In silico study of monoamine oxidase reversible inhibition with beta carbolines

β-Karbolini so naravne spojine, ki jih v večji količini najdemo v kavi in tobaku. Kljub temu da delujejo na več tarč v človeškem telesu, so najbolj znani po njihovem zaviralnem delovanju na obe izoobliki encima monoamin oksidaza, A in B. Monoamin oksidaza je najbolj zastopana v možganih, kjer je njena primarna naloga razgrajevanje v monoaminskem sistemu udeleženih živčnih prenašalcev. Pri tem kot sekundarni produkt encimske reakcije nastaja vodikov peroksid, ki lahko v višjih koncentracijah vodi v razvoj nevrodegenerativnih bolezni. Z zaviranjem monoamin oksidaz z β-karbolini lahko zmanjšamo stopnjo nevrodegeneracije. V sklopu magistrske naloge smo z metodami molekulskega modeliranja, ki so obsegale farmakoforno analizo, dinoforno analizo in metodo linearne interakcijske energije, geometrijsko in energijsko ovrednotili vezavo izbranih predstavnikov β-karbolinov v vezavno mesto monoamin oksidaze A. Pri tem smo ugotovili, da so najbolj pomembne hidrofobne interakcije z vezavnim mestom. Po podrobnejši analizi spojin 1, 6 in 10 smo ugotovili, da je za optimalno zaviranje encima pomembna vzporedna lega zaviralca z aktivnim mestom in prisotnost metoksi skupine na mestu C7. Vzporedna lega z aktivnim mestom zaviralcu omogoča interakcije z aromatskim predelom aktivnega mesta, ki ga sestavljata dva vzporedno ležeča tirozinska aminokislinska ostanka in flavinski obroč. Spojine, ki so imele na aromatskem obroču vezanih več alkilnih skupin, so izkazale močnejše zaviranje zaradi dodatnih hidrofobnih interakcij. Z metodo linearne interakcijske energije smo uspeli pridobiti rezultate, s katerimi smo grobo ocenili jakost vezave izbranih β-karbolinov v aktivo mesto monoamin oksidaze A. Ker je metoda linearne interakcijske energije robustna metoda, z njo nismo uspeli potrditi enakega razporeda spojin po jakosti inhibicije, kot so jo ugotovili z eksperimentalno določenimi prostimi energijami vezave. Za nadaljnji razvoj močnejših zaviralcev predlagamo optimizacijo strukture spojine 6. Predlagamo podaljšanje in razvejanje alkilne skupine na mestu C1 ter metoksi skupine na mestu C7. Za močnejše zaviranje encima je pomembno, da so vsi obroči proučevanega kemijskega sistema aromatizirani.β-Carbolines are naturally occurring compounds that can be found in coffee and tobacco in larger quantities. Although they act on multiple targets in the human body, they are best known for their inhibitory action on both isoforms A and B of the monoamine oxidase enzyme. Monoamine oxidase is mostly present in the brain, where its primary action is degradation of the neurotransmitters involved in the monoaminergic system. Hydrogen peroxide is a secondary product of the enzymatic reaction, which can in higher concentrations lead to development of neurodegenerative diseases. By inhibiting monoamine oxidase with β-carbolines, the rate of neurodegeneration can be reduced. In our master’s thesis, molecular modelling methods were used to evaluate geometric and energetic aspect of β carboline and monoamine oxidase interaction. Those include pharmacophore analysis, dynophore analysis and linear interaction energy method. We have concluded that hydrophobic interactions are the the most important for monoamine oxidase inhibition by β-carbolines. Detailed analysis of compounds 1, 6 and 10 showed that the parallel position of the inhibitor with the binding site and the presence of methoxy group at the C7 position coincided with optimal inhibition of the enzyme. Parallel position with the active site allows interactions with the aromatic region of the active site, which consists of two parallel tyrosine amino acid residues and a flavin ring. Compounds that had more alkyl groups attached to the aromatic ring showed greater inhibition due to additional hydrophobic interactions. Using the method of linear interaction energy, we were able to obtain results that roughly estimated the binding strength of selected β-carbolines to the active site of MAO A. The linear interaction energy method is a robust method as we have not been able to obtain the same arrangement of compounds in terms of inhibition strength, which coincide with the experimental free binding energies. In further research to develop more potent inhibitors, we suggest optimizing the structure of compound 6. We suggest keeping the tricyclic ring aromatic and the extension and branching of the alkyl group at the C1 position and at the methoxy group site