[show abstract][hide abstract] ABSTRACT: This paper reports the synthesis of a series of evodiamine derivatives. We assayed the ability to inhibit cell growth on three human tumour cell lines (H460, MCF-7 and HepG2) and we evaluated the capacity to interfere with the catalytic activity of topoisomerase I both by the relaxation assay and the occurrence of the cleavable complex. Moreover, whose effect on sirtuins 1, 2 and 3 was investigated. Finally, molecular docking analyses were performed in an attempt to rationalize the biological results.
[show abstract][hide abstract] ABSTRACT: In the past few years sirtuins have gained growing attention for their involvement in many biological processes such as cellular metabolism, apoptosis, aging and inflammation. In this paper, we report the synthesis of a library of thioacetylated pseudopeptides that were screened against human sirtuins 1-3 to reveal their in vitro inhibition activities. Molecular modeling studies were performed to acquire data about the binding modes of the inhibitors. Three sirtuin inhibitors were subjected to cellular studies and all of them showed an increase in acetylation of Lys382 of p53 after DNA damage. Furthermore, two of the compounds were able to inhibit both A549 lung carcinoma and MCF-7 breast carcinoma cell growth in micromolar concentration with the ability to arrest cancer cell cycle in the G1 phase.
Journal of Medicinal Chemistry 08/2013; · 5.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: Tuberculosis (TB) is a contagious disease caused by Mycobacterium tuberculosis (M. tuberculosis), and remains one of the most life-threatening plagues for public health in the world. The emergence of drug resistant strains of TB and co-infection with HIV has further complicated TB treatment. Here, the synthesis and characterizaton of a series of compounds were described, and these were followed by evaluating for their antibacterial activity against M. tuberculosis. Several novel arylthiourea derivatives exhibited excellent activity (lowest MIC=0.09 µg/ml) against M. tuberculosis including drug resistant strains of M. tuberculosis. The results suggest that these compounds are promising candidates for new anti-TB agent development.
Letters in Drug Design & Discovery 08/2013; 10(7):640-650. · 0.85 Impact Factor
[show abstract][hide abstract] ABSTRACT: Inhibition of the key hydrolytic enzymes of the endocannabinoid system, fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase (MAGL), has been proposed as potential mode of action for various therapeutic applications. Continuing our previous work, we take the first steps of structure-activity relationship exploration and show that 1,3,4-oxadiazol-2-ones can serve as scaffold for both selective FAAH and MAGL inhibitors, and also function as a dual FAAH/MAGL inhibitor at sub-micromolar IC50 values. Moreover, 10-fold selectivity against MAGL over FAAH was achieved with compound 3d (FAAH and MAGL IC50; 2.0 and 0.22 μM). Lastly, enzyme and ligand features contributing to the potency and selectivity differences are analysed by molecular docking.
European Journal of Pharmaceutical Sciences 04/2013; · 2.99 Impact Factor
[show abstract][hide abstract] ABSTRACT: SIRT3 is a member of the sirtuin family of histone deacetylases. It is a mitochondrial protein, which has an important role in metabolic homeostasis but it may also act as a tumor suppressor or promoter. Increased SIRT3 transcription has been associated with node-positive breast cancer and oral squamous cell carcinoma. To identify novel SIRT3 inhibitors we have established a virtual screening workflow by using shape-based filtering and flexible docking protocol. The Chembridge database was screened and 40 molecules were selected and tested in an in vitro assay. Two novel scaffolds were identified among the tested hits. The 5-amino-2-phenyl-benzoxazole scaffold was selected for further structure-activity studies and a series of its analogs was tested. The SIRT3 inhibition for this series ranged between 13% and 71%.
[show abstract][hide abstract] ABSTRACT: Large neutral amino acid transporter 1 (LAT1) is predominantly expressed at the blood-brain barrier and it has a major role in transporting neutral amino acids into the brain. LAT1 has the potential to function as a drug carrier for improved drug brain delivery which makes it an intriguing target protein for central nervous system disorders e.g., Alzheimer's disease, Parkinson's disease and brain tumors. In this study, a 3D pharmacophore was generated for a set of LAT1 substrates whose binding affinities were studied using competitive inhibition of the brain uptake of [(14)C]-L-leucine with an in situ rat brain perfusion method. The pharmacophore highlights the most important molecular features shared by efficient LAT1-binding compounds and elucidates their 3D-arrangement in detail. This clarifies the structure-activity relationships of LAT1 substrates and provides insights for making a binding hypothesis. The results can be further applied in the design of novel efficient LAT1 substrates.
European journal of pharmaceutical sciences: official journal of the European Federation for Pharmaceutical Sciences 12/2012; · 2.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: Chemical changes performed on 1a (sirtinol) led to a series of SIRT1/2 inhibitors in some cases more potent than 1a mainly against SIRT1. Tested in human leukemia U937 cells, the benzamide and anilide derivatives 1b, 1c, 2b, and 2c as well as the 4-(2-phenylpropyl)thioanalogue 4c showed huge apoptosis induction, while some sulfinyl and sulfonyl derivatives (5b, 5c, and 6a-c) were highly efficient in granulocytic differentiation. When assayed in human leukemia MOLT4 as well as in human breast MDA-MB-231 and colon RKO cancer cell lines, the anilide 2b (salermide) and the phenylpropylthio analogue 4b emerged as the most potent antiproliferative agents. Tested on colorectal carcinoma and glioblastoma multiforme cancer stem cells (CSCs) from patients, 2b was particularly potent against colorectal carcinoma CSCs, while 4b, 6a and the SIRT2-selective inhibitor AGK-2 showed the highest effect against glioblastoma multiforme CSCs. Such compounds will be further explored for their broad-spectrum anticancer properties.
Journal of Medicinal Chemistry 11/2012; · 5.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: CYP2E1 is an important enzyme oxidizing ethanol as well as several drugs and other xenobiotics in the human liver. We determined the inhibition potency of structurally diverse compounds against human CYP2E1, and analyzed their interactions with the enzyme active site by molecular docking and 3D-QSAR approaches. The IC(50) values for the tested compounds varied from 1.4μM for γ-undecanolactone to over 46mM for glycerol. This data set was used to create a comparative molecular field analysis (CoMFA) model. The most important interactions for binding of inhibitors were identified by docking and key features for inhibitors were characterized via the COMFA model. Since the active site of CYP2E1 is flexible, long chain lactones and alkyl alcohols fitted best into the larger open form while the other compounds fitted better in the smaller closed form of the active site. Electrostatic interactions near the Thr(303) residue proved to be important for inhibition of the enzyme activity. Thus, docking analysis and the predictive CoMFA model proved to be efficient tools for revealing interactions between inhibiting compounds and CYP2E1. These approaches can be used to analyze CYP2E1-mediated metabolism and drug interactions in the development of new chemical entities.
European journal of pharmaceutical sciences: official journal of the European Federation for Pharmaceutical Sciences 10/2012; · 2.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: A series of substituted chromone/chroman-4-one derivatives has been synthesized and evaluated as novel inhibitors of SIRT2, an enzyme involved in aging-related diseases, e.g., neurodegenerative disorders. The analogues were efficiently synthesized in a one-step procedure including a base-mediated aldol condensation using microwave irradiation. The most potent compounds, with inhibitory concentrations in the low micromolar range, were substituted in the 2-, 6-, and 8-positions. Larger, electron-withdrawing substituents in the 6- and 8-positions were favorable. The most potent inhibitor of SIRT2 was 6,8-dibromo-2-pentylchroman-4-one with an IC(50) of 1.5 μM. The synthesized compounds show high selectivity toward SIRT2 over SIRT1 and SIRT3 and represent an important starting point for the development of novel SIRT2 inhibitors.
Journal of Medicinal Chemistry 07/2012; 55(16):7104-13. · 5.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: The human CYP2A6 enzyme metabolises several xenobiotics including nicotine, the addictive component in tobacco. Reduced activity of CYP2A6, either for genetic reasons or by administering inhibitors of CYP2A6, reduces tobacco smoking. The aim was to design novel inhibitors of CYP2A6 using 3D-QSAR analysis combined with virtual screening. A 3D-QSAR model was utilised to identify the most important features of the inhibitors, and this knowledge was used to design inhibitors for CYP2A6. Chemical database screening yielded several potent inhibitor candidates such as alkylamine derivatives (compound no. 5, IC(50)=0.1 μM) and 1-benzothiophene-3-carbaldehyde that can be used as lead compounds in the development of drugs for smoking reduction therapy.
[show abstract][hide abstract] ABSTRACT: Kallikrein-related peptidase 3 (KLK3), also known as prostate-specific antigen (PSA), is the most useful biomarker for prostate cancer (PCa). KLK3 is suggested to play a role in regulating cancer growth through anti-angiogenic activity in vivo and in vitro. This feature, together with its specificity for prostate tissue, makes KLK3 an intriguing target for the design of new therapies for PCa. 3D pharmacophores for KLK3-stimulating compounds were generated based on peptides that bind specifically to KLK3 and increase its enzymatic activity. As a result of pharmacophore-based virtual screening, four small, drug-like compounds with affinity for KLK3 were discovered and validated by capillary differential scanning calorimetry. One of the compounds also stimulated the activity of KLK3, and is therefore the first published small molecule with such an activity.
[show abstract][hide abstract] ABSTRACT: The lack of substrate-bound crystal structures of SIRT1 and SIRT2 complicates the drug design for these targets. In this work, we aim to study whether SIRT3 could serve as a target structure in the design of substrate based pseudopeptidic inhibitors of SIRT1 and SIRT2. We created a binding hypothesis for pseudopeptidic inhibitors, synthesized a series of inhibitors, and studied how well the fulfillment of the binding criteria proposed by the hypothesis correlated with the in vitro inhibitory activities. The chosen approach was further validated by studying docking results between 12 different SIRT3, Sir2Tm, SIRT1 and SIRT2 X-ray structures and homology models in different conformational forms. It was concluded that the created binding hypothesis can be used in the design of the substrate based inhibitors of SIRT1 and SIRT2 although there are some reservations, and it is better to use the substrate-bound structure of SIRT3 instead of the available apo-SIRT2 as the target structure.
Journal of Medicinal Chemistry 09/2011; 54(19). · 5.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: Obtaining more structural information of human dopamine D(2) receptor may help in the design of better therapeutic agents against diseases such as Parkinson. In this study attempts have been made to develop a functional model for the catechol binding site of the human dopamine D(2) receptor, with two primary models being postulated based on the presence of a disulfide bridge in the second extracellular loop. The models have been subjected to subsequent molecular dynamics simulation and receptor based virtual screening of catechol structures. During steady state of the simulations, representative models with the reduced disulfide bridge were more capable of discriminating between active and inactive catechol structures. It is postulated that similar conformational changes of the second extracellular loop observed in 5-HT4 and β-adrenergic receptors, might also take place in the human D(2) receptor during its interaction with agonist ligands.
[show abstract][hide abstract] ABSTRACT: Sirtuins catalyze the NAD(+) dependent deacetylation of N(epsilon)-acetyl lysine residues to nicotinamide, O'-acetyl-ADP-ribose (OAADPR) and N(epsilon)-deacetylated lysine. Here, an easy-to-synthesize Ac-Ala-Lys-Ala sequence has been used as a probe for the screening of novel N(epsilon)-modified lysine containing inhibitors against SIRT1 and SIRT2. N(epsilon)-Selenoacetyl and N(epsilon)-isothiovaleryl were the most potent moieties found in this study, comparable to the widely studied N(epsilon)-thioacetyl group. The N(epsilon)-3,3-dimethylacryl and N(epsilon)-isovaleryl moieties gave significant inhibition in comparison to the N(epsilon)-acetyl group present in the substrates. In addition, the studied N(epsilon)-alkanoyl, N(epsilon)-alpha,beta-unsaturated carbonyl and N(epsilon)-aroyl moieties showed that the acetyl binding pocket can accept rather large groups, but is sensitive to even small changes in electronic and steric properties of the N(epsilon)-modification. These results are applicable for further screening of N(epsilon)-acetyl analogues.
[show abstract][hide abstract] ABSTRACT: As tautomerism and ionization may significantly change the interaction possibilities between a ligand and a target protein, these phenomena could have an effect on structure-based virtual screening. Tautomeric- and protonation-state enumeration ensures that the state with optimal interaction possibilities is included in the screening process, as the predicted state may not always be the optimal binder. However, there is very little information published if tautomer and protomer enumeration actually improves the enrichment of active molecules compared to the alternative of using a predicted form of each molecule. In this study, a retrospective virtual screening was performed using AutoDock on 19 drug targets with a publicly available data set. It is proposed that tautomer and protomer prediction can significantly save computing resources and can yield similar results to enumeration.
Journal of Chemical Information and Modeling 11/2009; 49(12):2742-8. · 4.30 Impact Factor
[show abstract][hide abstract] ABSTRACT: Fatty acid amide hydrolase (FAAH) and monoglyceride lipase (MGL) are the main enzymes responsible for the hydrolysis of endogenous cannabinoids N-arachidonoylethanolamide (AEA) and 2-arachidonoylglycerol (2-AG), respectively. Phenyl alkylcarbamates are FAAH inhibitors with anxiolytic and analgesic activities in vivo. Herein we present for the first time the synthesis and biological evaluation of a series of chiral 3-(2-oxazoline)-phenyl N-alkylcarbamates as FAAH inhibitors. Furthermore, the structural background of chirality on the FAAH inhibition is explored by analyzing the protein-ligand interactions. Remarkably, 10-fold difference in potency was observed for (R)- and (S)-derivatives of 3-(5-methyl-4,5-dihydrooxazol-2-yl)phenyl cyclohexylcarbamate (6a vs. 6b). Molecular modelling indicated an important interaction between the oxazoline nitrogen and FAAH active site.
European journal of medicinal chemistry 06/2009; 44(10):4179-91. · 3.27 Impact Factor
[show abstract][hide abstract] ABSTRACT: The uncertainty estimation of measurements in pharmaceutical manufacturing is often neglected in process optimization. For instance, tablet manufacturing consists of several process steps called unit operations where many measurements on the process conditions and quality are carried out. These measurements are assumed to be error-free and the possibility of the cumulative error throughout the process stages that only goes up has been ignored. Good manufacturing practices (GMP) guidelines provide regulations for the pharmaceutical industry on how to establish high quality production. However, they do not provide any instructions on pre-optimizing the process using a proper sampling scheme at each step. The uncertainty tests of measurements, for example in the tableting process, accounts for all significant sources of uncertainty in the production.In this study, the total error of the dissolution test according to the uncertainties described in the Pierre Gy's sampling theory has been studied. The present study shows that the overall uncertainty of the dissolution procedure could be clearly improved with optimization of the sampling chain.
Chemometrics and Intelligent Laboratory Systems - CHEMOMETR INTELL LAB SYST. 01/2009; 97(1):82-90.
[show abstract][hide abstract] ABSTRACT: The human constitutive androstane receptor (CAR, NR1I3) is an important regulator of xenobiotic metabolism and other physiological processes. So far, only few CAR agonists are known and no explicit mechanism has been proposed for their action. Thus, we aimed to generate a 3D QSAR model that could explain the molecular determinants of CAR agonist action. To obtain a sufficient number of agonists that cover a wide range of activity, we applied a virtual screening approach using both structure- and ligand-based methods. We identified 27 novel human CAR agonists on which a 3D QSAR model was generated. The model, complemented by coregulator recruitment and mutagenesis results, suggests a potential activation mechanism for human CAR and may serve to predict potential activation of CAR for compounds emerging from drug development projects or for chemicals undergoing toxicological risk assessment.
Journal of Medicinal Chemistry 12/2008; 51(22):7181-92. · 5.61 Impact Factor
[show abstract][hide abstract] ABSTRACT: SIRT2 inhibitors with a N-(3-phenylpropenoyl)-glycine tryptamide backbone were studied. This backbone has been developed in our group, and it is derived from a compound originally found by virtual screening. In addition, compounds with a smaller 3-phenylpropenoic acid tryptamide backbone were also included in the study. Binding modes for the new compounds and the previously reported compounds were analyzed with molecular modelling methods. The approach, which included a combination of molecular dynamics, molecular docking and cluster analysis, showed that certain docking poses were favourable despite the conformational variation in the target protein. The N-(3-phenylpropenoyl)-glycine tryptamide backbone is also a good backbone for SIRT2 inhibitors, and the series of compounds includes several potent SIRT2 inhibitors.