20.500.12556/RUL-167946 Računalniško podprto načrtovanje novih zaviralcev N-acetilglukozaminidaz s potencialnim protibakterijskim delovanjem Computer-aided design of new N-acetylglucosaminidase inhibitors with potential antibacterial activity Razvoj učinkovitih protibakterijskih učinkovin je izjemno pomemben pri reševanju naraščajočega problema bakterijske odpornosti. Avtolizin E (AtlE) bakterije Staphylococcus aureus je zanimiva potencialna tarča, ker razgrajuje celično steno s cepitvijo ß-1,4-glikozidne vezi med N-acetilglukozaminom in N-acetilmuraminsko kislino v peptidoglikanu, s tem pa vpliva na preoblikovanje celične stene, rast bakterij in tvorbo biofilma. Nove zaviralce AtlE smo iskali z računalniško podprtim načrtovanjem učinkovin na osnovi liganda in kristalne strukture AtlE iz S. aureus ter s pomočjo novo razvitih kot tudi prosto dostopnih računskih modelov za napoved topnosti v vodi in ostalih farmakoloških lastnosti. Zasnovali smo knjižnico 440 ligandov na osnovi piperidinil benzamidov (PBL), ki so edini predhodno znani zaviralci AtlE. Želeli smo izboljšati fizikalno-kemijske lastnosti, predvsem njihovo topnost v vodi. V ta namen smo razvili nove validirane modele za napovedovanje topnosti spojin v vodi na osnovi kemijske strukture (modeli QSPR) in ugotovili, da imajo modeli soglasja boljšo napovedno moč kot posamezni modeli. Najboljše virtualne zadetke so predstavljale spojine z ugodnimi vezavnimi konformacijami, pridobljenimi pri molekulskem sidranju, in z najbolj optimalno napovedano farmakološko aktivnostjo iz računskih študij. Nadalje smo po istem postopku preiskali še knjižnico spojin UL-FFA in iminosladkornih derivatov (ISL). Najboljše virtualne zadetke (n = 48) smo biološko ovrednotili z uporabo metod površinske plazmonske resonance in minimalne zaviralne koncentracije. Odkrili smo nove zaviralce AtlE iz strukturnega razreda iminosladkorjev z afiniteto vezave v nizkem mikromolarnem območju (spojini ISL-1 KD = 19 µM in MIC (S. aureus ATCC29213) = 8 µg/mL, ISL-8 KD = 88 µM in ISL-3 KD = 410 µM). Kljub ocenjeno izboljšani topnosti optimiziranih in novo sintetiziranih PBL, za te spojine vezave na AtlE in vrednosti MIC v nizkem mikromolarnem območju nismo uspeli doseči, zato predlagamo njihovo nadaljnjo strukturno optimizacijo. Z opravljenimi raziskavami smo razširili kemijski prostor zaviralcev in ustvarili temelje za nadaljnji razvoj učinkovitejših zaviralcev AtlE S. aureus. Development of effective antibacterial agents is crucial in addressing the growing issue of bacterial resistance. Autolysin E (AtlE) from Staphylococcus aureus presents a promising target due to its role in degrading the bacterial cell wall by cleaving the β-1,4-glycosidic bond between N-acetylglucosamine and N-acetylmuramic acid in peptidoglycan, thereby affecting cell wall remodeling, bacterial growth and biofilm formation. We sought to identify new AtlE inhibitors by utilizing the crystal structure of AtlE from S. aureus in computer-aided ligand-based and structure-based drug design, and employing newly developed computational models to predict water solubility and online pharmacological properties models. We designed a library of 440 ligands based on piperidinyl benzamides (PBL), the only previously known AtlE inhibitors, with the aim of improving their physicochemical properties, particularly their aqueous solubility. For this purpose, we developed and validated new QSPR models for predicting compound solubility based on chemical structure, finding that consensus models demonstrated better predictive power than individual models. The best virtual hits exhibited favorable binding conformations obtained from molecular docking and optimal predicted pharmacological activities from computational studies. Additionally, we investigated the UL-FFA compound library and iminosugar derivatives (ISL) through the same approach. The best virtual hits (n = 48) were biologically evaluated using surface plasmon resonance and minimum inhibitory concentration method. We identified new AtlE inhibitors from the iminosugar structural class with binding affinities in the low micromolar range (ISL-1: KD = 19 µM and MIC (S. aureus ATCC29213) = 8 µg/mL, ISL-8: KD = 88 µM, ISL-3: KD = 410 µM). Despite the improved solubility of the optimized and newly synthesized PBLs, these compounds did not achieve binding to AtlE or MICs values in the low micromolar range, indicating the need for further structural optimization. Through our research, we have expanded the chemical space of potential inhibitors and established further guidelines for the development of more effective AtlE inhibitors against S. aureus. N-acetilglukozaminidaze avtolizin E protibakterijske učinkovine zaviralci virtualno rešetanje QSP(A)R MIC SPR N-acetylglucosaminidases autolysin E antibacterial drugs inhibitors virtual screening QSP(A)R MIC SPR true false false Slovenski jezik Angleški jezik Doktorsko delo/naloga 2025-03-21 07:15:24 2025-03-21 07:15:31 2026-03-17 13:34:21 0000-00-00 00:00:00 2025 0 0 0000-00-00 NiDoloceno NiDoloceno NiDoloceno 0000-00-00 0000-00-00 0000-00-00 2027-03-11 30522 6737.pdf 6737.pdf 1 9169C4EF588E146DFB2E32AE0AE0E646 8c78884ad7c74a26efe0034412f222497919ea98a7ec9fcf77b03be637d15a18 e0cf338f-061a-11f0-b232-0050569b8976 https://repozitorij.uni-lj.si/Dokument.php?lang=slv&id=200879 Fakulteta za farmacijo 0 0 0