Načrtovanje novih modulatorjev kemokinskega receptorja CCR7 na osnovi strukture liganda in strukture tarče

Fleisinger, Črtomir (author), Gobec, Stanislav (mentor), Jukič, Marko (co-mentor)

Kemokinski receptorji so obetavne terapevtske tarče zaradi njihove vloge pri usmerjanju celic tekom fizioloških in patoloških stanj. CCR7 je kemokinski receptor, ključen za usmerjanje celic imunskega sistema, predvsem limfocitov T in B, na mesto njihovega delovanja. Ker je dosedanjih raziskav o zdravilnih učinkovinah, ki bi delovale na CCR7 malo, potencialna terapevtska vrednost receptorja pa visoka, smo z raziskovalnim delom želeli predlagati nabor spojin, ki nanj verjetno izražajo aktivnost. Zaradi predpostavljene določene mere podobnosti med strukturami kemokinskih receptorjev smo pregledali literaturo, da bi odkrili do sedaj poznane spojine, aktivne na ostale kemokinske receptorje, ter na podlagi teh ustvarili večjo knjižnico spojin, ki smo jo filtrirali z namenom izločiti molekule z neželenimi lastnostmi. S homolognim modeliranjem je bil na Fakulteti za farmacijo Univerze v Ljubljani na osnovi znanega aminokislinskega zaporedja ustvarjen model CCR7. S programom ProBiS-om smo določili možno vezavno mesto na osnovi podobnosti med CCR7 in CCR9, za katerega sta kristalna struktura in vezavno mesto že znana. Raziskali smo vse aminokisline v okolici vezavnega mesta ter s programom OPENEYE MakeReceptor izdelali njegov negativ, ki smo ga uporabili za virtualno rešetanje spojin iz knjižnice, ustvarjene na podlagi spojin aktivnih na ostale kemokinske receptorje. Rezultat našega dela je 20 spojin, ki jih predlagamo kot verjetno aktivne na CCR7, ter analiza njihove interakcije z modelom vezavnega mesta s posledično napovedjo ključnih lastnosti, ki vplivajo na moč interakcije med ligandom in vezavnim mestom CCR7. Aktivnosti naših spojin na CCR7 z gotovostjo na podlagi rezultatov magistrske naloge ne moremo napovedati, saj so zato potrebna in-vitro testiranja. Rezultati so dobra podlaga za nadaljevanje raziskav na CCR7, tako iskanje novih aktivnih spojin kot tudi izboljšanje modela vezavnega mesta.

• Language: Slovenian
• Keywords: kemokini, CCR7, vezavno mesto, homologno modeliranje, virtualno rešetanje
• Work type: Master's thesis/paper
• Organization: FFA - Faculty of Pharmacy
• Year: 2020
• PID: 20.500.12556/RUL-117041
• Publication date in RUL: 20.06.2020

Secondary language

• Language: English
• Title: Ligand based and structure based design of novel CCR7 chemokine receptor modulators

Abstract

Due to their involvement in cell homing in both physiological and pathological processes in the human body, chemokine receptors make for promising therapeutic targets. CCR7 is a chemokine receptor which has a key role in cell homing in the immune system, particularly for lymphocytes T and B. Taking into account the currently low amount of research done on possible compounds which are active on the CCR7 coupled with the high therapeutic value of the receptor, the goal of this thesis was to propose 20 compounds which could be active on the receptor. Since there is a certain amount of similarity among the chemokine receptor family structures we began by examining the currently available literature about compounds active on other currently known chemokine receptors. The compounds we found were then used as a foundation to forming a greater database of candidates based on their similarity to currently known active compounds. This database was filtered with the purpose of eliminating any inappropriate compounds. The amino acid sequence of the CCR7 is known and with the use of homology modelling a model of CCR7 was created at the Faculty of Pharmacy, University of Ljubljana. We analysed the model in ProBiS and through detection of similarity between CCR7 and CCR9 the programme proposed a possible binding site. We examined the immediate area around the proposed binding site in order to establish exactly which amino acid fragments were present. We created a negative of the binding site using OPENEYE MakeReceptor software and used it in virtual screening of the compounds we created based on those that are reported to be active on other chemokine receptors. The results are 20 compounds for which we foresee activity towards CCR7 and analysis of their interaction with the binding site model. We also suggest key properties which presumably affect the ligand-binding site interaction. The activity of the proposed 20 compounds is far from certain though, as in-vitro studies would have to be made in order to confirm it. However, we believe that the results presented here serve as a basis for further research on the structure of CCR7 and possible active compounds.

• Keywords: chemokines, CCR7, binding site, homology modelling, virtual screening