Conjugation at the oligonucleotide level based on isoxazole phosphoramidites generated by click chemistry

The versatility of the isoxazole generating nitrile oxide–alkyne Huisgen cycloaddition for provision of chemically modified oligonucleotides has been extended; in a novel approach isoxazole conjugated oligodeoxyribonucleotides have been constructed by phosphoramidite chemistry of isoxazole derivatives previously generated by nitrile oxide–alkyne click chemistry. The conjugation involves manual solid phase synthesis at room temperature in aqueous ethanol and proceeds in high yield

Isoxazole linked oligonucleotide conjugates by on resin and previously clicked nitrile oxide alkyne cycloadditions

Bioconjugation protocols in environments free from residual copper or other catalytic components are important for therapeutic and biomedical applications as well as in living systems. In this communication we discuss the versatility of the catalyst free, isoxazole generating nitrile oxide alkyne Huisgen cycloaddition for provision of chemically modified oligonucleotide conjugates. Two distinct approaches will be demonstrated. In the first we discuss on resin cylcoaddition between in situ generated nitrile oxide

Virtual screening, identification and in vitro validation of small molecule GDP-mannose dehydrogenase inhibitors †

Upon undergoing mucoid conversion within the lungs of cystic fibrosis patients, the pathogenic bacterium Pseudomonas aeruginosa synthesises copious quantities of the virulence factor and exopolysaccharide alginate. The enzyme guanosine diphosphate mannose dehydrogenase (GMD) catalyses the rate-limiting step and irreversible formation of the alginate sugar nucleotide building block, guanosine diphosphate mannuronic acid. Since there is no corresponding enzyme in humans, strategies that could prevent its mechanism of action could open a pathway for new and selective inhibitors to disrupt bacterial alginate production. Using virtual screening, a library of 1447 compounds within the Known Drug Space parameters were evaluated against the GMD active site using the Glide, FRED and GOLD algorithms. Compound hit evaluation with recombinant GMD refined the panel of 40 potential hits to 6 compounds which reduced NADH production in a time-dependent manner; of which, an usnic acid derivative demonstrated inhibition six-fold stronger than a previously established sugar nucleotide inhibitor, with an IC50 value of 17 μM. Further analysis by covalent docking and mass spectrometry confirm a single site of GMD alkylation

Structural basis of catalysis in the bacterial monoterpene synthases linalool synthase and 1,8-cineole synthase

Terpenoids form the largest and stereochemically most diverse class of natural products, and there is considerable interest in producing these by biocatalysis with whole cells or purified enzymes, and by metabolic engineering. The monoterpenes are an important class of terpenes and are industrially important as flavors and fragrances. We report here structures for the recently discovered Streptomyces clavuligerus monoterpene synthases linalool synthase (bLinS) and 1,8-cineole synthase (bCinS), and we show that these are active biocatalysts for monoterpene production using biocatalysis and metabolic engineering platforms. In metabolically engineered monoterpene-producing E. coli strains, use of bLinS leads to 300-fold higher linalool production compared with the corresponding plant monoterpene synthase. With bCinS, 1,8-cineole is produced with 96% purity compared to 67% from plant species. Structures of bLinS and bCinS, and their complexes with fluorinated substrate analogues, show that these bacterial monoterpene synthases are similar to previously characterized sesquiterpene synthases. Molecular dynamics simulations suggest that these monoterpene synthases do not undergo large-scale conformational changes during the reaction cycle, making them attractive targets for structured-based protein engineering to expand the catalytic scope of these enzymes toward alternative monoterpene scaffolds. Comparison of the bLinS and bCinS structures indicates how their active sites steer reactive carbocation intermediates to the desired acyclic linalool (bLinS) or bicyclic 1,8-cineole (bCinS) products. The work reported here provides the analysis of structures for this important class of monoterpene synthase. This should now guide exploitation of the bacterial enzymes as gateway biocatalysts for the production of other monoterpenes and monoterpenoids

Characterisation of the pro-inflammatory cytokine signature in severe COVID-19

Clinical outcomes from infection with SARS-CoV-2, the cause of the COVID-19 pandemic, are remarkably variable ranging from asymptomatic infection to severe pneumonia and death. One of the key drivers of this variability is differing trajectories in the immune response to SARS-CoV-2 infection. Many studies have noted markedly elevated cytokine levels in severe COVID-19, although results vary by cohort, cytokine studied and sensitivity of assay used. We assessed the immune response in acute COVID-19 by measuring 20 inflammatory markers in 118 unvaccinated patients with acute COVID-19 (median age: 70, IQR: 58-79 years; 48.3% female) recruited during the first year of the pandemic and 44 SARS-CoV-2 naïve healthy controls. Acute COVID-19 was associated with marked elevations in nearly all pro-inflammatory markers, whilst eleven markers (namely IL-1β, IL-2, IL-6, IL-10, IL-18, IL-23, IL-33, TNF-α, IP-10, G-CSF and YKL-40) were associated with disease severity. We observed significant correlations between nearly all markers elevated in those infected with SARS-CoV-2 consistent with widespread immune dysregulation. Principal component analysis highlighted a pro-inflammatory cytokine signature (with strongest contributions from IL-1β, IL-2, IL-6, IL-10, IL-33, G-CSF, TNF-α and IP-10) which was independently associated with severe COVID-19 (aOR: 1.40, 1.11-1.76, p=0.005), invasive mechanical ventilation (aOR: 1.61, 1.19-2.20, p=0.001) and mortality (aOR 1.57, 1.06-2.32, p = 0.02). Our findings demonstrate elevated cytokines and widespread immune dysregulation in severe COVID-19, adding further evidence for the role of a pro-inflammatory cytokine signature in severe and critical COVID-19

Conjugation at the oligonucleotide level based on isoxazole phosphoramidites generated by click chemistry

The versatility of the isoxazole generating nitrile oxide–alkyne Huisgen cycloaddition for provision of chemically modified oligonucleotides has been extended; in a novel approach isoxazole conjugated oligodeoxyribonucleotides have been constructed by phosphoramidite chemistry of isoxazole derivatives previously generated by nitrile oxide–alkyne click chemistry. The conjugation involves manual solid phase synthesis at room temperature in aqueous ethanol and proceeds in high yield

How to foster PPI with those excluded from public involvement itself

Background While there is encouragement of public involvement in the development of health interventions and healthcare issues, PPI seeks to go a step further with this involvement “with recognition of the need to engage citizens not only in providing feedback on health-care delivery or interventions, but in processes whereby decisions are made...” (Baxter, Clowes, Muir et al., 2016). But what happens to those citizens who find themselves socially excluded from their healthcare needs? One such group is our homeless population. This presentation, drawing upon previous research on health seeking behaviours of homeless individuals (Ní Cheallaigh, Cullivan, Sears, et al., 2017), will challenge PPI to go further in how it seeks to understand involvement. We argue that a way of achieving this is through applying experience- centred design (ECD), which gives “...people the chance to have a richer life, to include people who otherwise feel excluded, and to ensure that everybody has a chance to have their say. Especially those who often feel voiceless” (McCarthy and Wright, 2010). Methods Examples of ECD methodologies will be presented that naturally align with fostering PPI. The methods presented will attempt to equip researchers with a way to support a fluid dialogical research process, ensuring PPI across all health research contexts and not solely those of the socially included. These methods will respond to experience either in the form of digital health interventions or more service based responses. Findings & Discussion What we hope this presentation achieves is an entry point into a dialogue around how we ensure PPI, as well as responsive design of healthcare, within the homeless research context. While the presentation takes a positional stance, it seeks to provoke thought and reflection within the PPI community upon how we can achieve PPI with groups that are excluded from public involvement itself