Structure-Activity Relationship and Mode of Action of a Frog Secreted Antibacterial Peptide B1CTcu5 Using Synthetically and Modularly Modified or Deleted (SMMD) Peptides.

All life forms are equipped with rapidly acting, evolutionally conserved components of an innate immune defense system that consists of a group of unique and diverse molecules known as host defense peptides (HDPs). A Systematic and Modular Modification and Deletion (SMMD) approach was followed to analyse the structural requirement of B1CTcu5, a brevinin antibacterial peptide amide identified from the skin secretion of frog Clinotarsus curtipes, India, to show antibacterial activity and to explore the active core region. Seventeen SMMD-B1CTcu5 analogs were designed and synthesised by C and N-terminal amino acid substitution or deletion. Enhancement in cationicity by N-terminal Lys/Arg substitution or hydrophobicity by Trp substitution produced no drastic change in bactericidal nature against selected bacterial strains except S. aureus. But the sequential removal of N-terminal amino acids had a negative effect on bactericidal potency. Analog B1CTcu5-LIAG obtained by the removal of four N-terminal amino acids displayed bactericidal effect comparable to, or in excess of, the parent peptide with reduced hemolytic character. Its higher activity was well correlated with the improved inner membrane permeabilisation capacity. This region may act as the active core of B1CTcu5. Presence of C-terminal disulphide bond was not a necessary condition to display antibacterial activity but helped to promote hemolytic nature. Removal of the C-terminal rana box region drastically reduced antibacterial and hemolytic activity of the peptide, showing that this region is important for membrane targeting. The bactericidal potency of the D-peptide (DB1CTcu5) helped to rule out the stereospecific interaction with the bacterial membrane. Our data suggests that both the C and N-terminal regions are necessary for bactericidal activity, even though the active core region is located near the N-terminal of B1CTcu5. A judicious modification at the N-terminal region may produce a short SMMD analog with enhanced bactericidal activity and low toxicity against eukaryotic cells

DFT-based molecular modeling, NBO analysis and vibrational spectroscopic study of 3-(bromoacetyl)coumarin

WOS: 000295956500018PubMed ID: 21831702The NIR-FT Raman and FT-IR spectra of 3-(bromoacetyl)coumarin (BAC) molecule have been recorded and analyzed. Density functional theory (DFT) calculation of two BAC conformers has been performed to find the optimized structures and computed vibrational wavenumbers of the most stable one. The obtained vibrational wavenumbers and optimized geometric parameters were seen to be in good agreement with the experimental data. Characteristic vibrational bands of the pyrone ring and methylene and carbonyl groups have been identified. The lowering of HOMO-LUMO energy gap clearly explains the charge transfer interactions taking place within the molecule. (C) 2011 Elsevier B.V. All rights reserved.Ahi Evran UniversityAhi Evran University [A10/2009]We thank referees for their valuable suggestions. The author (Y. Erdogdu) would like to thank Ahi Evran University Research Fund for its financial support, Project Numbers: A10/2009. We also thank Assoc. Prof. Dr. Mustafa Kurt for the Gaussian 03W program package

Vibrational spectra, structural conformations, scaled quantum chemical calculations and NBO analysis of 3-acetyl-7-methoxycoumarin

WOS: 000311814300035PubMed ID: 23078790The powder form NIR-FT Raman and FT-IR spectra of 3-acetyl-7-methoxycoumarin (3A7MC) have been recorded in the regions 4000-400 and 3500-100 cm(-1), respectively. The equilibrium geometry, vibrational frequencies, band intensities, NMR spectra, NBO analysis and UV-Vis spectral studies of the most stable conformer have been calculated by density functional B3LYP method with the 6-311G(d,p) basis set. A complete vibrational analysis has been attempted on the basis of experimental infrared and Raman spectra, the calculated wavenumber and intensity of the vibrational bands and the potential energy distribution over the internal coordinates. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecules has been obtained by mapping the electron density isosurface with electrostatic potential surfaces (ESP). Natural bond orbital analysis has been carried out to understand the nature of different interactions responsible for the electron delocalization and the intramolecular charge transfer between the orbitals (n -> pi*, n -> sigma*, pi -> pi*). (c) 2012 Elsevier B.V. All rights reserved.University Grants Commission, New DelhiUniversity Grants Commission, India [MRP(S)-899/10-11/KLKE002/UGC-SWRO]; Ahi Evran University Research FundAhi Evran University [FBA-11-09]The author Lynnette Joseph would like to thank the University Grants Commission, New Delhi for its financial support, Project number: MRP(S)-899/10-11/KLKE002/UGC-SWRO. One of the authors (Y. Erdogdu) would like to thank Ahi Evran University Research Fund for its financial support, Project numbers: FBA-11-09

Antibacterial and hemolytic activity of synthetic B1CTcu5 and SMMD analogs.

<p>^a—MIC represents the lowest peptide concentration required to kill entire bacteria, NA-not active up to the highest concentration tested.</p><p>Antibacterial and hemolytic activity of synthetic B1CTcu5 and SMMD analogs.</p

Outer and inner membrane permeabilisation in <i>E</i>. <i>coli</i> cells.

<p>(A) <i>E</i>. <i>coli</i> cells(OD 0.5–0.6) were washed with 5mM HEPES, pH 7.2 and 5mM KCN. 1mL cells were treated with 10mM NPN and increasing concentrations of peptides were added. The uptake of NPN was noted by increase in fluorescence at an excitation of 350nm and emission of 420nmas a measure of outer membrane permeabilisation. (B) Inner membrane permeabilisation efficiency of the peptides were assayed by treating <i>E</i>. <i>coli</i> cells (OD 0.4–0.6) in PBS with 1μM SYTOX green at 37°C for 15 min. Fluorescence was measured at an excitation wavelength of 485nm and emission wavelength of 520nm after peptide addition.</p

Membrane depolarization of <i>E</i>. <i>coli</i> by B1CTcu5 and its analogs.

<p><i>E</i>. <i>coli</i> cells (10⁶ CFU/ml) were treated with peptides at their MICs for 1h and treated with 1μg/ml of [DiBAC₄ (3)].10,000 events were selected for the assay and the bacteria were differentiated from background signals. Membrane depolarization is indicated by a shift in the population.</p

Lignocellulose in future biorefineries: strategies for cost-effective production of biomaterials and bioenergy

Lignocellulosic biomass has been emerging as a biorefinery precursor for variety of biofuels, platform chemicals and biomaterials because of its specific surface morphology, exceptional physical, chemical and biological characteristics. The selection of proper raw materials, integration of nano biotechnological aspects, and designing of viable processes are important to attain a cost-effective route for the development of valuable end products. Lignocellulose-based materials can prove to be outstanding in terms of techno-economic viability, as well as being environmentally friendly and reducing effluent load. This review should facilitate the identification of better lignocellulosic sources, advanced pretreatments, and production of value-added products in order to boost the future industries in a cleaner and safer way

Cytotoxicity in human cells.

<p>The values represent averages ± s.d from three separated experiments.</p><p>Cytotoxicity in human cells.</p

Characterization and In vitro biocompatibility analysis of nanocellulose scaffold for tissue engineering application

Tissue engineering aims to exploit the regenerative capacity of cells and connect the inherent ability of the body to repair and regenerate. Cells are seeded onto a porous three-dimensional scaffold in tissue engineering, which will provide protection and direct cells to the development of new tissue-like structures. These scaffolds can provide a medium for the delivery, under controlled conditions of growth factors release and drug delivery. Herein, nanocellulose was extracted from Ixora coccinea L. plant root, plasticized scaffold of nanocellulose were prepared by using glycerol, gelatin, and PEG 600 followed by morphological characterized by FTIR, XRD, SEM, and tensile modulus analysis. FTIR indicated extracted nanocellulose is without any hemicelluloses, lignin, and non-cellulosic materials. XRD data displayed the extracted nanocellulose has a crystal size of around 3.6 nm while SEM data revealed the fiber diameter was around 20 µm. In the tensile modulus analysis, 1% PEG 600 exhibited the highest (tensile strength 69 MPa with young’s modulus 67.326 MPa) as compared to glycerol and gelatin and hence selected for further studies. The In vitro cytocompatibility studies revealed that nanocellulose and 1% PEG 600 incorporated nanocellulose scaffolds were cell-friendly, promote cell proliferation, and do not show RBC aggregation as well as haemolysis suggesting its potential in various tissue engineering applications. The novelty of this work is that the nanocellulose extracted from the root of I. coccineahas traditional medicinal values in Ayurveda

Effect of peptides against biofilm formation by <i>S</i>. <i>aureus</i> strains.

<p>Biofilm formed by <i>S</i>. <i>aureus</i> at 12 h were treated with 100μg/ml of peptides for 12 h and the biofilm formation was determined by measuring the absorbance at 570 nm.</p