58 research outputs found
Combined molecular dynamics and virtual screening studies to identify novel sirtuin 2 inhibitors
Sirtuins are highly conserved class of NAD+-dependent lysine deacetylases. Altered function of sirtuin 2 (Sirt2)
is related to pathogenesis of cancer, inflammation and neurodegeneration, which makes Sirt2 very attractive drug
target in novel epigenetic research [1]. A number of Sirt2 inhibitors have been recently developed, but for most
of them are missing structural information of their interaction with the enzyme [2, 3]. Our molecular dynamic
(MD) study was performed on recently resolved crystal structures of selective ligand-Sirt2 complexes [1]. In the
MD study were defined significant interactions with novel inhibitors, one of key residues responsible for
conformational stability of cofactor-binding pocket, and residue acting as gate-keeper for cofactor-binding loop.
Some residues completely changed orientation after the MD simulation, compared to the starting crystal
structures. This result indicates on the errors in the X-ray structures that may have influence on structure-based
design of novel inhibitors. After clustering of MD trajectory, 20 conformations (centroids) from 20 clusters of
Sirt2 have been selected as representative conformations for retrospective structure based virtual screening. The
virtual screening performances were significantly improved by use of the ensemble of conformations, selected
with this MD methodology, compared to screening against available X-ray structures.XXV EFMC International Symposium on Medicinal Chemistry, Ljubljana, Slovenia, September 2-6, 201
Molecular dynamicsābased virtual screening of sirtuin 2 inhibitors
Modulacija aktivnosti epigenetiÄkog brisaÄa, NADāzavisne protein deacetilaze
sirtuina 2 (SIRT2), poslednjih godina se pokazala kao obeÄavajuÄa strategija u leÄenju
Parkinsonove bolesti, depresije, odreÄenih tipova kancera, ishemijskoāreperfuzionih
povreda itd. Nasuprot terapijskom potencijalu, joÅ” uvek nijedan predstavnik ove grupe
farmakoloÅ”ki aktivnih supstanci nije naÅ”ao svoje mesto na tržiÅ”tu. NajÄeÅ”Äi problemi sa
dosada opisanim SIRT2 inhibitorima predstavljaju niska potentnost, loŔa selektivnost,
kao i loÅ”e farmakokinetiÄke osobine Å”to dalje opravdava razvoj novih predstavnika.
Cilj ovog rada je bio ispitivanje konformacionih promena SIRT2 u prisustvu
inhibitora i dalje poboljŔanje dostupnih kristalografskih modela u cilju razvoja
efikasnijeg protokola virtual screeningāa.
PolazeÄi od 5 razliÄitih kristalografskih struktura SIRT2āinhibitor kompleksa,
ukupno 1,5 Ī¼s simulacija molekulske dinamike u eksplicitnom solventu je izvedeno. 3D
deskriptori zasnovani na GRIDāu i linearna diskriminantna analiza su koriÅ”Äeni za
virtual screening (VS) studiju.
Konformaciona fleksibilnost SIRT2āinhibitor kompleksa zabeležena tokom
simulacija ukazuje na znaÄajnu fleksibilnost aktivnog mesta i poslediÄno na multiple
vezivne modove inhibitora. Nakon procedure klasterovanja trajektorije, nekoliko
relevantnih modela kompleksa je izdvojeno i ukljuÄeno u dalju VS studiju. VS modeli
generisani pomoÄu tri relevantna kompleksa dobijena studijom molekulske dinamike
su pokazali znaÄajno bolje performanse u poreÄenju sa modelima dobijenim pomoÄu do
danas opisanih kristalografskih struktura. Performanse generisanog VS protokola su
znaÄajno poboljÅ”ane i u odnosu na do danas publikovane protokole. Rezultati ove
studije jasno ukazuju na znaÄaj uraÄunavanja 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 realistiÄniji modeli aktivnog mesta sirtuina 2 kojima
su znaÄajno poboljÅ”ane performanse virtual screeningāa u odnosu na do danas
publikovane studije. Rezultati ove studije, ukljuÄujuÄi 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, NADādependent protein deacetylase
sirtuin 2 (SIRT2), recently emerged as promising therapeutic strategy for the treatment
of many diseases, including Parkinsonās 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 sirtuin2āinhibitor
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 coācrystalized
with inhibitors, total of 1.5 Ī¼s of molecular dynamics (MD) simulations in explicit
solvent has been performed. GRIDābased 3D descriptors and linear discriminant
analysis were used for virtual screening.
Significant conformational flexibility of SIRT2āinhibitor complexes was observed
during simulations indicating overall binding site flexibility and multiple binding modes
of inhibitors. Several atomistic models of SIRT2āinhibitor complexes were extracted
and used for structureābased VS study. VS models generated from three extracted
SIRT2āinhibitor 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 SIRT2āinhibitor 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.VII Kongres farmaceuta Srbije sa meÄunarodnim uÄeÅ”Äem
Zajedno stvaramo buduÄnost farmacije,
Beograd, 10-14. oktobar 201
Exploring conformational changes of sirtuin 2- molecular dynamic approach
Sirtuin 2 (Sirt2) se poslednjih godina sve viŔe povezuje sa patogenezom kancera,
neurodegeneracijom i inflamacijom zbog Äega predstavlja atraktivan target za razvoj novih lekova.
VeÄina do danas okarakterisanih inhibitora Sirt2 ne poseduje odgovarajuÄu aktivnost i/ili
selektivnost. Kristalografske strukture objavljene u poslednjih par godina obezbedile su odreÄeni
pomak u razvoju novih inhibitora, meÄutim i dalje postoje nedoumice u vezi sa mehanizmom
inhibicije koje su posledica visoke konformacone fleksibilnosti Sirt2 enzima. U cilju sticanja
detaljnijeg uvida u konformacionu fleksibilnost Sirt2, izvedeno je sedamnaest simulacija
molekulske dinamike u trajanju od po 100ns. Rezultati ove studije ukazali su na neke od kljuÄnih
rezidua neophodnih za stabilizaciju kompleksa Sirt2/inhibitor. TakoÄe, opisane konformacije daju
jasniji uvid u katalitiÄki ciklus deacilovanja. Opisan je i znaÄaj konformacije kofaktorske petlje na
konformaciju vezivnog mesta inhibitora. Rezultati ove studije Äe omoguÄiti racionalniji pristup
dizajnu selektivnijih i potentnijih inhibitora sirtuina2.Sirtuin 2 (Sirt2) has been implicated in pathogenesis of cancer, inflammation and neurodegeneration,
which makes Sirt2 attractive target for development of novel therapeutics. A number of small
molecule Sirt2 inhibitors have been reported, but most of them lack selectivity and/or high potency.
Very recently published X-ray structures of selective ligand/Sirt2 complexes have revealed more
details about mechanism of action of inhibitors, but some information still missing. Here, we will
try to answer on questions regarding the conformational changes during enzyme catalysis, based on
our recent molecular dynamic study of Sirt2. Total of seventeen 100 ns simulations have been
performed on five different crystal structures. Results of this study have suggested one of key
residues responsible for conformational stability of cofactor-binding loop and significant interaction
with novel inhibitors. Further, āclosingā of Sirt2 induced by presence of substrate has been described
as major factor responsible for conformational changes in substrate-binding site. In conclusion, this
study provides dynamic information on Sirt2 and may facilitate the rational design on novel, more
potent and selective inhibitors.Fifth Conference of Young Chemists of Serbia. September 29-30. 2017. Belgrade, Serbi
Sirtuin functions and modulation: from chemistry to the clinic
Sirtuins are NAD+
-dependent histone deacetylases regulating important metabolic pathways in prokaryotes and
eukaryotes and are involved in many biological processes such as cell survival, senescence, proliferation, apoptosis,
DNA repair, cell metabolism, and caloric restriction. The seven members of this family of enzymes are considered
potential targets for the treatment of human pathologies including neurodegenerative diseases, cardiovascular
diseases, and cancer. Furthermore, recent interest focusing on sirtuin modulators as epigenetic players in the
regulation of fundamental biological pathways has prompted increased efforts to discover new small molecules
able to modify sirtuin activity. Here, we review the role, mechanism of action, and biological function of the
seven sirtuins, as well as their inhibitors and activators
Computer-aided drug design of selective histone deacetylase inhibitors
The concept of gene expression is continuously explained with epigenetic modification. Post-translational histone acetylation and DNA methylation are dominant epigenetic alterations of the genome. Histone deacetylases (HDAC) play essential role in this process and therefore are very intensively investigated drug targets. The alteration in the structure and function of HDAC isoforms are identified in the pathogenesis of inflammation, cancer, and neurodegeneration. Eleven human HDAC isoforms are sharing a highly conserved catalytic domain. Among them, HDAC6 and SIRT2 are important for a wide range of diseases, due to their unique physiological functions. In our research, we have applied pharmacophore modelling, virtual screening, molecular docking and molecular dynamic methodologies for design and identification of selective HDAC6 and SIRT2 inhibitors. Recently resolved the crystal structure of catalytic domain II of human HDAC6 discovered a wide binding site essential for the substrate recognition. We have successfully used these structural features of human HDAC6 catalytic domain II to rationally design selective HDAC6 inhibitors. Newly published X-ray structures of selective ligand-SIRT2 complexes have revealed high conformational flexibility of this enzyme, and gave us more details about mechanism of action of sirtuin 2 inhibitors. Based on these findings we have performed molecular dynamic study of SIRT2 and tried to explain the conformational changes during enzyme catalysis. Since small number of selective HDAC modulators have been reported so far, rational design of HDAC6 and SIRT2 inhibitors are essential for further progress in discovery of epigenetic drugs.Journal of organic & inorganic chemistr
Novi protokol za poboljŔano uzorkovanje dinamike vezivnih mesta i njegova integracija u virtuelni skrining inhibitora sirtuina 2
Inhibitors of sirtuin 2 (SIRT2i) represent a promising group of novel therapeutics in
treatment of the age-related disorders, including carcinomas, neurodegenerative diseases,
metabolic syndrome etc. (1). Despite the promising preclinical results, none of the known
SIRT2i reached clinical trials. One of the main obstacles in the structure-based drug design of
novel SIRT2i represents intricate conformational dynamics of sirtuin 2 (SIRT2) binding
pocket (2). In order to facilitate the discovery of novel SIRT2i, we have developed the
protocol for enhanced sampling of the binding pocket dynamics and validated it by
integration into structure-based virtual screening (SBVS) pipeline for discovery of novel
SIRT2i. Developed protocol relies on well-tempered metadynamics simulations using the set
of pocket-related collective variables derived from time-lagged independent component
analysis (tICA). Our protocol outperformed classical molecular dynamics in search for
alternative conformational states of the binding pocket. Additionally, the protocol was able
to reveal the existence of cryptic subpocket inside SIRT2 binding pocket. To validate our
findings, the protocol was implemented into SBVS which resulted in significant expansion of
SIRT2i chemical space. To further probe the potential of expanded chemical space in
discovery of chemically novel groups of SIRT2i, a few virtual hit molecules were selected and
tested in vitro. Compound NDJ18 was shown to be potent and selective SIRT2i with
anticancer activity on triple-negative breast cancer cell line MDA-MB-231. Experimental
validation supported future generalization of the protocol by application on wider scope of
challenging protein targets.Inhibitori sirtuina 2 (SIRT2i) predstavljaju obeÄavajuÄu grupu novih terapeutika u
terapiji poremeÄaja povezanih sa starenjem, poput malignih oboljenja, neurodegenerativnih
oboljenja, metaboliÄkog sindroma itd. (1). Uprkos obeÄavajuÄim rezultatima prekliniÄkih
ispitivanja, nijedan SIRT2i nije doÅ”ao do kliniÄkih studija. Jedna od glavnih prepreka u
strukturno-zavisnom dizajnu novih SIRT2i predstavlja kompleksna konformaciona dinamika
vezivnog mesta sirtuina 2 (SIRT2) (2). U cilju poveÄanja efikasnosti racionalnog dizajna
novih SIRT2i, razvijen je protokol za poboljŔano uzorkovanje konformacione dinamike
vezivnog mesta SIRT2 koji se zasniva na metadinamiÄkim simulacijama uz set kolektivnih
varijabli izvedenih iz analize nezavisnih komponenti vremenskih zaostataka dinamike
vezivnog mesta (tICA). Razvijeni protokol nadmaÅ”io je klasiÄnu molekulsku dinamiku u
efikasnosti pretrage alternativnih konformacionih stanja vezivnog mesta. Dodatno,
primenom razvijenog protokola otkriveno je postojanje skrivenog džepa unutar vezivnog
mesta SIRT2. U cilju validacije, protokol je implementiran u strukturno-zavisni virtuelni
skrining SIRT2i Å”to je rezultovalo u znaÄajnoj ekspanziji postojeÄeg hemijskog prostora
SIRT2i. U daljem testiranju potencijala proÅ”irenog hemijskog prostora u otkriÄu potpuno
novih hemijskih skeleta SIRT2i, nekoliko najbolje rangiranih molekula je selektovano i
evaluirano in vitro. Jedinjenje NDJ18 se pokazalo kao potentan i selektivan novi SIRT2i.
Testiranjima na trostruko-negativnoj Äelijskoj liniji kancera dojke MDA-MB-231 utvrÄen je
znaÄajan antikancerski potencijal navedenog jedinjenja. Eksperimentalnom validacijom
podržan je dalji razvoj i generalizacija protokola kroz primenu na Ŕirem spektru proteinskih
targeta izazovnih sa aspekta tehnika racionalnog dizajna lekova.VIII Kongres farmaceuta Srbije sa meÄunarodnim uÄeÅ”Äem, 12-15.10.2022. Beogra
Tetrazole as a Replacement of the Electrophilic Group in Characteristic Prolyl Oligopeptidase Inhibitors
4-Phenylbutanoyl-aminoacyl-2(S)-tetrazolylpyrrolidines were studied as prolyl oligopeptidase inhibitors. The compounds were more potent than expected from the assumption that the tetrazole would also here be a bioisostere of the carboxylic acid group and the corresponding carboxylic acids are at their best only weak inhibitors. The aminoacyl groups L-prolyl and L-alanyl gave potent inhibitors with IC50 values of 12 and 129 nM, respectively. This was in line with typical prolyl oligopeptidase inhibitors; however, we did observe a difference with N-methyl-L-alanyl, which gave potent inhibitors in typical prolyl oligopeptidase inhibitors but not in our novel compound series. Furthermore, all studied 4-phenylbutanoyl-aminoacyl-2(S)-tetrazolylpyrrolidines decreased alpha-synuclein dimerization at the concentration of 10 mu M, also when they were only weak inhibitors of the proteolytic activity of the enzyme with an IC50 value of 205 mu M. Molecular docking studies revealed that the compounds are likely to bind differently to the enzyme compared to typical prolyl oligopeptidase inhibitors represented in this study by 4-phenylbutanoyl-aminoacyl-2(S)-cyanopyrrolidines.Peer reviewe
Rational design of selective histone deacetylase inhibitors
The concept of gene expression is continuously explained with epigenetic modifications. One of the most studied enzymes which have an influence on histone posttranslational modifications are histone deacetylases (HDACs). The overexpression and alterations in the structure of HDACs isoforms are described in the pathogenesis of cancer, inflammation and neurodegeneration. With different cellular function and tissue distribution of HDACs, scientists introduced them as attractive targets used in novel drug discovery protocols.
Rational drug design of novel small molecules is usually guided by computational approaches. In our laboratory, we use ligand-based (pharmacophore modeling and virtual screening) and structure-based (molecular docking and molecular dynamics) drug design methodologies. The main focus in our drug design project is identification of selective HDAC6 and SIRT2 inhibitors. With respect to all published data, very small number of selective HDAC modulators has been reported so far. Here, we present rational design of novel selective HDAC6 and SIRT2 inhibitors as promising drug candidates for further development and structure optimization.http://www.socphyschemserb.org/en/events/physical-chemistry-2018
The Identification of a SIRT6 Activator from Brown Algae Fucus distichus
peer-reviewedBrown seaweeds contain many bioactive compounds, including polyphenols, polysaccharides, fucosterol, and fucoxantin. These compounds have several biological activities, including anti-inflammatory, hepatoprotective, anti-tumor, anti-hypertensive, and anti-diabetic activity, although in most cases their mechanisms of action are not understood. In this study, extracts generated from five brown algae (Fucus dichitus, Fucus vesiculosus (Linnaeus), Cytoseira tamariscofolia, Cytoseira nodacaulis, Alaria esculenta) were tested for their ability to activate SIRT6 resulting in H3K9 deacetylation. Three of the five macroalgal extracts caused a significant increase of H3K9 deacetylation, and the effect was most pronounced for F. dichitus. The compound responsible for this in vitro activity was identified by mass spectrometry as fucoidan
Rational design, synthesis and in vitro testing of selective HDAC6 and SIRT2 inhibitors
Histone deacetylases (HDACs) are epigenetic enzymes involved in regulation of histone posttranslational
modifications and gene expression. Since changed function of HDACs is involved in pathogenesis of cancer 1-3,
the HDAC inhibitors are extensive examined as promising anticancer agents. In our in silico study we have
combined structure-based, ligand-based, and fragment-based methodologies to design selective inhibitors against
cytoplasmic isoforms of HDAC, such as histone deacetylase 6 inhibitors (HDAC6) and SIRT2. The drug design
study has defined several promising selective HDAC6 and SIRT2 inhibitors for further synthesis and in vitro
testing. Based on the in vitro activities of the novel compounds in a panel of biochemical HDAC assays as well
as various cell-based assays were selected the most promising candidates for further investigation.XXVI EFMC International Symposium on Medicinal Chemistry (EFMC-ISMC 2021), Virtual Event, August 29-September 2, 202
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