Medicinal Chemistry - Volume 9, Issue 3, 2013

The 1,2,4-triazoles are an important group of medicinal substances which exhibit a wide range of activity, such as analgesic, antibacterial, fungicidal, antinflammatory, antiviral and anticancer. As a part of our long-term study on 1,2,4- triazoles we synthesize 4-benzyl-3-[(1-methylpyrrol-2-yl)methyl]-4,5-dihydro-1H-1,2,4-triazol-5-one which is characterized with anticancer activity. Here, we present an exhaustive studies of its electronic and molecular structure, aimed to rationalize the observed pharmacological activity, supported by the molecular docking to the EGFR kinase domain ATP binding site. The structural studies include X-ray analysis, experimental and computed spectral analysis (1H and 13C NMR, IR) as well as conformational analysis and the frontal molecular orbitals (FMO) analysis. The results of molecular docking indicate that interaction of 4-benzyl-3-[(1-methylpyrrol-2-yl)methyl]-4,5-dihydro-1H-1,2,4-triazol-5-one with the EGFR kinase domain ATP binding site may be responsible for the observed anticancer activity of this 1,2,4-triazole derivative. Moreover, we find that formation of the respective ligand-protein complex is conditioned by the keto-enol tautomerism of the ligand, i.e. the energetic prevalence of the keto form.

A series of chromone derivatives were designed as potential topoisomerase I (Top I) inhibitors based on the docking simulation study. Sixteen synthesized compounds were evaluated for Top I inhibitory activity and some compounds were further tested for in vitro cytotoxic activity. The most potent inhibitor, chromone 11b showed greater inhibitory activity (IC50 = 1.46 μM) than the known Top I inhibitors, i.e., camptothecin, fisetin and morin, but inactive against breast cancer cell (MCF-7), oral cavity cancer cell (KB) and small cell lung cancer (NCI-H187). Chromone 11c, another potent inhibitor (IC50 = 6.16 μM), exhibited cytotoxic activity against KB (IC50 = 73.32 μM) and NCI-H187 (IC50 = 36.79 μM).

Two series of novel phenylaminopyrimidine derivatives were designed and synthesized. All target compounds were determined against the human acute monocytic leukemia cell line U937 and the human chronic myeloid leukemia cell line K562 in vitro. Some of the target compounds demonstrated significant inhibitory activity against both cell lines. Compared with the control drug VX-680, 8a, 8e, 8g, 8h, 8j, and 8k demonstrated more potent antitumor activity. The structures of all target compounds were identified by 1H-NMR, 13C-NMR, IR, MS, and EA.

This paper describes the synthesis and in vitro biological activities of imidazolidine and hexahydropyrimidine derivatives against bacteria (Escherichia coli, Staphylococcus aureus and Mycobacterium tuberculosis) and Leishmania protozoa. Out of sixteen heterocyclic derivatives tested, none were cytotoxic against mammalian cells. The compounds showed significant bacterial effects and leishmanicidal activity. Compounds 4a and 4c were active against S. aureus and E. coli, respectively. Compounds 3a-3f, 4h and 4i presented promising results against M. tuberculosis, with MIC values ranging from 12.5 to 25.0 μg/mL, comparable to the “first and second line” drugs used to treat tuberculosis. Compounds 4a, 4c and 4e were active against L major. Three of them were structurally characterized by single-crystal X-ray diffraction.

Suppression of HIF prolyl hydroxylase (PHD) activity by small molecule inhibitors leads to the stabilization of HIF and offers a potential therapeutic option for treating ischemic disorders. In this study, pharmacophore based QSAR modeling, virtual screening and molecular docking approaches were concurrently used to identify target-specific PHD inhibitors with better ADME properties and to readily minimize false positives and false negatives. A 3D-QSAR based method was used to generate a pharmacophore hypothesis (AAAN). The obtained 3D-QSAR model has an excellent correlation coefficient value (r2 = 0.99), Fisher ratio (F = 386) and exhibited good predictive power (q2 = 0.64). The hypothesis was validated and utilized for chemical database screening and the retrieved compounds were subjected to molecular docking for further refinement. Quantitative AAAN hypothesis comprised three H-bond accepter and one negative ionizable group feature and it give good predictive ability because all the QSAR information it was providing matched with the active site information. The hypothesis was validated and used as a 3D query for database screening. After manual selection, molecular docking and further refinement, based on the molecular interactions of inhibitors with the essential amino acids residues, 12 candidates with good ADME and blood brain barrier permeability values were selected as potential PHD inhibitors.

The present paper describes the design and synthesis of a series of some 2-naphthyloxy derivatives with their antiamnesic activity using mice as the animal model and piracetam as the reference drug. All the synthesized compounds were characterized by spectroscopic techniques and were screened for their efficacy as cognition enhancers by elevated plus maze test and acetylcholinestrase inhibitory assay. Molecular modeling and docking studies of the selected compounds into the crystal structure of acetylcholinestrase complexed with functional ligand succinylcholine using GRAMM software was performed in order to predict the affinity and orientation of the synthesized derivatives at the active site. The binding energy of ligands was calculated using ArgusLab software. The docking score and hydrogen bonds formed with surrounding amino acids show the good agreement with predicted binding affinities obtained by molecular docking studies, as verified by acetylcholinestrase activity.

New derivatives of 7-chloro-4-aminoquinoline Mannich base were prepared by selectively modifying the aliphatic diethyl amino function of isoquine with different aliphatic/aromatic heterocyclic primary amino moieties at Mannich side chain. The synthesized compounds were characterized by their analytical and spectral data, and screened for in-vitro antimalarial activity against a chloroquine-sensitive 3D7 strain of Plasmodium falciparum. All the compounds showed in-vitro antimalarial activity at the tested dose; which, however, was considerably less than that of the standard reference drug, chloroquine. Among synthesized compounds, compounds with cyclohexyl (2f), methyl (2c) substitutions showed better activity than compounds substituted with n-octyl (2a), propyl (2b), 3-aminopropyl (2d) and furan-2- ylmethyl (2e) moieties at aminomethyl side chain. The results clearly demonstrate that the compound substituted with saturated cycloalkyl moiety (cyclohexyl) exhibited to some extent increased activity as compared to the compound containing heterocyclic moiety (furan-2-ylmethyl), and compounds with short chain alkyl substitutions (methyl, propyl) were found to be more active than that of compounds with long chain alkyl substitution (n-octyl).

In order to meet the urgent need for novel antifungal agents with improved activity and broader spectrum, a series of 3/4-[[N-alkyl-2-(2,4-difluorophenyl)-2-hydroxy-3-(1H-1, 2, 4-triazole)] propylamino] benzylethyl carbonate were designed, synthesized and evaluated as antifungal agents. The MIC80 values indicate that all the compounds showed only moderate or even no antifungal activities against nearly all the tested fungal pathogens. Moreover, the interactions of the most active compounds in the drug binding site of CACYP51 were also explored with the help of docking studies.

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) studies were carried out for a series of thienopyrimidines, novel Histamine H1 receptor antagonists. Various models were generated. The best predictive CoMFA model gave significant correlation coefficients (cross-validated r2 (q2) = 0.514, non-cross-validated r2 = 0.925), showing the influence of steric and electrostatic fields. Likewise, the best predictive CoMSIA model gave cross-validated r2 (q2) = 0.541, non-cross-validated r2 = 0.862, eliciting the influence of steric, electrostatic, hydrophobic and hydrogen bond acceptor fields. The generated models were externally validated and well correlated with calculated (predicted) and experimental inhibitory concentration (IC50) values, using test sets. The analysis of the contour maps of both CoMFA and CoMSIA models offer important structural insight for designing novel and more active Histamine H1 receptor antagonists prior to their synthesis.

The LIM-Kinase 2 (LIMK2) inhibitory activity of a series of pyrrolopyrimidine analogs has been analyzed through combinatorial protocol in multiple linear regressions (CP-MLR) and partial least square (PLS) using different descriptors obtained from DRAGON software. The empirical, topological and charge descriptors have led to statistically significant QSAR models and showed good external predictivity as reflected in test set R2 values (0.782 to 0.888). The obtained structure-activity correlations underlined the significance of bulkiness and molecular polarizability in improving the activity. The topological descriptors suggested that open chain or branched substituents are favorable while cyclic /ring substituents are unfavorable for the activity. The descriptors identified in the study showed that pyrrolopyrimidine scaffold holds scope for modulating LIMK2 inhibitory activity. The study gives a direction for further exploration of chemical space of pyrrolopyrimidine analogs as LIMK2 inhibitors.

A quantitative structure-activity relationship (QSAR) study of aromatic inhibitors against aldose reductase (AR) activity was performed using variable selection from stepwise multiple linear regression (MLR) and genetic algorithm (GA)-MLR. As a result of variable selection, stepwise MLR and GA-MLR gave the same results with one, two, three and five descriptors and different results with four and six descriptors. GA-MLR produced higher values and was better in explanatory and predictive power than stepwise MLR in four variables. AR activity (pIC50) of aromatic derivatives was expressed with acceptable explanatory (74.6-81.2%) and predictive power (68.8-74.4%) in models 3 and 4. The resulting models with the given descriptors illustrate that hydrophobic and electrostatic interactions play a significant role in inhibition of AR activity. This study suggests that the QSAR models can be used as guidelines to predict improved aldose reductase inhibitory activity and to obtain reliable predictions in structurally diverse compounds.

HIV-1 integrase (HIVIN) plays a key role in the replication of the HIV-1 virus and represents an attractive target for anti-HIV drug design. Experimental observation suggests that pyrimidone analogues have potent anti-HIV activity. Then, we modeled an HIVIN catalytic core domain based on the crystal structure of the prototype foamy virus (PFV) integrase. Molecular docking and molecular dynamics simulations were used to investigate the interaction mechanism between pyrimidone analogues and the HIVIN catalytic core domain. MD results suggest that the most active molecule (6K) has more stable hydrogen bonds and hydrophobic contacts than the FDA approved anti-HIV drug Raltegravir. Furthermore, the analogues and Raltegravir might have similar binding modes with HIVIN. Finally, Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) methods were used to construct three dimensional quantitative structure–activity (3D-QSAR) models. Eleven test set compounds which are not included in the training set were used to evaluate these models. The results suggest that these models are robust and have good prediction abilities.

Farnesyltranseferase inhibitors (FTIs) are one of the most promising classes of anticancer agents, but though some compounds in this category are in clinical trials there are no marketed drugs in this class yet. Quantitative structureactivity relationship (QSAR) models can be used for predicting the activity of FTI candidates in early stages of drug discovery. In this study 192 imidazole-containing FTIs were obtained from the literature, structures of the molecules were optimized using Hyperchem software, and molecular descriptors were calculated using Dragon software. The most suitable descriptors were selected using genetic algorithms-partial least squares (GA-PLS) and stepwise regression, and indicated that the volume, shape and polarity of the FTIs are important for their activities. 2D-QSAR models were prepared using both linear methods, i.e., multiple linear regression (MLR), and non-linear methods, i.e., artificial neural networks (ANN) and support vector machines (SVM). The proposed QSAR models were validated using internal and external validation methods. The results show that the proposed 2D-QSAR models are valid and that they can be applied to predict the activities of imidazole-containing FTIs. The prediction capability of the 2D-QSAR (linear and non-linear) models is comparable to and somewhat better than that of previous 3D-QSAR models and the non-linear models are more accurate than the linear models.

Chondromodulating chimeric prodrugs of diacetylrhein were synthesized with an objective of potentiating its moderate anti-inflammatory effect and optimizing its hydrophilic/lipophilic balance by conjugating it with essential amino acids through a bioreversible amide linkage. In vitro release in HCl buffer (pH 1.2) showed insignificant release of diacetylrhein. However in phosphate buffer (pH 7.4), almost complete release of diacetylrhein was attained over a period of 4.5 h, following first order kinetics. The prodrug was screened extensively for therapeutic efficacy in monoiodoacetateinduced rat hyperalgesia model for levels of various markers of osteoarthritis, knee diameter and locomotor activity over a period of three months. Amongst the three prodrugs synthesized, diacetylrhein-L-tryptophan prodrug exhibited highest activity by reducing knee diameter, serum alkaline phosphatase and serum glucosaminoglycan to the baseline levels while increasing the spontaneous locomotor activity. It was found to provide maximum protection against Freund's adjuvant arthritis with minimum ulcerogenic potential and better chondroprotection than diacetylrhein.

A series of 2-thioxo-imidazolidin-4-one derivatives were synthesized and were characterized by IR, 1H NMR, 13C NMR, mass spectral data and elemental analysis. All compounds were tested for antifungal and antibacterial activity. Some of the compounds were found to exhibit promising antifungal activity. Molecular modeling investigations showed that the active compounds may interact at the active site of the fungal cytochrome P450- dependent sterol 14α- demethylase in the sterol biosynthesis pathway.

A novel series of benzimidazolo thiazolidinones, thiazinones and 5-arylidene-2-imino thiazolidinones were synthesized and evaluated for antibacterial activity. The compounds were synthesized in excellent yield and the structures were characterized on the basis of IR, 1H-NMR and MASS spectral data. Most of the synthesized compounds showed good antibacterial activity against Gram-positive and Gram-negative bacteria. QSAR study was carried out with synthesized compounds using molecular descriptors such as electronic, thermodynamic and steric. Molecular descriptors were used to derive QSAR models between antibacterial activity and structural properties. QSAR study suggested the need of a bulky group to enhance the antibacterial activity in these series of compounds.