Protac: redirigiendo los sistemas de degradación de proteínas a nuevos sustratos / Protac: redirecting protein degradation systems to new substrates

Tradicionalmente el diseño de fármacos se ha basado en el diseño de moléculas pequeñas hasta la aparición de terapias basadas en ácidos nucleicos, ya sea por la modificación de ciertos genes o por impedir que las proteínas se transcriban de forma efectiva. Empleando estas nuevas aproximaciones se han podido modificar dianas que hasta el momento se consideraban inmodificables o al menos no lo podían ser por moléculas pequeñas. Sin embargo, estas nuevas aproximaciones no están carentes de limitaciones como la baja biodisponibilidad debido a su limitada estabilidad y dificultad para poder atravesar las barreras celulares. Además, en muchas ocasiones las modificaciones que generan son irreversibles con el consiguiente riesgo de padecer efectos adversos de forma crónica. Como alternativa, han surgido con fuerza una serie de compuestos quiméricos heterobifuncionales denominados PROTACs (Protein Targeting Chimeras). Estos PROTACs son capaces de mantener en la proximidad de la ligasa E3 a una proteína de interés, marcándola con ubiquitina y finalmente, promoviendo su degradación mediada por el proteasoma. Esta aproximación permite la generación de diferentes estructuras de PROTAC por diseño racional o basado en la estructura y, además, permite las modificaciones estructurales necesarias para mejorar su perfil de estabilidad y farmacocinético manteniendo su actividad. Esta revisión pretende dar una visión general de qué son los PROTACs, qué ligasas E3 se emplean por el momento, factores relevantes a la hora de desarrollar un PROTAC y otras aproximaciones similares que no emplean el proteasoma como ruta de degradación.(AU)

The small molecules development has dominated the design of new drugs until the rise of nucleic acid-based therapies, either by modifying a gene or by preventing it from being effectively transcribed. Taking advantage of this new approaches, the pharmacological intervention in therapeutic targets that are considered unmodifiable up to now with small molecules were allowed. However, these new approaches are not devoid of defects such as low bioavailability due to their stability and pharmacokinetic problems, in addition to being irreversible DNA modifications in many cases, with the subsequent risk of suffering chronic adverse effects. Alternatively, a series of chimeric heterobifunctional compounds, called PROTACs (Protein Targeting Chimeras), have emerged with force in recent years. These PROTACs are able to bring E3 ligases closer with proteins of interest in space to label them with ubiquitin. Finally, it was degraded by the proteasome. This approach enables the generation of different PROTACs structures by rational design and, also, allows the chemical structure modification to improve their stability and pharmacokinetic profile keeping their activity. This review aims to give a comprehensive approach of what PROTACs are, what E3 ligases recruit, relevant factors in PROTAC development, and other approaches similar to this but that use non-proteasomal degradation pathways.(AU)

Determination of Effective Albumin in Patients With Decompensated Cirrhosis: Clinical and Prognostic Implications.

BACKGROUND AND AIMS: Circulating albumin in cirrhosis can be dysfunctional because of accumulating structural damages, leading to the concept of effective albumin concentration (eAlb), referring to the albumin portion presenting structural and functional integrity. We aimed to estimate eAlb in patients with decompensated cirrhosis and analyze its relationships with albumin function and clinical outcomes as compared to total albumin concentration (tAlb). APPROACH AND RESULTS: We evaluated 319 patients with cirrhosis hospitalized for acute decompensation (AD) with and without acute-on-chronic liver failure (ACLF) and 18 age- and sex-comparable outpatients with compensated cirrhosis. tAlb was quantified by standard assay, whereas eAlb was estimated combining liquid chromatography/electrospray ionization/mass spectrometry and standard methods. Albumin binding and detoxification efficiency were evaluated by electron paramagnetic resonance analysis. Circulating albumin in patients with decompensated cirrhosis displayed multiple structural abnormalities, with reversible oxidation and glycation being the most frequent. As a result, eAlb progressively declined with the worsening of cirrhosis and was superior to tAlb in stratifying patients between compensated cirrhosis, AD, and ACLF, as well as patients with and without complications. Moreover, eAlb, but not tAlb, was closely associated with binding capacities in ACLF. Finally, eAlb at admission predicted the occurrence of ACLF within 30 days and mortality at 90 days better than tAlb. CONCLUSIONS: This large, observational study provides the evidence in patients with decompensated cirrhosis that eAlb can be quantified and differentiated from tAlb routinely measured in clinical practice. As compared to tAlb, eAlb is more closely associated with disease severity and albumin dysfunction and carries a greater prognostic power. These results prompt future research assessing eAlb as a biomarker for predicting prognosis and treatment response.

Blood group antigen A on von Willebrand factor is more protective against ADAMTS13 cleavage than antigens B and H.

BACKGROUND: ADAMTS13 specifically cleaves the peptide bond between Y1605 and M1606 within the VWF-A2 domain. OBJECTIVE: The VWF contains ABO(H) blood group antigens, which may influence the susceptibility of VWF to ADAMTS13. METHODS: Using a unique monoclonal antibody recognizing the Y1605 residue, we have developed a sandwich ELISA to analyze the generation of a VWF-DP by ADAMTS13 quantitatively. RESULTS: Production of VWF-DP after exposure to four different degrees of high shear stress was validated in comparison to the reduction in high-molecular-weight multimers using VWF multimer analysis. In analysis of plasma from 259 healthy individuals, plasma levels of VWF antigen (VWF:Ag) were significantly lower in blood group O than in the other groups and were significantly correlated with plasma VWF-DP levels. The ratio between VWF-DP and VWF:Ag was significantly higher in blood group O than in blood groups A and AB. The ratio in blood group B was also significantly higher than those in A and AB, but did not differ from blood group O. Finally, to examine whether ABO(H) blood group antigens contributed to VWF cleavage, 82 plasma samples were exposed to high shear stress using a cone-plate shear stress inducer. The difference in the VWF-DP/VWF:Ag ratio before and after high shear stress in blood group O was significantly greater than those in groups A and AB. CONCLUSION: These results indicate that blood group antigen A on VWF was more protective against ADAMTS13 cleavage than antigens B and H.

Dietary Early Glycation Products Promote the Growth of Prostate Tumors More than Advanced Glycation End-Products through Modulation of Macrophage Polarization.

SCOPE: Glycation products are ubiquitous in food at high concentrations in the Western diet. The well-controlled glycation resulting in the production of early glycation products (EGPs) has been proposed as a strategy to improve the physicochemical properties of food proteins. However, the health effects of EGPs are unknown. It has been shown that the Western diet (glycation prone) is associated with a higher mortality in prostate cancer (PCa) patients than the prudent diet; therefore, the role of EGPs in prostate tumorigenesis is investigated. METHODS AND RESULTS: C57BL/6 male mice are treated with the vehicle (water), non-reacted samples, EGPs, and advanced glycation end-products (AGEs) by gavage. EGPs (600 mg kg-1 body weight per day) promoted the growth of subcutaneously transplanted TRAMP-C2 PCa cells the most among these groups. Significantly, increases in the circulation monocytes and tumor-associated M2 macrophages are observed in EGP-treated mice, and the M2/M1 ratio is also increased in the EGP group when compared to that of water and AGEs. In the human PCa cell and macrophage co-cultures, EGPs increase the spheroid size, and importantly, macrophages are also polarized toward M2. CONCLUSIONS: EGPs induce the proliferation of PCa cells either directly or by assisting PCa cells to polarize macrophages toward M2.

Haptoglobin degradation product as a novel serum biomarker for hematopoietic stem cell transplant-associated thrombotic microangiopathy.

BACKGROUND: Hematopoietic stem cell transplant (HSCT)-associated thrombotic microangiopathy (TA-TMA) is a well-known complication of HSCT and carries high risk of morbidity and mortality. A lack of consistent non-invasive diagnostic criteria can delay diagnosis and lead to irreversible organ damage. METHODS: Serum samples of 100 patients that underwent HSCT at Cincinnati Children's Hospital were serially collected. Unbiased proteomic profiling by SELDI-TOF-MS was performed on serum from TA-TMA patients at baseline (pre-HSCT), 2 weeks before TMA diagnosis (pre-TMA), and at clinical TMA diagnosis. Two proteins with mass to charge ratios of 12-13 kDa were consistently elevated at the 2 week pre-TMA time point by SELDI-TOF, compared to control samples. Potential peptides were isolated and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) on the Linear Trap Quadropole (LTQ). A MASCOT search identified haptoglobin fragments in the 12-17-kDa range. Western blot was performed to validate haptoglobin fragments as a potential biomarker. RESULTS: Western blot of TA-TMA patients showed haptoglobin fragments at 12, 14, and 17 kDa that varied between baseline, pre-TMA, and TMA time points for each patient. By densitometric analysis, the 17-kDa fragment in the pre-TMA samples differed significantly from TMA diagnosis (p < 0.0001). There was no significant difference in the concentrations of the 12-kDa and 14-kDa fragments. CONCLUSION: The 17-kDa haptoglobin degradation product may represent a novel early serum biomarker for TA-TMA that could potentially allow for earlier diagnosis and intervention.

A reference-based protein degradation assay without global translation inhibitors.

Although it is widely appreciated that the use of global translation inhibitors, such as cycloheximide, in protein degradation assays may result in artefacts, these inhibitors continue to be employed, owing to the absence of robust alternatives. We describe here the promoter reference technique (PRT), an assay for protein degradation with two advantageous features: a reference protein and a gene-specific inhibition of translation. In PRT assays, one measures, during a chase, the ratio of a test protein to a long-lived reference protein, a dihydrofolate reductase (DHFR). The test protein and DHFR are coexpressed, in the yeast Saccharomyces cerevisiae, on a low-copy plasmid from two identical P TDH3 promoters containing additional, previously developed DNA elements. Once transcribed, these elements form 5'-RNA aptamers that bind to the added tetracycline, which represses translation of aptamer-containing mRNAs. The selectivity of repression avoids a global inhibition of translation. This selectivity is particularly important if a component of a relevant proteolytic pathway (e.g. a specific ubiquitin ligase) is itself short-lived. We applied PRT to the Pro/N-end rule pathway, whose substrates include the short-lived Mdh2 malate dehydrogenase. Mdh2 is targeted for degradation by the Gid4 subunit of the GID ubiquitin ligase. Gid4 is also a metabolically unstable protein. Through analyses of short-lived Mdh2 as a target of short-lived Gid4, we illustrate the advantages of PRT over degradation assays that lack a reference and/or involve cycloheximide. In sum, PRT avoids the use of global translation inhibitors during a chase and also provides a "built-in" reference protein.

The novel mitochondrial matrix protease Ste23 is required for efficient presequence degradation and processing.

Approximately 70% of mitochondrial precursor proteins are imported from the cytosol via N-terminal presequences, which are cleaved upon exposure to the mitochondrial processing protease MPP in the matrix. Cleaved presequence peptides then need to be efficiently degraded, and impairment of this clearance step, for example, by amyloid ß peptides, causes feedback inhibition of MPP, leading ultimately to accumulation of immature precursor proteins within mitochondria. Degradation of mitochondrial peptides is performed by Cym1 in yeast and its homologue, PreP, in humans. Here we identify the novel mitochondrial matrix protease Ste23 in yeast, a homologue of human insulin-degrading enzyme, which is required for efficient peptide degradation. Ste23 and Cym1 tightly cooperate to ensure the correct functioning of the essential presequence processing machinery.

Improvement of succinate production by release of end-product inhibition in Corynebacterium glutamicum.

Succinate is a renewable-based platform chemical that may be used to produce a wide range of chemicals including 1,4-butanediol, tetrahydrofurane, and γ-butyrolactone. However, industrial fermentation of organic acids is often subject to end-product inhibition, which significantly retards cell growth and limits metabolic activities and final productivity. In this study, we report the development of metabolically engineered Corynebacterium glutamicum for high production of succinate by release of end-product inhibition coupled with an increase of key metabolic flux. It was found that the rates of glucose consumption and succinate production were significantly reduced by extracellular succinate in an engineered strain, S003. To understand the mechanism underlying the inhibition by succinate, comparative transcriptome analysis was performed. Among the downregulated genes, overexpression of the NCgl0275 gene was found to suppress the inhibition of glucose consumption and succinate production, resulting in a 37.7% increase in succinate production up to 55.4g/L in fed-batch fermentation. Further improvement was achieved by increasing the metabolic flux from PEP to OAA. The final engineered strain was able to produce 152.2g/L succinate, the highest production reported to date, with a yield of 1.1g/g glucose under anaerobic condition. These results suggest that the release of end-product inhibition coupled with an increase in key metabolic flux is a promising strategy for enhancing production of succinate.

C-terminally mutated tubby protein accumulates in aggresomes.

The tubby protein (Tub), a putative transcription factor, plays important roles in the maintenance and function of neuronal cells. A splicing defect-causing mutation in the 3'-end of the tubby gene, which is predicted to disrupt the carboxy-terminal region of the Tub protein, causes maturity-onset obesity, blindness, and deafness in mice. Although this pathological Tub mutation leads to a loss of function, the precise mechanism has not yet been investigated. Here, we found that the mutant Tub proteins were mostly localized to puncta found in the perinuclear region and that the C-terminus was important for its solubility. Immunocytochemical analysis revealed that puncta of mutant Tub co-localized with the aggresome. Moreover, whereas wild-type Tub was translocated to the nucleus by extracellular signaling, the mutant forms failed to undergo such translocation. Taken together, our results suggest that the malfunctions of the Tub mutant are caused by its misfolding and subsequent localization to aggresomes. [BMB Reports 2017; 50(1): 37-42].

Inhibition of the metabolic degradation of filtered albumin is a major determinant of albuminuria.

Inhibition of the degradation of filtered albumin has been proposed as a widespread, benign form of albuminuria. There have however been recent reports that radiolabeled albumin fragments in urine are not exclusively generated by the kidney and that in albuminuric states albumin fragment excretion is not inhibited. In order to resolve this controversy we have examined the fate of various radiolabeled low molecular weight protein degradation products (LMWDPs) introduced into the circulation in rats. The influence of puromycin aminonucleoside nephrosis on the processing and excretion of LMWDPs is also examined. The status and destinies of radiolabeled LMWDPs in the circulation are complex. A major finding is that LMWDPs are rapidly eliminated from the circulation (>97% in 2 h) but only small quantities (<4%) are excreted in urine. Small (<4%) but significant amounts of LMWDPs may have prolonged elimination (>24 h) due to binding to high molecular weight components in the circulation. If LMWDPs of albumin seen in the urine are produced by extra renal degradation it would require the degradation to far exceed the known catabolic rate of albumin. Alternatively, if an estimate of the role of extra renal degradation is made from the limit of detection of LMWDPs in plasma, then extra renal degradation would only contribute <1% of the total excretion of LMWDPs of albumin. We confirm that the degradation process for albumin is specifically associated with filtered albumin and this is inhibited in albuminuric states. This inhibition is also the primary determinant of the massive change in intact albuminuria in nephrotic states.

Oxidative stress and neurodegenerative diseases: a neurotrophic approach.

Neurotrophins are important neurotrophic factors involved in the survival, differentiation and function of a wide variety of neuron populations. A common feature for most neurotrophins is that they are synthesized as precursor proteins (pro-neurotrophins) that upon being processed by proteolysis render the mature active form responsible for most of their trophic functions. However, some of the pro-neurotrophin form of these proteins, such as the precursor form of NGF (pro-NGF), have been shown to induce opposite effects and trigger apoptosis on neurons through the p75NTR receptor. This suggests that the balance between the levels of proneurotrophin and neurotrophin must be tightly controlled. In this context, it has been shown that in conditions of oxidative stress due for instance to aging or the development of some neurodegenerative disease, neurotrophins are oxidatively modified at least by advanced glycation/lipoxidation end products (AGE/ALEs) which makes pro-NGF refractary to be processed. The lack of maturation and the imbalance in favor of the precursor form may change the pattern of active signaling pathways towards cell death, thus exacerbating the deleterious alterations, for instance during the development of neurodegenerative diseases. Besides that, AGE/ALEs also induce the processing of the pro-NGF receptor p75NTR by α- secretase which is followed by the processing by γ -secretase and the release of the intracellular domain of p75NTR (p75NTRICD). Once cleaved, p75NTRICD recruits two intracellular interactors, NRIF and TRAF6, which allows NRIF phosphorylation by JNK. The phosphorylated form of NRIF then translocates to the nucleus and induces the expression of pro-apoptotic proteins. In this chapter we will summarize the mechanisms by which ROS- induce protein modifications, which proteins are susceptible to be modified, how these modifications affect function and signaling and, finally, how they can be related to neurodegenerative diseases.

Oxygen restriction as challenge test reveals early high-fat-diet-induced changes in glucose and lipid metabolism.

Challenge tests stress homeostasis and may reveal deviations in health that remain masked under unchallenged conditions. Ideally, challenge tests are non-invasive and applicable in an early phase of an animal experiment. Oxygen restriction (OxR; based on ambient, mild normobaric hypoxia) is a non-invasive challenge test that measures the flexibility to adapt metabolism. Metabolic inflexibility is one of the hallmarks of the metabolic syndrome. To test whether OxR can be used to reveal early diet-induced health effects, we exposed mice to a low-fat (LF) or high-fat (HF) diet for only 5 days. The response to OxR was assessed by calorimetric measurements, followed by analysis of gene expression in liver and epididymal white adipose tissue (eWAT) and serum markers for e.g. protein glycation and oxidation. Although HF feeding increased body weight, HF and LF mice did not differ in indirect calorimetric values under normoxic conditions and in a fasting state. Exposure to OxR; however, increased oxygen consumption and lipid oxidation in HF mice versus LF mice. Furthermore, OxR induced gluconeogenesis and an antioxidant response in the liver of HF mice, whereas it induced de novo lipogenesis and an antioxidant response in eWAT of LF mice, indicating that HF and LF mice differed in their adaptation to OxR. OxR also increased serum markers of protein glycation and oxidation in HF mice, whereas these changes were absent in LF mice. Cumulatively, OxR is a promising new method to test food products on potential beneficial effects for human health.

Nitroxides prevent protein glycoxidation in vitro.

Seven nitroxides of different structures were studied for the ability to prevent glycoxidation of bovine serum albumin incubated with three monosaccharides (glucose, fructose, and ribose). Glycoxidation was estimated by fluorimetric parameters of protein modifications (formation of advanced glycation end products [AGEs], dityrosine, N'-formylkynurenine, and kynurenine) and enzyme-linked immunosorbent assay for AGEs. From among the nitroxides tested, (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO), 4-carboxy-TEMPO, and 4-hydroxy-TEMPO offered significant protection against glycoxidation induced by glucose and fructose, while 3-carbamoyl-PROXYL was not protective, enhancing glycoxidation. Lower protection was observed for glycoxidation induced by ribose where only 3-carbamoyl-PROXYL and 4-amino-TEMPO showed some protection. Loss of electron spin resonance signal of the nitroxides was observed during glycoxidation indicating occurrence of free radical reactions in this process. These results suggest for the first time that nitroxides may be promising compounds for preventing glycoxidation.

[The content of substances of low and medium molecular mass in biologic liquids in patients with erysipelas].

The endogenic intoxication is a metabolic response to any aggressive factor. The concentration of substances of low and medium molecular mass biologic liquids of organism w and medium molecular mass is a common indicator of intoxication syndrome. The study analyzed the role of uptake of substances of low and medium molecular mass in biologic liquids of organism in pathogenesis of erysipelas depending on period, form and ration of disease. The sampling included 76 patients with erysipelas aged from 27 to 62 years being in infection hospital for treatment. The concentration of substances of low and medium molecular mass was detected using M. Ya. Malakhova technique (1996). It is established that under erysipelas in organism occurs uptake of toxic substances in blood and gradual increase of concentration of substances of low and medium molecular mass in blood plasma and erythrocytes paralleled by corresponding changes of their concentration in urine. The altitude of increase of concentration level of substances of low and medium molecular mass and their reapportion between biologic mediums of organisms depends on period, form, ratio of course and degree of severity of pathologic process.

Salivary type I collagen degradation end-products and related matrix metalloproteinases in periodontitis.

AIM: Type I collagen degradation end-products and related matrix metalloproteinases (MMPs) were examined aiming to detect potential markers of periodontitis in saliva, with high sensitivity and specificity. MATERIALS AND METHODS: The salivary concentrations of MMP-8, MMP-9 and MMP-13, tartrate-resistant acid phosphatase serum type 5b, C-terminal cross-linked telopeptide of type I collagen (CTx), N-terminal cross-linked telopeptide of type I collagen (NTx) and cross-linked carboxyterminal telopeptide of type I collagen were analysed in 230 subjects. Oral health examination included panoramic radiography. RESULTS: The concentrations of MMP-8, MMP-9 and MMP-13 in saliva were higher in subjects with generalized periodontitis than in controls. Of the tested salivary markers, MMP-8 was the only marker capable of differentiating subjects with severe alveolar bone loss from those with slight bone loss (p < 0.001). The association between the salivary MMP-8 levels and periodontitis remained significant after the adjustment with age, gender and smoking. In addition, significant correlations were found between the tested markers and periodontal parameters. CONCLUSION: Enzymes and end-products of type I collagen degradation have different associations with each other and with periodontal status that may reflect their roles in the cascade leading to alveolar bone loss. MMP-8 is a strong biomarker candidate for detecting alveolar bone destruction.