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Cyclic lipodepsipeptides as lead structures for the discovery of new antiobiotics
Title
Cyclic lipodepsipeptides as lead structures for the discovery of new antiobiotics.
Creator
Bionda, Nina., Charles E. Schmidt College of Science, Department of Chemistry and Biochemistry
Abstract/Description
With antimicrobial resistance to current drugs steadily rising, the development of new antibiotics with novel mechanisms of action has become an imperative. The majority of life-threatening infections worldwide are caused by "ESKAPE" pathogens which are encountered in more than 40% of hospital-acquired infections, and are resistant to the majority of commonly used antibiotics. Naturally occurring cyclic depsipeptides, microbial secondary metabolites that contain one or more ester bonds in...
Show moreWith antimicrobial resistance to current drugs steadily rising, the development of new antibiotics with novel mechanisms of action has become an imperative. The majority of life-threatening infections worldwide are caused by "ESKAPE" pathogens which are encountered in more than 40% of hospital-acquired infections, and are resistant to the majority of commonly used antibiotics. Naturally occurring cyclic depsipeptides, microbial secondary metabolites that contain one or more ester bonds in addition to amide bonds, have emerged as an important source of pharmacologically active compounds or lead structures for the development of novel antibiotics. Some of those peptides are either already marketed (daptomycin) or in advanced stages of clinical development (ramoplanin). Structurally simple, yet potent, fusaricidin/LI-F and lysobactin families of naturally occurring antibiotics represent particularly attractive candidates for the development of new antibacterial agents capable of overco ming infections caused by multidrug-resistant bacteria. These natural products exhibit potent antimicrobial activity against a variety of clinically relevant fungi and Gram-positive bacteria. Therefore, access to these classes of natural products and their synthetic analogs, combined with elucidation of their mode of action represent important initial steps toward full exploitation of their antmicrobial potential. This dissertation describes a general approach toward the solid-phase synthesis of fusaricidin/LI-F and lysobactin analogs and an extensive structure-activity relationship (SAR) study. We have devised a simple and robust preparation strategy based on standard Fmoc solid-phase peptide synthesis protocols., The SAR study revealed key structural requirements for fusaricidin/LI-F and related cyclic lipopeptides antibacterial activity, including the presence of the guanidino moietly at the end of the lipidic tail, hydrophobic amino acid residues, and peptide conformation Moreover, substitution of the ester bond with an amide bond significantly improved stability under physiologically relevant conditions and reduced toxicity. In addition, we have shown that these antibacterial peptides exert their mode of action via a novel mechanism, which invloves bacterial membrane interactions, followed by peptide internalization. Altogether, the research described in this dissertation demonstrates that new antibiotics derived from fusaricidin/LI-F natural products, have the potential to meet the challenge of antibiotic resistance in Gram-positive bacteria.
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Date Issued
2013
PURL
http://purl.flvc.org/FAU/3360768
Subject Headings
Microbial peptides, Drugs, Design, Peptides, Therapeutic use, Genetic engineering, Antibacterial agents, Peptide antibiotics, Research, Methodology, Peptide antibiotics, Analysis
Format
Document (PDF)
extraction optimization and determination of the absolute configuartion of clathric acid
Title
An extraction optimization and determination of the absolute configuartion of clathric acid.
Creator
Rueda de Leon, Rolando, Charles E. Schmidt College of Science, Department of Chemistry and Biochemistry
Abstract/Description
Current research in natural products has heavily focused on the identification of potent biologically active compounds, specifically for drug development. The project detailed in this thesis focuses on the extraction of compounds from marine invertebrates as well as defining the absolute configuration for a compound. Utilizing marine invertebrates, the sonications method developed in this thesis provides an alternative approach to rapidly extract compounds for primary screening. This method...
Show moreCurrent research in natural products has heavily focused on the identification of potent biologically active compounds, specifically for drug development. The project detailed in this thesis focuses on the extraction of compounds from marine invertebrates as well as defining the absolute configuration for a compound. Utilizing marine invertebrates, the sonications method developed in this thesis provides an alternative approach to rapidly extract compounds for primary screening. This method is viable compared to a traditional overnight extraction method, without suffering compound degredation... Previously, clathric acid was isolated from an unknown Clathria sp. This compound is a bibyblic C-21 terpenoid shown to have mild antimicrobial activity against gram positive bacteria. With only its relative configuration established, additional amounts of clathric acid were required to define the overall absolute configuration. Identifying the Clathria sp. to be Clathria compressa, through spicule analysis, additional sponge tissues were then collected off the coast of Boca Raton, Florida to isolate additional quatities of clathric acid. The absolulte configuration was determined through circular dichroism and the octant rule to establish a final configuration for clathric acid's four carbon stereocenters to be: (3S, 7S, 8R, and 12S).
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Date Issued
2012
PURL
http://purl.flvc.org/FAU/3355874
Subject Headings
Organic compounds, Analysis, Extraction (Chemistry), Natural products, Therapeutic use, Marine biotechology, Marine resources, Research, Sponges, Ecology
Format
Document (PDF)
Light intensity influences on algal pigments, proteins and carbohydrates
Title
Light intensity influences on algal pigments, proteins and carbohydrates: implications for pigment-based chemotaxonomy.
Creator
Grant, Cidya S., Charles E. Schmidt College of Science, Department of Chemistry and Biochemistry
Abstract/Description
Phytoplankton Chlorophyll a (CHLa), total protein, colloidal carbohydrates, storage carbohydrates and taxonomic pigment relationships were studied in two cyanophytes (Microcystis aeruginosa and Synnechococcus elongatus), two chlorophytes (Dunaliella tertiolecta and Scenedesmus quadricauda), one cryptophyte (Rhodomonas salina), two diatoms (Cyclotella meneghiniana and Thalassiosira weissflogii) and one dinophyte (Amphidinium carterae) to assess if algal biomass could be expressed in other...
Show morePhytoplankton Chlorophyll a (CHLa), total protein, colloidal carbohydrates, storage carbohydrates and taxonomic pigment relationships were studied in two cyanophytes (Microcystis aeruginosa and Synnechococcus elongatus), two chlorophytes (Dunaliella tertiolecta and Scenedesmus quadricauda), one cryptophyte (Rhodomonas salina), two diatoms (Cyclotella meneghiniana and Thalassiosira weissflogii) and one dinophyte (Amphidinium carterae) to assess if algal biomass could be expressed in other indices than just chlorophyll a alone. Protein and carbohydrates are more useful currencies for expressing algal biomass, with respect to energy flow amongst trophic levels. These phytoplankton were grown at low light (LL = 37 (So(Bmol photons m-2 s-1), medium light (ML = 70-75 (So(Bmol photons m-2 s-1), and high light (HL= 200 (So(Bmol photons m-2 s-1)., Even though pigment per cell increased with increasing light intensity, statistically light had very little effect on the CHL a : taxonomic marker pigment ratios, as they covaried in the same way. Protein, colloidal carbohydrates and storage carbohydrates per cell all increased with increasing light intensity, but they did not covary with CHLa. Statistical data showed that light intensity had a more noticeable effect on protein: CHL a, colloidal carbohydrate: CHLa, storage CHO: CHLa, therefore a general mathematical expression for these relationships cannot be generated. This study showed that light intensity does have an influence on these biomass indices, therefore, seasonal and latitudinal formulas may be required for meaningful algal biomass estimation. However, more studies are needed if that goal is to be realized., While studying the effects of light intensity on algal pigment content and concentration, a new pigment was isolated from a cyanophyte (Scytonema hofmanii) growing between 300-1800 (So(Bmol photons¨m-2¨s-1 and from samples collected in areas of the Florida Everglades. This pigment was characterized and structurally determined to possess indolic and phenolic subunits that are characteristic of scytonemin and its derivatives. In addition, the pigment has a ketamine functionality which gives it its unique polarity and spectral properties. Based on the ultra violet/visible absorbance data, this pigment was postulated to be protecting the chlorophyll a and cytochrome Soret bands as well as a and (Sb (Bbands of the cytochromes (e.g. cytc-562) in the photosynthetic unit.
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Date Issued
2011
PURL
http://purl.flvc.org/FAU/3332257
Subject Headings
Plant pigments, Analysis, Photosynthetic pgiments, Analysis, Plant allometry, Enviornmental geochemistry, Marine algae, Analysis
Format
Document (PDF)
Study of cell penetrating peptides with Raman spectroscopy and microscopy
Title
Study of cell penetrating peptides with Raman spectroscopy and microscopy.
Creator
Ye, Jing., Charles E. Schmidt College of Science, Department of Chemistry and Biochemistry
Abstract/Description
Cell penetrating peptides (CPPs) have drawn the attention of researchers due to their ability to internalize large cargos into cells including cancer cells. The mechanism(s) with which the peptides enter the cell, however, is/are not clear and full of controversy. The peptide conformations and their microenvironment in live cells had been unknown until the development of a technique developed in our lab. As a first demonstration of principle, penetratin, a 16-residue CPP derived from the...
Show moreCell penetrating peptides (CPPs) have drawn the attention of researchers due to their ability to internalize large cargos into cells including cancer cells. The mechanism(s) with which the peptides enter the cell, however, is/are not clear and full of controversy. The peptide conformations and their microenvironment in live cells had been unknown until the development of a technique developed in our lab. As a first demonstration of principle, penetratin, a 16-residue CPP derived from the Antennapedia homeodomain protein of Drosophila, was measured in single, living melanoma cells. Carbon-13 labeling of the Phe residue of penetratin was used to shift the intense aromatic ring-breathing vibrational mode from 1003 to 967 cm-1, thereby enabling the peptide to be traced in cells. Difference spectroscopy and principal components analysis (PCA) were used independently to resolve the Raman spectrum of the peptide from the background cellular Raman signals., On the basis of the position of the amide I vibrational band in the Raman spectra, the secondary structure of the peptide was found to be mainly random coil and b-strand in the cytoplasm, and possibly assembling as b-sheets in the nucleus. Next, label-free transportan was studied with the same methodology. The peptide, besides predominantly a-helix, adopted a significant portion of b-sheet conformation in the cytoplasm and nucleolus, which is different from the peptide in aqueous solution. The peptide microenvironment was also probed through H-bonding reported by the tyrosine Fermi doublet. Transportan displayed a tendency to accumulate in the cytoplasm over time which was unlike penetratin, which concentrated in the nucleus. The relative concentration of CPPs in various locations of live melanoma cells was directly estimated from the Raman spectra using average Phe concentration in the cell as an internal standard., The rapid entry and almost uniform cellular distribution of both peptides, as well as the lack of correlation between peptide and lipid Raman signatures, indicated that the mechanism of CPP internalization under the conditions of study was probably non-endocytotic. Last, transportan and penetratin were studied using polarized Raman spectroscopy for more detailed vibrational spectroscopic information of the two peptides in water and TFE solutions. The majority of the bands in the Raman spectra of the peptides were highly polarized, consistent with the high symmetry of aromatic ring side chain vibrational bands dispersed throughout the spectra. This work has provided new insights into the structure of CPPs in live cells and in solutions.
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Date Issued
2011
PURL
http://purl.flvc.org/FAU/3342344
Subject Headings
Peptides, Analysis, Infrared spectroscopy, Raman spectroscopy, Cellular signal transduction
Format
Document (PDF)