SARS-CoV-2 Mpro responds to oxidation by forming disulfide and NOS/SONOS bonds.

The main protease (Mpro) of SARS-CoV-2 is critical for viral function and a key drug target. Mpro is only active when reduced; turnover ceases upon oxidation but is restored by re-reduction. This suggests the system has evolved to survive periods in an oxidative environment, but the mechanism of this protection has not been confirmed. Here, we report a crystal structure of oxidized Mpro showing a disulfide bond between the active site cysteine, C145, and a distal cysteine, C117. Previous work proposed this disulfide provides the mechanism of protection from irreversible oxidation. Mpro forms an obligate homodimer, and the C117-C145 structure shows disruption of interactions bridging the dimer interface, implying a correlation between oxidation and dimerization. We confirm dimer stability is weakened in solution upon oxidation. Finally, we observe the protein's crystallization behavior is linked to its redox state. Oxidized Mpro spontaneously forms a distinct, more loosely packed lattice. Seeding with crystals of this lattice yields a structure with an oxidation pattern incorporating one cysteine-lysine-cysteine (SONOS) and two lysine-cysteine (NOS) bridges. These structures further our understanding of the oxidative regulation of Mpro and the crystallization conditions necessary to study this structurally.

Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors.

Emerging RNA viruses, including SARS-CoV-2, continue to be a major threat. Cell entry of SARS-CoV-2 particles via the endosomal pathway involves cysteine cathepsins. Due to ubiquitous expression, cathepsin L (CatL) is considered a promising drug target in the context of different viral and lysosome-related diseases. We characterized the anti-SARS-CoV-2 activity of a set of carbonyl- and succinyl epoxide-based inhibitors, which were previously identified as inhibitors of cathepsins or related cysteine proteases. Calpain inhibitor XII, MG-101, and CatL inhibitor IV possess antiviral activity in the very low nanomolar EC50 range in Vero E6 cells and inhibit CatL in the picomolar Ki range. We show a relevant off-target effect of CatL inhibition by the coronavirus main protease α-ketoamide inhibitor 13b. Crystal structures of CatL in complex with 14 compounds at resolutions better than 2 Å present a solid basis for structure-guided understanding and optimization of CatL inhibitors toward protease drug development.

Improving hand hygiene of young children with a digital intervention: a cluster-randomised controlled field trial.

Contagious diseases that affect young children place a great burden on them and their families. Proper hand hygiene is an important measure to reduce the disease burden, however, its implementation in day care centres is challenging. This paper introduces a digital intervention to support independent and good handwashing among young children. The intervention leverages animated instructions triggered by water and soap use, together with a symbolic reward shown to children on a screen during and immediately after handwashing. We tested the intervention in a pre-registered, cluster-randomised controlled field trial in 4 day care centres in Finland and Germany with 162 children over 42 days. The intervention increased soaping time, used as a proxy for handwashing quality, by 5.30 s (+ 62%, p < 0.001). The effect occurs immediately at the onset of the intervention and is maintained throughout the intervention phase.

Assignment of individual structures from intermetalloid nickel gallium cluster ensembles.

Poorly selective mixed-metal cluster synthesis and separation yield reaction solutions of inseparable intermetalloid cluster mixtures, which are often discarded. High-resolution mass spectrometry, however, can provide precise compositional data of such product mixtures. Structure assignments can be achieved by advanced computational screening and consideration of the complete structural space. Here, we experimentally verify structure and composition of a whole cluster ensemble by combining a set of spectroscopic techniques. Our study case are the very similar nickel/gallium clusters of M12, M13 and M14 core composition Ni6+xGa6+y (x + y ≤ 2). The rationalization of structure, bonding and reactivity is built upon the organometallic superatom cluster [Ni6Ga6](Cp*)6 = [Ga6](NiCp*)6 (1; Cp* = C5Me5). The structural conclusions are validated by reactivity tests using carbon monoxide, which selectively binds to Ni sites, whereas (triisopropylsilyl)acetylene selectively binds to Ga sites.

SiteMine: Large-scale binding site similarity searching in protein structure databases.

Drug discovery and design challenges, such as drug repurposing, analyzing protein-ligand and protein-protein complexes, ligand promiscuity studies, or function prediction, can be addressed by protein binding site similarity analysis. Although numerous tools exist, they all have individual strengths and drawbacks with regard to run time, provision of structure superpositions, and applicability to diverse application domains. Here, we introduce SiteMine, an all-in-one database-driven, alignment-providing binding site similarity search tool to tackle the most pressing challenges of binding site comparison. The performance of SiteMine is evaluated on the ProSPECCTs benchmark, showing a promising performance on most of the data sets. The method performs convincingly regarding all quality criteria for reliable binding site comparison, offering a novel state-of-the-art approach for structure-based molecular design based on binding site comparisons. In a SiteMine showcase, we discuss the high structural similarity between cathepsin L and calpain 1 binding sites and give an outlook on the impact of this finding on structure-based drug design. SiteMine is available at https://uhh.de/naomi.

Time-resolved crystallography captures light-driven DNA repair.

Photolyase is an enzyme that uses light to catalyze DNA repair. To capture the reaction intermediates involved in the enzyme's catalytic cycle, we conducted a time-resolved crystallography experiment. We found that photolyase traps the excited state of the active cofactor, flavin adenine dinucleotide (FAD), in a highly bent geometry. This excited state performs electron transfer to damaged DNA, inducing repair. We show that the repair reaction, which involves the lysis of two covalent bonds, occurs through a single-bond intermediate. The transformation of the substrate into product crowds the active site and disrupts hydrogen bonds with the enzyme, resulting in stepwise product release, with the 3' thymine ejected first, followed by the 5' base.

Exceptional ultrafast nonlinear optical response of functionalized silicon nanosheets.

The present work reports on the ultrafast saturable absorption (SA), optical limiting (OL), and the nonlinear refractive response of hydride-terminated silicon nanosheets (SiNS-H) differently functionalized with styrene and tert-butyl methacrylate (tBuMA), namely, SiNS-styrene and SiNS-tBuMA, using 50 fs, 400 nm and 70 fs, 800 nm laser pulses. SiNS-styrene and SiNS-tBuMA exhibit dramatically enhanced nonlinear optical (NLO) responses compared to SiNS-H, with their absorptive nonlinearity strongly dependent on the laser excitation wavelength. More specifically, the studied functionalized SiNSs reveal strong SA behavior under 400 nm laser excitation, with NLO absorption coefficients, saturable intensities, and modulation depths comparable to various two-dimensional (2D) materials, known to exhibit strong SA, such as graphene, black phosphorous (BP), some transition metal dichalcogenides (TMDs), and some MXenes. On the other hand, under 800 nm laser excitation, SiNS-styrene and SiNS-tBuMA show highly efficient OL performance with OL onset values of about 0.0045 and 0.0065 J cm-2, respectively, which are significantly lower than those of other 2D nanostructures. In addition, it is shown that both SiNS samples have great potential in already existing Si-based optoelectronic devices for optical-switching applications since they exhibit very strong NLO refraction comparable to that of bulk Si. The results of the present work demonstrate that the chemical functionalization of SiNSs provides a highly efficient strategy for the preparation of 2D Si-based nanostructures with enhanced NLO response in view of several optoelectronic and photonic applications, such as OL, SA, and all-optical switching.

Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections.

Several drug screening campaigns identified Calpeptin as a drug candidate against SARS-CoV-2. Initially reported to target the viral main protease (Mpro), its moderate activity in Mpro inhibition assays hints at a second target. Indeed, we show that Calpeptin is an extremely potent cysteine cathepsin inhibitor, a finding additionally supported by X-ray crystallography. Cell infection assays proved Calpeptin's efficacy against SARS-CoV-2. Treatment of SARS-CoV-2-infected Golden Syrian hamsters with sulfonated Calpeptin at a dose of 1 mg/kg body weight reduces the viral load in the trachea. Despite a higher risk of side effects, an intrinsic advantage in targeting host proteins is their mutational stability in contrast to highly mutable viral targets. Here we show that the inhibition of cathepsins, a protein family of the host organism, by calpeptin is a promising approach for the treatment of SARS-CoV-2 and potentially other viral infections.

Versatile procedure for the correction of non-isochromatism in XPEEM spectroscopic imaging.

Non-isochromatism in X-ray PhotoEmission Electron Microscopy (XPEEM) may result in unwanted artifacts especially when working with large field of views. The lack of isochromatism of XPEEM images may result from multiple factors, for instance the energy dispersion of the X-rays on the sample or the effect of one or more dispersive elements in the electron optics of the microscope, or the combination of both. In practice, the photon energy or the electron kinetic energy may vary across the image, complicating image interpretation and analysis. The effect becomes severe when imaging at low magnification upon irradiation with high energy photons. Such imaging demands for a large X-ray illuminating spot size usually achieved by opening the exit slit of the X-ray monochromator while reducing the monochromaticity of the irradiating light. However, we show that the effect is linear and can be fully removed. A versatile correction procedure is presented which leads to true monochromatic photoelectron images at improved signal-to-noise ratio. XPEEM data recorded at the nanospectroscopy beamline of the Elettra synchrotron radiation facility illustrate the working principle of the procedure. Also, reciprocal space XPEEM data such as angle-resolved photoelectron spectroscopy (ARPES) momentum plots suffer from linear energy dispersion artifacts which can be corrected in a similar way. Representative data acquired from graphene synthesized on copper by chemical vapor deposition prove the benefits of the correction procedure.

Hand hygiene of kindergarten children-Understanding the effect of live feedback on handwashing behaviour, self-efficacy, and motivation of young children: Protocol for a multi-arm cluster randomized controlled trial.

Early implementation of interventions at a young age fosters behaviour changes and helps to adopt behaviours that promote health. Digital technologies may help to promote the hand hygiene behaviour of children. However, there is a lack of digital feedback interventions focusing on the hand hygiene behaviour of preschool children in childhood education and care settings. This study protocol aims to describe a study that evaluates the effectiveness of a gamified live feedback intervention and explores underlying behavioural theories in achieving better hand hygiene behaviour of preschool children in early childhood education and care settings. This study will be a four-arm cluster randomized controlled trial with three phases and a twelve-month follow-up by country stratification. The sample size is 106 children of which one cluster will have a minimum number of 40 children. During the baseline phase, all groups will have automated monitoring systems installed. In the intervention phase, the control group will have no screen activity. The intervention groups will have feedback displays during the handwashing activity. Intervention A will receive instructions, and intervention B and C groups will receive instructions and a reward. In the post-intervention phase, all the groups will have no screen activity except intervention C which will receive instructions from the screen but no reward. The outcome measures will be hand hygiene behaviour, self-efficacy, and intrinsic motivation. Outcome measures will be collected at baseline, intervention, and post-intervention phases and a 12-month follow-up. The data will be analysed with quantitative and qualitative methods. The findings of the planned study will provide whether this gamified live feedback intervention can be recommended to be used in educational settings to improve the hand hygiene behaviour of preschool children to promote health. The trial is registered with ClinicalTrials.gov (registration number NCT05395988 https://clinicaltrials.gov/ct2/show/NCT05395988?term=NCT05395988&draw=2&rank=1).

Probing dynamic covalent chemistry in a 2D boroxine framework by in situ near-ambient pressure X-ray photoelectron spectroscopy.

Dynamic covalent chemistry is a powerful approach to design covalent organic frameworks, where high crystallinity is achieved through reversible bond formation. Here, we exploit near-ambient pressure X-ray photoelectron spectroscopy to elucidate the reversible formation of a two-dimensional boroxine framework. By in situ mapping the pressure-temperature parameter space, we identify the regions where the rates of the condensation and hydrolysis reactions become dominant, being the key to enable the thermodynamically controlled growth of crystalline frameworks.

In Situ Observation of C-C Coupling and Step Poisoning During the Growth of Hydrocarbon Chains on Ni(111).

The synthesis of high-value fuels and plastics starting from small hydrocarbon molecules plays a central role in the current transition towards renewable energy. However, the detailed mechanisms driving the growth of hydrocarbon chains remain to a large extent unknown. Here we investigated the formation of hydrocarbon chains resulting from acetylene polymerization on a Ni(111) model catalyst surface. Exploiting X-ray photoelectron spectroscopy up to near-ambient pressures, the intermediate species and reaction products have been identified. Complementary in situ scanning tunneling microscopy observations shed light onto the C-C coupling mechanism. While the step edges of the metal catalyst are commonly assumed to be the active sites for the C-C coupling, we showed that the polymerization occurs instead on the flat terraces of the metallic surface.

Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease.

SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host's innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.

Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease.

The papain-like protease (PLpro) of SARS-CoV-2 is essential for viral propagation and, additionally, dysregulation of the host innate immune system. Using a library of 40 potential metal-chelating compounds we performed an X-ray crystallographic screening against PLpro. As outcome we identified six compounds binding to the target protein. Here we describe the interaction of one hydrazone (H1) and five thiosemicarbazone (T1-T5) compounds with the two distinct natural substrate binding sites of PLpro for ubiquitin and ISG15. H1 binds to a polar groove at the S1 binding site by forming several hydrogen bonds with PLpro. T1-T5 bind into a deep pocket close to the polyubiquitin and ISG15 binding site S2. Their interactions are mainly mediated by multiple hydrogen bonds and further hydrophobic interactions. In particular compound H1 interferes with natural substrate binding by sterical hindrance and induces conformational changes in protein residues involved in substrate binding, while compounds T1-T5 could have a more indirect effect. Fluorescence based enzyme activity assay and complementary thermal stability analysis reveal only weak inhibition properties in the high micromolar range thereby indicating the need for compound optimization. Nevertheless, the unique binding properties involving strong hydrogen bonding and the various options for structural optimization make the compounds ideal lead structures. In combination with the inexpensive and undemanding synthesis, the reported hydrazone and thiosemicarbazones represent an attractive scaffold for further structure-based development of novel PLpro inhibitors by interrupting protein-protein interactions at the S1 and S2 site.

Exploiting Cooperative Catalysis for the On-Surface Synthesis of Linear Heteroaromatic Polymers via Selective C-H Activation.

Regiospecific C-H activation is a promising approach to achieve extended polymers with tailored structures. While a recent on-surface synthetic approach has enabled regioselective homocoupling of heteroaromatic molecules, only small oligomers have been achieved. Herein, selective C-H activation for dehydrogenative C-C couplings of hexaazatriphenylene by Scholl reaction is reported for the first time. By combining low-temperature scanning tunneling microscopy (STM) and atomic force microscopy (AFM), we revealed the formation of one-dimensional polymers with a double-chain structure. The details of the growth process are rationalized by density functional theory (DFT) calculations, pointing out a cooperative catalytic action of Na and Ag adatoms in steering the C-H selectivity for the polymerization.

Nanometallurgy in solution: organometallic synthesis of intermetallic Pd-Ga colloids and their activity in semi-hydrogenation catalysis.

Nanoparticles (NPs) of Pd1--xGax (x = 0.67, 0.5, 0.33), stabilized in non-aqueous colloidal solution, were obtained via an organometallic approach under mild conditions using [Pd2(dvds)3] and GaCp* as all-hydrocarbon ligated metal-precursor compounds (dvds = 1,1,3,3-tetramethyl-1,3-divinyl-disiloxane; Cp* = η5-C5Me5; Me = CH3). The reaction of the two precursors involves the formation of a library of molecular clusters [PdnGamCp*y(dvds)z], as shown by liquid injection field desorption ionization mass spectrometry (LIFDI-MS). Full characterization of the catalytic system (HR-TEM, EDX, DLS, PXRD, XPS, NMR, IR, Raman) confirmed the formation of ultra-small, spherical NPs with narrow size distributions ranging from 1.2 ± 0.2 nm to 2.1 ± 0.4 nm (depending on the Pd : Ga ratio). The catalytic performance of the Pd1--xGax NPs in the semi-hydrogenation of terminal and internal alkynes and the influence of the gallium content on product selectivity were investigated. The highest activities (65%) and selectivities (81%) are achieved using colloids with a "stoichiometric" Pd/Ga ratio of 1 : 1 at 0 °C and 2.0 bar H2 pressure. While lower Ga ratios lead to an increase in activity, higher Ga contents increase the olefin selectivity but are detrimental to the activity.

Predicting Graphene Growth on Cu: Universal Kinetic Growth Model and Its Experimental Verification.

The kinetics of the chemical vapor deposition (CVD) of graphene on Cu in CH4 + H2 were investigated by monitoring the graphene flake size as a function of CVD growth time. A growth model was set up which relates the CVD parameters to the mass action constant Qexp of the methane decomposition reaction toward graphene at a given temperature T. Graphene growth was shown to proceed from pre-equilibrated adsorbed carbon (Cad) within a wide CVD parameter range. The model not only leads to the correct scaling relation of the growth kinetics but quantitatively determines how far the CVD parameters deviate from thermal equilibrium and correctly predicts the absolute flake size increase per time. Fitting experimental data delivers the energy barrier for carbon detachment from the graphene island edge (Edet = 4.7 ± 0.3 eV) and the methane decomposition entropy toward Cad on Cu (ΔdecS° = 260 ± 20 J mol-1 K-1). The latter value is used to estimate the vanishingly small Cad equilibrium concentration of 3 × 10-10 monolayers at 1045 °C. The universal validity of the model is proven by comparison with literature data providing the correct order of magnitude growth velocities up to 1000 µm/h. The performed reactor experiments deliver data that match the predicted flake growth velocity with a precision of about 50%. The obtained results can be used to calibrate any hot wall CVD reactor setup for the methane decomposition reaction toward graphene on Cu. The description can be directly applied for any hydrocarbon in the gas feed, and the technique can be easily applied for other catalytic support surfaces.

Frequency, Local Dynamics, and Genomic Characteristics of ESBL-Producing Escherichia coli Isolated From Specimens of Hospitalized Horses.

Previous research identified veterinary clinics as hotspots with respect to accumulation and spread of multidrug resistant extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli (EC). Therefore, promoting the prudent use of antibiotics to decrease selective pressure in that particular clinical environment is preferable to enhance biosecurity for animal patients and hospital staff. Accordingly, this study comparatively investigated the impact of two distinct perioperative antibiotic prophylaxis (PAP) regimens (short-term versus prolonged) on ESBL-EC carriage of horses subjected to colic surgery. While all horses received a combination of penicillin/gentamicin (P/G) as PAP, they were assigned to either the "single-shot group" (SSG) or the conventional "5-day group" (5DG). Fecal samples collected on arrival (t0), on the 3rd (t1) and on the 10th day after surgery (t2) were screened for ESBL-EC. All isolates were further investigated using whole genome sequences. In total, 81 of 98 horses met the inclusion criteria for this study. ESBL-EC identified in samples available at t0, t1 and t2 were 4.8% (SSG) and 9.7% (5DG), 37% (SSG) and 47.2% (5DG) as well as 55.6% (SSG) and 56.8% (5DG), respectively. Regardless of the P/G PAP regimen, horses were 9.12 times (95% CI 2.79-29.7) more likely to carry ESBL-EC at t1 compared to t0 (p < 0.001) and 15.64 times (95% CI 4.57-53.55) more likely to carry ESBL-EC at t2 compared to t0 (p < 0.001). ESBL-EC belonging to sequence type (ST) 10, ST86, ST641, and ST410 were the most prevalent lineages, with bla CTX - M - 1 (60%) being the dominant ESBL gene. A close spatio-temporal relationship between isolates sharing a particular ST was revealed by genome analysis, strongly indicating local spread. Consequently, hospitalization itself has a strong impact on ESBL-EC isolation rates in horses, possibly masking differences between distinct PAP regimens. The results of this study reveal accumulation and spread of multi-drug resistant ESBL-EC among horses subjected to colic surgery with different P/G PAP regimens, challenging the local hygiene management system and work-place safety of veterinary staff. Moreover, the predominance of particular ESBL-EC lineages in clinics providing health care for horses needs further investigation.

Method for the Manual Analysis of Moiré Structures in STM images.

A method is presented to manually determine the lattice parameters of commensurate hexagonal moiré structures resolved by STM. It solves the problem that lattice parameters of moiré structures usually cannot be determined by inspection of an STM image, so that computer-based analyses are required. The lattice vector of a commensurate moiré structure is a sum of integer multiples both of the two basis vectors of the substrate and of the adsorbed layer. The method extracts the two factors with respect to the adsorbed layer from an analysis of the Fourier transform of an STM image. These two factors are related to the two factors with respect to the substrate layer. Using the cell augmentation method, six possible moiré structures are identified by algebra. When the orientation and lattice constant of the substrate are roughly known, this information is usually sufficient to determine a unique moiré structure and its lattice parameters.

X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.

The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput x-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied x-ray fragment screening experiments with molecules of low complexity, our screen tested already-approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro In subsequent cell-based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.