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Search results for: HIV-1 INTEGRASE, INHIBITORS, DOCKING, ACTIVE SITE, ALLOSTERIC SITE,MOLECULAR DYNAMICS
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Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography
PublicationA novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...
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Synthesis of bicoumarin thiophosphate derivatives as steroid sulfatase inhibitors
PublicationBased on the frameworks of 7-hydroxy-2,3-dihydro-1H-cyclopenta[c]chromen-4-one, 3-hydroxy- 7,8,9,10-tetrahydro-6H-benzo[c]chromen-6-one and 3-hydroxy-8,9,10,11-tetrahydro-7H-cyclohepta[c] chromen-6-one, a series of bicoumarin thiophosphate analogs have been synthesized and biologically evaluated. Additionally, their binding modes have been modeled using docking techniques. The inhibitory properties of the synthesized compounds...
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Inhibitors of Matriptase‐2 Based on the Trypsin Inhibitor SFTI‐1
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Monoubiquitinated Histone H1B Is Required for Antiviral Protection in CD4+T Cells Resistant to HIV-1
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Coordination polymers and molecular structures among complexes of mercury(II) halides with selected 1-benzoylthioureas
PublicationSix new 1-benzoyl-3-phenylthiourea and 1-benzoyl-3-(2-methylphenyl)thiourea complexes of mercury( II) were obtained in the reactions of the ligands with HgX2 in methanol (X = Cl, Br, I). Their structures, determined by single-crystal X-ray diffraction analysis, exhibit different stoichiometries and molecular organization. Coordination centers adopt more or less distorted tetrahedral geometry (five structures) or distorted trigonal...
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Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study.
PublicationAmphotericin B (AmB) is an effective but very toxic antifungal antibiotic. In our laboratory a series of AmB derivatives of improved selectivity of action was synthesized and tested. To understand molecular basis of this improvement, comparative conformational studies of amphotericin B and its two more selectivederivatives were carried out in an aqueous solution and in a lipid membrane. These molecular simulation studies revealed...
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On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
PublicationAmphotericin B (AmB) is a well-known membrane-active antibiotic that has been used to treat systemicfungal infections for more than 45 years. Therapeutic application of AmB is based on the fact that it is moreactive against ergosterol-containing membranes of fungal cells than against mammalian membranes withcholesterol. In this paper, we examine the hypothesis according to which the selectivity of the AmB's membraneaction originates...
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Anisotropic mechanical behavior and auxeticity of penta-graphene: Molecular statics/molecular dynamics studies
PublicationWe investigate the mechanical properties of penta-graphene (PG), a recently proposed two-dimensional carbon allotrope using atomistic simulation techniques combined with the empirical description of interatomic interactions. We report on the dependence of its three in-plane mechanical moduli (i.e. Young's modulus, Poisson's ratio and shear modulus) on the deformation direction, strain and temperature. We show that PG displays a...
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Molecular aspects of the interaction between amphotericin B and a phospholipid bilayer: molecular dynamics studies.
PublicationAmfoterycyna B jest antybiotykiem z grupy polienów makrolidowych. Stosowany jest on w leczeniu układowych infekcji grzybowych. Wiadomo że związek ten oddziałuje ze składnikami błon lipidowych i tworzy kanały. W przedstawianej pracy prezentowane są wyniki symulacji przeprowadzonej dynamiką molekularną układu składającego się z 200 cząsteczek lipidów DMPC i jednej cząsteczki amfoterycyny ułożonej na powierzchni błony. Z przeprowadzonej...
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Collagen Type II—Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations
PublicationChitosan–collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence...
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Molecular dynamics simulations of ultraprecision machining of fcc monocrystals
PublicationArtykuł zawiera wyniki wielkoskalowych symulacji dynamiczno-molekularnych ultraprecyzyjnego skrawania monokryształów metali niedeformowalnym narzędziem. Zmiennymi parametrami symulacji były: szybkość i głębokość skrawania, temperatura, orientacja krystalograficzna skrawanego kryształu oraz kształt narzędzia.Analizie poddano zmiany strukturalne w obrabianym materiale.
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Synthesis, Molecular Structure, Anticancer Activity, and QSAR Study of N-(aryl/heteroaryl)-4-(1H-pyrrol-1-yl)Benzenesulfonamide Derivatives
PublicationA series of N-(aryl/heteroaryl)-4-(1H-pyrrol-1-yl)benzenesulfonamides were synthesized from 4-amino-N-(aryl/heteroaryl)benzenesulfonamides and 2,5-dimethoxytetrahydrofuran. All the synthesized compounds were evaluated for their anticancer activity on HeLa, HCT-116, and MCF-7 human tumor cell lines. Compound 28, bearing 8-quinolinyl moiety, exhibited the most potent anticancer activity against the HCT-116, MCF-7, and HeLa cell lines,...
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Biochemical Characterization and Validation of a Catalytic Site of a Highly Thermostable Ts2631 Endolysin from the Thermus scotoductus Phage vB_Tsc2631
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Tuning of the phase transition between site selective SCO and intermetallic ET in trimetallic magnetic cyanido-bridged clusters
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Site-selective cation–π interaction as a way of selective recognition of the caesium cation using sumanene-functionalized ferrocenes
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Machine Learning-Based Wetland Vulnerability Assessment in the Sindh Province Ramsar Site Using Remote Sensing Data
PublicationWetlands provide vital ecological and socioeconomic services but face escalating pressures worldwide. This study undertakes an integrated spatiotemporal assessment of the multifaceted vulnerabilities shaping Khinjhir Lake, an ecologically significant wetland ecosystem in Pakistan, using advanced geospatial and machine learning techniques. Multi-temporal optical remote sensing data from 2000 to 2020 was analyzed through spectral...
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Identification of pollutants at the adjacent areas to the landfill site using two dimensional gas chromatography with mass spectrometry technique
PublicationMunicipal landfills are considered one of the main sources of air pollutants. In this article is presented the use of a modern analytical technique: a two dimensional gas chromatography to identify the substances in the atmospheric air near a waste processing plant located in Gdansk. In order to determine the types of substances occurring in different atmospheric conditions, the study was conducted from February to April 2016....
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Study of the Interactions between Neurophysin II and Dipeptide Ligand by Means of Molecular Dynamics
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Development of Sulfamoylated 4‑(1-Phenyl‑1H‑1,2,3-triazol-4-yl)phenol Derivatives as Potent Steroid Sulfatase Inhibitors for Efficient Treatment of Breast Cancer
PublicationWe present here the advances achieved in the development of new sulfamoylated 4-(1-phenyl-1H-1,2,3-triazol-4-yl)phenol derivatives as potent steroid sulfatase (STS) inhibitors for the treatment of breast cancer. Prompted by promising biological results and in silico analysis, the initial series of similar compounds were extended, appending a variety of m-substituents at the outer phenyl ring. The inhibition profiles of the newly...
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Application 2D Descriptors and Artificial Neural Networks for Beta-Glucosidase Inhibitors Screening
PublicationBeta-glucosidase inhibitors play important medical and biological roles. In this study, simple two-variable artificial neural network (ANN) classification models were developed for beta-glucosidase inhibitors screening. All bioassay data were obtained from the ChEMBL database. The classifiers were generated using 2D molecular descriptors and the data miner tool available in the STATISTICA package (STATISTICA Automated Neural...
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Interactions of N-alkyl-N-methylmorpholinium based ionic liquids with acetonitrile studied by density and velocity of sound measurements and molecular dynamics simulations
PublicationMorpholinium-based ionic liquids (ILs) and their mixtures with polar co-solvents are an interesting class of emerging electrolytes in electrochemistry that is relatively poorly studied. In this work, densities and sound velocities of four ILs, N-ethyl-N-methylmorpholinium tetrafluoroborate, N-butyl-N-methylmorpholinium tetrafluoroborate, N-octyl-N-methylmorpho-linium tetrafluoroborate and N-decyl-N-methylmorpholinium tetrafluoroborate...
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Potential allosteric modulators of the proteasome activity
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Molecular dynamics study of the influence of calcium ions on the conformation of gelsolin S2 domain
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Molecular dynamics study on the influence of C-terminal sugar substitution on dynamics and conformation of vancomycin derivatives
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Molecular dynamics study on the role of solvation water in the adsorption of hyperactive AFP to the ice surface
PublicationUsing computer simulations, the early stages of the adsorption of the CfAFP molecule to the ice surface were analyzed. We found that the ice and the protein interact at least as early as when the protein is about 1 nm away from the ice surface. These interactions are mediated by interfacial solvation water and are possible thanks to the structural ordering of the solvent. This ordering leads to positional preference of the protein...
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Recent progress in the development of steroid sulfatase inhibitors – examples of the novel and most promising compounds from the last decade
PublicationThe purpose of this review article is to provide an overview of recent achievements in the synthesis of novel steroid sulfatase (STS) inhibitors. STS is a crucial enzyme in the biosynthesis of active hormones (including estrogens and androgens) and, therefore, represents an extremely attractive molecular target for the development of hormone-dependent cancer therapies. The inhibition of STS may effectively reduce the availability...
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In silico design of telomerase inhibitors.
PublicationTelomerase is a reverse transcriptase enzyme involved in DNA synthesis at the end of linear chromosomes. Unlike in most other cells, telomerase is reactivated most cancerous cells and, therefore, has become a promising new anticancer target. Despite extensive research, direct telomerase inhibitors have yet not been introduced to the clinics because of the complexity of this enzyme. Structures of this protein from simple organisms...
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Surface Site Modulations by Conjugated Organic Molecules To Enhance Visible Light Activity of ZnO Nanostructures in Photocatalytic Water Splitting
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The impact of potential leakage from the sub-seabed CO2 storage site on the phosphorus transformation in marine sediments – An experimental study
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Interactions of vasopressin and oxytocin receptors with vasopressin analogues substituted in position 2 with 3,3′-diphenylalanine - a molecular docking study
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Long-range, water-mediated interaction between a moderately active antifreeze protein molecule and the surface of ice
PublicationUsing molecular dynamics simulations, we show that a molecule of moderately active antifreeze protein (type III AFP, QAE HPLC-12 isoform) is able to interact with ice in an indirect manner. This interaction occurs between the ice binding site (IBS) of the AFP III molecule and the surface of ice, and it is mediated by liquid water which separates these surfaces. As a result, the AFP III molecule positions itself at a specific orientation...
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The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide–Doxorubicin Binding to DNA
PublicationMatrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide-DOX, the product of the MMPs' cleavage of carrier-linked DOX, into dsDNA was investigated using stationary and time-resolved fluorescence spectroscopy, UV-Vis...
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Influence of Protonation State on the Excited State Dynamics of a Photobiologically Active Ru(II) Dyad
PublicationThe influence of ligand protonation on the photophysics of a ruthenium (Ru) dyad bearing the 2-(1-pyrenyl)-1H-imidazo[4,5-f][1,10]-phenanthroline (ippy) ligand was investigated by time-resolved transient absorption spectroscopy. It was found that changes in the protonation state of the imidazole group led to changes in the electronic configuration of the lowest lying excited state. Formation of the fully deprotonated imidazole...
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A spline-based FE approach to modelling of high frequency dynamics of 1-D structures
PublicationIn this paper a computational methodology leading to the development of a new class of FEs, based on the application of continuous and smooth approximation polynomials, being splines, has been presented. Application of the splines as appropriately defined piecewise elemental shape functions led the authors to the formulation of a new approach for FEM, named as spFEM, where contrary to the well-known NURBS approach, the boundaries...
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Characterization of Bioactivity of Selective Molecules in Fruit Wines by FTIR and NMR Spectroscopies, Fluorescence and Docking Calculations
PublicationFourier transform infrared (FTIR) and proton nuclear magnetic resonance (1H NMR) spectroscopies were applied to characterize and compare the chemical shifts in the polyphenols’ regions of some fruit wines. The obtained results showed that FTIR spectra (1800–900 cm−1) and 1H NMR (δ 6.5–9.3 ppm) of different fruit wines can be used as main indices of the year of vintage and quality of fruit wines. In addition to the classical determination...
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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA
PublicationG-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully...
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Conformational Studies of Two Bradykinin Antagonists by Using Two-dimensional NMR Techniques and Molecular Dynamics Simulations
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Molecular-dynamics simulation of clustering processes in sea-ice floes
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Molecular Dynamics of a Vasopressin V2 Receptor in a Phospholipid Bilayer Membrane
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The structure of rarefied and densified PbSiO3 glass: a molecular dynamics study.
PublicationArtykuł przedstawia wyniki symulacji dynamiczno-molekularnychstruktury rozrzedzonego i zagęszczonego szkła PbSiO3 (w zakresie gęstości od 3000 kg/m3 do 8000 kg/m3). Otrzymane wyniki dokładnie przedyskutowano pod kątem blisko- i średnio-zasięgowego uporządkowania atomów i porównano ze strukturą szkła PbSiO3 o normalnej gęstości (5970kg/m3) oraz ze strukturą rozrzedzonych i zagęszczonych szkieł PbGeO3.
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Synthesis, molecular structure, and metabolic stability of new series of N' -(2-alkylthio-4-chloro-5-methylbenzenesulfonyl)-1-(5-phenyl-1 H -pyrazol-1-yl)amidine as potential anti-cancer agents
PublicationA series of new N'-(2-alkylthio-4-chloro-5-methylbenzenesulfonyl)-1-(5-phenyl-1H-pyrazol-1-yl)amidine 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 studied compounds display selective activity mainly against HCT-116 and HeLa cells. Thus, five compounds show selective cytotoxic...
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Studies of the Interaction Dynamics in Albumin-Chondroitin Sulfate Systems by Recurrence Method
PublicationThe physicochemical basis of lubrication of articular cartilage is still not fully understood. However, the synergy between components of the synovial fluid can be a crucial factor that could explain this phenomenon. This work presents a nonlinear data analysis technique named the recurrence method, applied to the system involving two components of synovial fluid: albumin and chondroitin sulfate (CS) immersed in a water environment....
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Comparative study of numerical modelling and experimental investigation for vessel-docking operations
PublicationA comparative study between numerical modelling and experimental investigation is performed to validate the developed numerical method for simulating floating dock operations with a vessel on board. Both model-scale and full-scale experimental tests are performed on floating docks with a vessel on board, and the draughts using draught meters, floating positions and bending of the floating dock are measured. The present numerical...
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Cloning and characterization of a novel cold-active glycoside hydrolase family 1 enzyme with beta-glucosidase, beta-fucosidase and beta-galactosidase activities.
PublicationBackground: Cold-active enzymes, sourced from cold-adapted organisms, are characterized by high catalytic efficiencies at low temperatures compared with their mesophilic counterparts, which have poor activity. This property makes them advantageous for biotechnology applications as it: (i) saves energy costs, (ii) shortens the times for processes operated at low temperatures, (iii) protects thermosensitive substrates or products...
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A. Computational analysis by molecular docking of thirty alkaloid compounds from medicinal plants as potent inhibitors of SARS-CoV-2 main protease(2020). Focused on analysis of the Medicinal plants that have potential therapeutic ability against COVID-19.
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Genotoxic effects of antitumor 1-nitroacridines C-857 and its novel analoque 4-methyl-1-nitroacridine C-1748
Publication4-podstawione 1-nitroakrydyny reprezentują nową grupę pochodnych akrydyny zsyntetyzowanych na Politechnice Gdańskiej. W przeprowadzonych badaniach nad pochodnymi C-1748 i C-857 zastosowano dwie metody badawcze: test kometowy oraz zmodyfikowany test mikrojąderkowy (CBMN assay). W teście kometowym wykazano wzrost uszkodzeń DNA w zależności od czasu i stężenia badanych pochodnych 1-nitroakrydyny. Badania aberracji chromosomalnych...
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Cardiovascular risks in HIV patients
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The oldest osseous mining tools in Europe? New discoveries from the chocolate flint mine in Orońsko, site 2 (southern Poland)
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Effective calcium doping at the B-site of BaFeO3−δ perovskite: towards low-cost and high-performance oxygen permeation membranes
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Built Heritage, Sustainable Development, and Natural Hazards: Flood Protection and UNESCO World Heritage Site Protection Strategies in Krakow, Poland
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