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Search results for: HIV-1 INTEGRASE, INHIBITORS, DOCKING, ACTIVE SITE, ALLOSTERIC SITE,MOLECULAR DYNAMICS
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Ce site dilution effects in the antiferromagnetic heavy fermion CeIn3
PublicationLa-doped intermetallic single crystals of Ce1−xLaxIn3 were synthesized via an In self-flux method throughout the entire range (x = 0–1). The prototypical heavy-fermion compound CeIn3 shows an antiferromagnetic phase transition at 10.1 K and becomes superconducting near a critical pressure where TN is completely suppressed. As the La concentration increases, Ce moments are diluted, and the lattice constant increases linearly, satisfying Vegard’s...
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Albumin–Hyaluronan Interactions: Influence of Ionic Composition Probed by Molecular Dynamics
PublicationThe lubrication mechanism in synovial fluid and joints is not yet fully understood. Nevertheless, intermolecular interactions between various neutral and ionic species including large macromolecular systems and simple inorganic ions are the key to understanding the excellent lubrication performance. An important tool for characterizing the intermolecular forces and their structural consequences is molecular dynamics. Albumin...
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New Pr3+ site in β-SiAlON red phosphor
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Interatomic potential suitable for the modeling of penta-graphene: Molecular statics/molecular dynamics studies
PublicationWe test the potentials available for elemental carbon, with the scope to choose the potential suitable for the modeling of penta-graphene, the latest two dimensional carbon allotrope. By using molecular statics and molecular dynamics simulations we show that there is only one potential e namely the Tersoff-type potential proposed by Erhart and Albe in 2005 e which is able to correctly describe all the important features of penta-graphene....
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Design of new cholinesterase inhibitors based on phosphorus analogs of tacrine as potential anti-Alzheimer’s disease agents
PublicationBased on the analysis of the determined free binding energy (using the AutoDock Vina 1.1.2 docking program), the most potent cholinesterase inhibitors were selected. Moreover, studies of 3D visualization of the results of molecular modeling led to the identification of potential sites for the interaction of new potential inhibitors with amino acid residues building active sites of investigated cholinesterases.
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Structural and dynamic insights on the EmrE protein with TPP+ and related substrates through molecular dynamics simulations
PublicationEmrE is a bacterial transporter protein that forms an anti-parallel homodimer with four transmembrane helices in each monomer. EmrE transports positively charged aromatic compounds, such as TPP+ and its derivatives. We performed molecular dynamics (MD) simulations of EmrE in complex with TPP+, MeTPP+, and MBTPP+ embedded in a membrane. The detailed molecular properties and interactions were analysed for all EmrE-ligand complexes....
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Spatiotemporal dynamics of the active perirheic zone in a natural wetland floodplain
PublicationAbstract The ecologically and biogeochemically significant perirheic zone is a part of the floodplain where waters originating from both the river and adjacent floodplain are present. In this study, we investigate the spatiotemporal dynamics of the active perirheic zone, i.e. river and floodplain waters and their transient mixing extent. This is achieved by using the Hydraulic Mixing-Cell method, a complement to a fully integrated...
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Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
PublicationIn drug optimization calculations, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method can be used to compute free energies of binding of ligands to proteins. The method involves the evaluation of the energy of configurations in an implicit solvent model. One source of errors is the force field used, which can potentially lead to large errors due to the restrictions in accuracy imposed by its empirical nature....
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Assessment of urinary cystatin C levels in HIV-1-infected patients with preserved kidney function
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Induction of Secreted Human Immunodeficiency Virus Type 1 (HIV-1) Resistance Factors in CD4-Positive T Lymphocytes by Attenuated HIV-1 Infection
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An efficient molecular docking using conformational space annealing
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Anion–water interactions of weakly hydrated anions: molecular dynamics simulations of aqueous NaBF4 and NaPF6
PublicationIn aqueous ionic solutions, both the structure and the dynamics of water are altered dramatically with respect to the pure solvent. The emergence of novel experimental techniques makes these changes accessible to detailed investigations. At the same time, computational studies deliver unique possibilities for the interpretation of the experimental data at the molecular level. Here, using molecular dynamics simulations, we demonstrate...
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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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Integrating web site services into application through user interface
PublicationThe issue of integrating applications which are only accessible through visual user interface is not thoroughly researched. Integration of web applications running remotely and controlled by separate organizations becomes even more complicated, as their user interface can display differently in different browsers or change without prior notification as a result of application maintenance. While possible, it is generally not common...
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Geometry optimization of steroid sulfatase inhibitors - the influence on the free binding energy with STS
PublicationIn the paper we review the application of two techniques (molecular mechanics and quantum mechanics) to study the influence of geometry optimization of the steroid sulfatase inhibitors on the values of descriptors coded their chemical structure and their free binding energy with the STS protein. We selected 22 STS-inhibitors and compared their structures optimized with MM+, PM7 and DFT B3LYP/6–31++G* approaches considering separately...
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The significance of the properties of water for the working cycle of the kinesin molecular motor
PublicationExplicit solvent molecular dynamics simulations were performed in this study to investigate and discuss several aspects of the influence of the properties of water on the working cycle of a molecular motor from the kinesin superfamily. The main objects of attention were: the binding of the neck linker and the association of the kinesin and the tubulin. The docking of the neck linker is considered a crucial event during the working...
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Synthesis and biological evaluation of fluorinated N-benzoyl and N-phenylacetoyl derivatives of 3-(4-aminophenyl)-coumarin-7-O-sulfamate as steroid sulfatase inhibitors
PublicationIn the present work, we report convenient methods for the synthesis of 3-(4-aminophenyl)-coumarin-7-O-sulfamate derivatives N-acylated with fluorinated analogues of benzoic or phenylacetic acid as steroid sulfatase (STS) inhibitors. The design of these potential STS inhibitors was supported by molecular modeling techniques. Additionally, computational docking methods were used to determine the binding modes of the synthesized inhibitors...
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Thermodynamic Studies of Interactions between Sertraline Hydrochloride and Randomly Methylated β-Cyclodextrin Molecules Supported by Circular Dichroism Spectroscopy and Molecular Docking Results
PublicationThe interaction between sertraline hydrochloride (SRT) and randomly methylated β-cyclodextrin (RM β CD) molecules have been investigated at 298.15 K under atmospheric pressure. The method used—Isothermal Titration Calorimetry (ITC) enabled to determine values of the thermodynamic functions like the enthalpy (DH), the entropy (DS) and the Gibbs free energy (DG) of binding for the examined system. Moreover, the stoichiometry coefficient...
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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).
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Prediction of Pile Shaft Capacity in Tension Based on Some Direct CPT Methods—Vistula Marshland Test Site
PublicationThis paper presents different CPT methodologies for the prediction of the pile shaft resistance in tension on the example of three reference screw piles of the Jazowa test site in Poland. The shaft capacity was estimated based on the cone resistance, sleeve friction and CPT excess pore water pressure. Three piles with diameter 0.4 m and the length varied from 8 m to 14.6 m were subjected to static load tests in tension. Their...
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Conformational studies of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy in conjunction with molecular dynamics calculations
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Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations
PublicationThis work presents the analysis of the conformation of albumin in the temperature range of 300K – 312K, i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from...
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Prediction of pile shaft capacity in tension based on some direct CPT methods – Vistula Marshland test site
PublicationThis paper presents different CPT methodologies for the prediction of the pile shaft resistance in tension on the example of three reference screw piles of the Jazowa test site in Poland. The shaft capacity was estimated based on the cone resistance, sleeve friction and CPT excess pore water pressure. Three piles with a diameter of 0.4 m and the length...
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Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules
PublicationSingle-particle cryogenic electron microscopy (cryo-EM) has revolutionized the field of the structural biology, providing an access to the atomic resolution structures of large biomolecular complexes in their near-native environment. Today’s cryo-EM maps can frequently reach the atomic-level resolution, while often containing a range of resolutions, with conformationally variable regions obtained at 6 Å or worse. Low resolution...
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Molecular dynamics and verisimilitude - to what extent can one trust a computational simulation?
PublicationFor the last several tens of years, computer simulations have become of undeniable importance. Molecular Dynamics (MD) simulation techniques are used to examine the phenomena which occur at the level that cannot be observed directly. Thus, they can be successfully exploited in many different scientific fields such as: materials science, applied mathematics and theoretical physics, biochemistry, biophysics or drug design. Despite...
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Inhibitors of glucosamine-6-phosphate synthase as potential antimicrobials or antidiabetics – synthesis and properties
PublicationGlucosamine-6-phosphate synthase (GlcN-6-P synthase) is known as a promising target for antimicrobial agents and antidiabetics. Several compounds of natural or synthetic origin have been identified as inhibitors of this enzyme. This set comprises highly selective L-glutamine, amino sugar phosphate or transition state intermediate cis-enolamine analogues. Relatively low antimicrobial activity of these inhibitors, poorly penetrating...
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Some remarks on problem of site characterisation - a subjective experience on theory and practice
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Site environment type – The main factor of urban road dust toxicity?
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Sensitivity analysis of the contractor’s financial effects achieved on a single building site
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The Baltic Sea as a dumping site of chemical munitions and chemical warfare agents
PublicationW pracy przedstawiono problem składowania w Morzu Bałtyckim aminucji chemicznej i bojowych środków trujących. Przedstawiono typy oraz charakterystykę BST składowanych na dnie Morza Bałtyckiego. Omówiono potencjalne zagrożenia dla środowiska abiotytcznego oraz dla organizmów żywych związanych z tego typu składowiskami. Przedstawiono również podstawowe informacje o procedurach analitycznych, które mogą być wykorzystane do wykrywania...
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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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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Phenazine - 2,6-dihydroxybenzoic acid (1/1)
PublicationOtrzymano krystaliczny kompleks fenazyny z kwasem 2,6-dihydroksybenzoesowym o stechiometrii 1:1. Badania struktury kompleksu za pomocą metod rentgenograficznych wykazały, że powiązane wiązaniami wodorowymi typu OH...N cząsteczki fenazyny układają się w stosy, które stabilizowane są poprzez oddziaływania typu π-π pierścieni aromatycznych. Cząsteczki kwasu zajmują przestrzenie kanałów tworzonych pomiędzy kolumnami pierścieni aromatycznych...
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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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Novel steroid sulfatase inhibitors based on N ‐thiophosphorylated 3‐(4‐aminophenyl)‐coumarin‐7‐O‐sulfamates
PublicationIn the present work, we described convenient methods for the synthesis ofN-thiophosphorylated 3-(4-aminophenyl)-coumarin-7-O-sulfamates as steroid sulfatase(STS) inhibitors. To design the structures of the potential STS inhibitors, molecularmodeling techniques were used. A computational docking method was used to deter-mine the binding modes of the synthesized inhibitors as well as to identify potentialinteractions between specified...
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Spectroscopic, molecular docking and molecular dynamic simulation studies on the complexes of β-lactoglobulin, safranal and oleuropein
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Reactive metabolites of acridinone antitumor agents, C-1311 and C-1305, are trapped within the active site of CYP1A2 and CYP3A4, causing irreversible enzymes inactivation
PublicationZwiązki C-1305 i C-1311, zsyntetyzowane w Katedrze Technologii Leków i Biochemii, wykazują najsilniejsze właściwości przeciwnowotworowe wśród pochodnych, odpowiednio, triazolo- i imidazoakrydonu. Obecnie prowadzone są badania mające na celu określenie biochemicznego mechanizmu działania, jak również potencjalnych szlaków biotransformacji C-1305 i C-1311.W bieżącym etapie podjęto próbę określenia mechanizmu obserwowanej inhibicji...
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Effect of Chitosan Deacetylation on Its Affinity to Type III Collagen: A Molecular Dynamics Study
PublicationThe ability to form strong intermolecular interactions by linear glucosamine polysaccharides with collagen is strictly related to their nonlinear dynamic behavior and hence bio-lubricating features. Type III collagen plays a crucial role in tissue regeneration, and its presence in the articular cartilage affects its bio-technical features. In this study, the molecular dynamics methodology was applied to evaluate the effect of...
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How acidic amino acid residues facilitate DNA target site selection
PublicationDespite the negative charge of the DNA backbone, acidic residues (Asp/Glu) commonly participate in the base readout, with a strong preference for cytosine. In fact, in the solved DNA/protein structures, cytosine is recognized almost exclusively by Asp/Glu through a direct hydrogen bond, while at the same time, adenine, regardless of its amino group, shows no propensity for Asp/Glu. Here, we analyzed the contribution of Asp/Glu...
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Tailoring structural properties of lanthanum orthoniobates through an isovalent substitution on the Nb-site
PublicationTetragonal polymorph of lanthanum orthoniobate can be stabilized to room temperature by the substitution of Nb with an isovalent element. LaNb1-xAsxO4 (0 < x ≤ 0.3), where As is an element stabilizing tetragonal structure, were successfully synthesized with combined co-precipitation and solid-state reaction method. The phase transition temperature, above which the material has tetragonal structure, decreases linearly with increasing...
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Synthesis, crystal structure and electrical properties of A-site cation ordered BaErMn2O5 and BaErMn2O6
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The new fluorogenic substrates of neutrophil proteinase 3 optimized in prime site region
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Reclamation of phosphogypsum deposition site Wiślinka near Gdańsk with municipal sewage sludge.
PublicationOmówiono zastosowanie osadów ściekowych do rekultywacji składowiska fosfogipsów w Wiślince k. Gdańska. Głównie pojawiają się problemy ze stabilizacją stoków oraz z sukcesją roślinności i zwalczaniem erozji wiatrowej.
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Surgical Site Infection after Breast Surgery: A Retrospective Analysis of 5-Year Postoperative Data from a Single Center in Poland
PublicationBackground and Objectives: Surgical site infection (SSI) is a significant complication of non-reconstructive and reconstructive breast surgery. This study aimed to assess SSI after breast surgery over five years in a single center in Poland. The microorganisms responsible for SSI and their antibiotic susceptibilities were determined. Materials and Methods: Data from 2129 patients acquired over five years postoperatively by the...
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Molecular Dynamics simulations of thermal conductivity of penta-graphene
PublicationThe thermal conductivity of penta-graphene (PG), a new two dimensional carbon allotrope and its dependence on temperature, strain, and direction are studied in this paper. The thermal conductivity of PG is investigated using a non-equilibrium molecular dynamics simulation (NEMD) with the Two Region Method by applying the optimized Tersoff interatomic potential. Our study shows that the thermal conductivity of PG (determined for...
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Structure of liquid gold from tight-binding driven molecular-dynamics
PublicationPraca przedstawia wyniki symulacji ciekłego złota w nadkomórce periodycznej przy użyciu stworzonego przez autorów programu komputerowego, za pomocą połączonych metod dynamiki molekularnej (MD) i ciasnego wiązania (TB). Omówiono strukturę tak symulowanej cieczy, porównując ją z dostępnymi danymi doświadczalnymi oraz wynikami innych symulacji, pod kątem radialnej i kątowej funkcji rozkładu i elektronowej gęstości stanów.A tight-binding...
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Golden artefacts, resin figurines, body adhesives and tomb sediments from the pre-Columbian burial site El Caño (Gran Coclé, Panamá): tracing organic contents using molecular archaeometry
PublicationThis research aimed to determine the origin of organic residues from funerary contexts in the El Ca~no settlement (Gran Cocl�e area, Panam�a, Central America) by means of multiple molecular probing techniques (GC-MS of organic solvent extracts and pyrolysis-GC-MS, THM-GC-MS and FTIR of solid samples). The samples include particles of precious resin figurines, fillings of golden objects, tomb sediments, plant exudates from extant...
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Hydration of amino acids: FTIR spectra and molecular dynamics studies
PublicationThe hydration of selected amino acids, alanine, glycine, proline, valine, isoleucine and phenylalanine, has been studied in aqueous solutions by means of FTIR spectra of HDO isotopically diluted in H2O. The difference spectra procedure and the chemometric method have been applied to remove the contribution of bulk water and thus to separate the spectra of solute-affected HDO. To support interpretation of obtained spectral results,...
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The Distribution of Glucosinolates in Different Phenotypes of Lepidium peruvianum and Their Role as Acetyl- and Butyrylcholinesterase Inhibitors—In Silico and In Vitro Studies
PublicationThe aim of the study was to present the fingerprint of different Lepidium peruvianum tu- ber extracts showing glucosinolates-containing substances possibly playing an important role in preventinting dementia and other memory disorders. Different phenotypes of Lepidium peruvianum (Brassicaceae) tubers were analysed for their glucosinolate profile using a liquid chromatograph coupled with mass spectrometer (HPLC-ESI-QTOF-MS/MS platform)....
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Microarray analysis of differentially expressed genes in cells resistant to HIV-1
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