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Ensemble Docking Coupled to Linear Interaction Energy Calculations for Identification of Coronavirus Main Protease (3CLpro) Non-Covalent Small-Molecule Inhibitors
Marko Jukič, Dušanka Janežič, Urban Bren, 2020, original scientific article

Abstract: SARS-CoV-2, or severe acute respiratory syndrome coronavirus 2, represents a new strain of Coronaviridae. In the closing 2019 to early 2020 months, the virus caused a global pandemic of COVID-19 disease. We performed a virtual screening study in order to identify potential inhibitors of the SARS-CoV-2 main viral protease (3CLpro or Mpro). For this purpose, we developed a novel approach using ensemble docking high-throughput virtual screening directly coupled with subsequent Linear Interaction Energy (LIE) calculations to maximize the conformational space sampling and to assess the binding affinity of identified inhibitors. A large database of small commercial compounds was prepared, and top-scoring hits were identified with two compounds singled out, namely 1-[(R)-2-(1,3-benzimidazol-2-yl)-1-pyrrolidinyl]-2-(4-methyl-1,4-diazepan-1-yl)-1-ethanone and [({(S)-1-[(1H-indol-2-yl)methyl]-3-pyrrolidinyl}methyl)amino](5-methyl-2H-pyrazol-3-yl)formaldehyde. Moreover, we obtained a favorable binding free energy of the identified compounds, and using contact analysis we confirmed their stable binding modes in the 3CLpro active site. These compounds will facilitate further 3CLpro inhibitor design.
Keywords: COVID-19, SARS-CoV-2, Mpro, 3CLpro, 3C-like protease, virtual screening, inhibitors, in silico drug design, free-energy calculations
Published: 10.12.2020; Views: 239; Downloads: 49
.pdf Full text (2,99 MB)

Hemicelluloses application for synthetic polymer surfaces functionalisation
Nena Dimitrušev, 2016, doctoral dissertation

Abstract: The main aim of this thesis was development of thin functional layers from hemicelluloses xylans on the polyethylene terephthalate (PET) surfaces. Hemicelluloses, xylans, as renewable polymers, were chemically modified in order to introduce anionic and cationic functional groups. Two types of chemical modifications were performed: carboxymethylation in order to increase anionic nature of xylans and improve their hydrophilic character and cationization for introducing of amino groups and antimicrobial characteristics. Both types of modifications were successful, which was proved by ATR FTIR and raman techniques, elemental analysis, total bound nitrogen determination, size exclusion chromatography and polyelectrolyte titrations. Polyelectrolyte titration results showed increased amounts of deprotonated carboxyl groups in carboxymethylated xylans as well as increased amounts of protonated groups in cationized xylans. Antimicrobial activity of xylans was investigated by the determination of minimal inhibitory concentration (MIC) against S. aureus, E. coli, and C. albicans and it was found out that the samples with higher amounts of active amino groups showed lower MIC. Cationised glucuronoxylan showed significantly higher antimicrobial activities against S. aureus in comparison to cationised arabinoxylan and nonmodified xylan samples. However, none of xylan samples was active against fungi. In order to analyze surface properties of solid surfaces, films from xylan (nonmodified and modified) water solution was formed by casting method. The surface chemical composition of films were investigated by x-ray photoelectron spectroscopy (XPS), and the results showed that films made from carboxymethylated xylans had significantly higher amounts of carbon fraction involved in O=C-O bonds, compared to nonmodified xylans. Such surface chemical structure caused higher surface free energy with higher electron-donor contribution and thus high hydrophilicity of these films. Films made by cationized xylans had higher amount of carbon involved in C-C and C-H bonds compared to nonmodified and lower surface free energy with increase of dispersive Lifshitz Van der Waals contribution. In order to thoroughly investigate the adsorption of xylans onto synthetic surfaces Quartz crystal microbalance with dissipation unit (QCM-D) was used. For these measurements model films were prepared from PET by spin coating technique. Adsorption studies were performed at different conditions, such as pH, concentration and ionic strength of xylan solutions. For all the chemically modified xylans the adsorption was improved at pH 5 and with increased ionic strength with divalent ions. The adsorption increased as well with increasing of xylan solution concentration. In order to improve binding of adsorbed xylans so-called anchoring polymers were applied. When anchoring polymers were applied, better adsorption and fixation of adsorbed layer was confirmed, thus the adsorbed masses of xylans after rinsing with water were significantly higher in comparison to the adsorption without immediate anchoring layer. On the basis of these results, real PET fabric surfaces were treated using chemically modified xylans. The xylan solutions were applied onto PET fabric samples using spray coating technique, which is the best approximate to the large-scale procedures. In the first step, PET fabric was activated by alkaline hydrolysis and after that, anchoring agents and carboxymethylated and/or cationized xylans were adsorbed. The success of these treatments was evaluated by the determination of negative and positive charge of the treated PET fabric samples by titration techniques, methylene blue and acid orange 7 adsorption methods, water contact angles and wettability determination. From the potentiometric titrations results it was clearly seen that each new adsorbed layer onto PET fabric totally screened the charge of the former one. FESEM images showed rather thick layers covering the
Keywords: hemicellulose, polyethylene terephthalate, glucuronoxylan, arabinoxylan, carboxymethylation, cationization, PET model films, quartz crystal microbalance, PET fabric, surface free energy, wettability, antimicrobial properties
Published: 11.03.2016; Views: 1213; Downloads: 82
.pdf Full text (4,53 MB)

Electrochemical impedance spectroscopy as a tool in the plate making process optimization
Tomislav Cigula, Regina Fuchs-Godec, Miroslav Gojo, Mojca Slemnik, 2012, original scientific article

Abstract: The structure of the porous aluminium-oxide layer, which builds non-image areas, has the most significant influence on the quality of final graphical product. This paper presents the results of the application of EIS in the characterisation and detection of changes on the aluminium-oxide layer caused by chemical processing in highly alkaline solution. The Al2O3 layer was characterised using SEM, fractal dimension and surface free energy calculationand EIS analysis. The results of the investigation showed that chemical processing has a significant influence on the structure of aluminiumoxide which could lead to a decrease in the quality of the printing plate. EIS enables the detection of changes on the aluminium- oxide layer. Thetwo equivalent circuits are proposed. Based on modelling with the obtained EIS spectra, precise evaluation of developing time in which complete removal of the photoactive layer is achieved. This makes EIS a powerful tool in optimizing chemical processing of lithographic printing plates.
Keywords: printing plate, chemical processing, SEM, surface free energy, EIS
Published: 10.07.2015; Views: 757; Downloads: 66
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Tine Curk, 2012, master's thesis

Abstract: A grafted polymer layer can be used to prevent the deposition of colloidal particles on a solid surface. This thesis presents Monte Carlo simulations of hard-sphere colloids pushed to a polymer brush under the influence of external fields (e.g. gravity). For weak fields colloids can not penetrate the brush and the effective potential acting on a single colloid is approximately quadratic. The phase diagram of three-dimensional hard-sphere colloids, that in one dimension are constrained to a plane by a harmonic potential, is presented. Under the influence of sufficiently strong external fields colloids penetrate the brush and form internally ordered, columnar structures that span the polymer layer. The morphology of the patterns that form depends sensitively on the strength of the applied field. We propose a simple phenomenological theory that accounts for the main characteristics of the observed behaviour. The present results suggest a simple experimental method to determine the surface polymer coverage.
Keywords: Soft Matter, Monte Carlo Method, Wang-Landau Algorithm, Free Energy, Polymer Brush, Colloids, Ordering
Published: 04.03.2013; Views: 1639; Downloads: 73
.pdf Full text (6,75 MB)

Heike M. A. Ehmann, 2012, doctoral dissertation

Abstract: The goal of this thesis is the structuring of cellulose nanocrystals using different organofunctional silane compounds and different cationic species to prepare highly functional materials with tailored properties. In addition different new aspects and approaches for the structural characterization of functionalised cellulose nanocrystals (CNC) functionalised with different organofunctionalalkoxysilanes as well as cationic species have been introduced. Cellulose nanocrystals (CNC) are prepared using three different acidic conditions to hydrolyse microcrystalline cellulose (MCC). The sulphuric acid hydrolysis introduces highly negative charged sulphate groups on the CNC. The aqueous nanocrystalline cellulose suspensions (aNCS) are analysed in terms of ζ-potential related to the pH and concentration to investigate the stability while dynamic light scattering (DLS) is used to investigate the size distribution. The hydrochloric acid hydrolysis in contrast only removes the amorphous regions but the so obtained CNC are less stabilized (decreased ζ-potential) and tend to agglomerate very fast. The use of the mixture of both acids (HCl and H2SO4) during the hydrolysis of MCC introduces less sulphate groups compared with the sulphuric acid hydrolysis. AFM investigations show that the shapes of the CNC are highly influenced by the hydrolysis conditions. While the shape of the H2SO4 hydrolysed CNC is rod like, while the shape of the other two CNC samples is more spherical in nature. One of the major topic in this work is the analysis of aNCS in aqueous solutions by small angle x-ray scattering (SAXS). The use of the generalized indirect Fourier transformation (GIFT) method allows the analysis of these systems and structural properties such as shape, size and surface charge of aNCS can be assessed. Using this kind of characterisation it can be seen that the shape of the H2SO4 hydrolysed CNC is definitely rod like while the other CNC sample can be described with spheres. In addition to the aNCS characterisation different substrates (Si-wafer, glass slides, polystyrene, etc.) are equipped with aNCS using a variety of different deposition methods (e.g. spin coating, solution casting, dip coating). The resulting films are studied in terms of morphology AFM, SARFUS and SEM. Sophisticated scattering techniques are employed for surface structural characterisation as grazing incidence small angel x-ray scattering. The determination of surface free energies allows conclusions about the hydrophilicity and hydrophobicity as well as the interaction capacity with different liquids. It can be seen that besides the hydrophilic nature of the CNC also hydrophobic interactions are present. The highly negative charged CNC sample which was prepared using sulphuric acid hydrolysis is found to be best suitable for the further hybridization with different organofunctional silanes and for the layer by layer approach (LBL) with different cationic species. The organofunctionalalkoxysilanes which were used in this study can be divided into three groups (e.g filler, surface functionalisation silanes, cross linking silanes). Depending on the nature of the organic residue the silanes are capable to introduce functionalities with enhanced hydrophobic and olephobic properties. The surface energies are investigated using contact angle method, while the surface energies are calculated using three different model approaches (OWRK, Wu, Acid-Base). The most increased hydrophobic and oleophobic properties were measured for trimethylfluorophenylsilantriol (PFTEOS). The morphology of the coated silanes is investigated using SAFRUS technique. It can be seen that nearly all silanes can be coated as homogeneous films onto different substrates (Si-wafer, SURFs, glass slides) with different methods (spin coating, solution casting). The macroscopic appearance of solution casted silanes is investigated using optical microscopy. The differences of the structural nature of the so obtained coatings and detaching films were investigated...
Keywords: Cellulose nanocrystals, sol-gel chemistry, organofunctionalalkoxysilanes, hybrid materials, small angle x-ray scattering, generalized indirect Fourier Transformation, quartz crystal microbalance dissipation, surface free energy, surface functionalisation, layer by layer
Published: 28.11.2012; Views: 1866; Downloads: 121
.pdf Full text (8,59 MB)

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