Retrosintezno zasnovana in silico optimizacija protivirusnih učinkovin z delovanjem na 3C in 3CL proteaze

Breznik, Marko (author), Gobec, Stanislav (mentor), Wolber, Gerhard (comentor)

Obstaja nujna potreba po razvoju novih rešitev za zdravljenje virusnih bolezni brez komercialno dostopnih zdravil. Raziskave protivirusnih učinkovin ostajajo ključnega pomena in ponujajo osnovo za spopadanje z izbruhi virusnih bolezni v prihodnosti, tveganje katerih se ne sme ponovno zanemariti. 3C proteaza (3Cpro) ter funkcionalno in strukturno podobna 3C podobna proteaza (3CLpro) igrata ključno vlogo pri virusni replikaciji in imata izrazito ohranjeno aktivno mesto med različnimi vrstami virusov, zaradi česar sta odlični tarči za zdravljenje pikornavirusnih, kalicivirusnih in/ali koronavirusnih okužb. V tej nalogi opisujemo retrosintezno voden pristop k optimizaciji spojine MLC3 - novega tipa inhibitorja 3Cpro Enterovirusa 68, ki z encimom tvori Meisenheimerjev kompleks. MLC3 domnevno zaseda samo S1 žepek aktivnega mesta. Ker je struktura S1 žepka ena glavnih skupnih značilnosti 3Cpro in 3CLpro, smo po enterovirusno usmerjeni optimizaciji in silico ovrednotili potencial širokospektralnega protivirusnega delovanja izbranih derivatov MLC3. Naš pristop k optimizaciji je bil sestavljen iz dveh metod. Prva metoda je »rast fragmenta« - dodajanje substituentov, ki tvorijo dodatne interakcije z aktivnim mestom, hkrati pa ohranjajo že obstoječe interakcije MLC3 ogrodja. Z retrosintezo smo prepoznali komercialno dostopne primarne reaktante za sintezo derivatov in z uporabo analitične platforme ustvarili virtualno knjižnico z 153.675 derivati spojine MLC3. Predstavljamo dve hipotezi o vezavi MLC3 in na njuni podlagi dva farmakoforja, tvorjena z namenom virtualnega rešetanja MLC3 derivatov. Rezultati virtualnega rešetanja so bili sidrani v aktivno mesto 3Cpro. Vsako spojino smo nato ocenili glede na prileganje značilnostim izvirne farmakoforne poizvedbe. Izrazito ugodne interakcije z encimom smo prepoznali pri devetnajstih derivatih, ki so predstavljeni v nalogi. Druga metoda optimizacije je analiza razmerja med strukturno in aktivnostjo »ogrodja« - MLC3. V katalogih komercialno dostopnih spojin smo odkrili trinajst strukturnih analogov MLC3, ki so navedeni za nadaljnje in vitro preskuse.

• Language: Slovenian
• Keywords: načrtovanje učinkovin, hit to lead, pikornavirus, enterovirus, inhibitor
• Work type: Master's thesis/paper
• Organization: FFA - Faculty of Pharmacy
• Year: 2021
• PID: 20.500.12556/RUL-125352
• Publication date in RUL: 12.03.2021

Secondary language

• Language: English
• Title: Retrosynthesis-driven in silico optimization of antiviral agents targeting 3C and 3C-like proteases

Abstract

There is an urgent unmet need for the development of therapies to treat a wide range of devastating viral diseases for which there are no accessible curative medications. Antiviral research remains essential and provides critical resources for tackling viral disease outbreaks in the future, the risk of which should not be underestimated again. The 3C protease (3Cpro) and the functionally and structurally similar 3C like protease (3CLpro) play an essential role in viral replication and have a remarkably conserved active site among different virus species, making them an excellent target for the treatment of picornavirus , calicivirus-, and/or coronavirus induced diseases. In this thesis, we describe a retrosynthesis-based approach to the optimization of MLC3 – a novel Meisenheimer complex-forming inhibitor of Enterovirus 68 3Cpro which is presumed to occupy only the S1 pocket of the active site. Since the S1 pocket structure is one of the main characteristics linking the 3CLpro to the 3Cpro, the broad-spectrum inhibitor potential of the selected derivatives was examined in silico following the enterovirus-focused optimization. The optimization is planned by a combination of two approaches. The first one is fragment growing – the addition of substituents that form additional interactions with the active site, while retaining the preexisting ones of the MLC3 scaffold. Retrosynthesis and an analytics platform were used to identify available starting materials allowing the synthesis of 153,675 derivatives. Two binding hypotheses of MLC3 are presented, and two pharmacophores optimized for the screening of the derivatives were created based on them. The hits of the pharmacophore-based virtual screenings were docked and energy minimized. Each compound was scored by how well it fulfilled the features of the original query pharmacophore. Favorable enzyme-substituent interactions were recognized by visual inspection in nineteen derivatives. The second approach is the structure-activity relationship analysis of the MLC3 scaffold. Thirteen MLC3 structural analogs have been found in the catalogs of commercially available compounds and are listed for subsequent in vitro assays.

• Keywords: drug design, hit to lead, picornavirus, enterovirus, inhibitor