Proučevanje vezave zaviralca bakterijske DNA-giraze in topoizomeraze IV s sidranjem in simulacijami molekulske dinamike

Zupančič, Tina (author), Tomašič, Tihomir (mentor)

Odpornost bakterij proti protibakterijskim učinkovinam se v zadnjih letih poglablja. V prihodnosti zato pričakujemo vse več smrti zaradi doslej ozdravljivih bolezni, kar je zelo zastrašujoče. Dodatna težava je posledica dejstva, da je vlaganje v razvoj novih protibakterijskih učinkovin za farmacevtsko industrijo vse prej kot privlačno, saj je donos takih zdravil v primerjavi z zdravili za dolgotrajno zdravljenje kroničnih bolezni zelo nizek. Pomembno vlogo pri upočasnitvi razvoja odpornosti bakterij proti protibakterijskim učinkovinam imajo nove učinkovine z novimi mehanizmi delovanja. Eden od možnih pristopov je zaviranje bakterijske DNA-giraze in topoizomeraze IV. Ta dva encima imata ključno vlogo pri procesih prepletanja in razpletanja dvojne verige DNA, saj olajšata zvijanje in premikanje te verige, to pa vpliva na replikacijo, transkripcijo in rekombinacijo DNA v bakteriji. Oba encima imata podobno strukturo, zato lahko z isto protibakterijsko učinkovino zaviramo oba encima hkrati. Naš namen je bil proučiti nove zaviralce DNA-giraze in topoizomeraze IV, ki so konjugirani z mimetiki sideroforov, s pomočjo računalniških metod kot sta sidranje in simulacije molekulske dinamike. Ti konjugati z vezavo v ATP-vezavno mesto obeh encimov zavirajo njihovo delovanje, s čimer dosežemo protibakterijsko delovanje. Mimetik siderofora potencialno omogoči večji privzem v bakterijsko celico in na ta način ojača protibakterijsko delovanje. Ker zaviralci DNA-giraze in topoizomeraze IV ob uvedbi mimetika siderofora v strukturo ohranijo močno encimsko zaviralno aktivnost, nas je zanimalo, ali mimetik siderofora tvori dodatne interakcije v vezavnem mestu. Simulacije molekulske dinamike so pokazale, da tako v vezavnem mestu DNA-giraze kot v vezavnem mestu topoizomeraze IV mimetik siderofora tvori dodatne vodikove vezi in π-π interakcije, kar bi lahko prispevalo k močni zaviralni aktivnosti proučevane spojine LMD-266. Rezultati magistrske naloge pomembno prispevajo k nadaljnjemu razvoju potencialnih protibakterijskih učinkovin. Spojina LMD-266 močno zavira DNA-girazo in topoizomerazo IV, ima močno protibakterijsko delovanje, zato je smiseln nadaljnji razvoj spojin tega tipa.

• Language: Slovenian
• Keywords: DNA-giraza, topoizomeraza IV, bakterijska rezistenca, benzotiazolni zaviralci, konjugati, siderofori, protibakterijske spojine
• Work type: Master's thesis/paper
• Organization: FFA - Faculty of Pharmacy
• Year: 2023
• PID: 20.500.12556/RUL-151193
• Publication date in RUL: 30.09.2023

Secondary language

• Language: English
• Title: Studying binding modes of a bacterial DNA gyrase and topoisomerase IV inhibitor by docking and molecular dynamics simulations

Abstract

Antibacterial drug resistance has increased in recent years. An increasing number of deaths from previously curable diseases is expected in the future. The problem is that investment in research and development of new antibacterial agents is far from attractive for the pharmaceutical industry, as the return on investment of such drugs is very low compared to drugs for long-term treatment of chronic diseases. New agents with novel mechanisms of action play an important role in slowing the development of bacterial resistance to antimicrobial agents. One possible approach is to inhibit bacterial DNA gyrase and topoisomerase IV. These two enzymes play key roles in the processes of unwinding and uncoiling the DNA double strand by facilitating the twisting and movement of this chain, which affects DNA replication, transcription, and recombination in bacteria. Both enzymes have a similar structure, so the same antibacterial agent can inhibit both enzymes simultaneously. Our goal was to investigate new inhibitors of DNA gyrase and topoisomerase IV conjugated to siderophore mimetics using computational methods such as docking and molecular dynamics simulations. These conjugates inhibit the activity of both enzymes by binding to the ATP-binding site of both enzymes, resulting in an antibacterial effect. Siderophore mimetics possibly enhance uptake into bacterial cells, thus enhancing antibacterial activity. Because inhibitors of DNA gyrase and topoisomerase IV retain potent enzyme inhibitory activity when a siderophore mimetic is included in the structure, we were interested to see if the siderophore mimetic forms additional interactions in the binding site. Molecular dynamics simulations showed that the siderophore mimetic forms additional hydrogen bonds and π-π interactions in the binding site of both DNA gyrase and topoisomerase IV, which could contribute to the strong inhibitory activity of the investigated compound LMD-266. The results of the master's thesis make an important contribution to the further development of potential antibacterial agents. The compound strongly inhibits DNA gyrase and topoisomerase IV and exhibits potent antibacterial activity, which warrants further development of compounds of this type.

• Keywords: DNA gyrase, antibacterial compounds, bacterial resistance, benzothiazole inhibitors, conjugates, topoisomerase IV, siderophores