Search results for: peptide hydration
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Inhibitory syntazy glukozamino-6-fosforanu o zwiększonej lipofilowości i ich peptydy - synteza i właściwości biologiczne
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Kallikrein-Related Peptidase 14 Activates Zymogens of Membrane Type Matrix Metalloproteinases (MT-MMPs)—A CleavEx Based Analysis
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Evaluating the antibacterial activity of muramyl dipeptide derivatives, retro-tuftsin derivatives, and anthraquinone oligopeptides against a range of pathogenic bacteria
PublicationSearch for new and efficient antibiotic is crucial because of microbial drug resistance and problems with side effects of the administered medication. In this study, we evaluate the in vitro microbiological activity of muramyl dipeptide derivatives, retro-tuftsin derivatives (i.e., tuftsin with reversed amino acid sequences), and combinations of retro-tuftsin derivatives with substituted anthraquinones. The potency of the investigated...
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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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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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General Mechanism of Osmolytes’ Influence on Protein Stability Irrespective of the Type of Osmolyte Cosolvent
PublicationThe stability of proteins in an aqueous solution can be modified by the presence of osmolytes. The hydration sphere of stabilizing osmolytes is strikingly similar to the enhanced hydration sphere of a protein. This similarity leads to an increase in the protein stability. Moreover, the hydration sphere of destabilizing osmolytes is significantly different. These solutes generate in their surroundings so-called “structurally different...
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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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A Novel Biological Role for Peptidyl-Arginine Deiminases: Citrullination of Cathelicidin LL-37 Controls the Immunostimulatory Potential of Cell-Free DNA
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Kallikrein-related peptidase 14 activates zymogens of membrane type matrix metalloproteinases (MT-MMPs) - a CleavEx library-based analysis
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Whole-genome sequencing and antimicrobial potential of bacteria isolated from Polish honey
PublicationThe aim of this study was the whole-genome analysis and assessment of the antimicrobial potential of bacterial isolates from honey harvested in one geographical location—the north of Poland. In total, 132 strains were derived from three honey samples, and the antimicrobial activity of CFAM (cell-free after-culture medium) was used as a criterion for strain selection and detailed genomic investigation. Two of the tested isolates...
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Właściwości otoczki hydratacyjnej wokół różnych konformacji poliseryny - analiza wyników dynamiki molekularnej
PublicationRozpuszczalnik w istotny sposób wpływa na preferencje peptydu do przyjmowania określonej struktury drugorzędowej. Przykładem tego może być fakt, iż w przypadku polialaniny stabilność konformacji helikalnej w wodzie jest niższa aniżeli w próżni, podczas gdy w przypadku poliseryny mamy do czynienia ze zjawiskiem odwrotnym. W celu lepszego zrozumienia tego zjawiska badano właściwości otoczek hydratacyjnych dookoła czterech konformacji...
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Analiza in silico bioaktywnych peptydów pochodzących z keratyny z piór drobiowych
PublicationKeratyna należy do najbardziej powszechnie występujących białek strukturalnych pochodzenia zwierzęcego. Stanowi ok. 90% masy piór wytwarzanych w dużych ilościach przez przemysł drobiarski. Ten odpadowy produkt pozostaje w dużym stopniu niezagospodarowany. Celem pracy była analiza bioinformatyczna pierwszorzędowej struktury keratyny z piór kurzych pod kątem występowania w niej peptydów bioaktywnych....
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Design, Synthesis, and Enzymatic Evaluation of Novel ZnO Quantum Dot-Based Assay for Detection of Proteinase 3 Activity
PublicationHerein, the synthesis and application of functionalized quantum dot-based protease probes is described. Such probes are composed of nontoxic ZnO nanocrystals decorated by amino groups followed by linker and labeled peptide attachment. Spherical NH2-terminated ZnO quantum dots (QDs) with the average size ranging from 4 to 8 nm and strong emission centered at 530 nm were prepared using the sol−gel method. The fluorescence of ZnO...
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Pigment production and secretion by psychrotolerant yeast-like fungi at 25 °C for 2 days
Open Research DataThree strains, named Red, Pink and Black, were grown in five different media with the following compositions: 1% peptone K, 2% glucose; 2% peptone K, 2% glucose; 1% yeast extract, 2% glucose; 1% peptone K, 1% yeast extract, 2% glucose; 1% peptone K, 2% yeast extract, 2% glucose (YPD) for 2 days at 25°C with shaking 180 rpm. The cultures were then centrifuged...
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Pigment production and secretion by psychrotolerant yeast-like fungi at 15 °C for 4 days
Open Research DataThree strains, named Red, Pink and Black, were grown in five different media with the following compositions: 1% peptone K, 2% glucose; 2% peptone K, 2% glucose; 1% yeast extract, 2% glucose; 1% peptone K, 1% yeast extract, 2% glucose; 1% peptone K, 2% yeast extract, 2% glucose (YPD) for 4 days at 15°C with shaking 180 rpm. The cultures were then centrifuged...
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Pigment production and secretion by psychrotolerant yeast-like fungi at 20 °C for 2 days
Open Research DataThree strains, named Red, Pink and Black, were grown in five different media with the following compositions: 1% peptone K, 2% glucose; 2% peptone K, 2% glucose; 1% yeast extract, 2% glucose; 1% peptone K, 1% yeast extract, 2% glucose; 1% peptone K, 2% yeast extract, 2% glucose (YPD) for 2 days at 20°C with shaking 180 rpm. The cultures were then centrifuged...
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Pigment production and secretion by psychrotolerant yeast-like fungi at 15 °C for 2 days
Open Research DataThree strains, named Red, Pink and Black, were grown in five different media with the following compositions: 1% peptone K, 2% glucose; 2% peptone K, 2% glucose; 1% yeast extract, 2% glucose; 1% peptone K, 1% yeast extract, 2% glucose; 1% peptone K, 2% yeast extract, 2% glucose (YPD) for 2 days at 15°C with shaking 180 rpm. The cultures were then centrifuged...
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Hydration of molecules and intermolecular interactions 2023
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Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighbouring space around these molecules were investigated. It was found, that water forms a well-defined layer - the first solvation shell - around the peptide molecule, and thickness of this layer is independent of the peptide structure, and it equals to approximately 0.28 nm....
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Transport deficiency is the molecular basis of Candida albicans resistance to antifungal oligopeptides
Publication(FMDP), an inhibitor of glucosamine-6-phosphate synthase, exhibited growth inhibitory activity against Candida albicans, with minimal inhibitory concentration values in the 0.05–50 mg/L range. Uptake by the peptide permeases was found to be the main factor limiting an anticandidal activity of these compounds. Di- and tripeptide containing FMDP (F2 and F3) were transported by Ptr2p/Ptr22p peptide transporters (PTR) and FMDP-containing...
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Unspecified peptic ulcer as acute or chronic, without haemorrhage or perforation - Male, 55 - Tissue image [12050630013026341]
Open Research DataThis is the histopathological image of STOMACH tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Unspecified peptic ulcer as acute or chronic, without haemorrhage or perforation - Male, 55 - Tissue image [12050630013036061]
Open Research DataThis is the histopathological image of STOMACH tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format.
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Structural and Dynamic Properties of Water within the Solvation Layer around Various Conformations of the Glycine-based Polypeptide
PublicationSeveral conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer—the first solvation shell—around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within...
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Two-particle entropy and structural ordering in liquid water
PublicationEntropies of simple point charge (SPC) water were calculated over the temperature range 278-363 K using the two-particle correlation function approximation. Then, the total two-particle contribution to the entropy of the system was divided into three parts, which we call translational, configurational, and orientational. The configurational term describes the contribution to entropy, which originates from spatial distribution of...
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Systematic Water Uptake Energetics of Yttrium-Doped Barium Zirconate—A High Resolution Thermochemical Study
PublicationA combination of surface area analyzer and microcalorimetry was employed to investigate the in situ water uptake energetics and the mechanism of proton incorporation in yttrium-doped barium zirconate in the temperature range 200–400 °C. The BaZr1–xYxO3 solid solutions are made with variable yttrium content (x = 10, 20, and 30 mol %) by a controlled oxidant-peroxo synthesis method. The water uptake increases as the partial pressure...
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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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Sławomir Milewski prof. dr hab. inż.
PeopleSławomir Milewski, born in 1955 in Puck, Poland, graduated in 1979 in Chemistry from the Faculty of Chemistry, Gdańsk University of Technology (GUT). In 1984 was employed at the Department of Pharmaceutical Technology and Biochemistry. In 1985 he got his PhD, in 1994 became a DSc (habilitation) and in 2002 got the professorship in chemical sciences. Currently he is a full professor and Head of the Department of Pharmaceutical Technology...
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Optical fiber aptasensor for label-free bacteria detection in small volumes
PublicationHighly sensitive devices for fast bacteria detection are sought to be developed with the task of quantifying the worldwide problem of pathogenic bacteria and thus helping to take control over spreading bacterial infections. This work concerns a sensing solution based on microcavity in-line Mach-Zehnder interferometer (μIMZI) induced in an optical fiber. Such a device exhibits ultrahigh sensitivity to refractive index changes...
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Enzymatic cleavage of specific dipeptide conjugated with ferrocene as a flexible ultra-sensitive and fast voltammetric assay of matrix metalloproteinase-9 considered a prognostic cancer biomarker in plasma samples
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Solubilization of keratins and functional properties of their isolates and hydrolysates
PublicationThe keratinous wastes of the textile industry and poultry slaughterhouses may be used as sources of soluble keratins or hydrolysates. This review presents methods for processing raw keratin-based materials into bioproducts with functional and bioactive properties suitable for biomedical, cosmetic, food, and agricultural applications. Soluble keratin can be obtained by thermal treatment in some organic solvents, reduction, or oxidation...
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Water uptake kinetics and electrical transport in BaCe0.6Zr0.2Y0.1M0.1O3−δ (M = Tb, Pr, Fe) protonic conductors
PublicationBaCe0.6Zr0.2Y0.1M0.1O3−d (M = Fe, Pr, Tb) is a mixed conducting oxide in which three mobile charge carriers – oxygen ion, electron/hole, and protonic defects – are present. These types of materials have gained much interest as electrode materials for protonic ceramic fuel cells (PCFCs) and protonic ceramic electrolysis cells (PCECs). In this study, the water uptake and oxygen transport properties of different BaCe0.6Zr0.2Y0.1M0.1O3−d...
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Multicopy Suppressor Analysis of Strains Lacking Cytoplasmic Peptidyl-Prolyl cis/trans Isomerases Identifies Three New PPIase Activities in Escherichia coli That Includes the DksA Transcription Factor
PublicationConsistent with a role in catalyzing rate-limiting step of protein folding, removal of genes encoding cytoplasmic protein folding catalysts belonging to the family of peptidyl-prolyl cis/trans isomerases (PPIs) in Escherichia coli confers conditional lethality. To address the molecular basis of the essentiality of PPIs, a multicopy suppressor approach revealed that overexpression of genes encoding chaperones (DnaK/J and GroL/S),...
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Understanding ion–ion and ion–solvent interactions in aqueous solutions of morpholinium ionic liquids with N-acetyl-L-alaninate anion through partial molar properties and molecular dynamics simulations
PublicationAmino acid ionic liquids (AAILs) provide a low toxicity, biodegradable alternative to conventional ionic liquids, while also maintaining solubility in water. Densities and sound velocities of aqueous solutions of four amino acid ionic liquids (AAILs), based on the N-alkyl-N-methylmorpholinium ([Mor1,R], R = 2, 3, 6, 8) cation and N-acetyl-L-alaninate ([N-Ac-L-Ala]) anion were measured at T = (293.15–313.15) K and at atmospheric...
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Taurine as a water structure breaker and protein stabilizer
PublicationThe enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as “structure breaking” solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between...
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Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations
PublicationHydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the...
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Fatty acyl benzamido antibacterials based on inhibition of DnaK-catalyzed protein folding
PublicationWe have reported that the hsp70 chaperone DnaK from Escherichia coli might assist protein folding by catalyzing the cis/trans isomerization of secondary amide peptide bonds in unfolded or partially folded proteins. In this study a series of fatty acylated benzamido inhibitors of the cis/trans isomerase activity of DnaK was developed and tested for antibacterial effects in E. coli MC4100 cells. Nα-[Tetradecanoyl-(4-aminomethylbenzoyl)]-l-asparagine...
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Monitoring of concrete curing in extradosed bridge supported by numerical simulation
PublicationThe paper describes a mathematical model of concrete curing taking into account kinetics of setting reactions. The numerical model is implemented in the author’s program that was used to monitor thermal effects recorded in the concrete bottom plate of the extradosed bridge. Numerical approach was verified by experimental measurements and used for assessment of the current compressive strength due to degree of hydration of fresh...
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Structural changes of water caused by non-electrolytes: Volumetric and compressibility approach for urea-like analogues
PublicationHydration of thiourea (TU), hydroxyurea (HU, hydroxycarbamide), acetone (AC, 2-propanone) and dimethyl sulfoxide (DMSO) has been investigated with the help of the volumetric and compression measurement. The apparent molar volumes and the apparent molar isentropic (adiabatic) compression have been calculated from the density and speed of sound data at temperatures ranging from 288.15 to 308.15 K at atmospheric pressure (0.1 MPa)....
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The importance of the shape of the protein–water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationA single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water are not very different from bulk water. The local...
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The importance of the shape of the protein-water interface of a kinesin motor domain for dynamics of the surface atoms of the protein
PublicationSingle kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in solvation shell change along with the nature of neighboring protein surface. However, a detailed analysis leads to the conclusion that the geometrical features of hydrogen bonds and overall structure of kinesin hydration water is not very different from bulk water. The local values of...
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Bacteriophages as Factories for Eu2O3 Nanoparticle Synthesis
PublicationThe use of phage display to identify peptides with an ability to bind and synthesize Eu2O3 nanoparticles is demonstrated in this report. This is the first report of modified phages specifically binding a lanthanide. The peptides exposed on virions revealed very strong binding to Eu2O3 nanoparticles and the ability to catalyze Eu2O3 nanoparticles’ formation from Eu(OH)3 and Eu(NO3)3 solutions. The luminescence emission spectrum...
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Design and synthesis of new analogues of batracylin linked to tuftsin and retro-tuftsin derivatives
PublicationThe synthesis of derivatives of batracylin with several peptides was elaborated followed by their cytotoxic activity investigation.
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Mercury intrusion porosimetry (MIP) results of cement pastes containing iron oxide (Fe3O4) nanoparticles (nanomagnetite)
Open Research DataMercury intrusion porosimetry (MIP) data - curves of cement pastes containing iron oxide (Fe3O4) nanoparticles (nanomagnetite) in *.opju (Origin) format.
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An optimal designed experiment for the alkaline hydrolysis of feather keratin
PublicationFeathers, burdensome waste from the poultry industry, can be a cheap source of keratin, a protein with excellent physico- chemical, biological, and mechanical properties. Acid and alkaline hydrolyses are usually adopted for isolation of keratin from its natural resources. This study aimed at assessing the statistically significant effect of input variables in the alkaline hydrolysis of keratin from chicken feathers on the process...
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Gracjana Klein-Raina dr hab.
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Baktericyna o aktywności gronkowcobójczej wytwarzana przez Staphylococcus xylosus - identyfikacja, oczyszczanie oraz wstępna charakterystyka
PublicationCelem badań prowadzonych w ramach realizacji niniejszej pracy była identyfikacja szczepów bakterii z rodzaju Staphylococcus produkujących substancje o działaniu przeciwbakteryjnym, w tym szczególnie bakteriocyny. W trakcie badań przesiewowych, których przedmiotem było 206 szczepów z kolekcji Katedry Technologii Leków i Biochemii Politechniki Gdaoskiej z gatunków Staphylococcus aureus, Staphylococcus epidermidis oraz Staphylococcus...
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The effect of lyophilization on selected biologically active components (vitamin c, catalase, lysozyme), total antioxidant capacity and lipid oxidation in human milk
PublicationHuman milk is rich in polyunsaturated fatty acids, as well as lysozyme, vitamin C and other bioactive compounds. The effect of lyophilization on the content of antioxidants (vitamin C and catalase CAT), bactericidal compounds (lysozyme), total antioxidant capacity (TAC) and lipid peroxidation in human milk was investigated in this study. Samples of mature human milk were collected from five healthy women who gave birth on the scheduled...
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Butyrylcholinesterase signal sequence self-aggregates and enhances amyloid fibril formation in vitro
PublicationAlzheimer’s disease (AD) pathogenesis has been attributed to extracellular aggregates of amyloid β (Aβ) plaques and neurofibrillary tangles in the human brain. It has been reported that butyrylcholinesterase (BChE) also accumulates in the brain Aβ plaques in AD. We have previously found that the BChE substitution in 5′UTR caused an in-frame N-terminal extension of 41 amino acids of the BChE signal peptide. The resultant variant...
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Emerging anticancer activity of candidal glucoseamine-6-phosphate synthase inhibitors upon nanoparticle-mediated delivery
PublicationNumerous glutamine analogues have been reported as irreversible inhibitors of the glucosamine-6-phosphate (GlcN-6-P) synthase in pathogenic Candida albicans in the last 3.5 decades. Among the reported inhibitors, the most effective N3-(4-methoxyfumaroyl)-L-2,3- diaminopropanoic acid (FMDP) has been extensively studied in order to develop its more active analogues. Several peptide−FMDP conjugates were tested to deliver FMDP to its...
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Chitosan, Collagen and Gelatin in the design of novel materials with antimicrobial acticity
PublicationMedical devices containing and releasing antiinfective agents directly on the site of injury are a common group of materials available and widely used in treating difficult to heal wounds. Sustained contact of the active agent to the damaged tissue, needed to inhibit infection and preservation of microbiological purity of the wound, is provided by the immobilization antimicrobial agents on the surface of the matrix material or...