Modelling the effect of surface charging on plasma synthesis of ammonia using DFT.

Non-equilibrium plasma has been found to have a synergistic effect on catalytic synthesis of NH3. The non-equilibrium plasma and catalyst surface together could affect NH3 synthesis through several mechanisms. Charging of the catalyst surface in the presence of non-equilibrium plasma is one such mechanism. We employed density functional theory (DFT) calculations to understand the effect of surface charge on surface reactivity of γ-Al2O3 supported single metal atom catalysts and a metal cluster. We investigated the effect of surface charge on adsorption energies of common adsorbates involved in NH3 synthesis. It is found that adsorption energy of N, N2, H, H2, NH and NH2 on metal atoms increases by up to ∼1.2 eV, whereas NH3 desorption is increased by up to 0.45 eV upon surface charging. The present results provide a new mechanism of plasma enhanced catalysis potentially explaining why Ni, Pt and Co have better catalytic performance compared to Ru and Fe in ammonia plasma catalysis. Furthermore, we found that the correlations between adsorption energies of adsorbates change significantly with surface charging. These findings suggest that surface charging might play an important role in plasma synthesis of NH3.

A coating strategy to achieve effective local charge separation for photocatalytic coevolution.

Semiconductors of narrow bandgaps and high quantum efficiency have not been broadly utilized for photocatalytic coevolution of H2 and O2 via water splitting. One prominent issue is to develop effective protection strategies, which not only mitigate photocorrosion in an aqueous environment but also facilitate charge separation. Achieving local charge separation is especially challenging when these reductive and oxidative sites are placed only nanometers apart compared to two macroscopically separated electrodes in a photoelectrochemical cell. Additionally, the driving force of charge separation, namely the energetic difference in the barrier heights across the two type of sites, is small. Herein, we used conformal coatings attached by nanoscale cocatalysts to transform two classes of tunable bandgap semiconductors, i.e., CdS and GaInP2, into stable and efficient photocatalysts. We used hydrogen evolution and redox-mediator oxidation for model study, and further constructed a two-compartment solar fuel generator that separated stoichiometric H2 and O2 products. Distinct from the single charge-transfer direction reported for conventional protective coatings, the coating herein allows for concurrent injection of photoexcited electrons and holes through the coating. The energetic difference between reductive and oxidative catalytic sites was regulated by selectivity and local kinetics. Accordingly, the charge separation behavior was validated using numerical simulations. Following this design principle, the CdS/TiO2/Rh@CrOx photocatalysts evolved H2 while oxidizing reversible polysulfide redox mediators at a maximum rate of 90.6 µmol⋅h-1⋅cm-2 by stacking three panels. Powered by a solar cell, the redox-mediated solar water-splitting reactor regenerated the polysulfide repeatedly and achieved solar-to-hydrogen efficiency of 1.7%.

Plasma-Assisted Chemical-Looping Combustion: Low-Temperature Methane and Ethylene Oxidation with Nickel Oxide.

The chemical reaction network of low-temperature plasma-assisted oxidation of methane (CH4) and ethylene (C2H4) with nickel oxide (NiO) was investigated in a heated plasma reactor through time-dependent species measurements by electron-ionization molecular beam mass spectrometry (EI-MBMS). Methane (ethylene) oxidation by NiO was explored in temperature ranges from 300-700 °C (300-500 °C) and 300-800 °C (300-600 °C) for the plasma and nonplasma conditions. Significant enhancement of methane oxidation was observed with plasma between 400 and 500 °C, where no oxidation was observed under nonplasma conditions. For the oxidation of methane at higher temperatures, three different oxidation stages were observed: (I) a period of complete oxidation, (II) a period of incomplete CO oxidation, and (III) a period of carbon buildup. For the C2H4 experiments, and unlike the CH4 experiments, the plasma resulted in a significant amount of new intermediate oxygenated species, such as CH2O, CH3OH, C2H4O, and C2H6O. Carbon deposits were observed under both methane and ethylene conditions and verified by X-ray photoelectron spectroscopy (XPS). ReaxFF (reactive force field) simulations were performed for the oxidation of CH4 and C2H4 in a nonplasma environment. The simulated intermediates and products largely agree with the species measured in the experiments, though the predicted intermediate oxygenated species such as CH2O and C2H6O were not observed in experiments under nonplasma conditions. A reaction pathway analysis for CH4 and C2H4 reacting with NiO was created based on the observed species from the MBMS spectra along with ReaxFF simulations.

Temperature and organic carbon quality control the anaerobic carbon mineralization in peat profiles via modulating microbes: A case study of Changbai Mountain.

Peatlands account for a significant fraction of the global carbon stock. However, the complex interplay of abiotic and biotic factors governing anaerobic carbon mineralization in response to warming remains unclear. In this study, peat sediments were collected from a typical northern peatland-Changbai Mountain to investigate the behavior and mechanism of anaerobic carbon mineralization in response to depth (0-200 cm) and temperature (5 °C, 15 °C and 20 °C), by integrating geochemical and microbial analysis. Several indices including humification indexes (HI), aromaticity, and water extractable organic carbon (WEOC) components were applied to evaluate carbon quality, while 16S rRNA sequencing was used to measure microbial composition. Regardless of temperature, degradations of carbon quality and associated reduction in microbial abundance as well as diversity resulted in a decrease in anaerobic carbon mineralization (both CO2 and CH4) towards greater depth. Warming either from 5 °C to 15 °C or 20 °C significantly increased anaerobic carbon mineralization in all depth profiles by improving carbon availability. Enhanced carbon availabilities were mediated by the change in microbial composition (p < 0.01) and an increase in metabolic activities, which was particularly evident in the enhanced ß-glucosidase activity and microbial collaborations. A remarkable increase of over 10-fold in the relative abundance of the Geothrix genus was observed under warming. Overall, warming resulted in an enhanced contribution of CH4 emission and a higher ratio of hydrogenotrophic methanogenesis, as evidenced by carbon isotope fractionation factors. In addition, deep peat soils (>100 cm) with recalcitrant carbon demonstrated greater temperature sensitivity (Q10: ∼2.0) than shallow peat soils (Q10:∼1.2) when temperature increased from 15 °C to 20 °C. The findings of this study have significantly deepened our understanding for mechanisms of carbon quality and microbe-driven anaerobic carbon mineralization in peatlands under global warming.

Functional characterization of Nosema bombycis (microsporidia) trehalase 3.

Nosema bombycis, an obligate intracellular parasite, is a single-celled eukaryote known to infect various tissues of silkworms, leading to the manifestation of pebrine. Trehalase, a glycosidase responsible for catalyzing the hydrolysis of trehalose into two glucose molecules, assumes a crucial role in thermal stress tolerance, dehydration, desiccation stress, and asexual development. Despite its recognized importance in these processes, the specific role of trehalase in N. bombycis remains uncertain. This investigation focused on exploring the functions of trehalase 3 in N. bombycis (NbTre3). Immunofluorescence analysis of mature (dormant) spores indicated that NbTre3 primarily localizes to the spore membrane or spore wall, suggesting a potential involvement in spore germination. Reverse transcription-quantitative polymerase chain reaction results indicated that the transcriptional level of NbTre3 peaked at 6 h post N. bombycis infection, potentially contributing to energy storage for proliferation. Throughout the life cycle of N. bombycis within the host cell, NbTre3 was detected in sporoplasm during the proliferative stage rather than the sporulation stage. RNA interference experiments revealed a substantial decrease in the relative transcriptional level of NbTre3, accompanied by a certain reduction in the relative transcriptional level of Nb16S rRNA. These outcomes suggest that NbTre3 may play a role in the proliferation of N. bombycis. The application of the His pull-down technique identified 28 proteins interacting with NbTre3, predominantly originating from the host silkworm. This finding implies that NbTre3 may participate in the metabolism of the host cell, potentially utilizing the host cell's energy resources.

Design, Synthesis, Biological Evaluation, and Molecular Dynamics Simulation of Influenza Polymerase PB2 Inhibitors.

The PB2 subunit of the influenza RNA-dependent RNA polymerase (RdRp) has been identified as a promising target for the treatment of influenza. To expand the chemical space of the known influenza polymerase PB2 inhibitor-pimodivir (formerly VX-787) and improve its pharmacokinetic profile, two pimodivir analogs containing 2,3-dihydro-imidazopyridine fragment (comp. I and comp. II) were designed, synthesized, and evaluated for anti-influenza virus activity. In the cytopathic effect (CPE) inhibition assay, comp. I and comp. II showed IC50 values of 0.07 and 0.09 µM for A/Puerto Rico/8/34 (H1N1) and 0.04 and 0.07 µM for A/Hong Kong/8/68 (H3N2), respectively. Protein-binding affinity assay results showed a concentration-dependent association and dissociation pattern, with KD values of 1.398 and 1.670 µM, respectively. In vitro metabolic stability assays showed that comp. I and comp. II exhibited good stability to liver microsomes and considerably less sensitivity to aldehyde oxidase compared to pimodivir. The binding modes of comp. I and comp. II were similar to those of VX-787; however, comp. I and comp. II had lower structural adaptability to PB2 than VX-787. Our results provide helpful information regarding the structure-activity relationship for the design of novel PB2 inhibitors and a reference for the development of drugs containing 2,3-dihydro-imidazopyridine fragments.

Design, Synthesis, Bioactivity Evaluation, Crystal Structures, and In Silico Studies of New α-Amino Amide Derivatives as Potential Histone Deacetylase 6 Inhibitors.

Hydroxamate, as a zinc-binding group (ZBG), prevails in the design of histone deacetylase 6(HDAC6) inhibitors due to its remarkable zinc-chelating capability. However, hydroxamate-associated genotoxicity and mutagenicity have limited the widespread application of corresponding HDAC6 inhibitors in the treatment of human diseases. To avoid such side effects, researchers are searching for novel ZBGs that may be used for the synthesis of HDAC6 inhibitors. In this study, a series of stereoisomeric compounds were designed and synthesized to discover non-hydroxamate HDAC6 inhibitors using α-amino amide as zinc-ion-chelating groups, along with a pair of enantiomeric isomers with inverted L-shaped vertical structure as cap structures. The anti-proliferative activities were determined against HL-60, Hela, and RPMI 8226 cells, and 7a and its stereoisomer 13a exhibited excellent activities against Hela cells with IC50 = 0.31 µM and IC50 = 5.19 µM, respectively. Interestingly, there is a significant difference between the two stereoisomers. Moreover, an evaluation of cytotoxicity toward human normal liver cells HL-7702 indicated its safety for normal cells. X-ray single crystal diffraction was employed to increase insights into molecule structure and activities. It was found that the carbonyl of the amide bond is on the different side from the amino and pyridine nitrogen atoms. To identify possible protein targets to clarify the mechanism of action and biological activity of 7a, a small-scale virtual screen using reverse docking for HDAC isoforms (1-10) was performed and the results showed that HDAC6 was the best receptor for 7a, suggesting that HDAC6 may be a potential target for 7a. The interaction pattern analysis showed that the α-amino amide moiety of 7a coordinated with the zinc ion of HDAC6 in a bidentate chelate manner, which is similar to the chelation pattern of hydroxamic acid. Finally, the molecular dynamics simulation approaches were used to assess the docked complex's conformational stability. In this work, we identified 7a as a potential HDAC6 inhibitor and provide some references for the discovery of non-hydroxamic acid HDAC6 inhibitors.

Asymmetric Radical Process for General Synthesis of Chiral Heteroaryl Cyclopropanes.

A highly efficient catalytic method has been developed for asymmetric radical cyclopropanation of alkenes with in situ-generated α-heteroaryldiazomethanes via Co(II)-based metalloradical catalysis (MRC). Through fine-tuning the cavity-like environments of newly-synthesized D2-symmetric chiral amidoporphyrins as the supporting ligand, the optimized Co(II)-based metalloradical system is broadly applicable to α-pyridyl and other α-heteroaryldiazomethanes for asymmetric cyclopropanation of wide-ranging alkenes, including several types of challenging substrates. This new catalytic methodology provides a general access to valuable chiral heteroaryl cyclopropanes in high yields with excellent both diastereoselectivities and enantioselectivities. Combined computational and experimental studies further support the underlying stepwise radical mechanism of the Co(II)-based olefin cyclopropanation involving α- and γ-metalloalkyl radicals as the key intermediates.

UL28 and UL33 homologs of Marek's disease virus terminase complex involved in the regulation of cleavage and packaging of viral DNA are indispensable for replication in cultured cells.

Processing and packaging of herpesvirus genomic DNA is regulated by a packaging-associated terminase complex comprising of viral proteins pUL15, pUL28 and pUL33. Marek's disease virus (MDV) homologs UL28 and UL33 showed conserved functional features with high sequence identity with the corresponding Herpes simplex virus 1 (HSV-1) homologs. As part of the investigations into the role of the UL28 and UL33 homologs of oncogenic MDV for DNA packaging and replication in cultured cells, we generated MDV mutant clones deficient in UL28 or UL33 of full-length MDV genomes. Transfection of UL28- or UL33-deleted BAC DNA into chicken embryo fibroblast (CEF) did not result either in the production of visible virus plaques, or detectable single cell infection after passaging onto fresh CEF cells. However, typical MDV plaques were detectable in CEF transfected with the DNA of revertant mutants where the deleted genes were precisely reinserted. Moreover, the replication defect of the UL28-deficient mutant was completely restored when fragment encoding the full UL28 gene was co-transfected into CEF cells. Viruses recovered from the revertant construct, as well as by the UL28 co-transfection, showed replication ability comparable with parental virus. Furthermore, the transmission electron microscopy study indicated that immature capsids were assembled without the UL28 expression, but with the loss of infectivity. Importantly, predicted three-dimensional structures of UL28 between MDV and HSV-1 suggests conserved function in virus replication. For the first time, these results revealed that both UL28 and UL33 are essential for MDV replication through regulating DNA cleavage and packaging.

Enhancements of electric field and afterglow of non-equilibrium plasma by Pb(ZrxTi1-x)O3 ferroelectric electrode.

Manipulating surface charge, electric field, and plasma afterglow in a non-equilibrium plasma is critical to control plasma-surface interaction for plasma catalysis and manufacturing. Here, we show enhancements of surface charge, electric field during breakdown, and afterglow by ferroelectric barrier discharge. The results show that the ferroelectrics manifest spontaneous electric polarization to increase the surface charge by two orders of magnitude compared to discharge with an alumina barrier. Time-resolved in-situ electric field measurements reveal that the fast polarization of ferroelectrics enhances the electric field during the breakdown in streamer discharge and doubles the electric field compared to the dielectric barrier discharge. Moreover, due to the existence of surface charge, the ferroelectric electrode extends the afterglow time and makes discharge sustained longer when alternating the external electric field polarity. The present results show that ferroelectric barrier discharge offers a promising technique to tune plasma properties for efficient plasma catalysis and electrified manufacturing.

The influence of eyelid pressure and eye contour factors on rigid corneal contact lens fitting.

PURPOSE: This study aimed to investigate the impact of eyelid pressure (ELP) and eye contour factors on rigid corneal contact lens fitting. METHODS: This prospective cross-sectional study involved 20 participants (one eye per person). Rigid corneal contact lenses with three different base curves were selected for each participant. The base curves were calculated according to the average keratometry value. The original value and its variations (+0.1 mm and - 0.1 mm) were considered. Eye contour factors, lens decentration under natural eye position (LD I) and full eyelid exposure (LD II), and lens vertical movement were taken by a Canon camera mounted on a digital slit lamp biomicroscope. Upper and lower ELPs were measured by a novel blepharo-tensiometer. RESULTS: The mean values of LD I, LD II, and lens vertical movement significantly increased as the base curve increased (P＜0.001, ＜0.001, and = 0.005). Upper ELP was positively correlated with lens vertical movement of the three base curves (P = 0.047, 0.001, and 0.004). Furthermore, upper ELP (odds ratio [OR]: 1.039; 95 % confidence [CI]: 1.009-1.069; P = 0.009) and flat keratometry values (OR: 0.873; 95 % CI: 0.786-0.969; P = 0.011) independently influenced lens vertical movement. CONCLUSIONS: ELP and base curve independently influenced rigid corneal contact lens fitting. Thus, ELP should be considered during rigid corneal contact lens fitting in clinical practice.

Enhancing arsenic adsorptions by optimizing Fe-loaded biochar and preliminary application in paddy soil under different water management strategies.

Arsenic (As) is widely distributed in nature and is a highly toxic element impacting human health through drinking water and rice. In this study, an optimized approach was attempted to improve As adsorption capabilities by combining pre- and post-pyrolysis modification of Fe(oxy)hydroxides to rice husk biochar (FRB), of which the method is rarely addressed in previous studies. Maghemite and goethite were successfully loaded onto biochar, characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), and X-ray photoemission spectroscopy (XPS) analyzer. The FRB had maximum As(III) and As(V) adsorption capabilities of 7908 and 11,268 mg/kg, respectively, which was significantly higher than that of Fe-modified biochar in the pre-pyrolysis and/or post-pyrolysis process. Adsorption mechanisms for As explored by Fourier-transform infrared spectroscopy (FTIR), XPS analysis mainly included electronic attraction and ligand exchange with hydroxyl groups on the FRB. It was noteworthy that more than half of the As(II) species loaded on FRB were converted into less toxic As(V) species, which could be mediated by the redox-active groups on the biochar. The preliminary application of FRB in soil indicated that it has an effective remediation potential for As-contaminated soil under flooded conditions, while promoted As release under dry conditions. Finding of this study highlighted that the loading of metal oxides onto biochar by combining pre- and post-pyrolysis modification could potentially increase As adsorption capabilities and further help in strategic water management.

Discovery of AI-2 Quorum Sensing Inhibitors Targeting the LsrK/HPr Protein-Protein Interaction Site by Molecular Dynamics Simulation, Virtual Screening, and Bioassay Evaluation.

Quorum sensing (QS) is a cell-to-cell communication mechanism that regulates bacterial pathogenicity, biofilm formation, and antibiotic sensitivity. Among the identified quorum sensing, AI-2 QS exists in both Gram-negative and Gram-positive bacteria and is responsible for interspecies communication. Recent studies have highlighted the connection between the phosphotransferase system (PTS) and AI-2 QS, with this link being associated with protein-protein interaction (PPI) between HPr and LsrK. Here, we first discovered several AI-2 QSIs targeting the LsrK/HPr PPI site through molecular dynamics (MD) simulation, virtual screening, and bioassay evaluation. Of the 62 compounds purchased, eight compounds demonstrated significant inhibition in LsrK-based assays and AI-2 QS interference assays. Surface plasmon resonance (SPR) analysis confirmed that the hit compound 4171-0375 specifically bound to the LsrK-N protein (HPr binding domain, KD = 2.51 × 10-5 M), and therefore the LsrK/HPr PPI site. The structure-activity relationships (SARs) emphasized the importance of hydrophobic interactions with the hydrophobic pocket and hydrogen bonds or salt bridges with key residues of LsrK for LsrK/HPr PPI inhibitors. These new AI-2 QSIs, especially 4171-0375, exhibited novel structures, significant LsrK inhibition, and were suitable for structural modification to search for more effective AI-2 QSIs.

Design, Synthesis, Evaluation and Molecular Dynamics Simulation of Dengue Virus NS5-RdRp Inhibitors.

Dengue virus (DENV) is a major mosquito-borne human pathogen in tropical countries; however, there are currently no targeted antiviral treatments for DENV infection. Compounds 27 and 29 have been reported to be allosteric inhibitors of DENV RdRp with potent inhibitory effects. In this study, the structures of compounds 27 and 29 were optimized using computer-aided drug design (CADD) approaches. Nine novel compounds were synthesized based on rational considerations, including molecular docking scores, free energy of binding to receptor proteins, predicted Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) parameters, structural diversity, and feasibility of synthesis. Subsequently, the anti-DENV activity was assessed. In the cytopathic effect (CPE) assay conducted on BHK-21 cells using the DENV2 NGC strain, both SW-b and SW-d demonstrated comparable or superior activity against DENV2, with IC50 values of 3.58 ± 0.29 µM and 23.94 ± 1.00 µM, respectively, compared to that of compound 27 (IC50 = 19.67 ± 1.12 µM). Importantly, both SW-b and SW-d exhibited low cytotoxicity, with CC50 values of 24.65 µmol and 133.70 µmol, respectively, resulting in selectivity indices of 6.89 and 5.58, respectively. Furthermore, when compared to the positive control compound 3'-dATP (IC50 = 30.09 ± 8.26 µM), SW-b and SW-d displayed superior inhibitory activity in an enzyme inhibitory assay, with IC50 values of 11.54 ± 1.30 µM and 13.54 ± 0.32 µM, respectively. Molecular dynamics (MD) simulations elucidated the mode of action of SW-b and SW-d, highlighting their ability to enhance π-π packing interactions between benzene rings and residue W795 in the S1 fragment, compared to compounds 27 and 29. Although the transacylsulphonamide fragment reduced the interaction between T794 and NH, it augmented the interaction between R729 and T794. In summary, our study underscores the potential of SW-b and SW-d as allosteric inhibitors targeting the DENV NS5 RdRp domain. However, further in vivo studies are warranted to assess their pharmacology and toxicity profiles.

Antagonistic effects of N-acetylcysteine on lead-induced apoptosis and oxidative stress in chicken embryo fibroblast cells.

Lead (Pb) is a heavy metal that can have harmful effects on the environment, which has severe cytotoxicity in many animal tissues. N-acetylcysteine (NAC) has antioxidant activity, reducing lead-induced oxidative stress and apoptosis, but its role in chicken cells is unknown. The current study explored the antagonistic effect of NAC on lead-induced apoptosis and oxidative stress in chicken embryo fibroblast (CEF). In this study, CEF was used as a model to measure the cytotoxic effects of lead nitrate at different concentrations, demonstrating a dose-dependent effect on CEF activity. Employing inverted microscopy, the investigation of morphological alterations in CEF cells was conducted. Fluorescence staining methodology enabled the assessment of reactive oxygen species (ROS) levels within CEF cells. Moreover, an enzyme-linked immunosorbent assay was utilized to detect the presence of oxidative damage indicators encompassing superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), catalase (CAT) activity, malondialdehyde (MDA) content, and total antioxidant capacity (T-AOC) within CEF cells. Furthermore, the determination of the apoptosis rate of CEF cells was accomplished through the utilization of the Hoechst 33258 staining method in combination with the Annexin V-FITC dual staining method. By using RT-qPCR for detection, lead treatment increased expression of pro-apoptotic genes, caspase-3, and caspase-9, and reduced expression of anti-apoptotic genes, Bcl-2, and BI-1. Reduced antioxidant capacity was shown by increased ROS and MDA levels in CEF cells after lead treatment. The results showed that NAC inhibited the expression of caspase-3 and caspase-9 in lead-treated CEF cells, while NAC had a certain inhibitory effect on the relative expression of Bcl-2 and BI-1 mRNA in lead-induced CEF cells. NAC significantly reduced lead-induced oxidative damage and apoptosis. Overall, our results demonstrate a novel protective effect of NAC against lead-induced injury in chicken cells, providing a theoretical basis for future investigations of drugs that are effective in preventing lead poisoning in animals.

Inulin: properties and health benefits.

Inulin, a soluble dietary fiber, is widely found in more than 36 000 plant species as a reserve polysaccharide. The primary sources of inulin, include Jerusalem artichoke, chicory, onion, garlic, barley, and dahlia, among which Jerusalem artichoke tubers and chicory roots are often used as raw materials for inulin production in the food industry. It is universally acknowledged that inulin as a prebiotic has an outstanding effect on the regulation of intestinal microbiota via stimulating the growth of beneficial bacteria. In addition, inulin also exhibits excellent health benefits in regulating lipid metabolism, weight loss, lowering blood sugar, inhibiting the expression of inflammatory factors, reducing the risk of colon cancer, enhancing mineral absorption, improving constipation, and relieving depression. In this review paper, we attempt to present an exhaustive overview of the function and health benefits of inulin.

Virtual screening-based discovery of AI-2 quorum sensing inhibitors that interact with an allosteric hydrophobic site of LsrK and their functional evaluation.

Introduction: Quorum sensing (QS) is a bacterial intracellular and intercellular communication system that regulates virulence factor production, biofilm formation, and antibiotic sensitivity. Quorum-sensing inhibitors (QSIs) are a novel class of antibiotics that can effectively combat antibiotic resistance. Autoinducer-2 (AI-2) is a universal signaling molecule that mediates inter- and intraspecies QS systems among different bacteria. Furthermore, LsrK plays an important role in regulating the activity and stability of the intracellular AI-2 signaling pathway. Thus, LsrK is considered an important target for the development of QSIs. Methods: We designed a workflow integrating molecular dynamic (MD) simulations, virtual screening, LsrK inhibition assays, cell-based AI-2-mediated QS interference assays, and surface plasmon resonance (SPR)-based protein affinity assays to screen for potential LsrK kinase inhibitors. Results: MD simulation results of the LsrK/ATP complex revealed hydrogen bonds and salt bridge formation among four key residues, namely, Lys 431, Tyr 341, Arg 319, and Arg 322, which are critical for the binding of ATP to LsrK. Furthermore, MD simulation results indicated that the ATP-binding site has an allosteric pocket that can become larger and be occupied by small molecule compounds. Based on these MD simulation results, a constraint of forming at least one hydrogen bond with Arg 319, Arg 322, Lys 431, or Tyr 341 residues was introduced when performing virtual screening using Glide's virtual screening workflow (VSW). In the meantime, compounds with hydrophobic group likely to interact with the allosteric hydrophobic pocket are preferred when performing visual inspection. Seventy-four compounds were selected for the wet laboratory assays based on virtual screening and the absorption, distribution, metabolism, and excretion (ADME) properties of these compounds. LsrK inhibition assays revealed 12 compounds inhibiting LsrK by more than 60% at a 200 µM concentration; four of these (Y205-6768, D135-0149, 3284-1358, and N025-0038) had IC50 values below 50 µM and were confirmed as ATP-competitive inhibitors. Six of these 12 LsrK inhibitors exhibited high AI-2 QS inhibition, of which, Y205-6768 had the highest activity with IC50 = 11.28 ± 0.70 µM. The SPR assay verified that compounds Y205-6768 and N025-0038 specifically bound to LsrK. MD simulation analysis of the docking complexes of the four active compounds with LsrK further confirmed the importance of forming hydrogen bonds and salt bridges with key basic amino acid residues including Lys 431, Tyr 341, Arg 319, and Arg 322 and filling the allosteric hydrophobic pocket next to the purine-binding site of LsrK. Discussion: Our study clarified for the first time that there is an allosteric site near the ATP-binding site of Lsrk and that it enriches the structure-activity relationship information of Lsrk inhibitors. The four identified compounds showed novel structures, low molecular weights, high activities, and novel LsrK binding modes, rendering them suitable for further optimization for effective AI-2 QSIs. Our work provides a valuable reference for the discovery of QSIs that do not inhibit bacterial growth, thereby avoiding the emergence of drug resistance.

Optimal production of bioflocculant from Pseudomonas sp. GO2 and its removal characteristics of heavy metals.

Bioflocculant may be a promising bioactivator for heavy metal removal duo to its eco-friendly properties and remarkable ability to adsorb heavy metals. In this study, bioflocculant production from a bacterium, Pseudomonas sp. GO2, was optimized and its removal efficiency for two heavy metal ions was evaluated. Results demonstrated that the maximal flocculation efficiency was achieved with concentration levels of 5 g/L glucose, 3 g/L casein, and 5 g/L NaCl, with an initial pH of 9.0, and a fermentation time of 48 h. Bioflocculant produced by GO2 had a stronger removal efficiency for Cd2+ than that of Pb2+, with highest removal efficiencies of 85.38% and 80.87%, respectively. The adsorption process was mainly dependent on the monolayer and chemisorption based on the adsorption isotherm and kinetic models. This study demonstrated that bioflocculant produced by the GO2 strain has the potential to be used in heavy metal treatment from industrial wastewater.

Effect of Autoinducer-2 Quorum Sensing Inhibitor on Interspecies Quorum Sensing.

Bacterial drug resistance caused by overuse and misuse of antibiotics is common, especially in clinical multispecies infections. It is of great significance to discover novel agents to treat clinical bacterial infections. Studies have demonstrated that autoinducer-2 (AI-2), a signal molecule in quorum sensing (QS), plays an important role in communication among multiple bacterial species and bacterial drug-resistance. Previously, 14 AI-2 inhibited compounds were selected through virtual screening by using the AI-2 receptor protein LuxP as a target. Here, we used Vibrio harveyi BB170 as a reporter strain for the preliminary screening of 14 inhibitors and compound Str7410 had higher AI-2 QS inhibition activity (IC50 = 0.3724 ± 0.1091 µM). Then, co-culture of Pseudomonas aeruginosa PAO1 with Staphylococcus aureus ATCC 25923 was used to evaluate the inhibitory effects of Str7410 on multispecies infection in vitro and in vivo. In vitro, Str7410 significantly inhibited the formation of mixed bacterial biofilms. Meanwhile, the combination of Str7410 with meropenem trihydrate (MEPM) significantly improved the susceptibility of mixed-species-biofilm cells to the antibiotic. In vivo, Str7410 significantly increased the survival rate of wild-type Caenorhabditis elegans N2 co-infected by P. aeruginosa PAO1 and S. aureus ATCC 25923. Real-time quantitative PCR analysis showed that Str7410 reduced virulence factor (pyocyanin and elastase) production and swarming motility of P. aeruginosa PAO1 by downregulating the expression of QS-related genes in strain PAO1 in co-culture with S. aureus ATCC 25923. Compound Str7410 is a candidate agent for treating drug-resistant multispecies infections. The work described here provides a strategy for discovering novel antibacterial drugs.

The CDK1 inhibitor, Ro-3306, is a potential antiviral candidate against influenza virus infection.

Many viruses use the host cell division cycle to facilitate replication. Cyclin-dependent kinases (CDKs) are a group of serine/threonine kinases that play a central role in regulating cell cycle progression. However, the prospect of using CDKs for anti-influenza virus treatment remains to be elucidated. We conducted this study to investigate the potential of the CDK1 inhibitor Ro-3306 in preventing influenza virus infection and to elucidate the underlying mechanism. We showed that Ro-3306, a CDK1 inhibitor, exerts anti-influenza activity both in vitro and in vivo. Proof-of-concept studies revealed that knockdown of host CDK1 might affect the splicing of M2 viral mRNA, leading to the restriction of viral replication. Moreover, Ro-3306 directly bound to viral PB2 protein and inhibited viral RNA replication. Transcriptome analysis further revealed that Ro-3306 treatment inhibited the expression of MAPK-regulated genes, which might also contribute to the antiviral activity of Ro-3306. This study highlighted the multifunctional role of Ro-3306 as a novel anti-influenza virus agent.