Exceptional stability of the sugammadex-solasodine complex: Insights from experimental and theoretical studies.

Sugammadex (SGM) is the first cyclodextrin (CD)-based selective relaxant binding agent. We investigated its ability to capture natural aminosteroid phytotoxins, and assessed its potential as an antidote for intoxication. Solasodine (SS), a toxic alkaloid from the Solanaceae family, was chosen as the model compound.

Adsorption of common greywater pollutants and nutrients by various biochars as potential amendments for nature-based systems: Laboratory tests and molecular dynamics.

Spruce wood and Typha (wetland plant) derived biochars pyrolyzed at 350 °C and 600 °C were tested for their sorption affinity for organic pollutants (diclofenac, methylparaben, benzotriazole and sodium 1-decanesulfonate) and nutrients (nitrate, ammonium, phosphate and boron) commonly found in greywater. Batch and column studies combined with molecular dynamics modelling determined the sorption capacity, kinetics, and described the underlying mechanisms. The spruce biochar (600 °C) exhibited the highest sorption capacity mainly for the tested organics.

Local and cooperative structural transitions of double-stranded DNA in choline-based deep eutectic solvents.

The possibility of using deep eutectic solvents (DESs) as co-solvents for stabilizing and preserving the native structure of DNA provides an attractive opportunity in the field of DNA biotechnology. The rationale of this work is a systematic investigation of the effect of hydrated choline-based DES on the structural stability of a 30-base-pair double-stranded DNA model via a combination of spectroscopic experiments and MD simulations. UV absorption and CD experiments provide evidence of a significant contribution of DESs to the stabilization of the double-stranded canonical (B-form) DNA structure.

Computational Study of Complex Formation between Hyaluronan Polymers and Polyarginine Peptides at Various Ratios.

Hyaluronic acid, a naturally occurring carbohydrate biopolymer in human tissues, finds wide application in cosmetics, medicine, and material science. Its anionic properties play a crucial role in its interaction with positively charged macromolecules and ions. Among these macromolecules, positively charged arginine molecules or polyarginine peptides demonstrate potential in drug delivery when complexed with hyaluronan.

Hexahelicene DNA-binding: Minor groove selectivity, semi-intercalation and chiral recognition.

In this contribution, we focused on a fundamental study targeting the interaction of water-soluble [6]helicene derivative 1 (1-butyl-3-(2-methyl[6]helicenyl)-imidazolium bromide) with double-stranded (ds) DNA. A synthetic 30-base pair duplex, plasmid, chromosomal calf thymus and salmon DNA were investigated using electrochemistry, electrophoresis and spectroscopic tools supported by molecular dynamics (MD) and quantum mechanical approaches. Both experimental and theoretical work revealed the minor groove binding of 1 to the dsDNA.

Competitive formation of molecular inclusion complexes of chlordecone and β-hexachlorocyclohexane with natural cyclodextrins: DFT and molecular dynamics study.

Context: Chlordecone (CLD) and β-hexachlorocyclohexane (β-HCH) are chlorinated pesticides that coexist as persistent organic pollutants in the groundwater of several countries in the Caribbean, being an environmental issue. This work evaluates theoretically the competitive formation of host-guest complexes pesticides@cyclodextrines (CDs) as an alternative for water purification and selective separation of pesticides.

Methods: Quantum mechanical calculations based on density functional theory (DFT) and classical molecular dynamics (MD) simulations were used to achieve information on geometries, energies, structure, and dynamics of guest-host complexes in the gas phase, implicit solvent medium, and in aqueous solutions.

Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme.

Low solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the polypeptide precursors into mature viral components, a very crucial step for virus life cycle.

Adsorption of Hexavalent Chromium Using Activated Carbon Produced from ssp.: Comparison between Lab Experiments and Molecular Dynamics Simulations.

Adsorption is one of the most successful physicochemical approaches for removing heavy metal contaminants from polluted water. The use of residual biomass for the production of adsorbents has attracted a lot of attention due to its cheap price and environmentally friendly approach. The transformation of Sargassum-an invasive brown macroalga-into activated carbon (AC) via phosphoric acid thermochemical activation was explored in an effort to increase the value of Sargassum seaweed biomass.

Explaining the interaction of mangiferin with MMP-9 and NF-ƙβ: a computational study.

Mangiferin is a glycosylated xanthone widely distributed in nature, which exhibits wide pharmacological activities, highlighting its anti-cancer properties. Mangiferin interferes with inflammation, lipid, and calcium signaling, which selectively inhibits multiple NFkB target genes as interleukin-6, tumor necrosis factor, plasminogen, and matrix metalloproteinase, among others. In this work, the interactions of this polyphenol with MMP-9 and NF-κβ are characterized by using computational chemistry methods.

Modulation of global stability, ligand binding and catalytic properties of trypsin by anions.

Specific salts effect is well-known on stability and solubility of proteins, however, relatively limited knowledge is known regarding the effect on catalytic properties of enzymes. Here, we examined the effect of four sodium anions on thermal stability and catalytic properties of trypsin and binding of the fluorescent probe, p-aminobenzamidine (PAB), to the enzyme. We show that the specific anions effect on trypsin properties agrees with the localization of the anions in the Hofmeister series.

Specific anion effect on properties of HRV 3C protease.

Specific salts effect is intensively studied from the prospective of modification of different physico-chemical properties of biomacromolecules. Limited knowledge of the specific salts effect on enzymes led us to address the influence of five sodium anions: sulfate, phosphate, chloride, bromide, and perchlorate, on catalytic and conformational properties of human rhinovirus-14 (HRV) 3C protease. The enzyme conformation was monitored by circular dichroism spectrum (CD) and by tyrosines fluorescence.

Metallic Effects on p-Hydroxyphenyl Porphyrin Thin-Film-Based Planar Optical Waveguide Gas Sensor: Experimental and Computational Studies.

Metal effects on the gas sensing behavior of metal complexes of 5,10,15,20-tetrakis(4-hydroxyphenyl)porphyrin (THPP) thin film was investigated in terms of detecting NO gas by the planar optical waveguide. For this purpose, several THPP and metal complexes were synthesized with different central metal ions: Co(II), Ni(II), Cu(II), and Zn(II). Planar optical gas sensors were fabricated with the metalloporphyrins deposited on K ion-exchanged soda-lime glass substrate with the spin coating method serving as host matrices for gas interaction.

Interactions between a dsDNA Oligonucleotide and Imidazolium Chloride Ionic Liquids: Effect of Alkyl Chain Length, Part I.

Ionic liquids (ILs) have become nearly ubiquitous solvents and their interactions with biomolecules has been a focus of study. Here, we used the fluorescence emission of DAPI, a groove binding fluorophore, coupled with molecular dynamics (MD) simulations to report on interactions between imidazolium chloride ([Im]) ionic liquids and a synthetic DNA oligonucleotide composed entirely of T/A bases (7(TA)) to elucidate the effects ILs on a model DNA duplex. Spectral shifts on the order of 500-1000 cm, spectral broadening (~1000 cm), and excitation and emission intensity ratio changes combine to give evidence of an increased DAPI environment heterogeneity on added IL.

Valorisation of agricultural waste derived biochars in aquaculture to remove organic micropollutants from water - experimental study and molecular dynamics simulations.

In this work, we evaluated the valorisation of agricultural waste materials by transforming coconut husks and shells, corncobs and rice straw into biochar for water treatment in aquaculture. We compared the biochars' suitability for removal of organic micropollutants (acetaminophen, oxytetracycline, tetracycline, enrofloxacin, atrazine, diuron and diclofenac) from surface water needed for aquaculture. The biochars were prepared by three methods ranging from inexpensive drum kilns (200 °C) to pyrolysis with biogasfication (350-750 °C).

Computational and experimental assessment of pH and specific ions on the solute solvent interactions of clay-biochar composites towards tetracycline adsorption: Implications on wastewater treatment.

Experimental and computational investigations have been conducted in this study to assess the influence of municipal waste pyrolyzed biochar impregnated clay composites on antibiotic removal as a material for wastewater treatment and simultaneous value-addition for waste. The surface potential (zeta potential) of the pristine biochar and composite samples are found to be within the range ~10 to ~ -40 mV in the pH range 2-10. The presence of different inorganic salt solutions influences the electrophoretic mobility of the dispersed phase in a suspension, as well as its zeta potential.

Substituent Effect on Porphyrin Film-Gas Interaction by Optical Waveguide: Spectrum Analysis and Molecular Dynamic Simulation.

Substituent effect on optical gas sensing performance in porphyrin-based optical waveguide detection system was studied by molecular dynamics simulation (MDS), absorption/emission spectrum analysis, and optical waveguide (OWG) detection. The affinities of porphyrin with seven types of substituents (-H, -OH, -tBu, -COOH, -NH, -OCH, -SO) on para position of meso-phenyl porphyrin toward gas molecules in adsorption process were studied in different size of boxes with the same pressure and concentration. Analyte gases (CO, HS, HCl, NO) were exposed to porphyrin film in absorption spectrophotometer, and in OWG with evanescent field excited by a guiding laser light with 670 nm wavelength.

Potential Application of Ionic Liquids in Pharmaceutical Dosage Forms for Small Molecule Drug and Vaccine Delivery System.

Ionic liquids are salts in which the ions are poorly coordinated, which causes them to exist in liquid form below 100°C, or at room temperature. Therefore, these are also defined as room temperature ionic liquids (RTILs). In ionic liquids, at least one ion has a delocalized charge and one component is organic, which prevents the formation of a stable solid form of crystal lattice.

NGR (Asn-Gly-Arg)-targeted delivery of coagulase to tumor vasculature arrests cancer cell growth.

Induction of selective thrombosis and infarction in tumor-feeding vessels represents an attractive strategy to combat cancer. Here we took advantage of the unique coagulation properties of staphylocoagulase and genetically engineered it to generate a new fusion protein with novel anti-cancer properties. This novel bi-functional protein consists of truncated coagulase (tCoa) and an NGR (GNGRAHA) motif that recognizes CD13 and αβ integrin receptors, targeting it to tumor endothelial cells.

Nonconjugated Acyloxy Group Deactivates the Intramolecular Charge-Transfer State in the Carotenoid Fucoxanthin.

We used ultrafast transient absorption spectroscopy to study excited-state dynamics of the keto-carotenoid fucoxanthin (Fx) and its two derivatives: 19'-butanoyloxyfucoxanthin (bFx) and 19'-hexanoyloxyfucoxanthin (hFx). These derivatives occur in some light-harvesting systems of photosynthetic microorganisms, and their presence is typically related to stress conditions. Even though the hexanoyl (butanoyl) moiety is not a part of the conjugated system of hFx (bFx), their absorption spectra in polar solvents exhibit more pronounced vibrational bands of the S state than for Fx.

Aggregation and metal-complexation behaviour of THPP porphyrin in ethanol/water solutions as function of pH.

The effect of pH change on 5,10,15,20-Tetrakis(4-hydroxyphenyl)-21H,23H-porphine (THPP) with its aggregation as function of water-ethanol mixture was studied with UV-vis, fluorescence, Raman and computational analysis. In neutral pH, THPP was present as free-base and, increasing the water amount, aggregation occurred with the formation of H- and J-aggregates. The aggregation constant and the concentration of dimers were calculated, other information about the dimer aggregation were evaluated by computational study.

RGD delivery of truncated coagulase to tumor vasculature affords local thrombotic activity to induce infarction of tumors in mice.

Induction of thrombosis in tumor vasculature represents an appealing strategy for combating cancer. Herein, we combined unique intrinsic coagulation properties of staphylocoagulase with new acquired functional potentials introduced by genetic engineering, to generate a novel bi-functional fusion protein consisting of truncated coagulase (tCoa) bearing an RGD motif on its C-terminus for cancer therapy. We demonstrated that free coagulase failed to elicit any significant thrombotic activity.

Structure and dynamics of solvated hydrogenoxalate and oxalate anions: a theoretical study.

Hydrogenoxalate (charge -1) and oxalate (charge -2) anions and their solvated forms were studied by various computational techniques. Ab initio quantum chemical calculations in gas phase, in implicit solvent and microsolvated (up to 32 water molecules) environment were performed in order to explore a potential energy surface of both anions. The solvation envelope of water molecules around them and the role of water on the conformation of the anions was revealed by means of Born-Oppenheimer molecular dynamics simulations and optimization procedures.