Simulacije molekulske dinamike i virtual screening studija inhibitora sirtuina 2

Abstract

Modulacija aktivnosti epigenetičkog brisača, NAD‐zavisne protein deacetilaze sirtuina 2 (SIRT2), poslednjih godina se pokazala kao obećavajuća strategija u lečenju Parkinsonove bolesti, depresije, određenih tipova kancera, ishemijsko‐reperfuzionih povreda itd. Nasuprot terapijskom potencijalu, još uvek nijedan predstavnik ove grupe farmakološki aktivnih supstanci nije našao svoje mesto na tržištu. Najčešći problemi sa dosada opisanim SIRT2 inhibitorima predstavljaju niska potentnost, loša selektivnost, kao i loše farmakokinetičke osobine što dalje opravdava razvoj novih predstavnika. Cilj ovog rada je bio ispitivanje konformacionih promena SIRT2 u prisustvu inhibitora i dalje poboljšanje dostupnih kristalografskih modela u cilju razvoja efikasnijeg protokola virtual screening‐a. Polazeći od 5 različitih kristalografskih struktura SIRT2‐inhibitor kompleksa, ukupno 1,5 μs simulacija molekulske dinamike u eksplicitnom solventu je izvedeno. 3D deskriptori zasnovani na GRID‐u i linearna diskriminantna analiza su korišćeni za virtual screening (VS) studiju. Konformaciona fleksibilnost SIRT2‐inhibitor kompleksa zabeležena tokom simulacija ukazuje na značajnu fleksibilnost aktivnog mesta i posledično na multiple vezivne modove inhibitora. Nakon procedure klasterovanja trajektorije, nekoliko relevantnih modela kompleksa je izdvojeno i uključeno u dalju VS studiju. VS modeli generisani pomoću tri relevantna kompleksa dobijena studijom molekulske dinamike su pokazali značajno bolje performanse u poređenju sa modelima dobijenim pomoću do danas opisanih kristalografskih struktura. Performanse generisanog VS protokola su značajno poboljšane i u odnosu na do danas publikovane protokole. Rezultati ove studije jasno ukazuju na značaj uračunavanja fleksibilnosti aktivnog mesta u racionalni dizajn SIRT2 inhibitora. Novi hemotipovi potenijalnih inhibitora SIRT2 su izdvojeni iz baza komercijalno dostupnih jedinjenja primenom generisanih VS modela. U ovoj studiji formirani su realističniji modeli aktivnog mesta sirtuina 2 kojima su značajno poboljšane performanse virtual screening‐a u odnosu na do danas publikovane studije. Rezultati ove studije, uključujući i opisane konformacione promene doprinose sveobuhvatnom razumevanju odnosa strukture i aktivnosti SIRT2 inhibitora i dodatno racionalizuju dizajn selektivnijih i potentnijih inhibitora.

Modulation of activity of epigenetic eraser, NAD‐dependent protein deacetylase sirtuin 2 (SIRT2), recently emerged as promising therapeutic strategy for the treatment of many diseases, including Parkinson’s disease, depression, some types of cancers, necrotic injuries (ischemic stroke, myocardial infarction) etc. Contrary to therapeutic potential, none of SIRT2 inhibitors reported to date has been approved for the market. Some of the most common problems with current SIRT2 inhibitors include poor potency, selectivity and pharmacokinetic properties which justify further development of novel inhibitors. The Aim of this study was to explore conformational space of sirtuin2‐inhibitor complexes and further refinement of available crystallographic structures in order to develop more efficient virtual screening (VS) protocol. Starting from five different crystallographic structures of SIRT2 co‐crystalized with inhibitors, total of 1.5 μs of molecular dynamics (MD) simulations in explicit solvent has been performed. GRID‐based 3D descriptors and linear discriminant analysis were used for virtual screening. Significant conformational flexibility of SIRT2‐inhibitor complexes was observed during simulations indicating overall binding site flexibility and multiple binding modes of inhibitors. Several atomistic models of SIRT2‐inhibitor complexes were extracted and used for structure‐based VS study. VS models generated from three extracted SIRT2‐inhibitor complexes were significantly better compared to VS models generated from available crystallographic structures. Generated VS protocol was also better in performance compared to published virtual screening studies. These results clearly indicate importance of considering flexibility of binding site in rational design of SIRT2 inhibitors. Obtained models were used for screening of commercial databases of compounds. Several chemotypes of potential novel SIRT2 inhibitors have been identified. Refined atomistic models of SIRT2‐inhibitor complexes have been generated and significant improvement of virtual screening performance has been achieved. These results further rationalize design of SIRT2 inhibitors with improved selectivity and potency.