Medicinal Chemistry - Volume 8, Issue 3, 2012

Artificial neural networks (ANNs) have been applied for the quantitative structure-activity relationships (QSAR) studies of antitumor activity of acridinone derivatives. Molecular modeling studies were performed with the use of HyperChem and Dragon computer programs and molecular geometry optimization using MM+ molecular mechanics and semi-empirical AM1 method, and several molecular descriptors of agents were obtained. A high correlation resulted between the ANN predicted antitumor activity and that one from biological experiments for the data used in the testing set of acridinones was obtained with correlation coefficient on the level of 0.9484. Moreover, the sensitivity analysis indicated that molecular parameters describing geometrical properties as well as lipophilicity of acridinone derivative molecule are important for acridinones antitumor activity.

A novel series of 3'-C-ethynyl and 3'-C-(1,4-disubstituted-1,2,3-triazolo) double-headed pyranonucleosides has been designed and synthesized. Reaction of 3-keto glucoside 1 with ethynyl magnesium bromide gave the desired precursor 3-C-ethynyl-1,2:5,6-di-O-isopropylidene-α-D-allofuranose (2). Hydrolysis followed by acetylation led to the 1,2,4,6-tetra-O-acetyl-3-C-ethynyl-β-D-allopyranose (3). Compound 3 was condensed with silylated 5-fluorouracil, uracil, thymine, N4-benzoylcytosine and N6-benzoyladenine, respectively and deacetylated to afford the target 1-(3'-C-ethynyl-β-D-allopyranosyl)nucleosides 5a-c,f,g. Copper-Catalyzed Azide-Alkyne Cycloaddition (CuAAC) reaction was utilized to couple the 3'-C-ethynyl pyranonucleoside derivatives with azidoethyl adenine, 5-fluorouracil and thymine, respectively to afford novel triazole double-headed nucleoside analogs 8a-h. 3'-C-Ethynyl pyranonucleosides and the new double-headed analogues were evaluated for their antiviral and cytostatic activities. Although none of the compounds showed pronounced cytostatic activity and were devoid of a significant antiviral potential, the double-headed nucleoside derivatives 8a, 8c and 8e showed a moderate cytostatic activity against human cervix carcinoma HeLa cells which may be the basis for the synthesis of analogous derivatives with improved cytostatic potential.

A series of fourteen (14) N-nitrophenyl-N'-(alkyl/aryl)urea and symmetrical 1,3-disubstituted urea derivatives were synthesized and evaluated for their antidepressant activity in mice. Among them, N-(4-nitrophenyl)-N'-(1'-phenylethyl)urea (1), demonstrated profound antidepressant property as reflected by significant reduction in the immobility time (89.83%), whereas compounds 2-6 showed activity values between 36 to 59% which were also larger than the standard phenelzine. Compounds 7-9 were less effective in reducing the immobility period of mice 26.20 to 31.01%). This variable magnitude of antidepressant activity appears to be related to the position of the nitro group to the parent molecules 1, 2, and 8. Compound 1 with the nitro group at para position showed to be the most effective antidepressant. However, the activity declined, if the nitro is attached to ortho and meta positions.

A series of 2-(1H-Benzotriazol-1-yl)-N'-[substituted]acetohydrazides were designed & synthesized keeping in view the structural requirement of pharmacophore and evaluated for anticonvulsant activity and neurotoxicity. The new compounds were characterized using FT-IR, 1H NMR, mass spectral data and elemental analysis. The anticonvulsant activity of the titled compounds was assessed using the 6 Hz psychomotor seizure test. The neurotoxicity was assessed using the rotorod method. The most active compound of the series was N'-[4-(1,3-Benzodioxol-5-yloxy)benzylidene]-2-(1H-benzotriazol-1-yl)acetohydrazide (BTA 9), which showed good activity with 75 % protection (3/4, 0.5 h) at a dose of 100 mg/kg in mice. All the compounds exhibited no neurotoxicity. A computational study was carried out for calculation of pharmacophore pattern and prediction of pharmacokinetic properties. Titled compounds have also exhibited good binding properties with epilepsy molecular targets such as glutamate, GABA (A) delta, GABA (A) alpha-1 receptors and Na/H exchanger, in Lamarckian genetic algorithm based flexible docking studies.

When a benzenesulfonyl moiety (BS) was bound to the N-piperazinyl ring of antibacterial fluoroquinolones (AMFQs) norfloxacin (NOR) or ciprofloxacin (CIP), the resulting benzenesulfonyl-fluoroquinolone (BSFQs) analogs showed an improved in vitro activity against Gram-positive strains. A bioisosterical replacement of the sulfonyl group for a carbonyl group led to the benzenecarboxamide-fluoroquinolones (BCFQs) that showed a similar trend in the antibacterial activity and spectrum. The BSFQs and BCFQs are considered members of the "dual targeting" fluoroquinolones, targeting both DNA gyrase and topoisomerase IV. To disclose the real contribution of the BS/BC moiety in anti-staphylococcal activity, a 3D-QSAR analysis that included calculation of theoretical molecular descriptors and pharmacophore generation was performed. Previous and present QSAR results have confirmed the positive influence on activity of small electron donating p-substituent on the BS or BC moiety. The generated phamacophore model showed that both phenyl and SO2/CO groups are involved in the interaction with receptor. We postulate that the enhanced potency of BSFQs against Staphylococcus aureus compared to CIP and NOR could be caused by the presence of the BS moiety that resulted in enhanced binding to DNA gyrase of Sa. Additionally, their greater ability to enter bacterial cells by diffusion and a reduced susceptibility to FQ-specific efflux pumps could also make a contribution.

A novel series of polycyclic amines, containing nitrogen monoxide donating moieties, were synthesised and tested for calcium channel and N-methyl-D-aspartate receptor modulating activity. The synthesised compounds were classified into two groups, based on their nitrogen monoxide donating moieties: unsaturated nitro compounds (1, 2 and 3) and nitro esters, or nitrates (4, 5 and 6). The nitrates were obtained via the reaction of hydroxyl functionalities with thionylchloride nitrate. All of the compounds synthesised exhibited significant (p < 0.01) S-nitrosylation capacity. The calcium channel activity of the polycyclic amines was evaluated using a KCl mediated fluorescent calcium flux assay. All the compounds exhibited better calcium channel antagonism than the lead structure, NGP1-01, with compound 1 exhibiting calcium channel blockade comparable to the commercially available nimodipine at concentrations of 10 μM and 1 μM. Compounds 3 and 4 inhibited calcium flux to these levels at 10 μM concentrations. NMDA/glycine mediated N-methyl-D-aspartate receptor (NMDAR) calcium influx inhibition was evaluated at a 100 μM concentration using a fluorescent calcium flux assay. All the compounds exhibited NMDAR antagonism with compounds 1 (25.4 %), 2 (20.24 %), 3 (33.14 %) and 6 (24.55 %) showing the most significant NMDAR inhibitory activity (p < 0.01). No clear correlation was observed between the S-nitrosylation capabilities of the compounds and their calcium channel activity or NMDAR channel antagonism, indicating that other factors probably play a more decisive role in the mechanism of pentacycloundecylamine channel modulation. This could include the geometric and steric bulk considerations that have been described to contribute to the channel activities of the pentacycloundecylamines. All the compounds synthesised exhibited promising calcium channel and NMDAR channel inhibitory activity and show promise as potential lead compounds for drug development against neurodegeneration.

Taking advantage of our in-house experimental data on 3-cyano-2-imino-1, 2-dihydropyridine and 3-cyano-2- oxo-1,2-dihydropyridine derivatives as inhibitors of the growth of the human HT-29 colon adenocarcinoma tumor cell line, we have established a highly significant CoMFA and CoMSIA models (q2 cv =0.70/0.639). The models were investigated to assure their stability and predictivity (r2 pred= 0.65/0.61) and successfully applied to design two new potential cell growth inhibitory agents with IC50s in the submicromolar range.

A novel trinuclear platinum compound with a cis-geometry for terminal metal centres coded as QH1 has been synthesized, characterized and investigated for activity against the human ovarian A2780, A2780cisR and A2780ZD0473R cancer cell lines. The cellular accumulation of platinum, level of platinum-DNA binding and the nature of interaction of the compound with pBR322 plasmid DNA have also been determined. QH1 is found to be more active against the resistant cell lines than the parent cell line, thus indicating that the compound has been able to overcome mechanisms of resistance operating in the A2780cisR and A2780ZD0473R cell lines. The high activity of QH1 is associated with high platinum accumulation and high level of platinum-DNA binding in all the three ovarian cancer cell lines. Provided QH1 has the right toxicity profile and its in vitro activity is matched with sufficient activity in vivo, the compound has the potential for development as a novel platinum-based anticancer drug targeted to the ovarian cancer.

Two series of compounds with the general formula of 4,6-diaryl-2-oxo-1,2 dihydropyridine-3-carbonitriles and their isosteric imino derivatives were synthesized through a one pot reaction of acetophenone, aldehyde and ammonium acetate with ethyl cyanoacetate or malononitrile, respectively. The synthesized compounds were evaluated for tumor cell growth inhibitory using the human HT-29 colon and MDA-MB-231 breast tumor cell lines. Compound 4-(2- Ethoxyphenyl)-2-imino-6-(4-fluorophenyl)-1,2-dihydropyridine-3 carbonitrile (6) showed IC50 value of 0.70 μM versus HT-29. Meanwhile, compound 4-(2-Hydroxyphenyl)-2-imino-6-(4-fluorophenyl)-1,2-dihydropyridine-3-carbonitrile (4) showed IC50 value of 4.6 μM versus MDA-MB-231. Docking compound 10 to possible molecular targets, survivin and PIM1 kinase showed appreciable interactions with both, which suggest possible targets for the antitumor activity of this novel class of anticancer compounds.

The anti-inflammatory effect of two new thiazoles derivatives CX-32 (N-[4-(4-hydroxy-3-methoxyphenyl)-1,3-thiazol-2-yl]acetamide ) and CX-35 (4-(2-amino-1,3-thiazol-4-yl)-2-methoxyphenol), was investigated in LPS-stimulated RAW 264.7 cell line. Synthesis, structure analysis and purity of these compounds were evaluated by high performance liquid chromatography, H1 NMR, and C13 NMR. Assessment of CX-32 and CX-35 inhibitory effect on cyclooxygenase-2 (COX-2) activity was achieved by incubating LPS-activated RAW cells with 25 μM, 50μM or 100μM of CX-32 or CX-35 respectively. Levels of secreted PGE2 were evaluated by enzyme immunoassay (EIA) and levels of COX-2 protein were measured by western blot. Finally, cell viability experiments were undertaken to assess the toxicity of each compound. Treatment of LPS-activated RAW cells with 25 μM, 50 μM, or 100 μM of CX-35 or CX-32 respectively, prevented the production of prostaglandins, but was without effect on COX-2 protein levels. Moreover, CX-35 and CX-32 reduced PGE2 production to levels comparable to those obtained in LPS-activated RAW cells incubated with the selective COX-2 inhibitor NS 398. Furthermore, both CX-32 and CX-35 showed no toxic effects, since viability of non-treated Hela cells was similar to Hela cells incubated with either CX-35 or CX-32. Our data demonstrated that CX-32 and CX-35 significantly blocked prostaglandin production induced during inflammatory cellular stress, possibly acting through specific COX-2 inhibition; confirmation of this hypothesis requires further investigation.

A series of mono, bis and mixed Schiff bases (1-7) were synthesised and evaluated for potential anti-glycation and anti-oxidant activities using the bovine serum albumin - glucose assay and 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical assay respectively. All compounds showed significant (p < 0.05) antiglycating activities with IC50 values (4.02 x10-24 ± 0.1 – 2.88 x 10-1 ± 1.35 mM) which were lower than the standard positive control aminoguanidine (IC50 : 1.51 x 10-3 ± 2.11 mM). Moreover, compounds 1-7 were found to possess significant (p < 0.05) DPPH radical scavenging properties with SC50 values (1.31 x 10-19 ± 0.05 to 2.25 x 10-1 ± 1.24 mM) lower than the standard ascorbic acid (SC50 : 5.50 x 10-3 ± 2.11 mM). Compound 6 was found to be the most potent anti-glycating molecule (IC50 value: 4.02 x10-24 ± 0.1 mM) while compound 5 was the most potent anti-oxidant molecule (SC50: 1.31 x 10-19 ± 0.05 mM); both being significantly lower (p < 0.05) than the respective positive controls used. The present data showed that the number of phenolic OH together with structural changes influence both the anti-glycation and anti-oxidant observed herein. This study provides for the first time a series of potential template molecules for possible pharmaceutical applications that warrant further investigation as potential anti-glycation and anti-oxidant agents which could be of importance in metabolic diseases including diabetes mellitus.

Kaempferol-3-O-α-L-rhamanopyranosyl-(1'''-6'')-β-D-glucopyranoside (1) (Nicotiflorin or kaempferol-3-O-rutinoside), isolated from the aerial parts of Osyris wightiana Wall. ex Wight, exhibited a potent antiglycation activity in vitro. A short and efficient route to kaempferol-3-O-rutinoside (1) is also described in this paper. To study the structure-activity relationship, few other derivatives of kaempferol were also evaluated for their antiglycation activity. Moreover the cytotoxicity analysis was also performed for these compounds. The Structure-Activity Relationship (SAR) studies showed that sugar derivatives of kaempferol possess a promising antiglycation activity.

Benzimidazole derivatives 1-24 have been synthesized and their in vitro β-glucuronidase inhibitory activitiy was evaluated. Compounds 15 (IC50 = 6.33 ± 0.40 μM), 7 (IC50 = 22.0 ± 0.33 μM), 2 (IC50 = 23.1 ± 1.78 μM), 17 (IC50 = 23.9 ± 1.46 μM), and 3 (IC50 = 33.8 ± 1.61 μM) showed more potent β-glucuronidase inhibitory activity than the standard (D-saccharic acid 1,4 lactone, IC50 = 48.4 ± 1.25 μM). This study has identified a new series of potential β-glucuronidase inhibitors. A structure-activity relationship has also been studied.

The 2,4,5-triaryl imidazole derivatives (API) were designed, screened and characterized kinetically & thermodynamically against Pepsin and their activity was also tested on the in silico platform. The docking studies of API with Pepsin show that these are novel and unique inhibitors of Aspartic protease. Drug like properties of these compounds were validated in silico based on Lipinski's rule of Five by calculating ClogP, LogS, H-bond acceptors, H-Bond donors, rotational bonds, PSA, PB and BBB values. The Et/Ki and Et/Km values of API show that they follow the Michaelis-Menten kinetics. The binding of inhibitors with proteases was explained by using Van't Hoff plot and thermodynamic parameters viz. free energy (ΔG), Entropy (ΔS) and Enthalpy (ΔH). The Van't Hoff analysis showed that the value of Ki decreases with increase in temperature and the binding of the inhibitor are entropically driven. API act as new potent aspartic protease inhibitors with Ki, for Pepsin, ranges from 3.7 μM to 16.7 μM. Strong hydrophobic groups at C-4 & C-5 position in API favor binding of inhibitors with Pepsin. Experiments also showed that among C-2 aryl substituted imidazole, a 4-substitution on aryl ring is preferred and less polar substituent makes the molecule more active whereas polar substituents at 2-position on C-2 aryl ring makes the molecule less active. The docking studies of API with Pepsin further intensify and validate our results.

In the present report, 3D-QSAR analysis was executed on the previously synthesized and evaluated derivatives of isoquinolin-1-ones and quinazolin-4-ones; potent inhibitors of tumor necrosis factor α (TNFα). Statistically significant 3D-QSAR models were generated using 42 molecules in the training set. The predictive ability of models was determined using a randomly chosen test set of 16 molecules, which gave excellent predictive correlation coefficients for 3-D models, suggesting good predictive index. Pharmacophore prediction generated a five point pharmacophore (AAHRR): two hydrogen bond acceptor (A), one hydrophobic (H) and two ring (RR) features. This pharmacophore hypothesis furnished a statistically meaningful 3D-QSAR model with partial least-square (PLS) factors seven having R2 = 0.9965, Q2 = 0.6185, Root Mean Squared Error = 0.4284 and Pearson-R = 0.853. Docking study revealed the important amino acid residues (His 15, Tyr 59, Tyr 151, Gly 121 and Gly 122) in the active site of TNFα that are involved in binding of the active ligand. Orientation of the pharmacophore hypothesis AAHRR.25 corresponded very closely with the binding mode recorded in the active site of ligand bound complex. The results of ligand based pharmacophore hypothesis and atom based 3D-QSAR furnished crucial structural insights and also highlighted the important binding features of isoquinolin-1-ones and quinazolin-4-ones derivatives, which may provide guidance for the rational design of novel and more potent TNFα inhibitors.

Syntheses of thirty 2,4,6-trichlorophenylhydrazine Schiff bases 1-30 were carried out and evaluated for their in vitro DPPH radical and super oxide anion scavenging activities. Compounds 1-30 have shown a varying degree of DPPH radical scavenging activity and their IC50 values range between 4.05-369.30 μM. The compounds 17, 28, 18, 14, 8, 15, 12, 2, 29, and 7 exhibited IC50 values ranging between 4.05 ± 0.06-24.42 ± 0.86 μM which are superior to standard n-propylgallate (IC50 = 30.12 ± 0.27 μM). Selected compounds have shown a varying degree of superoxide anion radical scavenger activity and their IC50 values range between 91.23-406.90 μM. The compounds 28 8, 17, 15, and 14, showed IC50 values between 91.23 ± 1.2-105.31 ± 2.29 μM which are superior to standard n-propylgallate (IC50 = 106.34 ± 1.6 μM).

Preliminary investigations of our research team have shown that some pyrrole hydrazones posses strong inhibitory activity against the tuberculosis bacilli, and thus represent a new perspective for development of anti-tuberculosis agents. In this work the anti-tuberculosis activity of an in-house series of pyrrole hydrazones was investigated by quantitative structure-activity relationships (QSAR) analysis and by pharmacophore modelling. Different constitutional, topological, physicochemical, and quantum-mechanical descriptors of the chemical structure were calculated. The QSAR models included the number of chlorine, fluorine and nitrogen atoms, molecular flexibility and shape indexes, and magnitudes of charged molecular surfaces areas and hydrophobic volumes, suggesting importance of these structural characteristics for the activity. Next, a pharmacophore analysis was applied. A possible pharmacophore responsible for the compound interactions with their biological target in the 3D space consisted of five features, including hydrophobic centres, a potential H-bond acceptor and a potential metal ligator.

The emergence of new diseases and the resurgence of several infections that were controlled in the past, associated with recent increase of bacterial resistance have created the necessity for more studies towards to the development of new antimicrobials and new treatment strategies. The aim of the present study was to evaluate the in vitro synergy between different classes of important glucosinolates hydrolysis products-isothiocyanates with antibiotics (gentamycin and vancomycin), against important pathogenic bacteria: Escherichia coli, Enterococcus faecalis, Listeria monocytogenes, Pseudomonas aeruginosa and Staphylococcus aureus. A disc diffusion method was used to evaluate the antibacterial activity. The antimicrobial activity of phytochemicals and combinations between gentamycin, vancomycin and phytochemicals were quantitatively assessed by measuring the inhibitory halos. The results showed a selective antimicrobial effect of isothiocyanates, and this effect was strictly related with their chemical structure. In general the benzylisothiocyanate was the most effective compound against both Gram-positive and Gram-negative bacteria. The Listeria monocytogenes and Staphylococcus aureus were the bacteria most affected either by the phytochemicals alone or by the combination phytochemical-antibiotic. The bacteria Pseudomonas aeruginosa was the less affected pathogen. The most important synergism detected occurred between the commercial antibiotics with benzylisothiocyanate and 2-phenylethylisothiocyanate. In conclusion, some isothiocyanates are effective inhibitors of in vitro bacterial growth, and they can act synergistically with antibiotics.

Alkylphenols have xenoestrogenic activity, which mimic the action of physiological estrogens and these mimicking activities are mainly mediated by nongenomic pathway. Nongenomic pathway plays a pivotal role in breast, endometrial and ovarian cancers' growth and development. In this study, various alkylphenol derivatives were prepared and screened for their anti-uterotrophic and uterotrophic activity. Among these compounds, 2-hydroxy-5-nonanoylbenzamide (compound 1b) showed 93.99% inhibitory activity in the anti-uterotrophic test performed, and was found inactive in the uterotrophic activity test. Moreover, all test compounds were examined for the effect on uterine histopathological changes, and plasma 17β-estradiol (E2) level. Compound 1b was also tested for in vitro anti-cancer activity against ER+, human breast cancer cell line MCF-7, and it reduced cell viability to 74.01% at 50 nM concentration.

A 2-Dimensional Quantitative Structure-Activity Relationship study has been performed on 2 series of hepatitis C virus (HCV) inhibitors, i.e., Isothiazoles and Thiazolones. In each case significant correlations are found between the anti-HCV potencies and some physicochemical, electronic and steric properties of the compounds, indicating that for the first series the activity is controlled by density and two indicator parameters (one for halogen and other for methyl), while for the second series density, Hammett constant and Kier's first order valence molecular connectivity index are important for anti-HCV activity. The validity of the correlation has been judged by leave-one-out jackknife procedure and predicting the activity of some test compounds. Using the correlations obtained, some new compounds of high potency have been predicted in each series.