Search results for: MOLECULAR DATA
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Anthrapyridones, a novel group of antitumour non-cross resistant anthraqui-none analogues. Synthesis and molecular basis of the cytotoxic activity towards K562/DOX cells
PublicationOpracowano syntezę nowej grupy związków z grupy antrapirydonów z odpowiednimi hydrofobowymi lub hydrofilowymi podstawnikami. Badano działanie tych związków na komórkach K562/S i K562/DOX (nadekspresja P-glikoproteiny). Stwierdzono, że zwiększenie lipofilowości zwiększa szybkość P-gp zależnego efluksu z komórki.
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An influence of molecular weight, deacetylation degree of chitosan xerogels on their antimicrobial activity and cytotoxicity. Comparison of chitosan materials obtained using lactic acid and CO2 saturation.
PublicationThis paper presents a comparison of the antimicrobial activity and cytotoxicity against L929 cells of chitosan xerogels prepared by dissolving the polymer in a solution of lactic acid (LA) or carbonic acid (CO2) and then freeze-drying. There was no simple relationship between the antimicrobial activity and cytotoxicity of the samples obtained using both techniques (LA and CO2). Chitosan materials obtained by the LA method in a...
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Design, synthesis, and molecular docking of new 5-HT reuptake inhibitors based on modified 1,2-dihydrocyclopenta[b] indol-3(4H)-one scaffold
PublicationA new group of serotonin reuptake inhibitors containing 1,2-dihydrocyclopenta[b]indol-3(4H)-one scaffoldwas synthesized, starting from indole 5-((1H-indol-3-yl)(1,3-dioxane-4,6-diones as a key intermediates. Following three transformations including intramolecular cyclization and formation of imines, a series of new ligand for human serotonin transporter was obtained. The ability of these ligands to inhibit human TS3 serotonin transporter...
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Versatile method employing basic techniques of genetic engineering to study the ability of low molecular weight compounds to bind covalently with DNA in cell free systems.
PublicationMechanizm działania większości leków przeciwnowotworowych oraz związków rakotwórczych polega na ich kowalencyjnym wiązaniu z DNA. Poziom tego wiązania jest zazwyczaj bardzo niski, co powoduje, że potrzebne są niezwykle czułe metody aby kowalencyjna modyfikacja mogła być w ogóle wykryta. My podjęliśmy próbę zastosowania w tym celu prostych, szybkich i sprawdzonych technik inżynierii genetycznej: metody PCR do uzyskania fragmentu...
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Experimental and Theoretical Screening for Green Solvents Improving Sulfamethizole Solubility
PublicationSolubility enhancement of poorly soluble active pharmaceutical ingredients is of crucial importance for drug development and processing. Extensive experimental screening is limited due to the vast number of potential solvent combinations. Hence, theoretical models can offer valuable hints for guiding experiments aimed at providing solubility data. In this paper, we explore the possibility of applying quantum-chemistry-derived...
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Electrochemical simulation of metabolism for antitumor-active imidazoacridinone C-1311 and in silico prediction of drug metabolic reactions
PublicationThe metabolism of antitumor-active 5-diethylaminoethylamino-8-hydroxyimidazoacridinone (C-1311) has been investigated widely over the last decade but some aspects of molecular mechanisms of its metabolic transformation are still not explained. In the current work, we have reported a direct and rapid analytical tool for better prediction of C-1311 metabolism which is based on electrochemistry (EC) coupled on-line with electrospray...
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Vibrational Sum-Frequency Generation Activity of a 2,4-Dinitrophenyl Phospholipid Hybrid Bilayer: Retrieving Orientational Parameters from a DFT Analysis of Experimental Data
PublicationThe vibrational nonlinear activity of films of 2,4-dinitrophenyl phospholipid (DNP) at the solid interface is measured by sum-frequency generation spectroscopy (SFG). Hybrid bilayers are formed by a LangmuirSchaefer approach in which the lipid layer is physisorbed on top of a self-assembled monolayer of dodecanethiol on Pt with the polar heads pointing out from the surface. The SFG response is investigated in two vibrational frequency...
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The imidazoacridinone C-1311 induces p53-dependent senescence or p53-independent apoptosis and sensitizes cancer cells to radiation
PublicationC-1311 is a small molecule, which has shown promise in a number of preclinical and clinical studies. However, the biological response to C-1311 exposure is complicated and has been reported to involve a number of cell fates. Here, we investigated the molecular signaling which determines the response to C-1311 in both cancer and non-cancer cell lines. For the first time we demonstrate that the tumor suppressor, p53 plays a key role...
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ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
PublicationA method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances...
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IoT for healthcare applications
PublicationThis chapter summarizes IRACON contributions related to the application of IoT in healthcare. It consists of the following three sections. Section 8.1 presents the measurement campaigns and the related statistical analysis to obtain various channel models for wearable and implantable devices. In addition, the importance of physical human-body phantoms used for channel, Specific Absorption Rate (SAR), and Electromagnetic (EM) exposure...
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Exploiting the S4–S5 Specificity of Human Neutrophil Proteinase 3 to Improve the Potency of Peptidyl Di(chlorophenyl)-phosphonate Ester Inhibitors: A Kinetic and Molecular Modeling Analysis
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Optimizing of MALDI-ToF-based low-molecular-weight serum proteome pattern analysis in detection of breast cancer patients; the effect of albumin removal on classification performance.
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Molecular cloning and initial characterization of African green monkey (Cercopithecus aethiops) corticotropin releasing factor receptor type 1 (CRF1) from COS-7 cells
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Molecular Docking-Based Study of Vasopressin Analogues Modified at Positions 2 and 3 with N-Methylphenylalanine: Influence on Receptor-Bound Conformations and Interactions with Vasopressin and Oxytocin Receptors
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Preferential solvation in (amide+alcohol) binary mixtures. Part 2. The N-methylpyrrolidinone+methanol mixture at T = 313.15 K: thermodynamic resultsand molecular dynamics calculations.
PublicationBadano zjawisko preferencyjnej solwatacji amidu (N-metylopyrrolidonu) przez metanol wykorzystując dwie uzupełniające się metody: bezpośrednich pomiarów własności termodynamicznych roztworu oraz symulacji komputerowych. W metodzie pierwszej dokonano pomiarów wielkości termodynamicznych takich jak: nadmiarowa energia swobodna mieszania, nadmiarowa objętość mieszania oraz współczynnika ściśliwości izotermicznej mieszaniny,...
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Preferential solvation in (amide+alcohol) binary mixtures. Part 1. The N- methylpyrrolidinone+ethanol mixture at T = 313.15 K: thermodynamic resultsand molecular dynamics calculations.
PublicationBadano zjawisko preferencyjnej solwatacji amidu (N-metylopyrrolidonu) przez etanol wykorzystując dwie uzupełniające się metody: bezpośrednich pomiarów własności termodynamicznych roztworu oraz symulacji komputerowych. W metodzie pierwszej dokonano pomiarów wielkości termodynamicznych takich jak: nadmiarowa energia swobodna mieszania, nadmiarowa objętość mieszania oraz współczynnika ściśliwości izotermicznej mieszaniny,...
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Novel 2-(2-alkylthiobenzenesulfonyl)-3-(phenylprop-2-ynylideneamino)guanidine derivatives as potent anticancer agents – Synthesis, molecular structure, QSAR studies and metabolic stability
PublicationA series of new 2-(2-alkylthiobenzenesulfonyl)-3-(phenylprop-2-ynylideneamino)guanidine derivatives have been synthesized and evaluated in vitro by MTT assays for their antiproliferative activity against cell lines of colon cancer HCT-116, cervical cancer HeLa and breast cancer MCF-7. The obtained results indicated that these compounds display prominent cytotoxic effect. The best anticancer properties have been observed for derivatives...
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How do sterols determine the antufungal activitiy of amphotericin B? Free energy of binding between the drug and its membrane targets.
PublicationAmphotericin B (AmB) is a well-known polyene antibiotic used to treat systemic fungal infections. It is commonly accepted that the presence of sterols in the membrane is essential for the AmB biological activity, that is, for the formation of transmembrane ion channels. The selective toxicity of AmB for fungal cells is attributed to the fact that it is more potent against fungal cell membranes containing ergosterol than against...
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Hyaluronan-Chondroitin Sulfate Anomalous Crosslinking Due to Temperature Changes
PublicationGlycosaminoglycans are a wide class of biopolymers showing great lubricating properties due to their structure and high affinity to water. Two of them, hyaluronic acid and chondroitin sulfate, play an important role in articular cartilage lubrication. In this work, we present results of the all-atom molecular dynamics simulations of both molecules placed in water-based solution. To mimic changes of the physiological conditions,...
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Analysis of the Factors Affecting Static In Vitro Pepsinolysis of Food Proteins
PublicationIn this meta-analysis, we collected 58 publications spanning the last seven decades that reported static in vitro protein gastric digestion results. A number of descriptors of the pepsinolysis process were extracted, including protein type; pepsin activity and concentration; protein concentration; pH; additives; protein form (e.g., ‘native’, ‘emulsion’, ‘gel’, etc.); molecular weight of the protein; treatment; temperature; and...
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A Novel Ru(II) Polypyridine Black Dye Investigated by Resonance Raman Spectroscopy and TDDFT Calculations
PublicationThe optical properties of a new(bipyridine)2Ru(4H-imidazole) complex presenting a remarkablebroad absorption in the visible range are investigated. Thestrong overlap of the absorption with the solar radiationspectrum renders the studied complex promising as a blackabsorber and hence as a starting structure for applications inthe field of dye-sensitized solar cells. The correlations betweenstructural and electronic features for...
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Phylogenetic trees of genus Oncidium Sw. based on analysis of DNA sequences
Open Research DataGenus Oncidium Sw. is widely regarded as a polyphiletic, and the taxonomic boundaries between him and such genera as Odontoglossum Kunth. or Miltonia Lindley remain blurred. The goal of the study was to determine the phylogenetic relationships within the genus Oncidium s.lato based on the DNA sequences analysis. The correlation between molecular data...
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Combined computational-experimental approach to predict blood–brain barrier (BBB) permeation based on “green” salting-out thin layer chromatography supported by simple molecular descriptors
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Effect of in vitro gastro‐pancreatic digestion on antioxidant activity of low‐molecular‐weight (<3.5 kDa) peptides from dry‐cured pork loins with probiotic strains of LAB
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Surface-enhanced Raman scattering (SERS) and tip-enhanced Raman scattering (TERS) in label-free characterization of erythrocyte membranes and extracellular vesicles at the nano-scale and molecular level
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Investigation of mechanism of desmopressin binding in vasopressin V2 receptor versus vasopressin V1a and oxytocin receptors: Molecular dynamics simulation of the agonist-bound state in the membrane–aqueous system
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Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics
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Targeting Spike‐ACE2 Interface of SARS‐CoV‐2 and its Omicron Variant: A Comparative Screening of Potential Inhibitors for Existing and Anticipating Variants Using Molecular Modelling Approach
PublicationThe recent COVID pandemic has shown major impact on public health and economic crisis. Despite the development of many vaccines and drugs against the severe acute respiratory syndrome (SARS) coronavirus 2, the pandemic still persists. The continued spread of the virus is largely driven by the emergence of viral variants such as α, β, γ, delta, epsilon spike, omicron and its subvariants (BA.1,2,3) which can evade the current vaccines...
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Relationship between Telomere Length, TERT Genetic Variability and TERT, TP53, SP1, MYC Gene Co-Expression in the Clinicopathological Profile of Breast Cancer
PublicationThe molecular mechanisms of telomerase reverse transcriptase (TERT) upregulation in breast cancer (BC) are complex. We compared genetic variability within TERT and telomere length with the clinical data of patients with BC. Additionally, we assessed the expression of the TERT, MYC, TP53 and SP1 genes in BC patients and in BC organoids (3D cell cultures obtained from breast cancer tissues). We observed the same correlation in the...
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Simultaneous determination of thermodynamic and kinetic parameters of aminopolycarbonate complexes of cobalt(II) and nickel(II) based on isothermal titration calorimetry data
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Modeling lignin extraction with ionic liquids using machine learning approach
PublicationLignin, next to cellulose, is the second most common natural biopolymer on Earth, containing a third of the organic carbon in the biosphere. For many years, lignin was perceived as waste when obtaining cellulose and hemicellulose and used as a biofuel for the production of bioenergy. However, recently, lignin has been considered a renewable raw material for the production of chemicals and materials to replace petrochemical resources....
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Interactions of protons with furan molecules studied by collision-induced emission spectroscopy at the incident energy range of 50–1000 eV
PublicationInvestigations of the ion-molecule reactions provide insight into many fields ranging from the stellar wind interaction with interstellar media, up to medicine and industrial applications. Besides the applications, the understanding of these processes is itself a problem of fundamental importance. Thus, interactions of protons with the gas-phase furan molecules have been investigated for the first time in the energy range of 50–1000...
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Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent
PublicationInfrared (IR) spectroscopy is a widely used and invaluable tool in the studies of solvation phenomena in electrolyte solutions. Using state-of-the-art chemometric analysis of a spectral series measured in a concentration-dependent manner, the spectrum of the solute-affected solvent can be extracted, providing a detailed view of the structural and energetic states of the solvent molecules influenced by the solute. Concurrently,...
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Elastic scattering of electrons from chloroform
PublicationWe present experimental and theoretical cross sections for elastic electron scattering from CHCl3. This is an important target because of its relevance to environmental chemistry and the plasma etching industry as a source of chlorine radicals. The experimental results were obtained at incident electron energies ranging from 0.5 to 800 eV in the 10deg-130deg scattering angle range. Theoretically, the scattering cross sections in...
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A DFT computational study on the molecular mechanism of the nitro group migration in the product derived from 3-nitro-2-(trifluoromethyl)-2 H -chromene and 2-(1-phenylpropylidene)malononitrile
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The role of solvent solubility parameters in the formation of intermittent low and high molecular weight polystyrene rich structures in a thin film resulting from water vapor induced phase separation
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Study of New Oxytocin Antagonist Barusiban (Fe200 440) Affinity Toward Human Oxytocin Receptor Versus Vasopressin V1a and V2 Receptors - Molecular Dynamics Simulation in POPC Bilayer
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Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures
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In silico modelling for predicting the cationic hydrophobicity and cytotoxicity of ionic liquids towards the Leukemia rat cell line, Vibrio fischeri and Scenedesmus vacuolatus based on molecular interaction potentials of ions
PublicationIn this study we present prediction models for estimating in silico the cationic hydrophobicity and the cytotoxicity (log [1/EC50]) of ionic liquids (ILs) towards the Leukemia rat cell line (IPC-81), the marine bacterium Vibrio fischeri and the limnic green algae Scenedesmus vacuolatus using linear free energy relationship (LFER) descriptors computed by COSMO calculations. The LFER descriptors used for the prediction model (i.e....
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Structural, magnetic and spectral properties of tetrahedral cobalt(II) silanethiolates: a variety of structures and manifestation of field-induced slow magnetic relaxation
PublicationBlue crystals of five heteroleptic cobalt(II) silanethiolates 1–5 have been obtained by the reaction of [Co{SSi (tBuO)3}2(NH3)]2 with aminopyridines and aminomethylpyridines at an appropriate molar ratio and their structural, spectral, thermal and magnetic properties have been established and described. All complexes 1–5 contain Co(II) ions in a tetrahedral CoN2S2 environment formed by (tBuO)3SiS− residues and pyridines and present...
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The Spatial and Temporal Distribution of Process Gases within the Biowaste Compost
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Geo-Questionnaire for Environmental Planning: The Case of Ecosystem Services Delivered by Trees in Poland
PublicationStudies on society and the environment interface are often based on simple questionnaires that do not allow for an in-depth analysis. Research conducted with geo-questionnaires is an increasingly common method. However, even if data collected via a geo-questionnaire are available, the shared databases provide limited information due to personal data protection. In the article, we present open databases that overcome those limitations....
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Intercalation complex of imidazoacridinone C-1311, a potential anticancer drug, with DNA helix d(CGATCG)2: stereostructural studies by 2D NMR spectroscopy.
PublicationImidazoacridinone C-1311 (Symadex®) is a powerful antitumor agent, which successfully made its way through the Phase I clinical trials and has been recommended for Phase II few a years ago. It has been shown experimentally that during the initial stage of its action C-1311 forms a relatively stable intercalation complex with DNA, yet it has shown no base-sequence specificity while binding to DNA. In this paper, the d(CGATCG)2:C-1311...
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Toward Mechanosynthesis of Diamondoid Structures: VI. Quantum-Chemical Molecular Dynamics Comparison of Conditions for the STM Tip Driven Mechanosynthesis on Hydrogenated Si(111), Si(110) and Si(100) Surfaces.
Publicationmożliwość prototypowania przejściowych generacji nano-urządzeń otrzymanych drogą pozycjonowanej mechanosyntezy za pomocą stm wyposażonego w ostrze typu swcnt są analizowane metodą kwantowo-chemicznej dynamiki molekularnej. proponowana strategia syntezy polega na insercji atomów si oraz cząsteczek sih2 we wiązania si-h na uwodornionej powierzchni si(111), si(110) oraz si(100) kryształu krzemu. rezultaty modelowania sugerują, że...
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Molecular epidemiology of Serratia marcescens in two hospitals in Danzig, Poland, over a 5-year period.Molecular epidemiology of Serratia marcescens in two hospitals in Gdańsk, Poland, over a 5-year period.
PublicationW pracy badano zmiany populacji Serratia marcescens w ciągu 5 lat w dwóch szpitalach klinicznych Gdańska. Posłużono się wartościami MIC, wynikami typowania genetycznego RAPD-PCR, PFGE i nową metodą ADSRRS-fingerprinting oraz analizą beta-laktamaz o rozszerzonym spektrum substratowym (ESBL). Dzięki określeniu lekowrażliwości na najnowsze antybiotyki beta-laktamowe wykryto fenotypy wykazujące derepresję cefalosporynazy AmpC u 23%...
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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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Synthesis and molecular structure of novel 2-(alkylthio)-4-chloro-N-(4,5-dihydro-5-oxo-1H-1,2,4-triazol-3-yl)-5-methylbenzenesulfonamideswith potential anticancer activity
PublicationOtrzymano 15 nowych związków: 2-(alkilotio)-4-chloro-N-(4,5-dihydro-5-oxo-1H-1,2,4-triazol-3-yl)-5-metylobenzenosulfonamidów, dla których opracowano nową metodę syntezy. Dla jednej pochodnej wyznaczono strukturę rentgenowską. Związek nr 36 wykazuje wysoką aktywność przeciwnowotworową w stosunku do 13 linii komórek nowotworowych o poziomie GI_50 w zakresie stężeń 1,9-3,0 μM.
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Ensemble fits of restrained peptides’ conformational equilibria to NMR data. Dependence on force fields: AMBER/8 ff03 versus ECEPP/3
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The effect of high molecular weight bio-based diamine derivative of dimerized fatty acids obtained from vegetable oils on the structure, morphology and selected properties of poly(ether-urethane-urea)s
PublicationIn this work, the effect of the high molecular weight bio-based diamine on the chemical structure and selected properties of poly(ether-urethane-urea)s has been investigated. The ether-urethane prepolymer was cured using 1,4-butanediol and/or bio-based diamine. Mentioned chain extenders were used separately or in the mixture, and their different molecular weight and chemical structure resulted in obtaining materials with diversified...
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Molecular basis of lipopolysaccharide heterogeneity in Escherichia coli: envelope stress-responsive regulators control the incorporation of glycoforms with a third 3-deoxy-α-D-manno-oct-2-ulosonic acid and rhamnose.
PublicationMass spectrometric analyses of lipopolysaccharide (LPS) from isogenic Escherichia coli strains with nonpolar mutations in the waa locus or overexpression of their cognate genes revealed that waaZ and waaS are the structural genes required for the incorporation of the third 3-deoxy-α-D-manno-oct-2-ulosonic acid (Kdo) linked to Kdo disaccharide and rhamnose, respectively. The incorporation of rhamnose requires prior sequential incorporation...