Crystallization of VHL-based PROTAC-induced ternary complexes.

X-ray crystal structures of PROTAC-induced ternary complexes provide invaluable insights into the critical species underpinning PROTAC mode of action, explain protein degradation selectivity profiles, and can guide rational degrader design. Nevertheless, crystallization of the ternary complexes formed by PROTACs remains an important bottleneck in employing this method. This is mainly due to the potential flexibility and heterogeneity that is inherent to a non-native protein-protein complex mediated by a small molecule, which together can hamper crystallization of the desired species. To overcome this limitation, selecting PROTAC compounds that enable the formation of stable, high-affinity and preferably cooperative ternary complexes in stoichiometric amount is, in our experience, critical to the success of co-crystallization studies. In this chapter, examples of stable PROTAC-mediated ternary complexes are illustrated. Learnings from biophysical & biochemical data are used as a guideline in achieving the highest "crystallizability" of ternary complexes. A case study of VHL-based SMARCA2 PROTAC degrader ternary complex crystallization is described. The procedure includes over-expression and purification of the E3 ligase and target protein, forming (and sometimes isolating) the ternary complex, and crystallizing it. The protocols can be applied for other combinations of E3 ligase, PROTAC and target protein.

Systems-Wide Dissection of Organic Acid Assimilation in Pseudomonas aeruginosa Reveals a Novel Path To Underground Metabolism.

The human pathogen Pseudomonas aeruginosa (Pa) is one of the most frequent and severe causes of nosocomial infection. This organism is also a major cause of airway infections in people with cystic fibrosis (CF). Pa is known to have a remarkable metabolic plasticity, allowing it to thrive under diverse environmental conditions and ecological niches; yet, little is known about the central metabolic pathways that sustain its growth during infection or precisely how these pathways operate. In this work, we used a combination of 'omics approaches (transcriptomics, proteomics, metabolomics, and 13C-fluxomics) and reverse genetics to provide systems-level insight into how the infection-relevant organic acids succinate and propionate are metabolized by Pa. Moreover, through structural and kinetic analysis of the 2-methylcitrate synthase (2-MCS; PrpC) and its paralogue citrate (CIT) synthase (GltA), we show how these two crucial enzymatic steps are interconnected in Pa organic acid assimilation. We found that Pa can rapidly adapt to the loss of GltA function by acquiring mutations in a transcriptional repressor, which then derepresses prpC expression. Our findings provide a clear example of how "underground metabolism," facilitated by enzyme substrate promiscuity, "rewires" Pa metabolism, allowing it to overcome the loss of a crucial enzyme. This pathogen-specific knowledge is critical for the advancement of a model-driven framework to target bacterial central metabolism. IMPORTANCE Pseudomonas aeruginosa is an opportunistic human pathogen that, due to its unrivalled resistance to antibiotics, ubiquity in the built environment, and aggressiveness in infection scenarios, has acquired the somewhat dubious accolade of being designated a "critical priority pathogen" by the WHO. In this work, we uncover the pathways and mechanisms used by P. aeruginosa to grow on a substrate that is abundant at many infection sites: propionate. We found that if the organism is prevented from metabolizing propionate, the substrate turns from being a convenient nutrient source into a potent poison, preventing bacterial growth. We further show that one of the enzymes involved in these reactions, 2-methylcitrate synthase (PrpC), is promiscuous and can moonlight for another essential enzyme in the cell (citrate synthase). Indeed, mutations that abolish citrate synthase activity (which would normally prevent the cell from growing) can be readily overcome if the cell acquires additional mutations that increase the expression of PrpC. This is a nice example of the evolutionary utility of so-called "underground metabolism."

A green extraction design for enhancing flavonoid compounds from Ixora javanica flowers using a deep eutectic solvent.

In this study, an environmentally friendly extraction method for flavonoid compound from Ixora javanica, as a new raw material candidate for herbal medicine and cosmetics, was developed. The objectives of the present work were to provide recommendations for the optimal extraction conditions and to investigate the effects of any extraction parameters on flavonoid yields from the I. javanica flower. The extraction process was performed using deep eutectic solvent (DES) (choline chloride and propylene glycol at molar ratio of 1 : 1) and the ultrasound-assisted extraction method. Both single-factor and response surface analyses using three-level and three-factor Box Behnken designs were conducted to obtain the optimum flavonoid concentrations. The results showed that the optimum extraction conditions for total flavonoids featured an extraction time of 40 min, 25% water content in DES and a solid-to-liquid ratio of 1 : 25 g ml-1. An extract obtained under optimum extraction conditions showed higher total flavonoid yields than an ethanolic extract which was used for comparison. Scanning electron microscope images demonstrated that both of the solvents also showed different effects on the outer surface of the I. javanica flower during the extraction process. In summary, our work succeeded in determining the optimum conditions for total flavonoids in the I. javanica flower using a green extraction method.

Air gun wound: bihemispheric penetrating brain injury in a paediatric patient.

Air guns are classified as low-velocity missiles and they usually considered safe and harmless. Despite that fact, air guns still can make serious or life-threatening injuries. Most of air gun injuries occur in paediatric population. A 2-year-old boy was shot in the forehead withan air gun accidentally. Skull radiography and non-contrast CT scan of the head were performed and showed penetrating bihemispheric brain injury from the left frontal to right occipital lobes at the level of the lateral ventricle with a metal-density foreign body at the right occipital. A projectile was successfully extracted via craniotomy, without complications. Air guns have the potential to cause fatal, life-threatening injury especially in children. Imaging is crucial for the evaluation of wound ballistics. Understanding about the mechanism of projectiles and wound ballistics is very helpful for radiologists to conceptualize these injuries when interpreting these cases. The role of radiology in ballistic wound cases is critical and important, both for clinical and forensic settings.

Loving the poison: the methylcitrate cycle and bacterial pathogenesis.

Propionate is an abundant catabolite in nature and represents a rich potential source of carbon for the organisms that can utilize it. However, propionate and propionate-derived catabolites are also toxic to cells, so propionate catabolism can alternatively be viewed as a detoxification mechanism. In this review, we summarize recent progress made in understanding how prokaryotes catabolize propionic acid, how these pathways are regulated and how they might be exploited to develop novel antibacterial interventions.