M.S. Theses

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Browsing M.S. Theses by Subject "Anti-infective agents."

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    Drug design against antimicrobial resistance
    (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2016., 2016.) Kalyon, Kevser Betül.; Özkırımlı, Elif.; Sarıyar, Berna.
    Cell penetrating peptides are extensively studied due to their potential for having antimicrobial properties. The purpose of this study is to understand the mechanisms of certain cell penetrating peptides in bacterial and mammalian membranes and to research their potential in antimicrobial drug design. In this study, melittin and pVEC peptide structures along with POPC and POPE membranes were constructed in VMD and the passage of each peptide through bilayers of each membrane type were simulated using SMD simulations. MD simulations were carried out by taking snapshots of SMD simulations while the peptide was located on the top, middle, and bottom of the bilayer. The simulations were examined by following energy, force and work vs. distance profiles of peptides. The results gave insight on melittin and pVEC interactions with POPE and POPC membranes as they are transported through bilayers. Compared to POPE membrane, the electrostatic energies were higher in POPC membrane making it harder for peptides to penetrate the bilayer. Melittin helicity was higher in POPE bilayer. The observed lower helicity in POPC membrane is thought to facilitate pore formation by increasing interactions of residues with membrane lipids and effecting lipid orders. In POPE membrane another mechanism might be at work. POPE membrane thinned more which may increase the probability of leakage. The pVEC peptide lead to more water insertion inside the bilayers compared to melittin peptide. Furthermore, pVEC caused more water molecules to penetrate POPC membrane. This may increase the permeability of the membrane and increase uptake of more peptides. In MD simulations, pVEC preferred POPE membrane over POPC membrane while melittin had affinity for both membranes. When melittin center of mass was pulled, due to energy barriers melittin penetrated the upper P layer of the bilayer with difficulty but caused more water penetration into the bilayer compared to other simulations. When melittin was pulled with 1/10th velocity, it stayed in a parallel position on the upper P layer of membrane in α-helix structure before penetration. After 151.68 ns, melittin only reached the center of the bilayer while in other melittin POPE simulations it took melittin 58, 50 and 38 ns to pass through the bilayer
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    Understanding the membrane penetration of antimicrobial
    (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2012., 2012.) Alaybeyoğlu, Begüm.; Özkırımlı, Elif.; Sarıyar, Berna.
    The studies on β-lactam antibiotics have found great interest since the use of antimicrobial therapy became widespread and as a result, bacteria started to develop resistance against β-lactam antibiotics. The most effective resistance mechanism is the production of β-lactamases. The need of successful inhibitors against β-lactamase led to the studies that revealed the structure of β-lactamase inhibitory protein (BLIP) and its interactions with β-lactamase. The structure of TEM-1-BLIP complex indicated that a type II β turn (residues 46-51) of BLIP made critical interactions with the active site of the TEM-1 β-lactamase, suggesting that a peptide including this loop would be a good lead toward the development of a peptide based inhibitor. In peptide based drug design, one of the most common challenges is penetration through the membrane. It was aimed to investigate the translocation mechanism of the cell-penetrating peptide pVEC (LLIILRRRIRKQAHAHSK) and to analyze it on a residue basis in order to identify mechanism by which bacterial uptake occurs. The wild-type pVEC, eight mutants, retro- and scramble pVEC were chosen to be studied using molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. The peptide transport was observed to occur in three main stages and it was distinguished that for peptides with increased uptake potential, the work performed was higher. Residues L1, R6, R7, R8, R10, K11 and K18 was shown to contribute to the interaction of pVEC with the lipid bilayer. In the experimental part of the study, effect of Peptide 1 (5-Fluorescein-NH-HA AGDYYAY- CONH2), Peptide 2 (5/6-Fluorescein-NH-RRGHYY-COOH) and Peptide 3 (5/6-Fluorescein-NH-LLIILHAAGDYYAY- CONH2) on growth of antibiotic resistant E. coli K12 pUC18 cells expressing β-lactamase was examined. Peptide 1 did not have an inhibitory effect on the cell growth. On the other hand, Peptide 3 was taken into the cells, as revealed by microscopy and incubation with this peptide led to cell death. Our studies showed that inclusion of the five hyrophobic residues at the N-terminus enhanced the uptake potential of the inhibitory peptide.