Browsing by Subject "Phage display library"
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Item Open Access Peptide drug candidates for pathogenic amyloids(2020-01) Özçelik, Cemile ElifAmyloid fibrils are very stable, ordered cross-β structured, resistant to protease degradation, proteinaceous composits. All amyloids have different peptide/protein sequences although they express similar structural properties. Some of amyloids possess advantageous functionalities such as protection, cell-cell communication, protein storage. However, most of amyloids are associated with various severe diseases such as neurodegenerative diseases. Although amyloids follow similar formation pathway, pathogenic amyloids are challenging since their formations are supported with secondary pathways. Up to now, there were several therapeutic approaches that are only effective in symptoms of disease conditions by masking or slowing down the symptom developments. Nonetheless, different approaches are developed for inhibiting amyloid aggregation. Today, most of the strategies are aiming to inhibit secondary nucleation, which is not fully understood yet. So, such approaches can be faced with lots of challenge in terms of secondary nucleation kinetics and formation mechanism. Thus, inhibition of monomeric amyloid units, which are developed into amyloid aggregates, can be another novel approach for halting disease-condition developments. In this thesis, candidate ligand peptides that cease aggregation of huntingtin, α-synuclein and amyloid-β were selected by using different types of display systems, which are bacterial surface display, yeast surface display and phage display. The monomeric amyloid units of these proteins were expressed on surfaces of bacterial cells and yeast cells in order to expressing monomeric units with a proper folding and avoiding aggregation after expression without interacting with each other. Candidate ligand peptides were selected against neurodegenerative amyloids by M13 phage display library. First, M13 phage display library was tried to be produced from using wild type M13 bacteriophage by basic cloning methods as well as commercially available M13 phage display library kit was used for peptide selection since the minor coat protein pIII of M13 is widely used for peptide display and ligand peptide selection studies. Thus, 12 amino acid-long peptides displayed on the minor coat protein pIII were selected against neurodegenerative amyloids for inhibiting protein aggregation purpose in the very first step of aggregation pathway.Item Open Access Synergistic screening of peptide-based biotechnological drug candidates for neurodegenerative diseases using yeast display and phage display(American Chemical Society, 2023-10-04) Özçelik, Cemile Elif; Beğli, Özge; Hınçer, Ahmet; Ahan, Recep Erdem; Kesici, M. S.; Oğuz, Oğuzhan; Kasırga, Talip Serkan; Özçubukçu, S.; Şeker, Urartu Özgür ŞafakPeptide therapeutics are robust and promising molecules for treating diverse disease conditions. These molecules can be developed from naturally occurring or mimicking native peptides, through rational design and peptide libraries. We developed a new platform for the rapid screening of the peptide therapeutics for disease targets. In the course of the study, we aimed to employ our platform to screen a new generation of peptide therapeutic candidates against aggregation-prone protein targets. Two peptide drug candidates were screened for protein aggregation-prone diseases, namely, Parkinson’s and Alzheimer’s diseases. Currently, there are several therapeutic applications that are only effective in masking or slowing down symptom development. Nonetheless, different approaches are being developed for inhibiting amyloid aggregation in the secondary nucleation phase, which is critical for amyloid fibril formation. Instead of targeting secondary nucleated protein structures, we tried to inhibit the aggregation of monomeric amyloid units as a novel approach for halting the disease condition. To achieve this, we combined yeast surface display and phage display library platforms. We expressed α-synuclein, amyloid β40, and amyloid β42 on the yeast surface, and we selected peptides by using phage display library. After iterative biopanning cycles optimized for yeast cells, several peptides were selected for interaction studies. All of the peptides have been used for in vitro characterization methods, which are quartz crystal microbalance-dissipation (QCM-D) measurement, atomic force microscopy (AFM) imaging, dot-blotting, and ThT assay, and some of them have yielded promising results in blocking fibrillization. The rest of the peptides, although, interacted with amyloid units which made them usable as a sensor molecule candidate. Therefore, peptides selected by yeast surface display and phage display library combination are good choice for diverse disease-prone molecule inhibition, particularly those inhibiting fibrillization. Additionally, these selected peptides can be used as drugs and sensors to detect diseases quickly and halt disease progression.