Cheminformatic analysis, design and examination of the proapoptotic activity of novel imidazoline receptor ligands

Ligandi imidazolinskih receptora predstavljaju veliku grupu biološki aktivnih jedinjenja koja svoju aktivnost ostvaruju delovanjem na imidazolinske receptore (I1-IR, I2-IR, and I3-IR) i na α2-adrenergičke receptore (α2-AR). Centralni antihipertenzivni efekat imidazolina kao što su klonidin, rilmenidin i moksonidin je rezultat aktivacije I1-IR and α2-AR. I2-imidazolinski receptori predstavljaju katalitičko mesto monoamino oksidaze B (MAO-B), enzima koji je uključen u nekolio neuroloških poremećaja. Jedinjenja kao što su idazoksan i njegovi analozi pokazuju visok afinitet za ovaj tip receptora. I3-IRs imaju ulogu u indukciju sekrecije insulina iz β-ćelija pankreasa i održavanje homeostaze glukoze. Imajući u vidu da većina liganada imidazolinskih receptora svoje efekate ostvaruje unutar centralnog nervnog sistema (CNS) delujući kao centralni antihipertenzivi i/ili su potencijalni lekovi u lečenju neuroloških oboljenja, procena njihove permeabilnosti kroz krvno-moždanu barijeru (KMB) je od suštinskog značaja u ranom otkriću lekova. U ovoj disertaciji KMB permeabilnost 18 liganda α2-adrenergičkih i/ili imidazolinskih receptora i 22 leka koja deluju na CNS je ispitana primenom paralelnog testa permeabilnosti na veštačkim membrana (eng. Parallel Artificial Membrane Permeability Assay, PAMPA) i bioparticione micelarne hromatografije (eng. Biopartitioning Micellar Chromatography, BMC). Vrednosti dobijene PAMPA (logPe) i BMC (logkBMC) su dalje analizirane kvantitativnim odnosom strukture i permeabilnosti jedinjenja (eng. Quantitative Structure-Permeability Relationship, QSPR). Dominantni molekulski/kajonski oblici na pH = 7,4 su određeni korišćenjem MarvinSketch 6.1.0 softvera. Geometrija odabranih molekulskih/katjonskih oblika ispitivanih jedinjenja je optimizovana primenom B3LYP /6-31G (d,p) nivoa Density Functional Theory (DTF) u ChemBio3D Ultra 13.0 programu. Deskriptori optimizovanih struktura su izračunati u ChemBio3D Ultra 13.0, Dragon 6.0 i ADMET Predictor 6.5 programima. logPe i logkBMC vrednosti su korišćene kao zavisne varijable (Y), dok su izračunati molekulski parametri predstavljali nezavisne varijable (X) u QSPR studiji.Imidazoline receptor ligands are a numerous family of biologically active compounds known to produce central hypotensive effect by interaction with both α2-adrenoreceptors (α2-AR) and imidazoline receptors (I1-IR, I2-IR, and I3-IR). The central hypotensive effect of imidazoline derivatives such as clonidine, rilmenidine and moxonidine is results of activation both I1-IR and α2-AR. I2-IRs have been shown to be modulatory site for monoamine oxidase-B, enzyme responsible for several neurological disorders. This type of imidazoline ligand receptors have high affinity for idazoxan and its analogues. I3-IRs are involved in induction of insulin secretion from β-cells and maintaining glucose homeostasis. Since the most IRs ligands are examined as centrally acting antihypertensives and/or drug candidates for treatment of various neurological diseases, predicting their brain penetration is a critical step in early drug discovery phase. In the framework of this doctoral dissertation, the effective Blood–Brain Barrier (BBB) permeability of 18 IRs/ α2-AR ligands and 22 Central Nervous System (CNS) drugs was experimentally determined by using both Parallel Artificial Membrane Permeability Assay (PAMPA) and Biopartitioning Micellar Chromatography (BMC) and further studied by the Quantitative-Structure-Permeability Relationship (QSPR) methodology. The dominant molecules/cations species of compounds have been calculated at pH = 7.4 by using MarvinSketch 6.1.0 software. The analyzed ligands were optimized using Density Functional Theory (B3LYP/6-31G(d,p)) included in ChemBio3D Ultra 13.0 program and molecule descriptors for optimized compounds were calculated using ChemBio3D Ultra 13.0, Dragon 6.0 and ADMET predictor 6.5 software. PAMPA effective permeabilities of examined compounds (logPe) and their logkBMC values were used as dependent variable (Y), while calculated molecular parametres were used as independent variables (X) in the QSPR study. SIMCA P+ 12.0 was used for Partial Least Square (PLS) analysis, while the stepwise Multiple Linear Regression (MLR) and Artificial Neural Networks (ANN) modeling were performed using STASTICA Neural Networks 4.0. Predictive potential of the formed models was confirmed by Leave-One-Out Cross- and external-validation and the most reliable models were selected. The descriptors that are important for model building are identified as well as their influence on BBB permeability..

Linear solvation energy relationship study of selected imidazoline receptor ligands on α1-acid glycoprotein column

The retention properties of 22 selected imidazoline receptor ligands were studied by high-performance liquid chromatography on α1-acid glycoprotein (AGP) column using 2-propanol as organic additive and Sørensen phosphate buffer (pH 7.0). Linear solvation energy relationships (LSER) were built using isocratic retention factors - log k5, log k8, log k10, log k12, log k15 obtained for (5, 8, 10, 12, 15)% of 2- propanol in mobile phase, respectively and extrapolated log Kw values as dependant variables. Independent variables (Abraham descriptors) for LSER analysis were calculated by ACD/i-Lab software. LSER analysis indicated on McGowan volume, hydrogen bond basicity and excess molar refraction as the most important parameters for all isocratic retention factors and log Kw values of 22 selected imidazoline receptor ligands

3D-QSAR modelovanje i analiza farmakofore antagonista serotoninskih 5-HT2A receptora

Creation of a statistically reliable 3D-QSAR (Quantitative Structure Activity Relationships) model enables definition of the structure of the pharmacophore for antagonists of serotonin 5-HT2A receptors and selection of the key molecular determinants for the design of new antagonists. A 3D-QSAR study was applied on a series of 50 antagonists of 5-HT2A receptors. The data set is divided into the training set, composed of 33 compounds, and test set containing 14 molecules. The training set was used to build the 3D-QSAR model, while test set was used for model validation. This 3D-QSAR study was performed by use of the Pentacle 1.07 programs. Obtained statistical and validation parameters for training set (R²= 0.96; Q²=0.75, RMSEE= 0.211); and for test set (R²pred=0.51; RMSEP= 0.558); indicate on reliability and good predictive potential of the 3D-QSAR model. Based on the most influential variables of the selected 3D-QSAR model, the molecular determinants for the antagonistic effect on the 5-HT2A receptors were selected: hydrogen bond acceptor and hydrogen bond donor at a distance of 10.4A-10.8A (v495: O-N1); carbonyl oxygen and a steric hot spot at a distance of 14.8A-15.2A (v640: N1-TIP); hydrophobic domain and hydrogen bond acceptor at a distance of 3.2A-3.6A (v276: DRY-O); two steric hot spots at a distance of 18.8A-19.2A (v248: TIP-TIP) .Formiranjem statistički pouzdanog 3D-QSAR (Quantitative Structure Activity Relationships) modela omogućeno je definisanje strukture farmakofore antagonista serotoninskih 5-HT₂A receptora i selekcija ključnih molekulskih determinanti za dizajn novih antagonista serotoninskih 5-HT₂A receptora. 3D-QSAR studija je primenjena na seriji od 50 antagonista serotoninskih 5-HT₂A receptora koji su podeljeni na trening set od 33 molekula i test set od 14 molekula. Trening set je korišćen za formiranje 3D-QSAR modela, dok je test set primenjen za validaciju modela. Za ovu 3D-QSAR studiju je upotrebljen Pentacle 1.07 program. Izračunati validacioni i statistički parametri 3D-QSAR modela (R²=0,96; Q²=0,75; RMSEE= 0,211), kao i parametri eksterne validacije na test setu (R²pred =0,51; RMSEP= 0,558), ukazuju na pouzdanost i dobru moć predviđanja izabranog 3D-QSAR modela. Na osnovu najuticajnijih varijabli izabranog 3D-QSAR modela definisana je struktura farmakofora za antagonističko dejstvo na serotoninskim 5-HT₂A receptorima: donor i akceptor vodonične veze na rastojanju od 10,4A-10,8A (v495: O-N1); karbonilni kiseonik i sterni centar na rastojanju od 14,8A-15,2A (v640: N1-TIP); hidrofobni centar i donor vodonične veze na rastojanju od 3,2A- 3,6A (v276: DRY-O); dva sterna centra na rastojanju od 18,8A-19,2A (v248: TIP-TIP)

3D-QSAR studija i razvoj farmakofore agonista serotoninskih 5-HT2A receptora

All tested compounds show agonistic activity onserotonin5-HT2areceptors, which activation causes neuronal excitations, behavioral changes and platelet aggregation. The main aims of this study were to create 3D-QSAR(3D-Quantitative structure-activity relationship)model, analyse 3D-structure of the pharmacophore, validate the 3D-QSARmodel, and propose structural modification for novel 5-HT2aagonists.3D-QSAR modeling was applied to 51 agonists of 5-HT2areceptors. Dominant forms at physiologic pHof the examined compounds were optimized using the PM3 method and used for QSAR modeling. Data set was divided in two groups, training set of38 compounds, and test set of 13 compounds. Training set was used to build 3D-QSAR model, while test set was examined for the model validation. PLS (Partial Least Square Regression)method was used to develop 3D-QSAR model. Statistical parameters of the created and validated 3D-QSAR model,R2= 0.93, Q2=0.72, RMSEE=0.178, RMSEP=0.190 and R2 pred=0.63, indicate good prognostic capacity of the model.The3D-QSAR model was applied to analyse pharmacophore and to predict activity of other agonists of serotonin 5-HT2areceptors. Information obtained from the 3D-QSAR study indicated that presence of hydrogen bond donor and steric hot spot at a distance 14.80-15.20Å (v477:O-TIP), hydrophobic region and hydrogen bond donor at a distance of 2.40-2.86Å (v226:DRY-O), hydrogen bond donor and hydrogen bond acceptor at a distance of 1.60-2.00Å (v389:O-N1) and two hydrophobic regions at a distance 9.20-9.60Å (v23:DRY-DRY) are essential for agonistic activity on 5-HT2aserotonin receptors.Ispitivana jedinjenja djeluju kao agonisti serotoninskih 5-HT2areceptora, i dovode do neuralne ekscitacije, promjene ponašanja i agregacije trombocita. Cilj ove studije je bio formiranje 3D-QSAR (3D-Quantitative structure-activity relationship) modela i 3D-strukture farmakofore agonista serotoninskih 5-HT2a receptora, validacija formiranog 3D-QSAR modela i definisanje strukturnih modifikacija za dizajn novih agonista serotoninskih 5-HT2areceptora. Iz literature su preuzete strukture i aktivnosti 51 agoniste 5-HT2areceptora. Definisani su dominantni oblici ispitivanih jedinjenja pri fiziološkom pH i optimizovane njihove konformacije primjenom PM3 (Parameterized Model revision 3) metode. Ispitivana jedinjenja su podijeljena u dvije grupe, trening set sa 38 jedinjenja i test set sa 13 jedinjenja. Trening set je korišćen za formiranje jednačine i građenje 3D-QSAR modela, a test set za validaciju 3DQSAR modela. Pomoću PLS (Partial Least Square Regression) metode kreira se novi 3DQSAR model i računaju statistički parametri modela: R2=0,93, Q2=0,72, RMSEE=0,178, RMSEP=0,190 i R2pred=0,63. Formirani i validirani 3D-QSAR model je dalje upotrijebljen za analizu 3D-strukture farmakofore i za predviđanje aktivnosti novih agonista serotoninskih 5-HT2areceptora. Analizom je utvrđeno da je za ispoljavanje agonističke aktivnosti na nivou 5-HT2a serotoninskih receptora neophodno prisustvo donora vodonične veze i sternog centra na rastojanju 14,80-15,20Å (v477:O-TIP), donora i akceptora vodonične veze na rastojanju 1,60- 2,00Å (v389:O-N1), hidrofobnog centra i donora vodonične veze na rastojanju 2,40-2,86Å (v226:DRY-O) i dva hidrofobna centra na rastojanju 9,20-9,60Å (v23:DRY-DRY)

Rational design of multi-target compounds with potential anticancer activity

Multi-target compounds are designed to act on at least two targets in synergistic way, in order to produce stronger biological effect. The link between cancer and inflammation has been intensively studied in last years and inhibition of both COX-2 and 5-LOX enzymes may be an effective therapeutic approach for colon cancer treatment [1]. Acridines are known as DNA-topoisomerase II inhibitors. These compounds intercalate into the DNA and inhibit topoisomerase II by their side chain. Recent studies showed additional activities of acridine derivatives, depending on the side chain structure, such as inhibition of Src, MEK and VEGFR2 kinases [2,3]. Altered activity of PI3K/mTOR signaling pathway is one of the most common aberrations found in various forms of neoplastic lesions. Dual inhibition of PI3K and mTOR represents a reasonably attractive concept in potential cancer treatment [4]. In this paper, design of three groups of multi-target compounds with potential anticancer activity is presented. Designed compounds are potential inhibitors of COX-2 and 5-LOX, DNA-topoisomerase II complex and kinases (Src, MEK and VEGFR2), as well as dual inhibitors of mTOR and PI3K. A set of 27 compounds with published inhibitory activity on COX-2 and 5-LOX was formed and two QSAR models, for both activities, were created in Pentacle program. On the basis of models’ interpretation, nine new compounds were designed and activity on both targets predicted by developed models. Twenty-three acridine derivatives were designed and their interactions with DNA-topoisomerase II complex, Src, MEK and VEGFR2 were tested using AutoDock Vina program. Nineteen designed compounds bind to DNA similarly to inhibitor amsacrine and among them, ten derivatives show key binding interactions with tested kinases and therefore possess potential to inhibit them. A dataset of eighty-five compounds with dual PI3K/mTOR inhibitory activities was formed, divided into two groups based on their structural analogy and 3D-QSAR analysis of each group was performed in Pentacle program, 9 resulting in four QSAR models. On the basis of these results, new compounds were designed and further evaluated by use of molecular docking, virtual screening and ADMET predictions. Finally, seven compounds were chosen as the most promising new dual mTOR/PI3K inhibitors

The Forty-Sixth Euro Congress on Drug Synthesis and Analysis: Snapshot

The 46th EuroCongress on Drug Synthesis and Analysis (ECDSA-2017) was arranged within the celebration of the 65th Anniversary of the Faculty of Pharmacy at Comenius University in Bratislava, Slovakia from 5-8 September 2017 to get together specialists in medicinal chemistry, organic synthesis, pharmaceutical analysis, screening of bioactive compounds, pharmacology and drug formulations; promote the exchange of scientific results, methods and ideas; and encourage cooperation between researchers from all over the world. The topic of the conference, Drug Synthesis and Analysis, meant that the symposium welcomed all pharmacists and/or researchers (chemists, analysts, biologists) and students interested in scientific work dealing with investigations of biologically active compounds as potential drugs. The authors of this manuscript were plenary speakers and other participants of the symposium and members of their research teams. The following summary highlights the major points/topics of the meeting

Cheminformatic analysis, design and examination of the proapoptotic activity of novel imidazoline receptor ligands

Ligandi imidazolinskih receptora predstavljaju veliku grupu biološki aktivnih jedinjenja koja svoju aktivnost ostvaruju delovanjem na imidazolinske receptore (I1-IR, I2-IR, and I3-IR) i na α2-adrenergičke receptore (α2-AR). Centralni antihipertenzivni efekat imidazolina kao što su klonidin, rilmenidin i moksonidin je rezultat aktivacije I1-IR and α2-AR. I2-imidazolinski receptori predstavljaju katalitičko mesto monoamino oksidaze B (MAO-B), enzima koji je uključen u nekolio neuroloških poremećaja. Jedinjenja kao što su idazoksan i njegovi analozi pokazuju visok afinitet za ovaj tip receptora. I3-IRs imaju ulogu u indukciju sekrecije insulina iz β-ćelija pankreasa i održavanje homeostaze glukoze. Imajući u vidu da većina liganada imidazolinskih receptora svoje efekate ostvaruje unutar centralnog nervnog sistema (CNS) delujući kao centralni antihipertenzivi i/ili su potencijalni lekovi u lečenju neuroloških oboljenja, procena njihove permeabilnosti kroz krvno-moždanu barijeru (KMB) je od suštinskog značaja u ranom otkriću lekova. U ovoj disertaciji KMB permeabilnost 18 liganda α2-adrenergičkih i/ili imidazolinskih receptora i 22 leka koja deluju na CNS je ispitana primenom paralelnog testa permeabilnosti na veštačkim membrana (eng. Parallel Artificial Membrane Permeability Assay, PAMPA) i bioparticione micelarne hromatografije (eng. Biopartitioning Micellar Chromatography, BMC). Vrednosti dobijene PAMPA (logPe) i BMC (logkBMC) su dalje analizirane kvantitativnim odnosom strukture i permeabilnosti jedinjenja (eng. Quantitative Structure-Permeability Relationship, QSPR). Dominantni molekulski/kajonski oblici na pH = 7,4 su određeni korišćenjem MarvinSketch 6.1.0 softvera. Geometrija odabranih molekulskih/katjonskih oblika ispitivanih jedinjenja je optimizovana primenom B3LYP /6-31G (d,p) nivoa Density Functional Theory (DTF) u ChemBio3D Ultra 13.0 programu. Deskriptori optimizovanih struktura su izračunati u ChemBio3D Ultra 13.0, Dragon 6.0 i ADMET Predictor 6.5 programima. logPe i logkBMC vrednosti su korišćene kao zavisne varijable (Y), dok su izračunati molekulski parametri predstavljali nezavisne varijable (X) u QSPR studiji.Imidazoline receptor ligands are a numerous family of biologically active compounds known to produce central hypotensive effect by interaction with both α2-adrenoreceptors (α2-AR) and imidazoline receptors (I1-IR, I2-IR, and I3-IR). The central hypotensive effect of imidazoline derivatives such as clonidine, rilmenidine and moxonidine is results of activation both I1-IR and α2-AR. I2-IRs have been shown to be modulatory site for monoamine oxidase-B, enzyme responsible for several neurological disorders. This type of imidazoline ligand receptors have high affinity for idazoxan and its analogues. I3-IRs are involved in induction of insulin secretion from β-cells and maintaining glucose homeostasis. Since the most IRs ligands are examined as centrally acting antihypertensives and/or drug candidates for treatment of various neurological diseases, predicting their brain penetration is a critical step in early drug discovery phase. In the framework of this doctoral dissertation, the effective Blood–Brain Barrier (BBB) permeability of 18 IRs/ α2-AR ligands and 22 Central Nervous System (CNS) drugs was experimentally determined by using both Parallel Artificial Membrane Permeability Assay (PAMPA) and Biopartitioning Micellar Chromatography (BMC) and further studied by the Quantitative-Structure-Permeability Relationship (QSPR) methodology. The dominant molecules/cations species of compounds have been calculated at pH = 7.4 by using MarvinSketch 6.1.0 software. The analyzed ligands were optimized using Density Functional Theory (B3LYP/6-31G(d,p)) included in ChemBio3D Ultra 13.0 program and molecule descriptors for optimized compounds were calculated using ChemBio3D Ultra 13.0, Dragon 6.0 and ADMET predictor 6.5 software. PAMPA effective permeabilities of examined compounds (logPe) and their logkBMC values were used as dependent variable (Y), while calculated molecular parametres were used as independent variables (X) in the QSPR study. SIMCA P+ 12.0 was used for Partial Least Square (PLS) analysis, while the stepwise Multiple Linear Regression (MLR) and Artificial Neural Networks (ANN) modeling were performed using STASTICA Neural Networks 4.0. Predictive potential of the formed models was confirmed by Leave-One-Out Cross- and external-validation and the most reliable models were selected. The descriptors that are important for model building are identified as well as their influence on BBB permeability..

Prediction of blood-brain barrier permeation of alpha-adrenergic and imidazoline receptor ligands using PAMPA technique and quantitative-structure permeability relationship analysis

Imidazoline receptor ligands are a numerous family of biologically active compounds known to produce central hypotensive effect by interaction with both alpha(2)-adrenoreceptors (alpha(2)-AR) and imidazoline receptors (IRs). Recent hypotheses connect those ligands with several neurological disorders. Therefore some IRs ligands are examined as novel centrally acting antihypertensives and drug candidates for treatment of various neurological diseases. Effective Blood-Brain Barrier (BBB) permeability (P-e) of 18 IRs/alpha-ARs ligands and 22 Central Nervous System (CNS) drugs was experimentally determined using Parallel Artificial Membrane Permeability Assay (PAMPA) and studied by the Quantitative-Structure-Permeability Relationship (QSPR) methodology. The dominant molecules/cations species of compounds have been calculated at pH = 7.4. The analyzed ligands were optimized using Density Functional Theory (B3LYP/6-31G(d,p)) included in ChemBio3D Ultra 13.0 program and molecule descriptors for optimized compounds were calculated using ChemBio3D Ultra 13.0, Dragon 6.0 and ADMET predictor 6.5 software. Effective permeability of compounds was used as dependent variable (Y), while calculated molecular parametres were used as independent variables (X) in the QSPR study. SIMCA P+ 12.0 was used for Partial Least Square (PLS) analysis, while the stepwise Multiple Linear Regression (MLR) and Artificial Neural Networks (ANN) modeling were performed using STASTICA Neural Networks 4.0. Predictive potential of the formed models was confirmed by Leave-One-Out Cross- and external-validation and the most reliable models were selected. The descriptors that are important for model building are identified as well as their influence on BBB permeability. Results of the QSPR studies could be used as time and cost efficient screening tools for evaluation of BBB permeation of novel alpha-adrenergic/imidazoline receptor ligands, as promising drug candidates for treatment of hypertension or neurological diseases

The use of biopartitioning micellar chromatography for determination of BBB penetration of alpha-adrenergic/imidazoline receptor ligands

Blood-Brain Barrier (BBB) plays an essential role in protecting Central Nervous System (CNS) from harmful agents present in the bloodstream. In order to estimate central nervous delivery of compounds a lot of useful in vitro models have been developed. ...21st International Symposium on Separation Sciences, June 30th - July 3rd, 2015, Ljubljana, Sloveni

RP-TLC in quantitative structure-retention relationships of some alpha adrenergic and imidazoline receptor ligands

The chromatographic behavior of 16 alpha adrenergic and imidazoline receptor ligands has been studied by reversed-phase thin-layer chromatography (RP-TLC). Retention constant RM 0 has been determined for all tested compounds in two different chromatographic systems (tetrahydrofuran-ammonia-water/RP-18, and tetrahydrofuran-ammoniawater/ CN) and together with computed molecular parameters of the examined compounds further used for the quantitative structure–retention relationship (QSRR) study. The QSRR modeling was performed with use of the partial least squares regression (PLS). Obtained results from leave-one out cross-validation (Q2 values: 0.923 and 0.873 for RP-18 and CN stationary phase, respectively) and external test set prediction (root mean square error of prediction, RMSEP: 0.339 and 0.218, for RP-18 and CN stationary phase, respectively) were proved high predictive power of the proposed models.12th International Conference on Fundamental and Applied Aspects of Physical Chemistry, September 22-26, 2014 Belgrade, Serbi