Računalniška analiza encima MurA in njegovih zaviralcev z vidika načrtovanja novih protibakterijskih učinkovin

Fazlić, Merima (avtor), Frlan, Rok (mentor)

Antibiotiki se uporabljajo približno 60 let in lahko zdravijo praktično vse danes poznane okužbe. Žal njihovo uporabo spremlja pojav odpornosti in posledično živimo v času, ko so bakterije razvile odpornost na večino antibiotikov. Pri bakterijah je celična stena tista, ki predstavlja ključni strukturni element in tako idealno tarčo pri odkrivanju in razvoju novih antibiotikov. S tem namenom smo se odločili za poseg v sintezo peptidoglikana, saj je le-ta prisoten v prokariontskih celicah in tako omogoča optimalno selektivno ciljanje mikrobnih vitalnih poti. Osredotočili smo se na encim MurA, ki katalizira prvi korak v biosintezi peptidoglikana tako grampozitivnih kot tudi gramnegativnih bakterijah. Pri izdelavi magistrske naloge smo uporabljali različna bioinformacijska orodja, s katerimi smo podrobneje analizirali encim. V prvem delu smo preverjali, ali je encim MurA esencialen za rast, razvoj in preživetje večine bakterij. Temu je sledilo preučevanje evolucijsko ohranjenih aminokislin in identifikacija vezavnih mest, s pomočjo katerega smo določili ključne aminokisline, pomembne za uspešno molekulsko sidranje spojin v aktivno mesto in razvoj potencialne protimikrobne učinkovine. V zadnjem delu smo preverili podatke o potencialnih zaviralcih encima in ovrednotili njihove fizikalno-kemijske lastnosti, lipofilnost, topnost v vodi, farmakokinetične lastnosti, podobnost z učinkovinami ter farmacevtsko-kemijske lastnosti. Pridobljene podatke smo z uporabo različnih programov tudi vizualizirali. Izkazalo se je, da je esencialnost gena MurA dokazana v enaindvajsetih različnih organizmih. S presekom aminokislin z najvišjim odstotkom evolucijske ohranjenosti in aminokislin z najvišjim odstotkom interakcij preko vodikovih vezi, smo kot končni rezultat dobili deset ključnih aminokislin: Lys-22, Asn-23, Asp-49, Arg-91, Arg-120, Glu-188, Thr-304, Asp-305, Arg-331, Arg-397. S pomočjo molekulskih deskriptorjev smo nato ovrednotili osemindvajset znanih zaviralcev encima MurA in naredili izbor treh spojin, ki izkazujejo najboljše lastnosti in so zato najbolj perspektivne za nadaljnji razvoj.

• Jezik: Slovenski jezik
• Ključne besede: MurA, protibakterijske učinkovine, bioinformacijska orodja, esencialnost, evolucijska ohranjenost, zaviralci.
• Vrsta gradiva: Magistrsko delo/naloga
• Organizacija: FFA - Fakulteta za farmacijo
• Leto izida: 2021
• PID: 20.500.12556/RUL-125672
• Datum objave v RUL: 01.04.2021

Sekundarni jezik

• Jezik: Angleški jezik
• Naslov: Computational analysis of the MurA enzyme and its inhibitors from the perspective of antibacterial agents design

Izvleček

Antibiotics have been in use for about 60 years, being applied in the treatment of almost all infectious diseases known today. Unfortunately, their application is accompanied by the emergence of resistance and we consequently live in a time when bacteria have developed resistance to almost all antibiotics. The cell wall in bacteria represents an essential structural element and is thus an ideal target for the discovery and development of new antibiotics. Therefore, we have decided to intervene in the synthesis of peptidoglycan, as it is present in prokaryotic cells and allows the optimal selective targeting of microbial vital pathways. We focused on the MurA enzyme, which catalyses the first step in the peptidoglycan biosynthesis of gram-positive and gram-negative bacteria. When writing our master’s paper, we used various bioinformatics tools, which allowed us to analyse the enzyme in detail. In the first part, we tested if the MurA enzyme is essential for the growth, development, and survival of a majority of bacteria. This was followed by the study of evolutionarily conserved amino acids and the identification of binding regions by which we determined amino acids important for successful molecular docking to the active site and the development of potential antimicrobial agents. In the last stage, we reviwed the data of potential enzyme inhibitors and evaluated their physicochemical properties, lipophilicity, water solubility, pharmacokinetics, druglikeness and medicinal chemistry. We also visualized the data obtained using various programs. The essentiality of the MurA gene has been proved in twenty-one different organisms. By intersecting the amino acids with the highest percentage of evolutionary conservations and the amino acids with the highest percentage of hydrogen bond interactions, we obtained ten important amino acids as a final result: Lys-22, Asn-23, Asp-49, Arg-91, Arg-120, Glu -188, Thr-304, Asp-305, Arg-331, Arg-397. With molecular descriptors, we evaluated twenty-eight MurA enzyme inhibitors in the following selection of three compounds that exhibit the best properties and thus the best prospects for further development.

• Ključne besede: MurA, antibacterial agents, bioinformatic tools, essential genes, evolutionary conservation, inhibitors.