Ispitivanje inhibitornog učinka derivata sintetskog peptidnog inhibitora na humanu kolagenazu fibroblasta metodom molekulskog sidrenja

master's thesis

• Title (english): A molecular docking study of synthetic peptide inhibitor derivatives as potential human fibroblast collagenase inhibitors
• Author: Ana Sentinella-Jerbić
• Mentor: Hrvoje Rimac (mentor)
• Mentor: Kristina Pavić (sumentor)
• Committee member: Hrvoje Rimac (predsjednik povjerenstva)
• Committee member: Kristina Pavić (član povjerenstva)
• Committee member: Mirela Matić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Pharmacy and Biochemistry; (Department of medicinal chemistry); Zagreb
• Defense date and country: 2023-06-28, Croatia
• Scientific / art field, discipline and subdiscipline: BIOMEDICINE AND HEALTHCARE; Pharmacy; Pharmacy

Abstract

Uzimajući u obzir čovjekov sve duži životni vijek, javlja se sve veća potreba za održavanjem optimalne razine kolagena tijekom još
duljeg perioda života. Padom razine kolagena nakon 25. godine za otprilike 2% godišnje osoba se tijekom procesa starenja susreće s
mnogim oslabljenim funkcijama organizma. Promjene su najprije vidljive u obliku boranja kože te njezine smanjene elastičnosti, a
kasnije se mogu razviti i razne bolesti zglobova (artritisi) s oticanjem i smanjenom pokretljivošću te poremećaji mineralizacije i
gustoće kostiju, što sve zajedno dovodi do smanjene kvalitete života. U ovom trenutku, najistraživanija mogućnost povećanja razine
kolagena u organizmu je pomoću dodataka prehrani temeljenih na kolagenu. Tržište je trenutno zasićeno mnogim farmaceutskim
oblicima kolagena, koji se dobivaju iz različitih životinjskih, posebice ribljih, izvora. Cilj ovog istraživanja je skrenuti pažnju na malo
drugačiji pristup održavanja koncentracija kolagena u organizmu, koji bi mogao biti puno učinkovitiji u praksi. Budući da je glavni
razlog smanjenja razine kolagena u organizmu njegova povećana razgradnja posredovana enzimima matriksnih metaloproteinaza
(MMP), smatra se da bi inhibicija upravo tih enzima dovela do sprječavanja razgradnje kolagena u organizmu te bi se na taj način
očuvala razina endogenog kolagena tijekom puno duljeg životnog razdoblja. Postojećim istraživanjem Borkakoti i sur. (1994)
pronađena je sintetski inhibitor koji se veže u katalitičko mjesto enzima humane kolagenaze fibroblasta te posljedično sprječava
razgradnju kolagena. Ovaj inhibitor je pokazao dobra i strukturna i ADMET svojstva, koja su poželjna kod razvoja novih lijekova.
Vodeći se navedenim saznanjima, cilj ovog istraživanja bio je poboljšati vezanje inhibitora u aktivno mjesto enzima te tako postići
jači inhibitorni učinak. Metodom molekulskog sidrenja ispitivao se inhibitorni učinak ukupno 765 molekula dizajniranih po uzoru na
prethodno nađeni sintetski inhibitor, pri čemu je njihova struktura prilagođena prirodi aminokiselinskih ostataka u aktivnom mjestu
enzima. Rezultati istraživanja pokazuju da ligandi 157 i 303 posjeduju najbolji inhibitorni učinak na ispitivani enzim s energijom
vezanja od ΔG = –9,2 kcal mol-1, što je za 2,8 kcal mol-1 niže od energije vezanja početne molekule sintetskog inhibitora. Međutim,
navedene dvije molekule imaju ponešto lošija farmakokinetička svojstva od početne molekule, a ono što se istaknulo posebno lošim
je njihov toksikološki profil. Dobivene molekule vrijedne su daljnjeg razmatranja s obzirom na izrazito povoljnu energiju vezanja u
aktivno vezno mjesto enzima, međutim da bi bile primjenjive u praksi, moraju proći daljnju optimizaciju prvenstveno toksikoloških,
a potom i farmakokinetičkih svojstava.

Abstract (english)

Given the current trend of longer life expectancy, there is an increasing need to maintain an optimal collagen levels during an even
more extended lifespan. Due to a decrease in collagen levels after the age of 25 by approximately 2% per year, a person encounters
many weakened body functions during the process of aging. Firstly, changes are visible in the form of skin wrinkles and its reduced
elasticity, but later on various joint diseases (like arthritis), as well as mineralization and bone density disorders can develop.
Currently, the most used method to increase collagen levels in the body is through collagen-based dietary supplements. The market
offers a wide range of pharmaceutical collagen products derived from various animal (especially fish) sources. The aim of this
research was to draw attention to a slightly different approach to maintaining collagen concentrations in the body, which could be
much more effective in practice. Particularly, since the main reason for the decrease in the collagen level in the body is the increased
collagen breakdown mediated by matrix metalloproteinases (MMP) enzymes, it is believed that inhibition of these enzymes would
lead to a prevention of collagen breakdown in the body, thus preserving the level of endogenous collagen much during a much longer
life expectancy. The existing research by Borkakoti et al. (1994) found a synthetic inhibitor that binds to the catalytic site of the
human fibroblast collagenase enzyme and consequently prevents collagen degradation. This molecule showed good structural and
ADMET properties, desirable in new drug development. Based on these findings, the goal of this research was to improve the binding
of the inhibitor to the enzyme active site and thus to achieve a stronger inhibitory effect. Using molecular docking, the inhibitory
effect of a total of 765 new molecules was predicted. The molecules were designed based on the model of the previously found
synthetic inhibitor and adapted to the nature of amino acid residues in the active site of the enzyme. The research results show that
ligands 157 and 303 have the best inhibitory effect on the tested enzyme with a binding energy of ΔG = –9.2 kcal mol-1, which is 2.8
kcal mol-1 lower than the binding energy of the initial synthetic inhibitor. However, the aforementioned two molecules exhibit slightly
inferior pharmacokinetic properties than the initial synthetic inhibitor, with their toxicological profile being particularly concerning.
The resulting molecules are worthy of further consideration due to the very favorable binding energy in the enzyme active site
however, in order to be applicable in practice, they must undergo further optimization primarily of toxicological and then
pharmacokinetic properties.

• Keywords: kolagen; humana kolagenaza fibroblasta; 2TCL; molekulsko sidrenje
• Keywords (english): collagen; human fibroblast collagenase; 2TCL; molecular docking
• Language: croatian
• URN:NBN: urn:nbn:hr:163:455254
• Study programme: Title: Pharmacy; Study programme type: university; Study level: integrated undergraduate and graduate; Academic / professional title: magistar/magistra farmacije (magistar/magistra farmacije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2024-01-04 14:52:33