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Search results for: THROMBIN BINDING APTAMER
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Mechanism of antifreeze protein functioning and the “anchored clathrate water” concept
PublicationIn liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case the interactions of water molecules with the protein surface shift...
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Fuzyjne polimerazy DNA – otrzymywanie, charakterystyka i zastosowanie
PublicationObecnie reakcje PCR (ang. Polymerase Chain Reaction) wykazują bardzo szerokie zastosowanie w diagnostyce medycznej, biologii molekularnej czy inżynierii genetycznej. Efektywność tych reakcji rozumiana jako wydajność i wierność przeprowadzonej amplifikacji jest nieodłącznie związana ze stosowaną polimerazą DNA i warunkami prowadzenia reakcji PCR. Aby sprostać wymaganiom stawianym przez nowoczesne metody diagnostyczne oraz współczesną...
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Thermodynamics aspects of interactions between acridine derivatives and DNA
PublicationDNA is a molecular target for many anticancer and antiviral drugs. Therefore, a clear understanding of the interaction of small molecules with DNA is important in the rational design of ligands that can bind to DNA with high affinity and selectivity. There are several methods to investigate interactions between drug and DNA. Some of them measure changing into DNA structures, such as lengthening and untwisting of helix of DNA. Other...
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Genotoxic properties of glucosinolates and isothiocyanates present in Brassica vegetables
PublicationThe bioactive phytochemicals found in Brassica vegetables, in this number glucosinolates (GLS), as well as products of their degradation such as isothiocyanates (ITC) and indoles, are regarded as the most promising chemopreventive compounds. These secondary metabolites display stron antibiological activity and constitute defence system preventing the development of agrophages attacking Brassica plants. Such properties suggest...
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Toward Mechanosynthesis of Diamondoid Structures: X. Commercial Capped CNT SPM Tip as Nowadays Available C2 Dimer Placement Tool for Tip-Based Nanofabrication
PublicationAccording to Drexler, advanced mechanosynthesis will employ advanced nano-machines, but advanced nano-machines will themselves be products of advanced mechanosynthesis. This circular relationship must be broken via TBN technology development. In this article, the possibility of using easily available commercial CNT tips to assemble carbon-based intermediate generations of nano-devices is considered. Mechanosynthesis of a target...
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Novel primosomal protein B from Clostridium pastuerianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Antioxidant activities and bioactive components in some berries
PublicationThe objective of this study was to evaluate the antioxidant and binding effects of gooseberry, a less-stud-ied berry, and to compare with blueberry and cranberry in the model of interaction with human serum albumin (HSA). The relationship between the scavenging properties of dietary polyphenols of the selected berries and their affinities for HSA were investigated by fluorescence anal- ysis. In order to perform the extraction and...
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Long range molecular dynamics study of interactions of the eukaryotic glucosamine-6-phosphate synthase with fructose-6-phosphate and UDP-GlcNAc
PublicationGlucosamine-6-phosphate synthase (EC 2.6.1.16) is responsible for catalysis of the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5 diphospho Nacetyl- d-glucosamine (UDP-GlcNAc), is an essential substrate for assembly of bacterial and fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which...
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The structurally similar TRFH domain of TRF1 and TRF2 dimers shows distinct behaviour towards TIN2
PublicationThe telomere repeat binding-factor 1 and 2 (TRF1 and TRF2) proteins of the shelterin complex bind to duplex telomeric DNA as homodimers, and the homodimerization is mediated by their TRFH (TRF-homology) domains. We performed molecular dynamic (MD) simulations of the dimer forms of TRF1TRFH and TRF2TRFH in the presence/absence of the TIN2TBM (TIN2, TRF-interacting nuclear protein 2, TBM, TRF-binding motif) peptide. The MD results...
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Novel primosomal protein B from Clostridium pasteurianum
PublicationPriB is a primosomal protein that catalyzes DNA replication in Procaryota. The replication pathway starts with PriA protein - the initiator protein that binds to a DNA replication fork, unwinds double-stranded DNA and role of PriB is to stabilize PriA on the DNA. However there are many biochemical differences in replication mechanism in bacteria and only some of them use PriB proteins. A few of PriB proteins were published and...
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Immunization with an anti-idiotypic antibody against the broadly lipopolysaccharide-reactive antibody WN1 222-5 induces Escherichia coli R3-core-type specific antibodies in rabbits
PublicationThe mouse monoclonal antibody (mAb) WN1 222-5 recognizes a carbohydrate epitope in the inner core region of LPS that is shared by all strains of Escherichia coli and Salmonella enterica and is able to neutralize their endotoxic activity in vitro and in vivo. Immunization of mice with mAb WN1 222-5 yielded several anti-idiotypic mAbs one of which (mAb S81-19) competitively inhibited binding of mAb WN1 222-5 to E. coli and Salmonella...
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Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition
PublicationFat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors...
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Comparative Study of the Mechanical Behaviour of Bitumen- and Cement-Dominated Mixtures with Reclaimed Asphalt
PublicationThe bitumen emulsion-based recycling is a commonly used maintenance treatment in the rehabilitation of low-and medium-volume roads in Europe. Nevertheless, the wide range of climatic conditions across the continent resulted in the variety of mixture concepts and the requirements being adopted for various local conditions. In this regard, the most commonly used parameter to distinguish between the main mixture concepts is bitumen...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow 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...
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Unraveling the Interplay between DNA and Proteins: A Computational Exploration of Sequence and Structure-Specific Recognition Mechanisms
PublicationMy PhD dissertation focused on DNA-protein interactions and the recognition of specific DNA sequences and structures. I discovered that acidic amino acid residues (Asp/Glu) play a crucial role by exhibiting a preference for cytosine. Their contribution to binding affinity depends on nearby cytosines, balancing electrostatic repulsion with specific interactions. Acidic residues act as negative selectors, discouraging non-cytosine...
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Flexibility in PAM recognition expands DNA targeting in xCas9
PublicationxCas9 is an evolved variant of the CRISPR-Cas9 genome editing system, engineered to improve specificity and reduce undesired off-target effects. How xCas9 expands the DNA targeting capability of Cas9 by recognising a series of alternative protospacer adjacent motif (PAM) sequences while ignoring others is unknown. Here, we elucidate the molecular mechanism underlying xCas9’s expanded PAM recognition and provide critical insights...
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Reduction of the strontium titanate doped by Ytrium ceramics observed by X-ray photoemission spectroscopy method
Open Research DataYtrium-doped strontium titanate (YSTF) ceramics materials were manufactured by three various methods: 1) standard solid-state reaction method from Y2O3 (Sigma Aldrich, 99,9%), TiO2 (Sigma Aldrich, 99%) and SrCO3 (Sigma Aldrich,98%), 2) Pechini method, 3) wet method.
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Lower rim substituted p-tert-butyl-calix[4]arene. Part 17. synthesis, extractive and ionophoric properties of p-tert-butylcalix[4]arene appended with hydroxamix acid moieties
PublicationThe synthesis and characterization of four p-tert-butylcalix[4]arene-hydroxamic acidc are reported. The dependence of the metal ion binding, assessed by liquid extraction of the metal nitrates from water into dichloromethane in individual and competitive experiments, on the ligand structure, is presented. The results showed that those ligands could be successfully used in separation process of trnasition and heavy metals often...
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Dissociation pathways of protonated water clusters
PublicationRelative abundances of positively ionized water clusters formed in a low-pressure electrical discharge as function of reduced electric field were obtained by using drift cell and quadrupole mass spectrometer. It was noticed that some clusters say with n=4 were more abundant than others, at comparable drift conditions. Dissociation energies have been derived from equilibrium conditions for relative clusters abundances. The Hartree-Fock...
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Iron(III)-selective materials based on a catechol-bearing amide for optical sensing
PublicationThe synthesis and ion-binding properties of a new amide L derived from 3,4-dihydroxybenzoic acid are described. Due to the presence of a catechol unit, the compound interacts selectively with iron(III) in organic solvent (dimethyl sulfoxide, DMSO) to produce a color change from pale yellow to green. The incorporation of the ligand L into polymeric matrices or its encapsulation into surfactant-based spheres enables analyte detection...
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Acceleration deforms exponential decays into generalized Zipf-Mandelbrot laws
PublicationAn exponentially decaying system looks as if its decay was a generalized power or double-exponential law, provided one takes into account the relativistic time dilation in a detector, the delay of the emitted signal, and the accelerations of both the source and the detector. The same mathematical formula can be found in generalizations of the Zipf-Mandelbrot law in quantitative linguistics and in the dynamics of ligand binding...
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Document transformations for data processing in information systems
PublicationAtrykuł przedstawia podejście do automatyzacji transformacjidokumentów użytkownika bazujące na technologii XML. W artykuleprzedstawiony został system Endoscopy Recommender System.ERS wykorzystuje dedykowane transformacje XML Schema do Java, Java dodokumentów XML. Dzięki tym transformacjom procesy pobierania iprzechowywania danych zostały w pełni zautomatyzowane.Zaimplementowane podejście XML data binding umożliwia walidacjępodstawowych...
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Antioxidant properties of ferrous flavanol mixtures
PublicationInteraction of metal, especially iron ions with flavanols is considered as an important feature of these compounds and is believed to contribute to their both antioxidant and prooxidant properties. The aim of this study was to examine how Fe2+ binding to form a 4:1 (flavanol:Fe2+) mixtures affects the antioxidant properties of flavanols. ABTS∗ scavenging, protection against fluorescence bleaching induced by AAPH and hypochlorite,...
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Azo group(s) in selected macrocyclic compounds
PublicationAzobenzene derivatives due to their photo- and electroactive properties are an important group of compounds finding applications in diverse fields. Due to the possibility of controlling the trans–cis isomerization, azo-bearing structures are ideal building blocks for development of e.g. nanomaterials, smart polymers, molecular containers, photoswitches, and sensors. Important role play also macrocyclic compounds well known for...
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Experiments on Preserving Pieces of Information in a Given Order in Holographic Reduced Representations and the Continuous Geometric Algebra Model
PublicationGeometric Analogues of Holographic Reduced Representations (GAc, which is the continuous version of the previously developed discrete GA model) employ role-filler binding based on geometric products.Atomic objects are real-valued vectors in n-dimensional Euclidean space and complex statements belong to a hierarchy of multivectors. The property of GAc and HRR studied here is the ability to store pieces of information in a given...
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Collagen type II–hyaluronan interactions – the effect of proline hydroxylation: a molecular dynamics study
PublicationHyaluronan–collagen composites have been employed in numerous biomedical applications. Understanding the interactions between hyaluronan and collagen is particularly important in the context of joint cartilage function and the treatment of joint diseases. Many factors affect the affinity of collagen for hyaluronan. One of the important factors is the ratio of 3- or 4-hydroxy proline to proline residues. This article presents...
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Methods for Elucidation of DNA-Anticancer Drug Interactions and Their Applications in the Development of New Drugs
PublicationDNA damaging agents including anthracyclines, camptothecins and platinum drugs are among most frequently used drugs in the chemotherapeutic routine. Due to their relatively low selectivity for cancer cells, administration is associated with adverse side effects, whereas the inherent genotoxicity of these drugs is associated with risk of developing secondary cancers. Development of new drugs, which could be spared of these drawbacks...
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Chemical, Aroma and Pro-Health Characteristics of Kaffir Lime Juice—The Approach Using Optimized HS-SPME-GC-TOFMS, MP-OES, 3D-FL and Physiochemical Analysis
PublicationThe study aimed to provide the chemical, aroma and prohealth characteristics of the kaffir lime juice. A procedure using solid-phase microextraction with gas chromatography (SPME-GC-TOFMS) was optimized and validated for the determination of terpenes of kaffir lime. Main physicochemical parameters: pH, vitamin C, citric acid and °Brix were evaluated. Micro- and macro elements were determined using microwave plasma optic emission...
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Phosphate and Thiophosphate Biphenyl Analogs as Steroid Sulfatase Inhibitors
PublicationIn the present work, we report convenient methods for the synthesis and biological evaluation of phosphate and thiophosphate biphenyl derivatives exhibiting steroid sulfatase (STS) activity. The described synthesis is based on straightforward preparation of biphenyl-4-ol and 40-hydroxybiphenyl- 4-carboxylic acid ethyl ester modified with various phosphate or thiophosphate moieties. The inhibitory effects of these compounds were...
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Dissociation energies of protonated water clusters
PublicationRelative abundances of positively ionized water clusters formed in a low-pressure electrical discharge as function of reduced electric field were obtained by using drift cell and quadrupole mass spectrometer. It was noticed that some clusters say with n = 4 were more abundant than others, at comparable drift conditions. Dissociation energies have been derived from equilibrium conditions for relative clusters abundances. The Hartree-Fock...
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Bridging the gap between business process models and use-case models
PublicationToday's software development methodologies are equipped with a plethora of methods and techniques for business process engineering and Requirements Engineering. However, heavy investments in IT have not brought forth expected results. What seems to be lacking is a systematic approach that consolidates both disciplines to gain a synergistic effect. To address this challenge we extend Use-Case Driven Approach (UCDA) by binding use...
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Chromogenic macrocyclic derivatives of azoles - synthesis and properties,
PublicationNew azocrown ethers comprising imidazoles in the macrocycle have been synthesized. Imidazole, 2-methyl-, 4-methyl-, and 4-phenylimidazole were incorporated to form macrocyclic units by coupling with the appropriate bis-diazonium salts. The syntheseswere performed under high dilution conditions. The X-ray structure of a water adduct of the 21-membered crown ether derivative of 4-methylimidazole 8 has been solved. Metal...
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Azomacrocyclic derivatives of imidazole: synthesis, structure, and metal ion complexation properties
PublicationNew azocrown ethers comprising imidazoles in the macrocycle have been synthesized. Imidazole, 2-methyl-, 4-methyl-, and 4-phenylimidazole were incorporated to form macrocyclic units by coupling with the appropriate bis-diazonium salts. The syntheseswere performed under high dilution conditions. The X-ray structure of a water adduct of the 21-membered crown ether derivative of 4-methylimidazole 8 has been solved. Metal...
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Preliminary study of linear viscoelasticity limits of cold recycled mixtures determined in Simple Performance Tester (SPT)
PublicationThe publication presents methodology developed for determination of linear viscoelasticity limits for cold recycled mixtures with cement and bituminous emulsion using Simple Performance Tester (SPT). Methodology was verified on reference materials (PCV and steel dummy specimens, cement concrete and asphalt concrete) to comply with elasticity and viscoelasticity theory. The developed methodology enabled determination of linear viscoelasticity...
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Investigation of interaction between xanthene dye rhodamine B and metagenomic-derivated methylthioadenosine phosphorylase RSFP
PublicationIn the previous study we found that the expression of the metagenomic - derived methylthioadenosine phosphorylase gene (rsfp) in E. coli cells and the presence of rhodamine B in the growth medium were crucial for the pink fluorescence of one E. coli colony from Antarctic soil metagenomic library (Cieśliński et al., 2009). In this study, rsfp gene expression was induced by an arabinose promoter in an LMG194 E. coli strain and the...
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The Ellenbogen's “Matter as Software” Concept for Quantum Computer Implementation. C60 and X@C60 Molecules as Available Molecular Building Blocks (MBBs) for Tip-Based Nanofabrication (TBN) of Quantum Computing Devices
PublicationThe TBN bottom-up strategy of building quantum devices from C60 and X@C60 MBBs is proposed as an extension of the Ellenbogen's “Matter as Software” idea to quantum information processing. The capped SW or DW CNT STM tip is considered as device for manipulating C60 and X@C60 molecules. In this article, the possibility of using easily available on the market C60 Fullerene and endohedral X@C60 molecules together with commercial CNT...
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Influence of steam cooking on pro-health properties of Small and Large variety of Momordica charantia
PublicationSteam cooking is one of the most common preparations of Momordicacharantia dishes. This method improved the tastiness of the fruits but at the same time, some changes occurred in the volatile and non-volatile parts of their food matrices. In this study, for the first time these properties were correlated with the found substances affecting the bioactivity of this fruit. Two varieties of Momordicacharantia were analysed and compared....
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Novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(1,3,5-triazin-2-ylamino)guanidine derivatives: Inhibition of human carbonic anhydrase cytosolic isozymes I and II and the transmembrane tumor-associated isozymes IX and XII, anticancer activity, and molecular modeling studies
PublicationA series of novel 2-(2-arylmethylthio-4-chloro-5-methylbenzenesulfonyl)-1-(6-substituted-4-chloro-1,3,5-triazin-2-ylamino)guanidine derivatives 9–20 have been synthesized by substitution of chlorine atom at the 1,3,5-triazine ring in compounds 5–8 with 3- or 4-aminobenzenesulfonamide and 4-(aminomethyl)benzenesulfonamide hydrochloride. All the synthesized compounds were evaluated for their inhibitory activity toward hCA I, II,...
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Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein
PublicationHsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP...
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Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants
PublicationThe genome feature of SARS-CoV-2 leads the virus to mutate and creates new variants of concern. Tackling viral mutations is also an important challenge for the development of a new vaccine. Accordingly, in the present study, we undertook to identify B- and T-cell epitopes with immunogenic potential for eliciting responses to SARS-CoV-2, using computational approaches and its tailoring to coronavirus variants. A total of 47 novel...
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A new division of bacterial UvrA homologues
PublicationThe UvrA protein is a DNA-binding and damage-recognition enzyme which participates in the prokaryotic type nucleotide excision repair (NER) pathway. It has recently been noted that some bacterial genomes comprise additional uvrA genes which encode five distinct types of UvrA homologue. We investigated the sequences of over 2400 bacterial genomes and found 130 examples of bacteria containing uvrA 2 genes. The sequence analyses conducted...
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Entropy Production Associated with Aggregation into Granules in a Subdiffusive Environment
PublicationWe study the entropy production that is associated with the growing or shrinking of a small granule in, for instance, a colloidal suspension or in an aggregating polymer chain. A granule will fluctuate in size when the energy of binding is comparable to k_{B}T, which is the “quantum” of Brownian energy. Especially for polymers, the conformational energy landscape is often rough and has been commonly modeled as being self-similar...
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Ion recognition properties of new pyridine-2,6-dicarboxamide bearing propeller-like pendant residues: multi-spectroscopic approach
PublicationThe synthesis and ion binding properties of new amide derived from propeller-like tris(2-pyridyl)amine and 2,6-pyridinedicarboxylic acid chloride were described. Amide binds divalent metal cations: copper(II), nickel(II), zinc(II), and lead(II) in acetonitrile. In acetonitrile:water mixture (9:1 v/v) amide interacts only with copper(II) and nickel(II) cations forming complexes of 1:1 stoichiometry. It was found that the introduction...
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Linear antenna microwave chemical vapour deposition of diamond films on long-period fiber gratings for bio-sensing applications
PublicationThe growth processes of nanocrystalline diamond (NCD) thin films on fused silica optical fibers with UV-induced long-period gratings (LPGs) were investigated with regard to biosensing applications. The films were deposited using a linear antenna microwave plasma enhanced chemical vapor deposition system, which allows for the growth of diamond at temperatures below 350°C. The films exhibited a high refractive index n = 2.32, as...
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Molecular docking studies towards development of novel Gly-Phe analogs for potential inhibition of Cathepsin C (dipeptidyl peptidase I).
PublicationCathepsin C is a cysteine protease required for activation of various pro-inflammatory serine proteases and, essentially, is of interest as a therapeutic target. Cathepsin C coordinate system was employed as a model to study the interaction of some already available inhibitors of Cathepsin C. Compounds containing Gly-Phe fragment with functional groups at its ends were designed by knowledge based approach. Using AutoDock and...
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Structural and mechanical properties of hydroxyapatite coatings formed by ion-beam assisted deposition
PublicationThe ion-beam assisted deposition (IBAD) is an advanced method capable of producing crystalline coatings at low temperatures. We determined the characteristics of hydroxyapatite Ca10(PO4)6(OH)2 target and coatings formed by IBAD using X-ray photoemission spectroscopy (XPS), X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM) and energy dispersive X-ray (EDX). The composition of the coatings'...
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Application of the 2-deoxyglucose scaffold as a new chiral probe for elucidation of the absolute configuration of secondary alcohols
PublicationHerein, we present the application of 2-deoxy-D-glucose derivatives as chiral probes for elucidation of the absolute configuration of chiral secondary alcohols. The probes are attached to the studied molecules via glycosylation reaction and the resulting products are examined by a set of standard 2D NMR experiments. The absolute configuration of an oxymethine carbon atom binding the probe is established on a basis of a set of diagnostic...
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Novel Diazocrowns with Pyrrole Residue as Lead(II) Colorimetric Probes
PublicationNovel 18- and 23-membered diazomacrocycles were obtained with satisfactory yields by diazocoupling of aromatic diamines with pyrrole in reactions carried under high dilution conditions. X-ray structure of macrocycle bearing five carbon atoms linkage was determined and described. Compounds were characterized as chromogenic heavy metal ions receptors. Selective color and spectral response for lead(II) was found in acetonitrile and...
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Desensitization of glucosamine-6-phosphate synthase to inhibition by UDP-GlcNAc
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase, known also as L-Glutamine: D-fructose-6-phosphate amidotransferase, catalyzes the first committed step in the pathway leading to the ultimate formation of UDP-GlcNAc. The final product of this pathway is an activated precursor of numerous macromolecules containing amino sugars, including chitin and mannproteins in fungi, peptidoglycan and lipopolysaccharides in bacteria, and glycoproteins...
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(4-(Bis(4-Fluorophenyl)Methyl)Piperazin-1-yl)(Cyclohexyl)Methanone Hydrochloride (LDK1229): A New Cannabinoid CB1 Receptor Inverse Agonist from the Class of Benzhydryl Piperazine Analogs
PublicationSome inverse agonists of cannabinoid receptor type 1 (CB1) have been demonstrated to be anorectic antiobesity drug candidates. However, the first generation of CB1 inverse agonists, represented by rimonabant (SR141716A), otenabant, and taranabant, are centrally active, with a high level of psychiatric side effects. Hence, the discovery of CB1 inverse agonists with a chemical scaffold distinct from these holds promise for developing...