摩尔电导率、红外光谱、紫外光谱、荧光光谱和热重分析手段进行表征,并研究了该三元配合物对常见的大肠杆菌、金黄色葡萄球菌和真菌黑曲霉的抑菌活性。结果表明:该三元配合物对大肠杆菌、金黄色葡萄球菌、黑曲霉菌都具有良好的抑菌效果。织物经该配合物的整理后,也具有了较强的抗菌作用。     

Studies on preparation,structure and fluorescence emission of polymer-rare earth complexes composed of aryl carboxylic acid-functionalized polystyrene and Tb(Ⅲ) ion

4-(Chloromethyl) benzoic acid (CMBA) was first bonded onto the side chains of polystyrene (PS) via a polymer reaction, Friedel–Crafts alkylation reaction, and aryl carboxylic acid-functionalized polystyrene (PSBA) was generated. The functionalized polystyrene was used to prepare rare earth metal complexes. By using PSBA as macromolecule ligand, the binary polymer-rare earth complexes, PS-(BA)_n-Tb(Ⅲ), were prepared, and at the same time, ternary polymer-rare earth complexes, PS-(BA)_n-Tb(Ⅲ)-(Phen)_m, i.e. the mixed complexes in which both polymer-based aryl carboxylic acid and 1,10-phenanthroline as ligands were also prepared. The complexes were fully characterized using FTIR and proton NMR spectroscopy. Both ultraviolet absorption and fluorescence emission spectra for the complexes were recorded. The relationship between complex structure and the intensity of fluorescence emission was established. The experimental results show that the fluorescence emission from the central metal ion in the complex is strongly sensitized by the aryl carboxylic acid ligands chemically attached to the side chains of PSBA, and an apparent “Antenna Effect” is produced for these complexes. In the dilute solution of PSBA, the formed complex belongs to intramolecular complex. For the binary intramolecular complex, the apparent saturated coordination number of Tb³⁺ ion is 10, and here the binary complex has the structure of PS-(BA)₅-Tb(Ⅲ) and it has the strongest fluorescence emission among all of the binary complexes. When small-molecule Phen is added into the binary complex solution, the ternary complex PS-(BA)_n-Tb(Ⅲ)-(Phen)_m will be formed. As compared with the conventional ternary complexes PS-(BA)₁-Tb(Ⅲ)-Phen₂ and PS-(BA)₁-Tb(Ⅲ)-(Phen)₃ (the molar ratio of the central ion and the two ligands is conventional), the ternary complex with the structure of PS-(BA)₅-Tb(Ⅲ)-(Phen)₁ has the strongest fluorescence emission because of the complete coordination of the ligands to Tb³⁺ ion and the removal of the substituted water molecules around Tb³⁺ ion.     

Ternary Ni2P/Bi2MoO6/g-C3N4 composite with Z-scheme electron transfer path for enhanced removal broad-spectrum antibiotics by the synergistic effect of adsorption and photocatalysis

Constructing the stable, low-cost, efficient, and highly adaptable visible light-driven photocatalyst to implement the synergistic effect of photocatalysis and adsorption has been excavated a promising strategy to deal with antibiotic pollution in water bodies. Herein, a novel 3D ternary Z-scheme heterojunction photocatalyst Ni₂P/Bi₂MoO₆/g-C₃N₄ (Ni₂P/BMO/CN) was fabricated by a simple solvothermal method in which the broad spectrum antibiotics (mainly tetracyclines and supplemented by quinolones) were used as target pollution sources to evaluate its adsorption and photocatalytic performance. Notably, the Z-scheme composite significantly exhibit the enhancement for degradation efficiency of tetracycline and other antibiotic by using Ni₂P nanoparticles as electron conductor. Active species capture experiment and electron spin resonance (ESR) technology reveal the mechanism of Z-scheme Ni₂P/BMO/CN photocatalytic reaction in detail. In addition, based on the identification of intermediates by liquid chromatography–mass spectroscopy (LC–MS), the possible photocatalytic degradation pathways of TC were proposed.     

E3 Ubiquitin Ligase APC/CCdh1 Negatively Regulates FAH Protein Stability by Promoting Its Polyubiquitination

Fumarylacetoacetate hydrolase (FAH) is the last enzyme in the degradation pathway of the amino acids tyrosine and phenylalanine in mammals that catalyzes the hydrolysis of 4-fumarylacetoacetate into acetoacetate and fumarate. Mutations of the FAH gene are associated with hereditary tyrosinemia type I (HT1), resulting in reduced protein stability, misfolding, accelerated degradation and deficiency in functional proteins. Identifying E3 ligases, which are necessary for FAH protein stability and degradation, is essential. In this study, we demonstrated that the FAH protein level is elevated in liver cancer tissues compared to that in normal tissues. Further, we showed that the FAH protein undergoes 26S proteasomal degradation and its protein turnover is regulated by the anaphase-promoting complex/cyclosome-Cdh1 (APC/C)^Cdh1 E3 ubiquitin ligase complex. APC/C^Cdh1 acts as a negative stabilizer of FAH protein by promoting FAH polyubiquitination and decreases the half-life of FAH protein. Thus, we envision that Cdh1 might be a key factor in the maintenance of FAH protein level to regulate FAH-mediated physiological functions.