Design principles for cyclin K molecular glue degraders.

Molecular glue degraders are an effective therapeutic modality, but their design principles are not well understood. Recently, several unexpectedly diverse compounds were reported to deplete cyclin K by linking CDK12-cyclin K to the DDB1-CUL4-RBX1 E3 ligase. Here, to investigate how chemically dissimilar small molecules trigger cyclin K degradation, we evaluated 91 candidate degraders in structural, biophysical and cellular studies and reveal all compounds acquire glue activity via simultaneous CDK12 binding and engagement of DDB1 interfacial residues, in particular Arg928. While we identify multiple published kinase inhibitors as cryptic degraders, we also show that these glues do not require pronounced inhibitory properties for activity and that the relative degree of CDK12 inhibition versus cyclin K degradation is tuneable. We further demonstrate cyclin K degraders have transcriptional signatures distinct from CDK12 inhibitors, thereby offering unique therapeutic opportunities. The systematic structure-activity relationship analysis presented herein provides a conceptual framework for rational molecular glue design.

The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K.

Molecular glue compounds induce protein-protein interactions that, in the context of a ubiquitin ligase, lead to protein degradation1. Unlike traditional enzyme inhibitors, these molecular glue degraders act substoichiometrically to catalyse the rapid depletion of previously inaccessible targets2. They are clinically effective and highly sought-after, but have thus far only been discovered serendipitously. Here, through systematically mining databases for correlations between the cytotoxicity of 4,518 clinical and preclinical small molecules and the expression levels of E3 ligase components across hundreds of human cancer cell lines3-5, we identify CR8-a cyclin-dependent kinase (CDK) inhibitor6-as a compound that acts as a molecular glue degrader. The CDK-bound form of CR8 has a solvent-exposed pyridyl moiety that induces the formation of a complex between CDK12-cyclin K and the CUL4 adaptor protein DDB1, bypassing the requirement for a substrate receptor and presenting cyclin K for ubiquitination and degradation. Our studies demonstrate that chemical alteration of surface-exposed moieties can confer gain-of-function glue properties to an inhibitor, and we propose this as a broader strategy through which target-binding molecules could be converted into molecular glues.

Antibacterial Activity of Nitric Oxide-Releasing Hyperbranched Polyamidoamines.

Hyperbranched polyamidoamines (h-PAMAM) were prepared using a one-pot reaction to have similar molecular weight to third generation PAMAM (G3-PAMAM) dendrimers, and then functionalized with N-diazeniumdiolate nitric oxide (NO) donors. A wide range of NO storage capacities (∼1-2.50 µmol mg-1) and NO-release kinetics (t1/2 ∼30-80 min) were achieved by changing the extent of propylene oxide (PO) modification. The therapeutic potential of these materials was evaluated by studying their antibacterial activities and toxicity against common dental pathogens and human gingival fibroblast cells, respectively. Our results indicate that the combination of NO release and PO modification is necessary to yield h-PAMAM materials with efficient bactericidal action without eliciting unwarranted cytotoxicity. Of importance, NO-releasing PO-modified h-PAMAM polymers exhibited comparable biological properties (i.e., antibacterial action and cytotoxicity) to defect-free G3-PAMAM dendrimers, but at a substantially lower synthetic burden.

Nitric Oxide-Releasing Alginates.

Low and high molecular weight alginate biopolymers were chemically modified to store and release potentially therapeutic levels of nitric oxide (NO). Carbodiimide chemistry was first used to modify carboxylic acid functional groups with a series of small molecule alkyl amines. The resulting secondary amines were subsequently converted to N-diazeniumdiolate NO donors via reaction with NO gas under basic conditions. NO donor-modified alginates stored between 0.4-0.6 µmol NO·mg-1. In aqueous solution, the NO-release kinetics were diverse (0.3-13 h half-lives), dependent on the precursor amine structure. The liberated NO showed bactericidal activity against Pseudomonas aeruginosa and Staphylococcus aureus with pathogen eradication efficiency dependent on both molecular weight and NO-release kinetics. The combination of lower molecular weight (∼5 kDa) alginates with moderate NO-release durations (half-life of ∼4 h) resulted in enhanced killing of both planktonic and biofilm-based bacteria. Toxicity against human respiratory epithelial (A549) cells proved negligible at NO-releasing alginate concentrations required to achieve a 5-log reduction in viability in the biofilm eradication assay.

Effect of Phosphorylated Chitosan on Dentin Erosion: An in vitro Study.

The aim of this study was to evaluate the antierosive effect of phosphorylated chitosan in dentin. Bovine dentin specimens were randomly distributed into the following groups: (1) no treatment (NoTx/negative control), (2) phosphate-buffered saline solution (PBS), (3) AmF/NaF/SnCl2 (positive control), (4) 0.5% chitosan solution (Chi), (5) 0.5% neutral phosphorylated (NP)-Chi, and (6) 0.5% alkaline phosphorylated (AP)-Chi. The specimens were submitted to de-remineralization treatment cycles for 5 days: 0.5% citric acid (2 min), remineralizing solution (30 min), and surface treatment according to assigned groups (2 min, 6×/day). The loss of dentin surface was measured by profilometry. Hardness and modulus of elasticity were measured using a nanoindenter equipped with a Berkovich diamond tip. The dentin surface was analyzed by scanning electron microscopy (SEM). The largest loss of dentin was observed in the No Tx and PBS groups (approx. 25 µm). The group treated with AmF/NaF/SnCl2 showed less loss of dentin (67% reduction vs. NoTx and PBS), followed by the groups treated with NP-Chi and AP-Chi (33% reduction), and Chi (18% reduction). Nanohardness and modulus of elasticity were similar in the NoTx and PBS groups, with a small increase in stiffness in all other groups. SEM revealed that the experimental solution of AP-Chi had a favorable effect on maintaining the integrity of collagen fibrils. AmF/NaF/SnCl2 showed a preserved mineralized collagen surface. Further studies are warranted to explore this nontoxic phosphorylated chitosan polymer as an effective agent in the prevention and treatment of dental erosion.

Encapsulation of N-Diazeniumdiolates within Liposomes for Enhanced Nitric Oxide Donor Stability and Delivery.

The rapid decomposition of nitric oxide (NO) donors in aqueous environments remains a limitation for applications requiring extended NO release. Herein, we report the synthesis of dipalmitoylphosphatidylcholine-based liposomes capable of extended NO release using low molecular weight NO donors and a reverse-phase evaporation technique. The encapsulation of the NO donors within the liposomes enabled both prolonged NO release and enhanced storage compared to free NO donors alone. The NO-releasing liposomes also demonstrated enhanced efficacy against human pancreatic cancer cells. These NO-release vehicles represent attractive anticancer therapeutics due to their potential to store the majority of their NO payload until reaching cancerous tissue at which time the lower pH inherent to such environments will trigger an avalanche of NO.

A nitric oxide-releasing heparin conjugate for delivery of a combined antiplatelet/anticoagulant agent.

Heparin is a widely used anticoagulant due to its ability to inhibit key components in the coagulation cascade such as Factor Xa and thrombin (Factor IIa). Its potential to preferentially bind to antithrombin (ATIII) results in a conformational change and activation that leads to the prevention of fibrin formation from fibrinogen and ultimately obstructs a hemostatic plug from forming. Nitric oxide (NO) exhibits potent antiplatelet activity attributed to its capacity to increase the amount of cyclic guanosine monophosphate (cGMP) within platelets, which decreases the Ca(2+) concentration required for platelet activation. Currently there is no single agent that combines the functions of both antiplatelet and anticoagulant (anti-Xa and anti-IIa) activities to effectively block both the extrinsic and the intrinsic coagulation pathways. The research reported herein demonstrates the ability to combine the physiological capabilities of both heparin and NO into one functional compound via use of a spermine derivative of heparin, thus enabling formation of a novel diazeniumdiolate (NONOate). The heparin-spermine NONOate has a half-life of 85 min at 25 °C (pH 7.4). The heparin backbone of the conjugate maintains its anticoagulant activity as demonstrated via an anti-Xa assay, providing an anticoagulant conversion of 3.6 µg/mL of the heparin-spermine-NONO conjugate being equivalent to 2.5 µg/mL (0.50 IU/mL) of underivatized heparin in terms of anti-Xa activity. Using standard platelet aggregometry, it is shown that the functionality of the NO release portion of the heparin conjugate prevents (nearly 100%) platelet aggregation in the presence of adenosine diphosphate (ADP, platelet agonist).

Mode of nitric oxide delivery affects antibacterial action.

Nitric oxide (NO) is a broad-spectrum antibacterial agent, making it an attractive alternative to traditional antibiotics for treating infections. To date, a direct comparison of the antibacterial activity of gaseous NO (gNO) versus water-soluble NO-releasing biopolymers has not been reported. In this study, the bactericidal action of NO-releasing chitosan oligosaccharides was compared to gNO treatment against cystic fibrosis-relevant Gram-positive and Gram-negative bacteria. A NO exposure chamber was constructed to enable the dosing of bacteria with gNO at concentrations up to 800 ppm under both aerobic and anaerobic conditions. Bacteria viability, solution properties (i.e., pH, NO concentration), and toxicity to mammalian cells were monitored to ensure a thorough understanding of bactericidal action and reproducibility for each delivery method. The NO-releasing chitosan oligosaccharides required significantly lower NO doses relative to gNO therapy to elicit antibacterial action against Pseudomonas aeruginosa and Staphylococcus aureus under both aerobic and anaerobic conditions. Reduced NO doses required for bacteria eradication using water-soluble NO-releasing chitosan were attributed to the release of NO in solution, removing the need to transfer from gas to liquid phase and the associated long diffusion distances of gNO treatment.

Anticancer potency of nitric oxide-releasing liposomes.

In this study, fast and slow nitric oxide (NO)-releasing liposomes (half-lives of 2.5 and >72 h, respectively) were prepared by encapsulation of N-propyl-1,3-propanediamine/NO (PAPA/NO) and diethylenetriamine/NO (DETA/NO), respectively, via reverse phase evaporation. The anticancer activity of the otherwise equivalent fast and slow NO-releasing systems was evaluated against several distinct pancreatic, colorectal, and breast cancer cell lines. The anticancer assays (via cytotoxicity) over 72 h revealed that the slower NO-releasing liposomes consistently required lower NO payloads (LD50 <3 µg/mL) relative to the fast NO-release system (LD50 >6 µg/mL) to elicit cytotoxicity. The mechanism of intracellular NO build-up in cancer cells was studied using confocal fluorescence microscopy and flow cytometry, the results of which indicated that a more gradual NO accumulation was characteristic of the slow NO-release system. Protein expression via Western blot analysis revealed that slower NO release resulted in more necrotic/apoptotic cells, while faster release reduced the number of mitotic cells to a greater extent. Overall, these studies demonstrate the potential of NO-releasing liposomes for anticancer therapy and highlight the significance of release kinetics (and NO payloads) required to induce cell death.

Controlled release of nitric oxide from liposomes.

We report the ability to readily tune NO release from N-diazeniumdiolate-encapsulated liposomal structures by altering the NO donor molecule structure and/or phospholipid composition (independently or in combination). While encapsulating more stable NO donors expectedly enhanced the NO release (up to 48 h) from the liposomes, the phospholipid headgroup surface area proved equally useful in controlling NO-release kinetics by influencing the water uptake and concomitant N-diazeniumdiolate NO donor breakdown (to NO). The potential therapeutic utility of the NO-releasing liposomes was further assessed in biological/proteinaceous fluids. The NO-release kinetics were similar in buffer and serum.

Selective monophosphorylation of chitosan via phosphorus oxychloride.

Chitosan was selectively monophosphorylated via reaction with phosphorus oxychloride (POCl3) to enhance water solubility while avoiding polyphosphate formation. The use of POCl3 resulted in negligible product degradation (i.e., breakdown of O-glycosidic bonds) even after a 3 d reaction period (<5% weight loss). X-ray photoelectron spectroscopy (XPS) characterization of the POCl3-phosphorylated chitosan (P-chitosan) revealed a phosphorus to nitrogen (P/N) atomic ratio of 0.30. Phosphorus-31 nuclear magnetic resonance (31P NMR) spectroscopy verified the monophosphorylation of chitosan's primary and secondary alcohols, and primary amines. The calcium chelation efficiency for the phosphorylated product approached 0.05 mg Ca2+ per mg of P-chitosan as measured by inductively coupled plasma-optical emission spectrometry (ICP-OES), indicating improved chelation over native chitosan. This selective monophosphorylation approach proved useful for modifying other biopolymers, including cellulose and alginate.