Računalne simulacije kompleksa derivata ibuprofena i naproksena s acil-CoA tioesterazom I (TesA) iz bakterije Pseudomonas aeruginosa

master's thesis

• Title (english): Computational investigation of acyl-CoA thioesterase I (TesA) from the bacteria Pseudomonas aeruginosa in complexes with ibuprofen and naproxen derivatives
• Author: Krunoslav Ilić
• Mentor: Branimir Bertoša (mentor)
• Committee member: Branimir Bertoša (predsjednik povjerenstva)
• Committee member: Martina Šeruga Musić (član povjerenstva)
• Committee member: Ivana Ivančić Baće (član povjerenstva)
• Committee member: Kristian Vlahoviček (član povjerenstva)
• Granter: University of Zagreb; Faculty of Science; (Department of Biology); Zagreb
• Defense date and country: 2015-05-28, Croatia
• Scientific / art field, discipline and subdiscipline: NATURAL SCIENCES; Biology

Abstract

GDSL hidrolaze su relativno slabo istražena porodica enzima. Karakterizira ih GDSL strukturni motiv koji se nalazi oko serina katalitičke trijade. Odlikuje se izraženim supstratnim promiskuitetom što ih čini zanimljivim područjem istraživanja, kako zbog fundamentalnog značaja, tako i zbog potencijalne primjene u farmaceutskoj i biotehnološkoj industriji. Jedan od enzima iz te porodice je Acil-CoA tioesteraza I (TesA) iz patogene bakterije Pseudomonas aeruginosa koji je istraživan u ovome radu.
Računalnim metodama prilagođenim istraživanju biokemijskih sustava, prvenstveno Monte Carlo konformacijskom pretragom i simulacijama molekulske dinamike, istražena je mogućnost produktivnog vezanja derivata ibuprofena i naproksena u aktivno mjesto enzima TesA. Pronađene su ključne interakcije za vezanje navedenih supstrata u aktivno mjesto enzima te interakcije koje se razlikuju između enatiomera istog lijeka. Računalno je istražen utjecaj mutacije L78F na enatioselektivnost enzima prema istraženim derivatima ibuprofena i naproksena. Produktivno vezanje utvrđeno je za derivat R-ibuprofena sa divljim tipom i mutantom enzima TesA te za derivat R-naproksena sa mutiranim enzimom. Također, pronađen je hidrofobni džep u blizini aktivnog mjesta enzima važan za vezanje supstrata i opisane su nevezne interakcije enzima i kovalentnog intermedijera supstrata potrebne za katalitičku reakciju te utjecaj mutacije L78F na navedene interakcije.

Abstract (english)

GDSL hydrolases are relatively poorly described enzyme family. They contain a GDSL structural motif centered around nucleophilic serine from catalytic triad. They are characterized by substrate promiscuity, which makes them an interesting area of research, both for fundamental scientific value and potential uses in pharmaceutic and biotech industry. One of the enzymes from that family shown to be an interesting research target is Acyl-CoA thioesterase (TesA) from Pseudomonas aeruginosa, which was studied in this thesis. Computational biochemistry methods, primarily Monte Carlo conformational search and molecular dynamics simulations, were used to test possibilities of catalytically productive substrate binding for ibuprofen and naproxen derivatives. Key interactions for active site binding were identified, as well as differences in binding between enantiomers of the same compound. Amino acid mutation L78F was introduced in silico and its effect on substrate binding and enantioselectivity was computationally assessed. Productive binding was obtained for R-ibuprofen derivate, both with wild-type enzyme and L78F mutant, as well as for R-naproxen derivate with mutated enzyme. Hydrophobic cavity for substrate binding was found in vicinity of the enzyme active site and non-bonding interactions required for catalysis were described, as well as the effect of L78F mutation on those interactions.

• Keywords: GDSL hidrolaze; enantioselektivnost; molekulska dinamika; Monte Carlo konformacijska pretraga
• Keywords (english): GDSL hydrolases; enantioselectivity; molecular dynamics; Monte Carlo conformational search
• Language: croatian
• URN:NBN: urn:nbn:hr:217:719027
• Study programme: Title: Molecular Biology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra molekularne biologije (magistar/magistra molekularne biologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2017-04-21 10:40:13