Rational design, synthesis and in vitro evaluation of selective histone deacetylase 6 inhibitors

Histon deacetilaze su metaloenzimi koji hidrolizuju acetilovane bočne amino grupe lizina na histonskim i nehistonskim proteinima. Uklanjanjem acetil grupe sa lizina generiše se pozitivno naelektrisanje na histonima, koje gradi jonske veze sa negativno naelektrisanim DNK molekulima. Kao posledica građenja jonskih veza, hromatin postaje gusto pakovan, teže dostupan transkripcionim faktorima, koji posledično dovodi do represije genske transkripcije. U epigenetičkim istraživanjima, derivati hidroksamskih kiselina se koriste u dizajniranju inhibitora histon deacetilaza. Posledica inhibicije histon deacetilaza je indukcija apoptoze, zastoj u ćelijskom ciklusu, smanjenje rasta tumora, inhibicija migracije i invazije malignih ćelija. U zavisnosti od homologije u primarnoj sekvenci i ćelijske lokalizacije, histon deacetilaze su podeljene u četiri klase. Klasi I pripadaju HDAC1, HDAC2, HDAC3 i HDAC8 izoforme. Klasa II se deli na dve podklase – klasu IIa (HDAC4, HDAC5, HDAC7 i HDAC9), dok klasi IIb pripadaju HDAC6 i HDAC10. Posebno se izdvaja izoforma HDAC11 u okviru klase IV humanih histon deacetilaza. Prva faza istraživanja u ovoj doktorskoj disertaciji je kompjutersko dizajniranje selektivnih inhibitora histon deacetilaze 6. Dizajniranje pomenutih inhibitora je omogućeno kombinovanjem studija kvantitativnog odnosa strukture i aktivnosti (3D-QSAR), pretrage novih fragmenata, kao i studija molekulskog dokinga na trodimenzionalnim strukturama histon deacetilaza 1 i 6. Druga faza istraživanja bila je sinteza odabranih jedinjenja na osnovu zaključaka in silico studija racionalnog dizajna selektivnih HDAC6 inhibitora. Treća faza istraživanja u ovoj doktorskoj disertaciji je određivanje vrednosti inhibitornih koncentracija (IC50) novosintetisanih jedinjenja na humanim HDAC1, HDAC3, HDAC6 i HDAC8 izoenzimima u in vitro enzimskim testovima. Ispitivanje antikancerskih osobina sintetisanih jedinjenja na ćelijama tumora dojke (MDA-MB-231 i MCF-7) predstavlja četvrtu fazu istraživanja u ovoj doktorskoj disertaciji. Kao rezultat kompjuterskog dizajniranja selektivnih inhibitora histon deacetilaze 6 izdvojeni se validni i prediktivni 3D-QSAR modeli. Tehnikom virtuelnog skrininga odabrani su odgovarajući fragmenti za dizajniranje selektivnih HDAC6 inhibitora. Molekulskim dokingom je predviđen način vezivanja dizajniranih jedinjenja za humane HDAC1 i HDAC6 izoforme. Sintetisane su dve klase derivata hidroksamskih kiselina, derivati 1-benzhidrilnog piperazina i klasa 5,5-difenil-2,4- imidazolidindiona i okarakterisani metodama strukturne analize. Na osnovu rezultata in vitro enzimskih testiranja, identifikovano je sedam nanomolarnih inhibitora histon deacetilaze 6, od kojih su dva inhibitora: BDR-6, IC50 = 186 nM i BDR-9, IC50 = 31 nM selektivna za HDAC6 izoformu i jedan inhibitor je izdvojen kao dualni HDAC6/8 inhibitor. Ispitivanjima uticaja sintetisanih inhibitora na ćelijsko preživljavanje, apoptozu, promene u ćelijskom ciklusu, migraciju i invaziju ćelija kancera dojke (MDA-MB-231 i MCF-7) izdvojen je neselektivni HDAC inhibitor, BDR-8 (HDAC1, IC50 = 408 nM; HDAC3 IC50 = 207 nM; HDAC6, IC50 = 124 nM i HDAC8, IC50 = 245 nM) sa najboljim antikancerskim osobinama. Najpotentniji sintetisani selektivni HDAC6 inhibitor, BDR-9 predstavlja necitotoksično jedinjenje sa antimigratornim osobinama na MCF-7 ćelijama kancera dojke. U ovoj doktorskoj disertaciji prikazan je sistematičan protokol za preklinički razvoj novih selektivnih inhibitora histon deacetilaze 6, koji može da bude iskorišćen u budućim istraživanjima u oblasti otkrića lekova koji deluju na kancerski epigenom.Histone deacetylases are metalloenzymes that hydrolyze acetylated lysine side chains on histone and non-histone proteins. Removal of the acetyl group from lysine generates a positive charge on histones that forms ionic bonds with negatively charged DNA molecules. As a consequence of forming ionic bonds, chromatin becomes densely packed, the access of the transcription factors is prevented, which in turn leads to the repression of gene transcription. In epigenetic drug discovery, hydroxamic acid derivatives are used in the design of histone deacetylase inhibitors. Inhibition of human histone deacetylases leads to induction of apoptosis, cell cycle arrest, tumor growth inhibition, inhibition of migration and invasion of malignant cells. Depending on the homology in the primary sequence and cell localization, histone deacetylases are classified into four classes. Class I is consisted of HDAC1, HDAC2, HDAC3 and HDAC8 isoforms. Class II is divided into two subclasses - class IIa (HDAC4, HDAC5, HDAC7 and HDAC9), and class IIb (HDAC6 and HDAC10). The HDAC11 is the unique isoform within the class IV HDACs. The first goal of research in this doctoral dissertation was computational drug design of selective histone deacetylase 6 inhibitors. The second goal of the research was the synthesis of selected compounds based on the predictions of in silico studies. The third research goal in this doctoral dissertation is to determine the inhibitory concentrations (IC50) of newly synthesized compounds against human HDAC1, HDAC3, HDAC6 and HDAC8 isoenzymes in in vitro enzyme assays. Evaluation of anticancer properties of synthesized compounds on breast tumor cells (MDA-MB- 231 and MCF-7) is the fourth goal set in this doctoral dissertation. As a result of computational drug design study, valid and predictive 3D-QSAR models were generated. The most promising fragments for the design of selective HDAC6 inhibitors were selected by virtual screening technique. Molecular docking study predicted the binding modes of designed compounds toward the human HDAC1 and HDAC6 isoforms. Two classes of hydroxamic acid derivatives, 1-benzhydryl piperazine derivatives and 5,5-diphenyl-imidazolidine- 2,4-dione derivatives were synthesized and characterized by NMR analysis and mass spectrometry. Considering the results of in vitro enzyme assays, seven nanomolar histone deacetylase 6 inhibitors were identified, of which two inhibitors: BDR-6, IC50 = 186 nM and BDR-9, IC50 = 31 nM are selective for HDAC6 isoform and one inhibitor was disclosed as dual HDAC6 / 8 inhibitor. Evaluation of the effects of synthesized inhibitors on cell survival, apoptosis, changes in cell cycle, migration and invasion of breast cancer cells (MDA-MB-231 and MCF-7) singled out a non- selective HDAC inhibitor, BDR-8 (HDAC1, IC50 = 408 nM; HDAC3 IC50 = 207 nM, HDAC6, IC50 = 124 nM and HDAC8, IC50 = 245 nM) with the best anticancer properties. The most potent selective HDAC6 inhibitor, BDR-9 is a non-cytotoxic compound with anti-migratory properties on MCF-7 breast cancer cells. In this doctoral dissertation, a systematic protocol for the preclinical drug discovery of novel selective histone deacetylase 6 inhibitors is presented, that can be used in future research of drug candidates that target the cancer epigenome

Fire analysis of partially delaminated curved reinforced concrete beam structures

In the dissertation a new partly coupled numerical model for non linear analysis of homogeneous and partly delaminated curved RC structures exposed to mechanical and temperature load is introduced. Due to its complexity the model is divided into two phases. In the first phase the time and spatial distribution of temperatures in fire compartment is defined by temperature-time fire curves and FDS models. Obtained temperatures from the first phase and mechanical load are used as input parameters in the second phase of the presented model, where the distribution of temperatures, pore pressures, gaseous mixture of dry air and water vapour and stress-strain state are calculated. One of the novelties of the introduced model is the second phase, where chemical-hygro-thermal part and mechanical part of the fire analysis are partly coupled. The connection between the parts is considered with the changed geometry of structure due to concrete spalling. The second novelty of the introduced model is the mechanical part of the fire analysis, where a new group of strain based finite elements for non linear analysis of homogeneous and partly delaminated curved RC structures during fire has been developed. Finite elements are based on kinematically exact planar beam theory of Reissner, non linear material models for concrete and steel at elevated temperatures and costitutive laws for contact surface between beam layers. With the principle of additivity of strain increments temperature strains of concrete and steel, viscous strains of steel, transient strains and creep strains at elevated temperatures for concrete are considered. The restraining effect of soil on tunnel structure is employed with discrete non linear springs. Detailed numerical analyses have revealed, that the introduced model has good efficiency and accuracy and it si perfectly suitable for fire analysis of all kinds of homogeneous and partly delaminated curved RC structures, even tunnels. The parametric studies have showed that the changed geometry of structure due to concrete spalling significantly affects the time and the form of failure of tunnels during fire and that the contact stiffness between the beam layers strongly influences the distribution of internal forces in curved RC structures during fire

Rational design, synthesis and in vitro evaluation of selective histone deacetylase 6 inhibitors

Histon deacetilaze su metaloenzimi koji hidrolizuju acetilovane bočne amino grupe lizina nahistonskim i nehistonskim proteinima. Uklanjanjem acetil grupe sa lizina generiše se pozitivnonaelektrisanje na histonima, koje gradi jonske veze sa negativno naelektrisanim DNK molekulima.Kao posledica građenja jonskih veza, hromatin postaje gusto pakovan, teže dostupantranskripcionim faktorima, koji posledično dovodi do represije genske transkripcije. Uepigenetičkim istraživanjima, derivati hidroksamskih kiselina se koriste u dizajniranju inhibitorahiston deacetilaza. Posledica inhibicije histon deacetilaza je indukcija apoptoze, zastoj u ćelijskomciklusu, smanjenje rasta tumora, inhibicija migracije i invazije malignih ćelija. U zavisnosti odhomologije u primarnoj sekvenci i ćelijske lokalizacije, histon deacetilaze su podeljene u četiriklase. Klasi I pripadaju HDAC1, HDAC2, HDAC3 i HDAC8 izoforme. Klasa II se deli na dvepodklase – klasu IIa (HDAC4, HDAC5, HDAC7 i HDAC9), dok klasi IIb pripadaju HDAC6 iHDAC10. Posebno se izdvaja izoforma HDAC11 u okviru klase IV humanih histon deacetilaza.Prva faza istraživanja u ovoj doktorskoj disertaciji je kompjutersko dizajniranje selektivnihinhibitora histon deacetilaze 6. Dizajniranje pomenutih inhibitora je omogućeno kombinovanjemstudija kvantitativnog odnosa strukture i aktivnosti (3D-QSAR), pretrage novih fragmenata, kao istudija molekulskog dokinga na trodimenzionalnim strukturama histon deacetilaza 1 i 6. Druga fazaistraživanja bila je sinteza odabranih jedinjenja na osnovu zaključaka in silico studija racionalnogdizajna selektivnih HDAC6 inhibitora. Treća faza istraživanja u ovoj doktorskoj disertaciji jeodređivanje vrednosti inhibitornih koncentracija (IC50) novosintetisanih jedinjenja na humanimHDAC1, HDAC3, HDAC6 i HDAC8 izoenzimima u in vitro enzimskim testovima. Ispitivanjeantikancerskih osobina sintetisanih jedinjenja na ćelijama tumora dojke (MDA-MB-231 i MCF-7)predstavlja četvrtu fazu istraživanja u ovoj doktorskoj disertaciji.Kao rezultat kompjuterskog dizajniranja selektivnih inhibitora histon deacetilaze 6 izdvojeni sevalidni i prediktivni 3D-QSAR modeli. Tehnikom virtuelnog skrininga odabrani su odgovarajućifragmenti za dizajniranje selektivnih HDAC6 inhibitora. Molekulskim dokingom je predviđen načinvezivanja dizajniranih jedinjenja za humane HDAC1 i HDAC6 izoforme. Sintetisane su dve klasederivata hidroksamskih kiselina, derivati 1-benzhidrilnog piperazina i klasa 5,5-difenil-2,4-imidazolidindiona i okarakterisani metodama strukturne analize. Na osnovu rezultata in vitroenzimskih testiranja, identifikovano je sedam nanomolarnih inhibitora histon deacetilaze 6, od kojihsu dva inhibitora: BDR-6, IC50 = 186 nM i BDR-9, IC50 = 31 nM selektivna za HDAC6 izoformu ijedan inhibitor je izdvojen kao dualni HDAC6/8 inhibitor. Ispitivanjima uticaja sintetisanih inhibitorana ćelijsko preživljavanje, apoptozu, promene u ćelijskom ciklusu, migraciju i invaziju ćelija kanceradojke (MDA-MB-231 i MCF-7) izdvojen je neselektivni HDAC inhibitor, BDR-8 (HDAC1, IC50 =408 nM; HDAC3 IC50 = 207 nM; HDAC6, IC50 = 124 nM i HDAC8, IC50 = 245 nM) sa najboljimantikancerskim osobinama. Najpotentniji sintetisani selektivni HDAC6 inhibitor, BDR-9 predstavljanecitotoksično jedinjenje sa antimigratornim osobinama na MCF-7 ćelijama kancera dojke. U ovojdoktorskoj disertaciji prikazan je sistematičan protokol za preklinički razvoj novih selektivnihinhibitora histon deacetilaze 6, koji može da bude iskorišćen u budućim istraživanjima u oblastiotkrića lekova koji deluju na kancerski epigenom.Histone deacetylases are metalloenzymes that hydrolyze acetylated lysine side chains on histoneand non-histone proteins. Removal of the acetyl group from lysine generates a positive charge onhistones that forms ionic bonds with negatively charged DNA molecules. As a consequence offorming ionic bonds, chromatin becomes densely packed, the access of the transcription factors isprevented, which in turn leads to the repression of gene transcription. In epigenetic drugdiscovery, hydroxamic acid derivatives are used in the design of histone deacetylase inhibitors.Inhibition of human histone deacetylases leads to induction of apoptosis, cell cycle arrest, tumorgrowth inhibition, inhibition of migration and invasion of malignant cells. Depending on thehomology in the primary sequence and cell localization, histone deacetylases are classified intofour classes. Class I is consisted of HDAC1, HDAC2, HDAC3 and HDAC8 isoforms. Class II isdivided into two subclasses - class IIa (HDAC4, HDAC5, HDAC7 and HDAC9), and class IIb(HDAC6 and HDAC10). The HDAC11 is the unique isoform within the class IV HDACs.The first goal of research in this doctoral dissertation was computational drug design of selectivehistone deacetylase 6 inhibitors. The second goal of the research was the synthesis of selectedcompounds based on the predictions of in silico studies. The third research goal in this doctoraldissertation is to determine the inhibitory concentrations (IC50) of newly synthesized compoundsagainst human HDAC1, HDAC3, HDAC6 and HDAC8 isoenzymes in in vitro enzyme assays.Evaluation of anticancer properties of synthesized compounds on breast tumor cells (MDA-MB-231 and MCF-7) is the fourth goal set in this doctoral dissertation.As a result of computational drug design study, valid and predictive 3D-QSAR models weregenerated. The most promising fragments for the design of selective HDAC6 inhibitors wereselected by virtual screening technique. Molecular docking study predicted the binding modes ofdesigned compounds toward the human HDAC1 and HDAC6 isoforms. Two classes ofhydroxamic acid derivatives, 1-benzhydryl piperazine derivatives and 5,5-diphenyl-imidazolidine-2,4-dione derivatives were synthesized and characterized by NMR analysis and mass spectrometry.Considering the results of in vitro enzyme assays, seven nanomolar histone deacetylase 6 inhibitorswere identified, of which two inhibitors: BDR-6, IC50 = 186 nM and BDR-9, IC50 = 31 nM areselective for HDAC6 isoform and one inhibitor was disclosed as dual HDAC6 / 8 inhibitor.Evaluation of the effects of synthesized inhibitors on cell survival, apoptosis, changes in cell cycle,migration and invasion of breast cancer cells (MDA-MB-231 and MCF-7) singled out a non-selective HDAC inhibitor, BDR-8 (HDAC1, IC50 = 408 nM; HDAC3 IC50 = 207 nM, HDAC6, IC50= 124 nM and HDAC8, IC50 = 245 nM) with the best anticancer properties. The most potentselective HDAC6 inhibitor, BDR-9 is a non-cytotoxic compound with anti-migratory properties onMCF-7 breast cancer cells. In this doctoral dissertation, a systematic protocol for the preclinicaldrug discovery of novel selective histone deacetylase 6 inhibitors is presented, that can be used infuture research of drug candidates that target the cancer epigenome

Understanding plasma spraying process and characteristics of DC-arc plasma gun (PJ-100)

The thermal spray processes are a group of coating processes used to apply metallic or non-metallic coatings. In these processes energy sources are used to heat the coating material (in the form of powder, wire, or rod form) to a molten or semi-molten state and accelerated towards a prepared surface by either carrier gases or atomization jets. In plasma spraying process, the spraying material is generally in the form of powder and requires a carrier gas to feed the powder into the plasma jet, which is passing between the hot cathode and the cylindrical nozzle-shaped anode. The design of DC plasma gun (PJ - 100) is designed and manufactured in Serbia. Plasma spaying process, the powder injection with the heat, momentum and mass transfers between particles and plasma jet, and the latest developments related to the production of DC plasma gun are described in this article

The Effect of Ball-Powder Ratio on The Mechanical and Structural Properties of CuZrB Composite Materials Fabricated by Powder Metallurgy

Copper matrix composites exhibit excellent mechanical and thermal properties. The composite consists of copper (Cu), zirconium (Zr), and boron (B) and is produced using the powder metallurgy technique. The high-energy ball milling was applied for mechanical alloying of the Cu-Zr-B powder mixture to achieve the desired ratio for obtaining a copper matrix reinforced with ZrB2 ceramic particles. The milling times of 10 and 40 hours for two different ball-to-powder ratios are investigated for a powder mixture with a composition of Cu-2.71Zr-2.27B (wt.%). XRD and SEM analyses were employed to determine structural and morphological changes in the mechanically alloyed powder mixture. Investigation of the morphological parameters shows that with prolonged milling, the shape of mixed particles becomes more uniform, while their structural parameters have been drastically changed. It is determined that during high-energy ball milling of the Cu-2.71Zr-2.27B (wt.%), the size of the copper powder decreases as the mechanical alloying increases for both ball-powder ratios. Dislocation densities reach their maximum value at around 30 hours of mechanical alloying for both ball-powder ratios, with dislocation density being higher for the 1:15 ratio, after which they decrease owing to the recrystallization of the copper matrix. XRD analysis shows no presence of ZrB2 reinforcement particles or oxides during milling

FIRE ANALYSIS OF CURVED REINFORCED CONCRETE BEAM

In the present study the fire analysis of a curved reinforced concrete beam exposed to concrete spalling is presented. Due to the complexity of physical and chemical processes in concrete at elevated temperatures, the proposed numerical model is divided into two consecutive mathematically uncoupled phases. In the second phase of the fire analysis a partially coupled numerical model is introduced in order to evaluate the effect of concrete spalling on the behaviour of curved RC beam in fire. In addition, the effect of depth, time development and the length of spalling area on the fire resistance of a curved RC beam is discussed

Prediction of hardness and electrical properties in ZrB2 particle reinforced metal matrix composites using artificial neural network

In the present study, the hardness and electrical properties of copper based composite prepared by hot pressing of mechanically alloyed powders were predicted using Artificial Neural Network (ANN) approach. Milling time (t, h), particles size of mechanically alloyed powders (d, nm), dislocation density (Ï, m-2) and compressive yield stress (σ0.2, MPa) were used as inputs. The ANN model was developed using general regression neural network (GRNN) architecture. Cu-based composites reinforced with micro and nano ZrB2 particles were consolidated via powder metallurgy processing by combining mechanical alloying and hot pressing. Analysis of the obtained results concerning hardness and electrical properties of the Cu-7 vol.% ZrB2 alloy showed that the distribution of micro and nano ZrB2 particles and the presence of agglomerates in the Cu matrix directly depend on the milling time. Also, the results show a strong influence of the milling time on hardness and electrical properties of Cu-7 vol.% ZrB2 alloy. Addition of ZrB2 particles decreases electrical conductivity of copper, but despite this fact Cu-7 vol.% ZrB2 alloy can be marked as highly conductive alloy (samples made of mechanically alloyed powders milled longer than 20 h). Experimental results of the samples have shown a consistency with the predicted results of ANN.  http://dx.doi.org/10.5937/metmateng1404255

In silico Methods for Design of Kinase Inhibitors as Anticancer Drugs

Rational drug design implies usage of molecular modeling techniques such as pharmacophore modeling, molecular dynamics, virtual screening, and molecular docking to explain the activity of biomolecules, define molecular determinants for interaction with the drug target, and design more efficient drug candidates. Kinases play an essential role in cell function and therefore are extensively studied targets in drug design and discovery. Kinase inhibitors are clinically very important and widely used antineoplastic drugs. In this review, computational methods used in rational drug design of kinase inhibitors are discussed and compared, considering some representative case studies

A theoretical study of interaction between HDAC-1 and HDAC-6 enzymes and in silico designed inhibitors

The disproportionate posttranslational histone modification as deacetylation has been associated with tumorigenesis and neurodegenerative diseases. Currently, there are five approved histone deacetylase (HDAC) inhibitors by FDA, which are defined as pan-HDAC inhibitors. By using ligand based virtual design approach (3D-QSAR) based on naphthalimide derivative scriptaid, we found molecular determinants important for selectivity towards histone deacetylase 6 isoform. After in silico design of novel inhibitors, we performed molecular docking studies using crystal structure of HDAC-1 enzyme (5ICN) and crystal structure of second human catalytic domain of HDAC-6 enzyme (5EDU). Molecular docking procedure was performed in GOLD 5.4.0 Software and ChemScore as scoring functions, and two in silico designed compounds D-48 and D-34 were selected as potential selective HDAC-6 inhibitors for synthesis. The shorter linker of selected compounds allows hydroxamic group to be more accessible to Zn2+ ion at the bottom of the active pocket. Both of them shown improved predicted selectivity according to the developed 3D-QSAR models.Book of Abstracts Fourth Conference of Young Chemists of Serbia Београд, 5. новембар 2016

A 3D-QSAR study on a set of MAPK1 inhibitors

Three different classes of mitogen-activated protein kinase 1 (MAPK1) inhibitors (derivatives of pyrimidine-pyridone, acetamidothiazole and pyrazolyl-pyrrole) were used to perform three-dimensional Quantitative Structure-Activity Relationship (3D-QSAR) study. The number of 92 MAPK1 inhibitors, split into training and test sets, was extracted from ChEMBL database, with their enzymatic inhibitory constants determined on human MAPK1. The statistically significant 3D-QSAR models were further validated. The 3D-QSAR model with the best statistical and validation parameters was further used to define main structural determinant for efficient inhibition of MAPK1 enzyme.14th International Conference on Fundamental and Applied Aspects of Physical Chemistry, September 24–28, 2018, Belgrad