prikaz prve stranice dokumenta Design strategies for SARS-CoV-2 spike protein mimetics based on peptide self-assembly
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master's thesis
Design strategies for SARS-CoV-2 spike protein mimetics based on peptide self-assembly
2021. urn:nbn:hr:193:059914
Budić, Katarina
University of Rijeka
Faculty of Biotechnology and Drug Development

Cite this document

Budić, K. (2021). Design strategies for SARS-CoV-2 spike protein mimetics based on peptide self-assembly (Master's thesis). Rijeka: University of Rijeka. Retrieved from https://urn.nsk.hr/urn:nbn:hr:193:059914

Budić, Katarina. "Design strategies for SARS-CoV-2 spike protein mimetics based on peptide self-assembly." Master's thesis, University of Rijeka, 2021. https://urn.nsk.hr/urn:nbn:hr:193:059914

Budić, Katarina. "Design strategies for SARS-CoV-2 spike protein mimetics based on peptide self-assembly." Master's thesis, University of Rijeka, 2021. https://urn.nsk.hr/urn:nbn:hr:193:059914

Budić, K. (2021). 'Design strategies for SARS-CoV-2 spike protein mimetics based on peptide self-assembly', Master's thesis, University of Rijeka, accessed 21 November 2024, https://urn.nsk.hr/urn:nbn:hr:193:059914

Budić K. Design strategies for SARS-CoV-2 spike protein mimetics based on peptide self-assembly [Master's thesis]. Rijeka: University of Rijeka; 2021 [cited 2024 November 21] Available at: https://urn.nsk.hr/urn:nbn:hr:193:059914

K. Budić, "Design strategies for SARS-CoV-2 spike protein mimetics based on peptide self-assembly", Master's thesis, University of Rijeka, Rijeka, 2021. Available at: https://urn.nsk.hr/urn:nbn:hr:193:059914

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Metadata
TitleDesign strategies for SARS-CoV-2 spike protein mimetics based on peptide self-assembly
Title (croatian)Dizajn peptidnih mimetika "Spike" proteina SARS-CoV-2 virusa na temelju sposobnosti samo-sastavljanja peptida
AuthorKatarina Budić
MentorDaniela Kalafatović (mentor)
MentorJelena Ban (komentor)
Committee memberNela Malatesti (predsjednik povjerenstva)
Committee memberIvana Ratkaj (član povjerenstva)
Committee memberDaniela Kalafatović (član povjerenstva)
GranterUniversity of Rijeka
(Faculty of Biotechnology and Drug Development)
Rijeka
Defense date and country2021-09-15, Croatia
Scientific / art field,
discipline and subdiscipline		BIOTECHNICAL SCIENCES
Biotechnology
Molecular Biotechnology
Abstract
Supramolecular chemistry is a discipline that studies the characteristics of non-covalent bonds between molecules and / or ions. Advances in supramolecular chemistry in the last two decades have enabled the fabrication and design of peptide nanostructures. Peptides are biological molecules whose sequences are naturally self-assembled in water and organized into nanostructures. They are often investigated as carriers in targeted drug delivery, and their purpose has been found in the fight against the pandemic caused by the SARS-CoV-2 virus. This member of the beta-coronavirus group infects cells and tissues by binding to ACE2 and NRP1 receptors with the S- protein. The aim of this study was to design and prepare a minimalist peptide version of the SARS-CoV-2 virus based on S-protein. Peptide mimetics consisted of amino acids identified at the S-protein binding site (RBM) that interact with the ACE2 and NRP1 receptors. After amino acid identification using Pymol computer applications, three peptide sequences were designed: FFLYY, FFLYYKK, and KYLFFQTY. Physiochemical characteristics of peptides were determined by MALDI TOF / TOF MS and OD measurements. The formation of spherical nanostructures was examined by determining the critical concentration of micellization (CMC) using fluorescent spectrophotometer and pyrene as a fluorescent probe. The peptides FFLYYKK and KYLFFQTY form micelles at 0.65 mM and 2.15 mM, respectively. The formation of micelles for the FFLYY peptide cannot be confirmed with certainty as it failed to dissolve completely in the DMSO/water mixture. It also showed the highest optical density, while the other peptides were well soluble in aqueous solution. In future research, additional confirmation of the micelle formation by ATF-FTIR spectroscopy and the atomic force microscope is required. It is also necessary to examine their toxicity and the possibility of binding and entering neurons and astrocytes whose morphological changes would be monitored by fluorescence microscopy. Successful binding of peptide mimetics to ACE2 and NRP1 may block virus entry and the influence on cells would explain possible neurocognitive difficulties caused by infection.
Abstract (croatian)
Supramolekularna kemija je disciplina koja proučava karakteristike nekovalentnih veza između molekula i/ili iona. Napredak u području supramolekularne kemije u posljednja dva desetljeća unaprijedio je dizajn i primjenu peptidnih nanostruktura. Peptidi su biološke molekuke čije se sekvence prirodnim procesom samo-sastavljanja u vodi organiziraju u nanostrukture. Njihovom manipulacijom nastaju funkcionalni biokompatibilni materijali. Često se istražuju kao nosači pri ciljanoj dostavi lijekova, a svoju svrhu pronašli su i u borbi protiv pandemije uzrokovane SARS-CoV-2 virusom. Ovaj pripadnik skupine betakoronavirusa inficira stanice i tkiva vežući se na ACE2 i NRP1 receptore pomoću S-proteina. Cilj ovog istraživanja bio je dizajnirati i pripremiti minimalističke peptidne verzije SARS-CoV-2 virusa. Peptidni mimetici sastojali su se od aminokiselina identificiranih na veznom mjestu S-proteina (RBM) kojim se veže na ACE2 i NRP1 receptore. Nakon identifikacije aminokiselina pomoću računalne aplikacije Pymol, dizajnirane su tri peptidne sekvence: FFLYY, FFLYYKK i KYLFFQTY. Fizio-kemijske karakteristike peptida određene su metodama matricom potpomognute laserske desorpcije/ionizacije (MALDI TOF/TOF MS) i mjerenjem optičke gustoće (eng. optical density, OD). Formiranje sfernih nanostruktura procesom samo-sastavljanja ispitivalo se određivanjem kritične koncentracije micelizacije (eng. critical micelle concentration, CMC) metodom spektrofotometrije i pirenom kao fluorescentnom probom. Peptidi FFLYYKK i KYLFFQTY formiraju micele pri 0.65 mM i 2.15 mM. Formiranje micela za peptid FFLYY ne može se sa sigurnošću potvrditi s obzirom da se nije uspio potpuno otopiti u otopini DMSO-a i vode. On je pokazao i najveću optičku gustoću, dok su ostali peptidi bili dobro topivi u vodenoj otopini. U budućim istraživanjima potrebno je provesti dodatnu potvrdu agregacije peptida pomoću infracrvene spektroskopije s Fourierovom transformacijom (ATFFTIR) i mikroskopa atomskih sila (eng. atomic force microscope, AFM).Također je potrebno ispitati njihovu toksičnost te mogućnost vezanja na receptore i ulazak peptidnih nanostruktura u stanice neurona i astrocita čije će se morfološke promjene pratiti fluorescentnim mikroskopom. Uspješno vezanje peptidnih mimetika za ACE2 i NRP1 može blokirati ulazak virusa, a djelovanje na moždane stanice objasnit će neurokognitivne poteškoće koje nastaju kao posljedica infekcije.
Keywords
Keywords (croatian)
Languageenglish
URN:NBNurn:nbn:hr:193:059914
ProjectNumber: UIP-2019-04-7999
Title: Dizajn katalitički aktivnih peptida i peptidnih nanostruktura
Title: Design of short catalytic peptides and peptide assemblies
Acronym: DeShPet
Leader: Daniela Kalafatović
Jurisdiction: Croatia
Funder: HRZZ
Funding stream: UIP
Study programmeTitle: Biotechnology in medicine
Study programme type: university
Study level: graduate
Academic / professional title: magistar/magistra biotehnologije u medicini (magistar/magistra biotehnologije u medicini)
Type of resourceText
File originBorn digital
Access conditionsClosed access
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Created on2021-09-22 15:46:08