Study of the binding of ΔFN3.1 fragments of the Bifidobacterium longum GT15 with TNFα and prevalence of domain-containing proteins in groups of bacteria of the human gut microbiota.

Aim: This study is mainly devoted to determining the ability of ∆FN3.1 protein fragments of Bifidobacterium (B.) longum subsp. longum GT15, namely two FN3 domains (2D FN3) and a C-terminal domain (CD FN3), to bind to tumor necrosis factor-alpha (TNF-α). Methods: Fragments of the fn3 gene encoding the 2D FN3 and CD FN3 were cloned in Escherichia (E.) coli. In order to assess the binding specificity between 2D FN3 and CD FN3 to TNFα, we employed the previously developed sandwich ELISA system to detect any specific interactions between the purified protein and any of the studied cytokines. The trRosetta software was used to build 3D models of the ∆FN3.1, 2D FN3, and CD FN3 proteins. The detection of polymorphism in the amino acid sequences of the studied proteins and the analysis of human gut-derived bacterial proteins carrying FN3 domains were performed in silico. Results: We experimentally showed that neither 2D FN3 nor CD FN3 alone can bind to TNFα. Prediction of the 3D structures of ΔFN3.1, 2D FN3, and CD FN3 suggested that only ΔFN3.1 can form a pocket allowing binding with TNFα to occur. Polymorphism analysis of amino acid sequences of ΔFN3.1 proteins in B. longum strains uncovered substitutions that can alter the conformation of the spatial structure of the ΔFN3.1 protein. We also analyzed human gut-derived bacterial proteins harboring FN3 domains which allowed us to differentiate between those containing motifs of cytokine receptors (MCRs) in their FN3 domains and those lacking them. Conclusion: Only the complete ∆FN3.1 protein can selectively bind to TNFα. Analysis of 3D models of the 2D FN3, CD FN3, and ΔFN3.1 proteins showed that only the ΔFN3.1 protein is potentially capable of forming a pocket allowing TNFα binding to occur. Only FN3 domains containing MCRs exhibited sequence homology with FN3 domains of human proteins.

In Vitro and In Silico Studies of Human Tyrosyl-DNA Phosphodiesterase 1 (Tdp1) Inhibition by Stereoisomeric Forms of Lipophilic Nucleosides: The Role of Carbohydrate Stereochemistry in Ligand-Enzyme Interactions.

Inhibition of human DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1) by different chiral lipophilic nucleoside derivatives was studied. New Tdp1 inhibitors were found in the series of the studied compounds with IC50 = 2.7-6.7 µM. It was shown that D-lipophilic nucleoside derivatives manifested higher inhibition activity than their L-analogs, and configuration of the carbohydrate moiety can influence the mechanism of Tdp1 inhibition.

The Lipophilic Purine Nucleoside-Tdp1 Inhibitor-Enhances DNA Damage Induced by Topotecan In Vitro and Potentiates the Antitumor Effect of Topotecan In Vivo.

The use of cancer chemotherapy sensitizers is a promising approach to induce the effect of clinically used anticancer treatments. One of the interesting targets is Tyrosyl-DNA Phosphodiesterase 1 (Tdp1), a DNA-repair enzyme, that may prevent the action of clinical Topoisomerase 1 (Top1) inhibitors, such as topotecan (Tpc). Tdp1 eliminates covalent Top1-DNA (Top1c) complexes that appear under the action of topotecan and determines the cytotoxic effect of this drug. We hypothesize that Tdp1 inhibition would sensitize cells towards the effect of Tpc. Herein, we report the synthesis and study of lipophilic derivatives of purine nucleosides that efficiently suppress Tdp1 activity, with IC50 values in the 0.3-22.0 µM range. We also showed that this compound class can enhance DNA damage induced by topotecan in vitro by Comet assay on human cell lines HeLa and potentiate the antitumor effect of topotecan in vivo on a mice ascitic Krebs-2 carcinoma model. Thereby, this type of compound may be useful to develop drugs, that sensitize the effect of topotecan and reduce the required dose and, as a result, side effects.

New Hybrid Compounds Combining Fragments of Usnic Acid and Thioether Are Inhibitors of Human Enzymes TDP1, TDP2 and PARP1.

Tyrosyl-DNA phosphodiesterase 1 (TDP1) catalyzes the cleavage of the phosphodiester bond between the tyrosine residue of topoisomerase 1 (TOP1) and the 3' phosphate of DNA in the single-strand break generated by TOP1. TDP1 promotes the cleavage of the stable DNA-TOP1 complexes with the TOP1 inhibitor topotecan, which is a clinically used anticancer drug. This article reports the synthesis and study of usnic acid thioether and sulfoxide derivatives that efficiently suppress TDP1 activity, with IC50 values in the 1.4-25.2 µM range. The structure of the heterocyclic substituent introduced into the dibenzofuran core affects the TDP1 inhibitory efficiency of the compounds. A five-membered heterocyclic fragment was shown to be most pharmacophoric among the others. Sulfoxide derivatives were less cytotoxic than their thioester analogs. We observed an uncompetitive type of inhibition for the four most effective inhibitors of TDP1. The anticancer effect of TOP1 inhibitors can be enhanced by the simultaneous inhibition of PARP1, TDP1, and TDP2. Some of the compounds inhibited not only TDP1 but also TDP2 and/or PARP1, but at significantly higher concentration ranges than TDP1. Leader compound 10a showed promising synergy on HeLa cells in conjunction with the TOP1 inhibitor topotecan.

Design, Synthesis, and Molecular Docking Study of New Tyrosyl-DNA Phosphodiesterase 1 (TDP1) Inhibitors Combining Resin Acids and Adamantane Moieties.

In this paper, a series of novel abietyl and dehydroabietyl ureas, thioureas, amides, and thioamides bearing adamantane moieties were designed, synthesized, and evaluated for their inhibitory activities against tyrosil-DNA-phosphodiesterase 1 (TDP1). The synthesized compounds were able to inhibit TDP1 at micromolar concentrations (0.19-2.3 µM) and demonstrated low cytotoxicity in the T98G glioma cell line. The effect of the terpene fragment, the linker structure, and the adamantane residue on the biological properties of the new compounds was investigated. Based on molecular docking results, we suppose that adamantane derivatives of resin acids bind to the TDP1 covalent intermediate, forming a hydrogen bond with Ser463 and hydrophobic contacts with the Phe259 and Trp590 residues and the oligonucleotide fragment of the substrate.

Toward green flotation: Interaction of a sophorolipid biosurfactant with a copper sulfide.

The United Nations' Sustainable Development Goals have sparked growing interest in biosurfactants from many surfactant-loaded industries including those utilizing froth flotation for mineral separation. However, the interaction of biosurfactants with mineral surfaces is currently poorly understood. We bridge this gap by studying adsorption of a yeast-derived bola acidic sophorolipid (ASL) biosurfactant on djurleite (Cu1.94S). The methods used include Hallimond flotation, contact angle, adsorption isotherm, zeta potential, leaching measurements, and X-ray photoelectron spectroscopy (XPS). To facilitate the interpretation of the adsorption results, we characterize the activity of ASL at the air-water interface and measure its critical micelle concentration (CMC) at different pH using static surface tension. We find ASL to be a multifunctional surfactant with an unusual, pH-sensitive interfacial behavior. At the air-water interface, ASL is most active at pH 8, while its CMC goes through minimum as low as 40 µM at pH 7. The surfactant adsorption at the djurleite-water interface makes the sulfide surface hydrophilic at acidic pH and hydrophobic at neutral and basic pH. In addition, ASL has strong affinity to copper sulfide and demonstrates metal leaching properties. Finally, ASL demonstrates detergency properties. We offer a mechanistic interpretation of these findings. Our results provide a basis for the application of acidic glycolipids in froth flotation and have implications for their application in ion separation using hydrometallurgical routes, as well as for the chemical stability of metal sulfides in environmental systems.

Inhibition of Tyrosyl-DNA Phosphodiesterase 1 by Lipophilic Pyrimidine Nucleosides.

Inhibition of DNA repair enzymes tyrosyl-DNA phosphodiesterase 1 and poly(ADP-ribose)polymerases 1 and 2 in the presence of pyrimidine nucleoside derivatives was studied here. New effective Tdp1 inhibitors were found in a series of nucleoside derivatives possessing 2',3',5'-tri-O-benzoyl-d-ribofuranose and 5-substituted uracil moieties and have half-maximal inhibitory concentrations (IC50) in the lower micromolar and submicromolar range. 2',3',5'-Tri-O-benzoyl-5-iodouridine manifested the strongest inhibitory effect on Tdp1 (IC50 = 0.6 µM). A decrease in the number of benzoic acid residues led to a marked decline in the inhibitory activity, and pyrimidine nucleosides lacking lipophilic groups (uridine, 5-fluorouridine, 5-chlorouridine, 5-bromouridine, 5-iodouridine, and ribothymidine) did not cause noticeable inhibition of Tdp1 (IC50 > 50 µM). No PARP1/2 inhibitors were found among the studied compounds (residual activity in the presence of 1 mM substances was 50-100%). Several O-benzoylated uridine and cytidine derivatives strengthened the action of topotecan on HeLa cervical cancer cells.

FN3 protein fragment containing two type III fibronectin domains from B. longum GT15 binds to human tumor necrosis factor alpha in vitro.

Most species of the genus Bifidobacterium contain the gene cluster PFNA, which is presumably involved in the species-specific communication between bacteria and their hosts. The gene cluster PFNA consists of five genes including fn3, which codes for a protein containing two fibronectin type III domains. Each fibronectin domain contains sites similar to cytokine-binding sites of human receptors. Based on this finding we assumed that this protein would bind specifically to human cytokines in vitro. We cloned a fragment of the fn3 gene (1503 bp; 501 aa) containing two fibronectin domains, from the strain B. longum subsp. longum GT15. After cloning the fragment into the expression vector pET16b and expressing it in E. coli, the protein product was purified to a homogenous state for further analysis. Using the immunoferment method, we tested the purified fragment's ability to bind the following human cytokines: IL-1ß, IL-6, IL-10, TNFα. We developed a sandwich ELISA system to detect any specific interactions between the purified protein and any of the studied cytokines. We found that the purified protein fragment only binds to TNFα.

Activation of CO2 at the electrode-electrolyte interface by a co-adsorbed cation and an electric field.

Carboxylate *CO2- has recently been identified as the first intermediate of the CO2 electroreduction independent of the reaction pathway. However, on the fundamental level, the structural and electronic properties of *CO2- remain poorly understood especially under the electrocatalytic conditions, which limits our capacity to rationally control the transformation of this reaction intermediate to CO or formate. To close this gap, we model using density functional theory (DFT) the interactions of *CO2- with the copper Cu(111) surface and a co-adsorbed sodium cation in the electric double layer (EDL), as well as the effects of electrode potential on these interactions. We demonstrate that *CO2- is activated by a co-adsorbed alkali cation most strongly when it forms with the cation a noncovalent bond (ion pair), where the cation is coordinated in the on-top position. The most stable structure of this ion pair with a sodium cation is hydration-shared. An external negative electric field not only enhances activation of *CO2- but also tilts it in the *CO2- plane, elongating the metal-C bond and contracting the metal-O bond. This tilting facilitates hydrogenation of the C atom and dissociation of the surface-coordinated C-O bond. Based on a detailed analysis of the projected density of states (pDOS), we interpret these findings in terms of electrostatic and chemical effects. The provided insights can help understand the relationship between properties of the catalytic system and its catalytic activity in the CO2 conversion to CO and formate, and hence help develop new CO2 electroreduction catalysts.

On the origin of the elusive first intermediate of CO2 electroreduction.

We resolve the long-standing controversy about the first step of the CO2 electroreduction to fuels in aqueous electrolytes by providing direct spectroscopic evidence that the first intermediate of the CO2 conversion to formate on copper is a carboxylate anion *CO2- coordinated to the surface through one of its C-O bonds. We identify this intermediate and gain insight into its formation, its chemical and electronic properties, as well as its dependence on the electrode potential by taking advantage of a cutting-edge methodology that includes operando surface-enhanced Raman scattering (SERS) empowered by isotope exchange and electrochemical Stark effects, reaction kinetics (Tafel) analysis, and density functional theory (DFT) simulations. The SERS spectra are measured on an operating Cu surface. These results advance the mechanistic understanding of CO2 electroreduction and its selectivity to carbon monoxide and formate.

Nitrogen-containing polymers as a platform for CO2 electroreduction.

Heterogeneous electroreduction of CO2 has received considerable attention in the past decade. However, none of the earlier reviews has been dedicated to nitrogen-containing polymers (N-polymers) as an emerging platform for conversion of CO2 to industrially useful chemicals. The term 'platform' is used here to underscore that the role of N-polymers is not only to serve as direct catalysts (through loaded metals) but also as co-catalysts/promoters and stabilizing agents. This review covers the current state, advantages, challenges, and prospects of the application of N-polymer-metal composites, also referred as polymer functionalized, coated, or modified electrodes, as well as functional hybrid materials, for the electrocatalytic conversion of CO2. It briefly surveys the efficiencies of the N-polymer-metal electrodes already used for this application, methods of their fabrication, and proposed mechanisms of their catalytic activities.

Stabilization of Silicon Carbide (SiC) micro- and nanoparticle dispersions in the presence of concentrated electrolyte.

Achieving a stable and robust dispersion of ultrafine particles in concentrated electrolytes is challenging due to the shielding of electrostatic repulsion. Stable dispersion of ultrafine particles in concentrated electrolytes is critical for several applications, including electro-codeposition of ceramic particles in protective metal coatings. We achieved the steric stabilization of SiC micro- and nano-particles in highly concentrated electroplating Watts solutions using their controlled coating with linear and branched polyethyleneimines (PEI) as dispersants. Branched polyethyleneimine of 60,000 MW effectively disperses both microparticles and nanoparticles at a concentration of 1000 ppm. However, lower polymer dosages and smaller polymers fail to disperse, presumably due to insufficient coverage and bridging flocculation. Dispersion stability correlates well with the adsorption density of PEI on microparticles. We discuss the results in the framework of DLVO theory and suggest possible dispersion mechanisms. However, though the dispersion is enhanced with extended adsorption time, the residual PEI in solution adversely affects electroplating. We overcome this drawback by precoating the particles with the polymer and resuspending them in Watts solution. With this novel approach, we obtained robust dispersions. These results offer new possibilities to control dispersion at high electrolyte concentration, as well as bring new insights into the dispersion phenomenon.

Beneficial effects of cerium oxide nanoparticles in development of chondrocyte-seeded hydrogel constructs and cellular response to interleukin insults.

The harsh inflammatory environment associated with injured and arthritic joints represents a major challenge to articular cartilage repair. In this study, we report the effect of cerium oxide nanoparticles, or nanoceria, in modulating development of engineered cartilage and in combating the deleterious effects of interleukin-1α. Nanoceria was found to be biocompatible with bovine chondrocytes up to a concentration of 1000 µg/mL (60,000 cells/µg of nanoceria), and its presence significantly improved compressive mechanical properties and biochemical composition (i.e., glycosaminoglycans) of engineered cartilage. Raman microspectroscopy revealed that individual chondrocytes with internalized nanoceria have increased concentrations of proline, procollagen, and glycogen as compared with cells without the nanoparticles in their vicinity. The inflammatory response due to physiologically relevant quantities of interluekin-1α (0.5 ng/mL) is partially inhibited by nanoceria. To the best of the authors' knowledge, these results are the first to demonstrate a high potential for nanoceria to improve articular cartilage tissue properties and for their long-term treatment against an inflammatory reaction.

Linking interfacial chemistry of CO2 to surface structures of hydrated metal oxide nanoparticles: hematite.

A better understanding of interaction with dissolved CO2 is required to rationally design and model the (photo)catalytic and sorption processes on metal (hydr)oxide nanoparticles (NPs) in aqueous media. Using in situ FTIR spectroscopy, we address this problem for rhombohedral 38 nm hematite (α-Fe2O3) nanoparticles as a model. We not only resolve the structures of the adsorbed carbonate species, but also specify their adsorption sites and their location on the nanoparticle surface. The spectral relationships obtained present a basis for a new method of characterizing the microscopic structural and acid-base properties (related to individual adsorption sites) of hydrated metal (hydr)oxide NPs using atmospherically derived CO2 as a probe. Specifically, we distinguish two carbonate species suggesting two principally different adsorption mechanisms. One species, which is more weakly adsorbed, has an inner-sphere mononuclear monodentate structure which is formed by a conventional ligand-exchange mechanism. At natural levels of dissolved carbonate and pH from 3 to 11, this species is attached to the most acidic/reactive surface cations (surface states) associated with ferrihydrite-like surface defects. The second species, which is more strongly adsorbed, presents a mixed C and O coordination of bent CO2. This species uniquely recognizes the stoichiometric rhombohedral {104} facets in the NP texture. Like in gas phase, it is formed through the surface coordination of molecular CO2. We address how the adsorption sites hosting these two carbonate species are affected by the annealing and acid etching of the NPs. These results support the nanosize-induced phase transformation of hematite towards ferrihydrite under hydrous conditions, and additionally show that the process starts from the roughened areas of the facet intersections.

Rational design of interfacial properties of ferric (hydr)oxide nanoparticles by adsorption of fatty acids from aqueous solutions.

Notwithstanding the great practical importance, still open are the questions how, why, and to what extent the size, morphology, and surface charge of metal (hydr)oxide nanoparticles (NPs) affect the adsorption form, adsorption strength, surface density, and packing order of organic (bio)molecules containing carboxylic groups. In this article, we conclusively answer these questions for a model system of ferric (hydr)oxide NPs and demonstrate applicability of the established relationships to manipulating their hydrophobicity and dispersibility. Employing in situ Fourier transform infrared (FTIR) spectroscopy and adsorption isotherm measurements, we study the interaction of 150, 38, and 9 nm hematite (α-Fe(2)O(3)) and ∼4 nm 2-line ferrihydrite with sodium laurate (dodecanoate) in water. We discover that, independent of morphology, an increase in size of the ferric (hydr)oxide NPs significantly improves their adsorption capacity and affinity toward fatty acids. This effect favors the formation of bilayers, which in turn promotes dispersibility of the larger NPs in water. At the same time, the local order in self-assembled monolayer (SAM) strongly depends on the morphological compatibility of the NP facets with the geometry-driven well-packed arrangements of the hydrocarbon chains as well as on the ratio of the chemisorbed to the physically adsorbed carboxylate groups. Surprisingly, the geometrical constraints can be removed, and adsorption capacity can be increased by negatively polarizing the NPs due to promotion of the outer-sphere complexes of the fatty acid. We interpret these findings and discuss their implications for the nanotechnological applications of surface-functionalized metal (hydr)oxide NPs.

Adsorption of fatty acids on iron (hydr)oxides from aqueous solutions.

The interaction of iron (hydr)oxides with fatty acids is related to many industrial and natural processes. To resolve current controversies about the adsorption configurations of fatty acids and the conditions of the maximum hydrophobicity of the minerals, we perform a detailed study of the adsorption of sodium laurate (dodecanoate) on 150 nm hematite (α-Fe(2)O(3)) particles as a model system. The methods used include in situ FTIR spectroscopy, ex situ X-ray photoelectron spectroscopy (XPS), measurements of the adsorption isotherm and contact angle, as well as the density functional theory (DFT) calculations. We found that the laurate adlayer is present as a mixture of inner-sphere monodentate mononuclear (ISMM) and outer-sphere (OS) hydration shared complexes independent of the solution pH. Protonation of the OS complexes does not influence the conformational order of the surfactant tails. One monolayer, which is filled through the growth of domains and is reached at the micellization/precipitation edge of laurate, makes the particles superhydrophobic. These results contradict previous models of the fatty acid adsorption and suggest new interpretation of literature data. Finally, we discovered that the fractions of both the OS laurate and its molecular form increase in D(2)O, which can be used for interpreting complex spectra. We discuss shortcomings of vibrational spectroscopy in determining the interfacial coordination of carboxylate groups. This work advances the current understanding of the oxide-carboxylate interactions and the research toward improving performance of fatty acids as surfactants, dispersants, lubricants, and anticorrosion reagents.

Tailoring (bio)chemical activity of semiconducting nanoparticles: critical role of deposition and aggregation.

The impact of deposition and aggregation on (bio)chemical properties of semiconducting nanoparticles (NPs) is perhaps among the least studied aspects of aquatic chemistry of solids. Employing a combination of in situ FTIR and ex situ X-ray photoelectron spectroscopy (XPS) and using the Mn(II) oxygenation on hematite (α-Fe(2)O(3)) and anatase (TiO(2)) NPs as a model catalytic reaction, we discovered that the catalytic and sorption performance of the semiconducting NPs in the dark can be manipulated by depositing them on different supports or mixing them with other NPs. We introduce the electrochemical concept of the catalytic redox activity to explain the findings and to predict the effects of (co)aggregation and deposition on the catalytic and corrosion properties of ferric (hydr)oxides. These results offer new possibilities for rationally tailoring the technological performance of semiconducting metal oxide NPs, provide a new framework for modeling their fate and transport in the environment and living organisms, and can be helpful in discriminating between weakly and strongly adsorbed species in spectra.