Quantum Chemical Characterization of Rotamerism in Thio-Michael Additions for Targeted Covalent Inhibitors.

Myotonic dystrophy type I (DM1) is the most common form of adult muscular dystrophy and is a severe condition with no treatment currently available. Recently, small-molecule ligands have been developed as targeted covalent inhibitors that have some selectivity for and covalently inhibit cyclin-dependent kinase 12 (CDK12). CDK12 is involved in the transcription of elongated RNA sections that results in the DM1 condition.

The importance of mA topology in chicken embryo mRNA: a precise mapping of mA at the conserved chicken β-actin zipcode.

-methyladenosine (mA) in mRNA regulates almost every stage in the mRNA life cycle, and the development of methodologies for the high-throughput detection of methylated sites in mRNA using mA-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIPSeq) or mA individual-nucleotide-resolution cross-linking and immunoprecipitation (miCLIP) have revolutionized the mA research field. Both of these methods are based on immunoprecipitation of fragmented mRNA. However, it is well documented that antibodies often have nonspecific activities, thus verification of identified mA sites using an antibody-independent method would be highly desirable.

Emergent SARS-CoV-2 variants: comparative replication dynamics and high sensitivity to thapsigargin.

The struggle to control the COVID-19 pandemic is made challenging by the emergence of virulent SARS-CoV-2 variants. To gain insight into their replication dynamics, emergent Alpha (A), Beta (B) and Delta (D) SARS-CoV-2 variants were assessed for their infection performance in single variant- and co-infections. The effectiveness of thapsigargin (TG), a recently discovered broad-spectrum antiviral, against these variants was also examined.

Diazophosphonates: Effective Surrogates for Diazoalkanes in Pyrazole Synthesis.

Diazophosphonates, readily prepared from α-ketophosphonates by oxidation of the corresponding hydrazones in batch or in flow, are useful partners in 1,3-dipolar cycloaddition reactions to alkynes to give N-H pyrazoles, including the first intramolecular examples of such a process. The phosphoryl group imbues a number of desirable properties into the diazo 1,3-dipole. The electron-withdrawing nature of the phosphoryl stabilizes the diazo compound making it easier to handle, whilst the ability of the phosphoryl group to migrate readily in a [1,5]-sigmatropic rearrangement enables its transfer from C to N to aromatize the initial cycloadduct, and hence its facile removal from the final pyrazole product.

Unusually high α-proton acidity of prolyl residues in cyclic peptides.

The acidity of the α-proton in peptides has an essential role in numerous biochemical reactions and underpins their stereochemical integrity, which is critical to their biological function. We report a detailed kinetic and computational study of the acidity of the α-proton in two cyclic peptide systems: diketopiperazine (DKP) and triketopiperazine (TKP). The kinetic acidity (protofugality) of the α-protons were determined though hydrogen deuterium exchange studies in aqueous solutions.

Mapping the interaction between eukaryotic initiation factor 4A (eIF4A) and the inhibitor hippuristanol using carbene footprinting and mass spectrometry.

Protein-ligand interactions are central to protein activity and cell functionality. Improved knowledge of these relationships greatly benefits our understanding of key biological processes and aids in rational drug design towards the treatment of clinically relevant diseases. Carbene footprinting is a recently developed mass spectrometry-based chemical labelling technique that provides valuable information relating to protein-ligand interactions, such as the mapping of binding sites and associated conformational change.

Thapsigargin Is a Broad-Spectrum Inhibitor of Major Human Respiratory Viruses: Coronavirus, Respiratory Syncytial Virus and Influenza A Virus.

The long-term control strategy of SARS-CoV-2 and other major respiratory viruses needs to include antivirals to treat acute infections, in addition to the judicious use of effective vaccines. Whilst COVID-19 vaccines are being rolled out for mass vaccination, the modest number of antivirals in use or development for any disease bears testament to the challenges of antiviral development. We recently showed that non-cytotoxic levels of thapsigargin (TG), an inhibitor of the sarcoplasmic/endoplasmic reticulum (ER) Ca ATPase pump, induces a potent host innate immune antiviral response that blocks influenza A virus replication.

CDK12 inhibition reduces abnormalities in cells from patients with myotonic dystrophy and in a mouse model.

Myotonic dystrophy type 1 (DM1) is an RNA-based disease with no current treatment. It is caused by a transcribed CTG repeat expansion within the 3' untranslated region of the dystrophia myotonica protein kinase () gene. Mutant repeat expansion transcripts remain in the nuclei of patients' cells, forming distinct microscopically detectable foci that contribute substantially to the pathophysiology of the condition.

The Impact of Macrocycle Conformation on the Taxadiene-Forming Carbocation Cascade: Insight Gained from Sobralene, a Recently Discovered Verticillene Isomer.

DFT calculations on the carbocation intermediates that connect the biosynthetic pathways leading to the sand fly pheromone sobralene and taxadiene have been made. Establishment of the conformation of the macrocyclic carbocation intermediate required to produce the ()-C8,C9 alkene bond in sobralene has identified new conformations of the verticillyl carbocation intermediates on the taxadiene biosynthetic pathway. These "sobralene-like" carbocation conformations provide an exothermic pathway to taxadiene and are validated by comparison to closely related structures (X-ray and NMR).

Atrial fibrillation in elderly patients with implantable loop recorders for unexplained syncope.

Background: An implantable loop recorder (ILR) assists in the diagnosis of unexplained syncope and atrial fibrillation (AF). Both become prevalent with age. Limited data exist describing the incidence of AF as the diagnostic rhythm underlying syncope in the elderly.

Implantable loop recorders in the real world: a study of two Canadian centers.

Purpose: Implantable loop recorders (ILRs) are increasingly being used for ambulatory electrocardiography. We sought to evaluate ILR indications, diagnostic yield, ILR-guided interventions, and complications in two Canadian centers.

Methods: This was a retrospective study using electronic medical records to identify ILR implants at Queen's University and the University of Manitoba.

Total synthesis of (-)-aritasone via the ultra-high pressure hetero-Diels-Alder dimerisation of (-)-pinocarvone.

This paper describes a total synthesis of the terpene-derived natural product aritasone via the hetero-Diels-Alder [4 + 2] cyclodimerisation of pinocarvove, which represents the proposed biosyntheic route. The hetero-Diels-Alder dimerisation of pinocarvone did not proceed under standard conditions, and ultra-high pressure (19.9 kbar) was required.

C-H Insertion as a Key Step to Spiro-Oxetanes, Scaffolds for Drug Discovery.

A new route to spiro-oxetanes, potential scaffolds for drug discovery, is described. The route is based on the selective 1,4-C-H insertion reactions of metallocarbenes, generated from simple carbonyl precursors in flow or batch mode, to give spiro-β-lactones that are rapidly converted into spiro-oxetanes. The three-dimensional and lead-like properties of spiro-oxetanes are illustrated by the conversion of the 1-oxa-7-azaspiro[3,5]nonane scaffold into a range of functionalized derivatives.

Extracellular matrix gene expression profiling using microfluidics for colorectal carcinoma stratification.

In cancer, biomarkers have many potential applications including generation of a differential diagnosis, prediction of response to treatment, and monitoring disease progression. Many molecular biomarkers have been put forward for different diseases but most of them do not possess the required specificity and sensitivity. A biomarker with a high sensitivity has a low specificity and vice versa.

Accessing low-oxidation state taxanes: is taxadiene-4(5)-epoxide on the taxol biosynthetic pathway?

We have shown for the first time that taxadiene () can be epoxidised in a regio- and diastereoselective manner to provide taxadiene-4(5)-epoxide () as a single diastereoisomer, and that this epoxide can be rearranged to give taxa-4(20),11(12)-dien-5α-ol (). Furthermore, the epoxide rearranges under acidic conditions to give taxa-4(20),11(12)-dien-5α-ol (), the known bridged ether OCT () and the new oxacyclotaxane (OCT2) . Contrary to previous speculation, taxadiene-4(5)-epoxide () is susceptible to rearrangement when exposed to an iron porphyrin, and these observations justify consideration of epoxide as a chemically competent intermediate on the taxol biosynthetic pathway.

Microfluidic droplet-based PCR instrumentation for high-throughput gene expression profiling and biomarker discovery.

PCR is a common and often indispensable technique used in medical and biological research labs for a variety of applications. Real-time quantitative PCR (RT-qPCR) has become a definitive technique for quantitating differences in gene expression levels between samples. Yet, in spite of this importance, reliable methods to quantitate nucleic acid amounts in a higher throughput remain elusive.

Synthesis of triazole-linked morpholino oligonucleotides via Cu(I) catalysed cycloaddition.

Triazole-linked morpholino ((TL)MO) oligonucleic acids were synthesised using the Cu(I) catalysed (3 + 2) azide-alkyne cycloaddition (CuAAC) reaction. The modified DNA analogues were incorporated into 13-mer sequences via solid phase synthesis. UV melting experiments showed that the (TL)MO modification gives higher Tm values than the corresponding (TL)DNA modification.

Stereoselective Synthesis of Functionalized Pyrrolidines by the Diverted N-H Insertion Reaction of Metallocarbenes with β-Aminoketone Derivatives.

A highly stereoselective route to functionalized pyrrolidines by the metal-catalyzed diverted N-H insertion of a range of diazocarbonyl compounds with β-aminoketone derivatives is described. A number of catalysts (rhodium(II) carboxylate dimers, copper(I) triflate, and an iron(III) porphyrin) are shown to promote the process under mild conditions to give a wide range of highly substituted proline derivatives. The reaction starts as a metallocarbene N-H insertion but is diverted by an intermolecular aldol reaction.

Stereoselective Synthesis of Highly Substituted Tetrahydrofurans through Diverted Carbene O-H Insertion Reaction.

Copper- or rhodium-catalyzed reactions of diazocarbonyl compounds with β-hydroxyketones give highly substituted tetrahydrofurans with excellent diastereoselectivity. Under mild conditions, the single-step process starts as a carbene O-H insertion reaction, but is diverted by an intramolecular aldol reaction.

Alkyl halide-free heteroatom alkylation and epoxidation facilitated by a recyclable polymer-supported oxidant for the in-flow preparation of diazo compounds.

Highly reactive metal carbenes, generated from simple ketones via diazo compounds, including diazo-amides and -phosphonates, using a recyclable reagent in-flow, are transient but versatile electrophiles for heteroatom alkylation reactions and for epoxide formation. The method produces no organic waste, with the only by-products being water, KI and nitrogen, without the attendant hazards of isolation of intermediate diazo compounds.

Bridgehead enolate or bridgehead organolithium? DFT calculations provide insights into a difficult bridgehead substitution reaction in the synthesis of the polycyclic polyprenylated acylphloroglucinol (PPAP) nemorosone.

A computational study (B3LYP), of the metallation of a bridged ketone, an important step in the synthesis of a polycyclic polyprenylated acylphloroglucinol (PPAP), nemorosone, shows three energetically distinct structural possibilities for the lithiated intermediate. These findings, along with observations of the reactivity of the intermediates in bridgehead substitutions, suggest that different intermediates may be formed depending upon the type of process used for lithiation.

High-content screening identifies small molecules that remove nuclear foci, affect MBNL distribution and CELF1 protein levels via a PKC-independent pathway in myotonic dystrophy cell lines.

Myotonic dystrophy (DM) is a multi-system neuromuscular disorder for which there is no treatment. We have developed a medium throughput phenotypic assay, based on the identification of nuclear foci in DM patient cell lines using in situ hybridization and high-content imaging to screen for potentially useful therapeutic compounds. A series of further assays based on molecular features of DM have also been employed.

Phosphoramidate synthesis via copper-catalysed aerobic oxidative coupling of amines and H-phosphonates.

The copper-catalysed oxidative coupling of amines and H-phosphonates to produce phosphoramidates has been achieved using CuI as the catalyst and O2 (present in air) as the sole oxidant.

Nucleophilic fluorination of β-ketoester derivatives with HBF4.

Treating readily available α-diazo-β-ketoesters with HBF(4) results in nucleophilic fluorination by the usually inert and stable tetrafluoroborate anion. The resulting α-fluoro-β-ketoesters are highly versatile synthetic intermediates, for example in the preparation of fluoro-heterocycles, as illustrated by the direct formation of fluoro-pyrimidines, -pyrazoles and -coumarins in a single step.