The Nitrile Bis-Thiol Bioconjugation Reaction.

Electron-poor aryl nitriles are promising reagents for bioconjugation due to their high electrophilicity and selectivity for reaction with thiols, albeit generally in a reversible manner. A transient species has previously been observed in such reactions, involving the addition of two thiols to the nitrile functional group, forming a tetrahedral amino dithioacetal (ADTA). In this work, the reaction of heteroaryl nitriles with bis-thiols is explored in an attempt to generate stable ADTAs, which could facilitate new bioconjugation protocols. By use of a 1,2-dithiol, or the incorporation of an electrophilic trap into the aryl nitrile design, the formation of stable products is achieved. The resultant "nitrile bis-thiol" (NBT) reaction is then explored in the context of protein modification, specifically to carry out antibody conjugation. By addition of these nitriles to the reduced disulfide bond of an antibody fragment, it is shown that, depending on the reagent design, cysteine-to-lysine transfer or disulfide bridged NBT products can be generated. Both represent site-selective conjugates and are shown to be stable when challenged with glutathione under physiological conditions and upon incubation in serum. Furthermore, the NBT reaction is tested in the more challenging context of a full antibody, and all four disulfide bonds are effectively modified by these new one-carbon bridging reagents. Overall, this reaction of heteroaryl-nitriles with bis-thiols is shown to be highly efficient and versatile, of tunable reversibility, and offers enticing prospects as a new addition to the toolbox of biocompatible "click"-type reactions.

Use of pyridazinediones for tuneable and reversible covalent cysteine modification applied to peptides, proteins and hydrogels.

Reversible cysteine modification has been found to be a useful tool for a plethora of applications such as selective enzymatic inhibition, activity-based protein profiling and/or cargo release from a protein or a material. However, only a limited number of reagents display reliable dynamic/reversible thiol modification and, in most cases, many of these reagents suffer from issues of stability, a lack of modularity and/or poor rate tunability. In this work, we demonstrate the potential of pyridazinediones as novel reversible and tuneable covalent cysteine modifiers. We show that the electrophilicity of pyridazinediones correlates to the rates of the Michael addition and retro-Michael deconjugation reactions, demonstrating that pyridazinediones provide an enticing platform for readily tuneable and reversible thiol addition/release. We explore the regioselectivity of the novel reaction and unveil the reason for the fundamental increased reactivity of aryl bearing pyridazinediones by using DFT calculations and corroborating findings with SCXRD. We also applied this fundamental discovery to making more rapid disulfide rebridging agents in related work. We finally provide the groundwork for potential applications in various areas with exemplification using readily functionalised "clickable" pyridazinediones on clinically relevant cysteine and disulfide conjugated proteins, as well as on a hydrogel material.

Room-Temperature One-Pot Synthesis of pH-Responsive Pyridine-Functionalized Carbon Surfaces.

Carbon surfaces (glassy carbon, graphite, and boron-doped diamond) were functionalized with layers composed of linked pyridinium and pyridine moieties using simple electrochemical reduction of trifluoroacetylpyridinium. The pyridinium species was generated in situ in solution by the reaction of trifluoroacetic anhydride and pyridine precursors and underwent electrochemical reduction at -1.97 V vs Fc/Fc+, as determined by cyclic voltammetry. The pyridine/pyridinium films were electrodeposited at room temperature, on a timescale of minutes, and were characterized using X-ray photoelectron spectroscopy. The as-prepared films have a net positive charge in aqueous solution at pH 9 and below due to the pyridinium content, confirmed by the electrochemical response of differently charged redox molecules at the functionalized surfaces. The positive charge can be enhanced further through protonation of the neutral pyridine component by controlling the solution pH. Moreover, the nitrogen-acetyl bond can be cleaved through base treatment to purposefully increase the neutral pyridine proportion of the film. This results in a surface that can be "switched" from functionally near neutral to a positive charge by treatment in basic and acidic solutions, respectively, through manipulation of the protonation state of the pyridine. The functionalization process demonstrated here is readily achievable at a fast timescale at room temperature and hence can allow for rapid screening of surface properties. Such functionalized surfaces present a means to test in isolation the specific catalytic performance of pyridinic groups toward key processes such as oxygen and CO2 reduction.

Regioselective Dehydration of Sugar Thioacetals under Mild Conditions.

Sugars are abundant in waste biomass, making them sustainable chiral building blocks for organic synthesis. The demand for chiral saturated heterocyclic rings for pharmaceutical applications is increasing as they provide well-defined three-dimensional frameworks that show increased metabolic resistance. A range of sugar thioacetals can be dehydrated selectively at C-2 under mild basic conditions, and the resulting ketene thioacetals can be applied to the production of useful chiral building blocks via further selective dehydration reactions.

Gold-Catalyzed Hydroamination of Propargylic Alcohols: Controlling Divergent Catalytic Reaction Pathways To Access 1,3-Amino Alcohols, 3-Hydroxyketones, or 3-Aminoketones.

A versatile approach to the valorization of propargylic alcohols is reported, enabling controlled access to three different products from the same starting materials. First, a general method for the hydroamination of propargylic alcohols with anilines is described using gold catalysis to give 3-hydroxyimines with complete regioselectivity. These 3-hydroxyimines can be reduced to give 1,3-amino alcohols with high syn selectivity. Alternatively, by using a catalytic quantity of aniline, 3-hydroxyketones can be obtained in high yield directly from propargylic alcohols. Further manipulation of the reaction conditions enables the selective formation of 3-aminoketones via a rearrangement/hydroamination pathway. The utility of the new chemistry was exemplified by the one-pot synthesis of a selection of N-arylpyrrolidines and N-arylpiperidines. A mechanism for the hydroamination has been proposed on the basis of experimental studies and density functional theory calculations.

Catalytic direct amidations in tert-butyl acetate using B(OCH2CF3)3.

Catalytic direct amidation reactions have been the focus of considerable recent research effort, due to the widespread use of amide formation processes in pharmaceutical synthesis. However, the vast majority of catalytic amidations are performed in non-polar solvents (aromatic hydrocarbons, ethers) which are typically undesirable from a sustainability perspective, and are often poor at solubilising polar carboxylic acid and amine substrates. As a consequence, most catalytic amidation protocols are unsuccessful when applied to polar and/or functionalised substrates of the kind commonly used in medicinal chemistry. In this paper we report a practical and useful catalytic direct amidation reaction using tert-butyl acetate as the reaction solvent. The use of an ester solvent offers improvements in terms of safety and sustainability, but also leads to an improved reaction scope with regard to polar substrates and less nucleophilic anilines, both of which are important components of amides used in medicinal chemistry. An amidation reaction was scaled up to 100 mmol and proceeded with excellent yield and efficiency, with a measured process mass intensity of 8.

Ring-Closing Synthesis of Dibenzothiophene Sulfonium Salts and Their Use as Leaving Groups for Aromatic 18F-Fluorination.

Herein, we report a novel intramolecular ring-closing reaction of biaryl thioethers that give access to highly functionalized dibenzothiophene sulfonium salts under mild conditions. The resulting precursors react regioselectively with [18F]fluoride to give [18F]fluoroarenes in predictable radiochemical yields. The strategy expands the available radiochemical space and provides superior labeling efficiency for clinically relevant PET tracers.

Silver-Free Palladium-Catalyzed C(sp3)-H Arylation of Saturated Bicyclic Amine Scaffolds.

Herein, we report a silver-free Pd(II)-catalyzed C(sp3)-H arylation of saturated bicyclic and tricyclic amine scaffolds. The reaction provides good yields using a range of aryl iodides and aryl bromides including functionalized examples bearing aldehydes, ketones, esters, free phenols, and heterocycles. The methodology has been applied to medicinally relevant scaffolds. Two of the intermediate palladium complexes in the catalytic cycle have been prepared and characterized, and a mechanism is proposed. Removal of the directing group proceeded with good yield under relatively mild conditions.

Conversion of Alcohols to Phosphorothiolates Using a Thioiminium Salt as Coupling Agent.

We report a method for the direct and rapid conversion of primary and secondary alcohols to the corresponding phosphorothiolates in yields ranging from 64% to 97%, using as a coupling agent the iminium salt prepared from N,N-dimethylthioformamide and Meerwein's salt. Selective reaction of primary alcohols in the presence of secondary alcohols is possible. The reaction of secondary alcohols proceeds stereospecifically with inversion of configuration.

Controlling electron emission from the photoactive yellow protein chromophore by substitution at the coumaric acid group.

Understanding how the interactions between a chromophore and its surrounding protein control the function of a photoactive protein remains a challenge. Here, we present the results of photoelectron spectroscopy measurements and quantum chemistry calculations aimed at investigating how substitution at the coumaryl tail of the photoactive yellow protein chromophore controls competing relaxation pathways following photoexcitation of isolated chromophores in the gas phase with ultraviolet light in the range 350-315 nm. The photoelectron spectra are dominated by electrons resulting from direct detachment and fast detachment from the 2(1)ππ* state but also have a low electron kinetic energy component arising from autodetachment from lower lying electronically excited states or thermionic emission from the electronic ground state. We find that substituting the hydrogen atom of the carboxylic acid group with a methyl group lowers the threshold for electron detachment but has very little effect on the competition between the different relaxation pathways, whereas substituting with a thioester group raises the threshold for electron detachment and appears to 'turn off' the competing electron emission processes from lower lying electronically excited states. This has potential implications in terms of tuning the light-induced electron donor properties of photoactive yellow protein.

The structure of tagetitoxin.

Based on detailed analysis of newly acquired NMR data, we show that the previously revised structure of tagetitoxin is incorrect. A new structure of tagetitoxin is proposed which is consistent with the NMR and MS data.

Multichannel Detection and Differentiation of Explosives with a Quantum Dot Array.

The sensing and differentiation of explosive molecules is key for both security and environmental monitoring. Single fluorophores are a widely used tool for explosives detection, but a fluorescent array is a more powerful tool for detecting and differentiating such molecules. By combining array elements into a single multichannel platform, faster results can be obtained from smaller amounts of sample. Here, five explosives are detected and differentiated using quantum dots as luminescent probes in a multichannel platform: 2,4-dinitrotoluene (DNT), 2,4,6-trinitrotoluene (TNT), tetryl (2,4,6-trinitrophenylmethylnitramine), cyclotrimethylenetrinitramine (RDX), and pentaerythritol tetranitrate (PETN). The sharp, variable emissions of the quantum dots, from a single excitation wavelength, make them ideal for such a system. Each color quantum dot is functionalized with a different surface receptor via a facile ligation process. These receptors undergo nonspecific interactions with the explosives, inducing variable fluorescence quenching of the quantum dots. Pattern analysis of the fluorescence quenching data allows for explosive detection and identification with limits-of-detection in the ppb range.

Irreversible endo-selective diels-alder reactions of substituted alkoxyfurans: a general synthesis of endo-cantharimides.

The [4+2] cycloaddition of 3-alkoxyfurans with N-substituted maleimides provides the first general route for preparing endo-cantharimides. Unlike the corresponding reaction with 3H furans, the reaction can tolerate a broad range of 2-substitued furans including alkyl, aromatic, and heteroaromatic groups. The cycloaddition products were converted into a range of cantharimide products with promising lead-like properties for medicinal chemistry programs. Furthermore, the electron-rich furans are shown to react with a variety of alternative dienophiles to generate 7-oxabicyclo[2.2.1]heptane derivatives under mild conditions. DFT calculations have been performed to rationalize the activation effect of the 3-alkoxy group on a furan Diels-Alder reaction.

Surfing π†clouds for noncovalent interactions: arenes versus alkenes.

A comparative study of molecular balances by NMR spectroscopy indicates that noncovalent functional-group interactions with an arene dominate over those with an alkene, and that a π-facial intramolecular hydrogen bond from a hydroxy group to an arene is favored by approximately 1.2 kJ mol(-1). The strongest interaction observed in this study was with the cyano group. Analysis of the series of groups CH2CH3, CH=CH2, C≡CH, and C≡N shows a correlation between conformational free-energy differences and the calculated charge on the C(α) atom of these substituents, which is indicative of the electrostatic nature of their π interactions. Changes in the free-energy differences of conformers show a linear dependence on the solvent hydrogen bond acceptor parameter ß.

Clinical performance of the BD Onclarity HPV assay using an adjudicated cohort of BD SurePath liquid-based cytology specimens.

OBJECTIVES: To compare the performance of the BD Onclarity HPV Assay (BD Diagnostics, Sparks, MD) in BD SurePath liquid-based cytology media with that of Hybrid Capture 2 (HC2, Qiagen, Germantown, MD) samples co-collected in specimen transport medium in an adjudicated patient cohort. METHODS: The performance of the BD Onclarity HPV Assay using BD SurePath media was compared with that of HC2 samples co-collected in specimen transport medium using 541 archived samples from a multicenter US clinical trial with histologically adjudicated cervical biopsy specimens. RESULTS: The sensitivity for cervical intraepithelial neoplasia (CIN) 2 positivity (n - 104) was 90.4% (95% confidence interval [CI], 83-95) and 93.3% (95% CI, 87-97) and specificity was 76.9% (95% CI, 73-81) and 77.8% (95% CI, 74-82) for the BD assay and HC2, respectively. Nine cases of CIN 2+ had results discordant with the high-risk HPV assay. All were found to have been correctly classified with the BD assay using a novel WAVE denaturing high-performance liquid chromatography double-stranded DNA sequencing method. CONCLUSIONS: The clinical performance of The BD Onclarity HPV Assay with respect to histology end points was similar to HC2. Moreover, discordant analysis revealed improved performance of the BD assay with respect to ability to provide extended genotyping information and lack of cross-reactivity with low-risk HPV types associated with cellular abnormalities. The relative risks for CIN 3 disease for HPV 31 and HPV 33/58 (combined) were comparable to that of HPV 18 in this population, suggesting that these genotypes may warrant monitoring in future studies.

Synthetic Studies Towards the Core Structure of Nakadomarin A by a Thioamide-Based Strategy.

The tricyclic BCD substructure of the marine natural product nakadomarin A has been synthesised. The strategy utilised a key carbon-carbon bond-forming reaction between a furan and an N-acyliminium ion derived from a secondary thiolactam. In addition, a novel three-component coupling reaction between a thioamide, an allylic bromide and an isocyanate, leading to the establishment of two new stereogenic centres, is reported. Two key steps in a projected total synthesis of nakadomarin A have been realised by using the unique chemistry of thioamides. Formation of the carbocyclic B ring can be effected by nucleophilic attack of a furan on a thiolactam-derived iminium ion, and the key quaternary centre can be established by a novel three-component coupling reaction.

Reversal of facial selectivity in a thia-Claisen rearrangement by incorporation of a vinylic bromine substituent.

Thia-Claisen rearrangements have been carried out using N-benzylpyrrolidine-2-thione and chiral allylic bromides derived from D-mannitol. Introduction of a bromine atom onto the double bond of the allylic bromide reverses the sense of diastereoselectivity in the [3,3]-sigmatropic rearrangement. Density functional theory calculations lead us to rationalise the observed selectivity in terms of a Cíeplak effect.

Synthesis of the reported structure of piperazirum using a nitro-Mannich reaction as the key stereochemical determining step.

Piperazirum, isolated from Arum palaestinum Boiss, was originally assigned as r-3,c-5-diisobutyl-c-6-isopropylpiperazin-2-one. The reported structure was synthesised diastereoselectively using a key nitro-Mannich reaction to set up the C5/C6 relative stereochemistry. The structure was unambiguously assigned by single crystal X-ray diffraction but the spectroscopic data did not match those reported for the natural product. The structure of the natural product must therefore be revised.

Long-term stability of human genomic and human papillomavirus DNA stored in BD SurePath and Hologic PreservCyt liquid-based cytology media.

We evaluated the effect of storage at 2 to 8°C on the stability of human genomic and human papillomavirus (HPV) DNA stored in BD SurePath and Hologic PreservCyt liquid-based cytology media. DNA retained the ability to be extracted and PCR amplified for more than 2.5 years in both medium types. Prior inability to detect DNA in archived specimens may have been due to failure of the extraction method to isolate DNA from fixed cells.

Inter- and intramolecular reactions of 1-deoxy-1-thio-1,6-anhydrosugars with α-diazoesters: synthesis of the tagetitoxin core by photochemical ylide rearrangement.

The one-carbon ring expansion of 1-deoxy-1-thio-1,6-anhydrosugars, mediated by metal carbenes and proceeding through the intermediacy of sulfur ylides, has been proposed as a route for the synthesis of the tagetitoxin skeleton. Intermolecular reactions of such thioanhydrosugars with diazoesters afford a range of undesired products derived from the initially formed ylide, whereas use of an intramolecular process generates stable ylides which can be converted to the tagetitoxin skeleton by photo-Stevens rearrangement. Computational studies using density functional theory indicate that the photochemical rearrangement likely proceeds through a homolysis-recombination pathway.