Načrtovanje pentapeptidov za vezavo na fc regijo protiteles : diplomsko delo visokošolskega strokovnega študijskega programa I. stopnje

Stradar, Benjamin

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Title:	Načrtovanje pentapeptidov za vezavo na fc regijo protiteles : diplomsko delo visokošolskega strokovnega študijskega programa I. stopnje
Authors:	ID Stradar, Benjamin (Author) ID Jukič, Marko (Mentor) More about this mentor... ID Bren, Urban (Comentor)
Files:	VS_Stradar_Benjamin_2023.pdf (6,20 MB) MD5: 3DC60B0F0232C63502B2E12BF93608C1
Language:	Slovenian
Work type:	Bachelor thesis/paper
Typology:	2.11 - Undergraduate Thesis
Organization:	FKKT - Faculty of Chemistry and Chemical Engineering
Abstract:	Razvoj novih peptidnih zdravilnih učinkovin je zelo zahtevna naloga kemijske in farmacevtske industrije. Delo lahko olajša uporaba računalniških pristopov in simulacij. Z njimi lahko uspešno modeliramo interakcije, ki so ključne pri razumevanju delovanja in razvoja novih zdravilnih učinkovin. Peptidi zajemajo prednosti majhnih molekul ter tarčno specifičnost večjih struktur, kot so proteini. V diplomski nalogi smo za načrtovanje novih potencialnih struktur peptidov uporabili računalniške in bioinformacijske pristope kot sta mulekulsko sidranje in kemoinformacijska analiza. Za načrtovanje peptidov smo se osredotočili predvsem na tarčo Fc regije protiteles, kjer smo ustrezno strukturo pridobili na prosto dostopnem spletnem mestu https://www.rcsb.org/ (PDB ID: 5U52). Načrtovali in identificirali smo potencialne pentapeptide z uporabo struktur iz predhodno načrtovane knjižnice tetrapeptidov. Za pripravo knjižice struktur pentapeptidov in analizo rezultatov pa smo uporabili 100 najboljših predhodno identificiranih tetrapeptidov. Nato smo izvedli molekulsko sidranje in uporabili programsko opremo CmDock. Podatke smo nato analizirali z uporabo programov PyMOL in PLIP. Uporabljen protokol je v primerjavi z uporabo kombinatoričnih knjižnic omogočil učinkovitejše
Keywords:	pentapeptidi, Fc regija, molekulsko sidranje, PyMol, CmDock, peptidno sidranje
Place of publishing:	Maribor
Place of performance:	Maribor
Publisher:	[B. Stradar]
Year of publishing:	2023
Number of pages:	1 spletni vir (1 datoteka PDF (IX, 40 f.))
PID:	20.500.12556/DKUM-85806
UDC:	543.645.6:[604.4:615.331](043.2)
COBISS.SI-ID:	171018243
Publication date in DKUM:	25.09.2023
Views:	682
Downloads:	101
Metadata:
Categories:	KTFMB - FKKT
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Licences

License:	CC BY-NC-ND 4.0, Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International

Link:	http://creativecommons.org/licenses/by-nc-nd/4.0/
Description:	The most restrictive Creative Commons license. This only allows people to download and share the work for no commercial gain and for no other purposes.
Licensing start date:	12.09.2023

Secondary language

Language:	English
Title:	Peptide antibody fc region binding optimization
Abstract:	The development of new peptide active substances is a challenging task for the chemical and pharmaceutical industries. This can be facilitated with the use of computational approaches and simulations. With their help, we can successfully model the interactions that are key to understanding the activity and development of new active substances. Peptides capture the advantages of small molecules and the target specificity of larger structures such as proteins. In this thesis, computational and bioinformatics approaches such as molecular anchoring and chemoinformatics analysis have been used to design new potential peptide structures. For peptide design, we focused mainly on the target Fc region of antibodies where the corresponding structure was obtained from the freely available website https://www.rcsb.org/ (PDB ID: 5U52). We designed and identified candidate pentapeptides using structures from a previously designed tetrapeptide library. The top 100 previously identified tetrapeptides were used to prepare the pentapeptide structure library and analyse the results. Molecular anchoring was then performed using CmDock software. The data were then analysed using PyMOL and PLIP. The protocol used allowed a more efficient design of the pentapeptides and analysis of their potential binding conformations compared to the use of combinatorial libraries.
Keywords:	pentapeptides, Fc region, molecular docking, PyMol, CmDock, peptide docking

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