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1.
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: 237; Downloads: 49
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2.
Selection of non-small cell lung cancer patients for intercalated chemotherapy and tyrosine kinase inhibitors
Matjaž Zwitter, Antonio Rossi, Massimo Di Maio, Maja Pohar Perme, Gilberto Lopes, 2017, original scientific article

Abstract: Background: When treating patients with advanced non-small cell lung cancer (NSCLC) with tyrosine kinase inhibitors and chemotherapy, intercalated schedule with time separation between the two classes of drugs should avoid their mutual antagonism. In a survey of published trials, we focus on relation between eligibility criteria and effectiveness of intercalated treatment. Methods: Published documents were identified using major medical databases, conference proceedings and references of published trials. Median progression-free survival (PFS) was taken as the basic parameter of treatment efficacy. Correlation between characteristics of patients and median PFS was assessed through the Pearson's correlation coefficient and the coefficient of determination, separately for first-line and second-line setting. Results: The series includes 11 single-arm trials and 18 randomized phase II or phase III trials with a total of 2903 patients. Treatment-naive patients or those in progression after first-line treatment were included in 16 and 13 trials, respectively. In 14 trials, only patients with non-squamous histology were eligible. Proportion of patients with nonsquamous carcinoma (in first-line setting), proportion of never-smokers (both in first- and second-line setting) and proportion of epidermal growth factor receptor (EGFR) mutant patients (both in first- and second-line setting) showed a moderate or strong correlation with median PFS. In six trials of intercalated treatment applied to treatment-naive EGFR-mutant patients, objective response was confirmed in 83.1% of cases and median PFS was 18.6 months. Conclusions: Most suitable candidates for intercalated treatment are treatment-naive patients with EGFR-mutant tumors, as determined from biopsy or liquid biopsy. For these patients, experience with intercalated treatment is most promising and randomized trials with comparison to the best standard treatment are warranted.
Keywords: lung cancer, NSCLC, intercalated treatment, EGFR, tyrosine -kinase inhibitors
Published: 30.10.2017; Views: 656; Downloads: 223
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3.
Modified surface of Cu, Zn, Cu10Zn and Cu40Zn with expression of hydrophobic properties for the purpose of corrosion protection
Gregor Žerjav, 2015, doctoral dissertation

Abstract: Copper and its alloys are soft and malleable metals and are often used for fabricating structures and monuments open to the atmosphere where they are subject to corrosion attack. There are many ways to protect metal against corrosion: corrosion inhibitors, protective layers, hydrophobic layers. He aim was to develop a simple technological process for forming hydrophobic, protective coatings for protection of Cu, Cu10Zn, Cu40Zn and Zn under conditions of atmospheric corrosion as tested in simulated urban rain. Carboxylic acids form self-assembled hydrophobic layers by adsorption to the positively charged metal surfaces via their carboxylic group. Corrosion inhibitors are often used to protect metals against corrosion in closed system. Most used corrosion inhibitors to protect Cu and its alloys is benzotriazole (BTAH) which showed good results in different environments. 2-mercaptobenzimidazole (2-MBI) is a derivative of BTAH with stronger affinity to adsorb on the Cu surface and showed good corrosion protection results in acidic solutions. Corrosion protection properties of the layers were tested with the use of electrochemical methods: potentiodynamic polarization and electrochemical impedance spectroscopy. The results were complement with immersion test where the weight loss was obtained. The properties of the layers were explored with surface-analytical methods: measurement of the contact angles, X-ray photoelectron spectroscopy, scanning electron microscopy with a chemical analysis and glow discharge optical emission spectroscopy. First the optimal conditions to produce hydrophobic coatings with the use of carboxylic acids were explored. The inhibition efficiency increased with increasing carbon chain length, longer preparation time in ethanol solution and increasing concentration of carboxylic acid. The inhibition of corrosion of Cu, Cu10Zn, Cu40Zn and Zn in simulated urban rain was further studied using the self-assembly of BTAH, 2-MBI and SA in ethanol solution, as individual inhibitors and in combinations. The morphology of layers differed greatly. The results of electrochemical measurements and weight loss immersion test ruled out BTAH as a possible inhibitor, unless combined with stearic acid. In the cases of Cu40Zn and Zn it even promoted corrosion. In contrast, 2-MBI gave good results, and even better in combination with stearic acid. SA layers provided the best long term corrosion protection of all tested inhibitors and exhibited the highest contact angles. 2-MBI provided less protection than SA. Combining organic inhibitor and stearic acid improves the corrosion protection properties of the self-assembled layers compare to individual layers. To make the procedure of layer preparation more appropriate for industrial application the time of immersion was decreased. Layers prepared on Cu with 1 min immersion time showed adequate corrosion protection of Cu in simulated urban rain. We also studied the possibility of combining SA with vitamin E in the layer preparation procedure. The modified layers formed with combination of Vitamin E and SA showed better corrosion inhibition properties for Cu and Cu40Zn in simulated urban rain as individual layers. Combining inhibitor and carboxylic acid together to prepare corrosion protective layers has a positive effect on the corrosion properties of the layers. Layers made combining corrosion inhibitor and carboxylic acid showed better corrosion protection than individual layers. The self-assembling process is a fast process shown by the tests made on the Cu layers with shorter immersion time. The addition of Vitamin E in the preparation of layers with carboxylic acids shows a positive effect on the corrosion properties of layers.
Keywords: copper, brass, corrosion, simulated urban rain, inhibitors, carboxylic acid, benzotriazole, 2-mercaptobenzimidazole
Published: 30.11.2015; Views: 929; Downloads: 105
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4.
Interakcije zdravil z zaviralci angiotenzinske konvertaze
Marjetka Pal, Polonca Ferk, 2012, review article

Abstract: V članku predstavljamo pregled potencialno klinično pomembnih interakcij zdravil (DDIs) z zaviralci angiotenzinske konvertaze (ACE). Na osnovi pregleda dveh knjig Stockleyʼs Drug Interactions in dveh preko spleta dostopnih podatkovnih zbirk o DDIs smo opisali več kot deset takih DDIs, razložili njihove mehanizme, opredelili njihov klinični pomen ter navedli možnosti za njihovo preprečevanje oz. ustrezno obravnavo. Večina DDIs z zaviralci ACE je farmakodinamičnih, le nekaj jih je na nivoju farmakokinetike. Največ DDIs z zaviralci ACE se odraža kot prekomerno znižanje krvnega tlaka, hiperkaliemija ali nefrotoksičnost. Dokazali so tudi, da zaviralci ACE zvečajo toksičnost litija in da lahko vplivajo na pojav hudih preobčutljivostnih reakcij pri bolnikih, ki so prejeli parenteralne pripravke železa, ali pri bolnikih, ki sočasno jemljejo alopurinol. Prav tako je zaviralce ACE zaradi njihove lastne hepatotoksičnosti potrebno previdno kombinirati z drugimi hepatoksičnimi zdravili. Zaradi velike porabe zaviralcev ACE je pogostost neželenih učinkov zdravil zaradi DDIs z zaviralci ACE visoka. Ugodno pa je, da lahko v večini primerov teh DDIs ustrezno ukrepamo že s primernim kliničnim in laboratorijskim spremljanjem bolnikov oz. s prilagoditvijo odmerkov sočasno predpisanih zdravil.
Keywords: angiotensin-converting enzyme inhibitors, drug-drug interactions, drug-interaction databases
Published: 10.07.2015; Views: 1476; Downloads: 51
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5.
An effect of sodium dodecylsulfate on the corrosion of copper in sulphuric acid media
Regina Fuchs-Godec, Valter Doleček, 2004, original scientific article

Abstract: The effect of sodium dodecylsulfate (SDS) on copper corrosion in a solution of 0.5 M H2SO4 + x M SDS was studied using electrochemical polarisation measurements. The critical micelle concentration (CMC) of SDS in 0.5 M H2SO4 is 8 * 10-4 M, and the experimental concentrations of SDS were in the range below and above the CMC. It was found that SDS is a good anodic inhibitor at lower anodic overpotentials, i.e. very close to the rest potential. Adsorptionof the inhibitor obeys the Langmuir isotherm. Plots of log [▫$theta$▫/(1-▫$theta$▫)] versus log ▫$c_{inh}$▫ yielded straight lines with a slope change at the CMC. Accordingly, the CMC could be determined from these electrochemical measurements. The values of ▫$Delta$▫▫$G_{ads}$▫ calculated from the Langmuir plots are negative, suggesting that the inhibitive action of SDS in 0.5 M H2SO4 results from the electrostatic adsorption of C12H25SO4- ions onto the positively charged copper surface.
Keywords: electrochemistry, corrosion inhibitors, surfactants, potentiodynamic polarisation, corrosion kinetic parameters, copper, Langmuir isotherm, critical micelle concentration, sulphuric acid
Published: 01.06.2012; Views: 1204; Downloads: 87
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6.
Inhibitory effect of non-ionic surfactants of the TRITON-X series on the corrosion of carbon steel in sulphuric acid
Regina Fuchs-Godec, 2007, original scientific article

Abstract: The corrosion inhibition characteristics of non-ionic surfactants of the TRITON-X series, known as TRITON-X-100 and TRITON-X-405, on stainless steel (SS) type X4Cr13 in sulphuric acid were investigated by potentiodynamic polarisation measurements. It was found that these surfactants act as good inhibitors of the corrosion of stainless steel in 2 mol L-1 H2SO4 solution, but the inhibition efficiency strongly depends on the electrode potential. Thepolarisation data showed that the non-ionic surfactants used in this study acted as mixed-type inhibitors and adsorb on the stainless steel surface, in agreement with the Flory-Huggins adsorption isotherm. Calculated Gads values are -57.79 kJ mol-1 for TRITON-X-100, and -87.5 kJ mol-1 for TRITON-X-405. From the molecular structure it can be supposed that these surfactants adsorb on the metal surface through two lone pairs of electrons on the oxygen atoms of the hydrophilic head group, suggesting a chemisorption mechanism.
Keywords: electrochemistry, corrosion inhibitors, non-ionic surfactants, Flory-Huggins isotherm, critical micelle concentration, sulphuric acid
Published: 01.06.2012; Views: 1403; Downloads: 84
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7.
Protection of copper and its alloys using corrosion inhibitor-literature review
Milorad V. Tomić, Miomir Pavlović, Milovan Jotanović, Regina Fuchs-Godec, 2010, original scientific article

Abstract: A review of the literature dealing with the electrochemical corrosion of copper and its alloys with purpose to find the most suitable inhibitor for its protection has been done. According to their chemical composition of corrosion inhibitors are divided into inorganic and organic inhibitors. Inhibition of alloying metals are possible (such as the addition of arsenic alloy components in brass, preventing its unzincanization). The paper reviews the theoretical basis of application of inhibitors to protect metals from corrosion as well as an overview of current research application of inhibitorsto protect copper and copper alloys. Benzotriazole (BTA) is most often used corrosion inhibitor for copper and its alloys in acidic and alkaline solution, because of its high inhibition efficiency. The lowest concentration of inhibitor for protection of copper in various solutions was 0.05%, and for the protection of copper in contact with steel is 0.1%. On the surface of copper and brass BTA forms a protective Cu-BTA film. However, BTA is like many other synthesized organic inhibitors is very toxic and if used invery small concentrations. It turnedout that the AETD, AETDA and PTAT good corrosion inhibitors of copper mixed type with the efficiency of inhibition increases with concentration. Due to the adverse effects on the environment, health and other bodies in recent times the focus of researchis transferred to the inhibiting action of biological molecules or mixtures of natural compounds called "Green inhibitors".
Keywords: corrosion inhibitors, protection of metals, inorganic inhibitors, organic inhibitors, alloys elements, green inhibitors
Published: 31.05.2012; Views: 1728; Downloads: 96
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8.
Inhibition properties of TRITON-X-100 on ferritic stainless steel in sulphuricacid at increasing temperature
Regina Fuchs-Godec, Gregor Žerjav, 2009, original scientific article

Abstract: The inhibiting action of a non-ionic surfactant of the TRITON-X series (TRITON-X-100) on stainless steel type X4Cr13 in 1.0 M H2SO4 solution at five different temperatures was investigated by the potentiodynamic polarisation measurements. The inhibition efficiency has been calculated in the presence and in the absence of the inhibitor. The experimental data suggest that the inhibition efficiency increases with increasing concentration of the TRITON-X-100, and decreases with the increasing temperature. Adsorption of the non-ionic surfactant used here obeys the Flory- Huggins isotherm. The thermodynamic parameters, such as, the heat of adsorption, adsorption entropy, and the adsorption free energy, have been calculated by employing thermodynamic equations. Kinetic parameters, also been evaluated.
Keywords: non-ionic surfactants, corrosion inhibitors, sulphuric acid, Flory-Huggins adsorption isotherm
Published: 31.05.2012; Views: 1387; Downloads: 63
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9.
The adsorption, CMC determination and corrosion inhibition of some N-alkyl quaternary ammonium salts on carbon steel surface in 2 M H2SO4
Regina Fuchs-Godec, 2006, original scientific article

Abstract: Electrochemical measurements were performed to investigate the effectiveness of cationic surfactants of the N-alkyl quaternary ammonium salt type, i.e. myristyltrimethylammonium chloride (MTACl), cetyldimethylbenzylammonium chloride (CDBACl), and trioctylmethylammonium chloride (TOMACl), as corrosion inhibitors for type X4Cr13 ferritic stainless steel in 2 M H2SO4 solution. Potentiodynamic polarization measurements showed that these surfactants hinder both anodic and cathodic processes, i.e. act as mixed-type inhibitors. It was found that the adsorption of the N-alkyl ammonium ion in 2 M H2SO4 solution follows the Langmuir adsorption isotherm. Plots of log ▫$[/theta$▫/(1-▫$/theta$▫)] versus log▫$c_{inh}$▫ yielded straight lines with a slope, which changed drasticallyat the critical micelle concentration (CMC) of the surfactants studied. Accordingly, the CMC could be accurately determined from these measurements. The calculated values of the free energy of adsorption ▫$/Delta$▫▫$G_{ads}$▫ are, in cases when the charge on the metal surface is negative with respect to the PZC, relatively high what is characteristically for the chemisorption. On the other hand, for positive metal surfaces it is assumed that ▫$SO_4^{2-}$▫ anions are adsorbed first, so the cationic species would be limited by the surface concentration of anions. Accordingly ▫$/Delta$▫▫$G_{ads}$▫ values were lower in this case and the adsorption is due to merely electrostatic attraction, which is characteristically of physisorption.
Keywords: electrochemistry, corrosion inhibitors, cationic surfactants, Langmuir isotherm, corrosion kinetic parameters, critical micelle concentration, sulphuric acid
Published: 30.05.2012; Views: 2015; Downloads: 86
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