Comparative molecular field analysis (CoMFA) for phosphodiesterase (PDE) IV inhibitors

A comparative molecular field analysis (CoMFA) for phosphodiesterase (PDE) IV inhibitors has been performed to correlate their chemical structures with their observed biological activity. In this study, CoMFA model based on docking mode for active site of PDE IV can describe the relative change in magnitude of the steric and electrostatic fields as a function of the compounds. Pyridine N-oxide and pyridine group of each compound are aligned toward the metal ion in S2-sub pocket of PDE IV. The study provided a statistically valid model with good correlation and predictive power, and consequently we identified some key features that may be used to design new derivatives.     

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of thiazolone derivatives as hepatitis C virus NS5B polymerase allosteric inhibitors

Three-dimensional quantitative structure-activity relationship (3D-QSAR) models for a series of thiazolone derivatives as novel inhibitors bound to the allosteric site of hepatitis C virus (HCV) NS5B polymerase were developed based on CoMFA and CoMSIA analyses. Two different conformations of the template molecule and the combinations of different CoMSIA field/fields were considered to build predictive CoMFA and CoMSIA models. The CoMFA and CoMSIA models with best predictive ability were obtained by the use of the template conformation from X-ray crystal structures. The best CoMFA and CoMSIA models gave q (2) values of 0.621 and 0.685, and r (2) values of 0.950 and 0.940, respectively for the 51 compounds in the training set. The predictive ability of the two models was also validated by using a test set of 16 compounds which gave r (pred) (2) values of 0.685 and 0.822, respectively. The information obtained from the CoMFA and CoMSIA 3D contour maps enables the interpretation of their structure-activity relationship and was also used to the design of several new inhibitors with improved activity.     

Comparative molecular field analysis (CoMFA) of new herbicidal sulfonylurea compounds

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Comparative molecular field analysis and energy interaction studies of thrombin-inhibitor complexes

A Comparative Molecular Field Analysis (CoMFA) and an interaction energy-based method were applied on a database holding the 3D structures of 29 thrombin-inhibitor complexes. Several parameters were optimized in both methods in order to obtain the best correlation between theoretical and experimentally determined binding (Ki) data. CoMFA, which only uses the information of the inhibitors, performed best (r = 0.99, q2 = 0.46, N = 29) when HF 6-31G charges were used in combination with a pharmacophore-based alignment. Inclusion of hydrophobic fields did not lead to improvements. The interaction energy-based approach uses the information of the whole thrombin-inhibitor complex. A statistically significant correlation (r = 0.74, N = 14) could only be obtained for a subset of the database containing the high resolution structures. Geometry optimization of the ligand only in combination with downscaled electrostatics performed best.     

MM3(96) parameterization for camptothecin analogs: An ab initio and molecular mechanics study

Torsional parameters for MM3(96) were derived for the missing atom types present in thenatural product camptothecin (CPT). Potential energy curves were calculated via ab initiocalculations on representative compounds for dihedral angles containing these missingparameters. Gaussian 92 at the restricted Hartree–Fock level of theory using thestandard 6-31G** and 4-31G** basis sets, was used for all the quantum-mechanicscalculations. Missing MM3 torsional terms were obtained by optimizing the V1, V2 and V3parameters such that MM3 could reproduce the ab initio torsional profile. MM3 calculatedmolecular structures that compare well with the ab initio results. Using the newly developedparameters, conformational analyses and QSAR studies of camptothecin analogs wereundertaken. MM3 predicts two distinct boatlike conformations for the -hydroxy lactonemoiety. The low-energy lactone conformation predicted by MM3 is in general agreement withreported X-ray crystal structures of CPT iodoacetate and 7-ethyl-10-(4-piperidino)piperidinylcarbonyloxy CPT HCl as well as the ab initio structure of a CPT-like-hydroxy lactone.     

Comparative molecular field analysis and comparative molecular similarity index analysis studies on 1H NMR chemical shift of NH group of diaryl triazene derivatives

Comparative molecular field analysis (CoMFA), comparative molecular field analysis region focusing (CoMFA‐RF) for optimizing the region for the final partial least square analysis, and comparative molecular similarity indices analysis (CoMSIA) methods were employed to develop three‐dimensional quantitative structure–activity relationship (3D‐QSAR) models of ¹H NMR chemical shift of NH proton of diaryl triazene derivatives. The best orientation was searched by all‐orientation search (AOS) strategy to minimize the effect of the initial orientation of the structures. The predictive abilities of CoMFA‐RF and CoMSIA models were determined using a test set of ten compounds affording predictive correlation coefficients of 0.721 and 0.754, respectively, indicating good predictive power. For further model validation, cross validation (leave one out), progressive scrambling, and bootstrapping were also applied. The accuracy and speed of obtained 3D‐QSAR models for the prediction of ¹H NMR chemical shifts of NH group of diaryl triazene derivatives were greater compared to some computational well‐known procedures. Copyright © 2013 John Wiley & Sons, Ltd.     

20(S)-20-O-Camptothecin β-Aminopropionate: Novel Synthesis and Antitumor Activity in vitro

To improve the biological anticancer activity of 20(S)-camptothecin, a novel class of 20(S)-20-O-camptothecin β-aminopropionates were designed and synthesized with camptothecins as the starting materials, through acylation with acryloyl chloride followed by Michael′s addition. Twelve esters, 1a-1d, 4a-4d and 5a-5d, were synthesized and evaluated by using MTT assay method. The results demonstrate that all these compounds show a potential cytotoxicity on KB, HT-29, HCT-8, and Bel7402 tumor cell lines. Some compounds, 1d, 4c, 5b, 5c and 5d, show a higher cytoto-xicity on KB and HCT-8 compared with camptothecin.     

Evaluation of proposed modes of binding of (2S)-2-[4-[[(3S)-1-acetimidoyl-3-pyrrolidinyl]oxy]phenyl]-3-(7-amidino-2-naphthyl)propanoic acid hydrochloride and some analogs to Factor Xa using a comparative molecular field analysis

The binding mode of (2S)-2-[4-[[(3S)-1-acetimidoyl-3-pyrrolidinyl]oxy]phenyl]-3-(7-amidino-2-naphthyl)propanoic acid hydrochloride (DX-9065a, 4) to Factor Xa is examined using inhibition data for a series of analogs that have a hydrophobic group as well as basic or dibasic functionality. Comparative molecular field analysis is utilized on a series of DX-9065a analogs in a series of proposed alternative binding modes. A quantitative measure is provided that distinguishes between the proposed binding modes that describes how well the binding mode explains the structure-activity relationship or the best 3D QSAR agrees with the crystallographically determined binding mode. The best model is in agreement with recently available data [Brandstetter et al., J. Biol. Chem., 271 (1996) 29988]. The highest statistical correlation occurs with the second basic group accommodated in the vicinity of Glu97 and a hydrophobic group accommodated in the pocket defined by Phe174, Tyr99 and Trp215. Also, the best model arises when the conformation of the Glu97 side chain is modified such that an H-bond interaction is maintained with the inhibitor if possible. The model also shows a tightening of the S1 pocket as is shown in the recent data described above.     

Combination of pharmacophore modeling and 3D-QSAR analysis of potential glyoxalase-I inhibitors as anticancer agents

Glyoxalase system is an ubiquitous system in human cells which has been examined thoroughly for its role in different diseases. It comprises two enzymes; Glyoxalase I (Glo-I) and Glyoxalase II (Glo-II) which perform detoxifying endogenous harmful metabolites, mainly methylglyoxal (MG) into non-toxic bystanders. In silico computer Aided Drug Design approaches were used and ninety two diverse pharmacophore models were generated from eighteen Glyoxalase I crystallographic complexes. Subsequent QSAR modeling followed by ROC evaluation identified a single pharmacophore model which was able to predict the expected Glyoxalase I inhibition. Screening of the National Cancer Institute (NCI) database using the optimal pharmacophore Hypo(3VW9) identified several promising hits. Thirty eight hits were successfully predicted then ordered and evaluated in vitro. Seven hits out of the thirty eight tested compounds showed more than 50% inhibition with low micromolar IC₅₀.     

CoMFA and CoMSIA studies on C-aryl glucoside SGLT2 inhibitors as potential anti-diabetic agents

SGLT2 has become a target of therapeutic interest in diabetes research. CoMFA and CoMSIA studies were performed on C-aryl glucoside SGLT2 inhibitors (180 analogues) as potential anti-diabetic agents. Three different alignment strategies were used for the compounds. The best CoMFA and CoMSIA models were obtained by means of Distill rigid body alignment of training and test sets, and found statistically significant with cross-validated coefficients (q ²) of 0.602 and 0.618, respectively, and conventional coefficients (r ²) of 0.905 and 0.902, respectively. Both models were validated by a test set of 36 compounds giving satisfactory predicted correlation coefficients (r ² _pred) of 0.622 and 0.584 for CoMFA and CoMSIA models, respectively. A comparison was made with earlier 3D QSAR study on SGLT2 inhibitors, which shows that our 3D QSAR models are better than earlier models to predict good inhibitory activity. CoMFA and CoMSIA models generated in this work can provide useful information to design new compounds and helped in prediction of activity prior to synthesis.     

20 （S） -20-O- Camptothecin β-Aminopropionate： Novel Synthesis and Antitumor Activity in vitro

IntroductionCamptothecin(CPT,1, Scheme 1), a pentacyclicalkaloid isolated from theCamptotheca acuminatebyWallet al. in 1966, shows a broad-spectrum antitumoractivity[1]. However, because of its lowwater solubilityand high toxicity, its clinical applicatio…     

Synthesis,modeling, and biological studies of new thiazole-pyrazole analogues as anticancer agents

A series of various substituted thiazole-pyrazole hybrids 5, 7, 8, and 9 were synthesized, and their chemical structures were confirmed by spectral data (infrared, ¹H & ¹³C NMR and Mass). The frontier molecular orbital structural and energetic properties of the targeting thiazole-pyrazole hybrids were explored using the DFT/B3LYP methodology. The data indicated that they had a low energy gap (ΔE_H-L), 1.51–2.42 eV, and may be sorted as 6 < 9 < 7 < 8 < 4 < 3 < 5. The synthesized thiazole-pyrazole hybrids were explored for their activities towards HepG2, MCF-7, and HCT-116 in contrast to doxorubicin. The newly synthesized thiazole-pyrazole analogues demonstrated an acceptable efficiency towards the HepG2 cancer cell line in accordance with this order: 8 > 9 > 7 > 6. Meanwhile, most of the synthesized analogues displayed a significant reduction for the activity of the CAIX inhibitor, with IC₅₀ = 0.071 ± 0.015 to 0.902 ± 0.043 µM. Likewise, they revealed an IC₅₀ = 0.119 ± 0.043 to 0.906 ± 0.04 µM for CAXII inhibitor. Moreover, the newly synthesized thiazole-pyrazole analogues were exposed to the theoretical molecular docking study with PDB:1RHJ as the crystal structure of caspase-3 to examine their antiapoptotic effect as well as their certain properties on the caspase-3 enzyme.     

Comparative molecular field analysis of non-steroidal aromatase inhibitors related to fadrozole

Summary A series of non-steroidal inhibitors of aromatase, structurally related to fadrozole (2), was investigated with the aim of developing a 3D QSAR model using the Comparative Molecular Field Analysis (CoMFA) technique. The alignment of the molecules was performed following two approaches (atom-by-atom and field fit), both starting from an initial hypothesis of superimposition of fadrozole to a steroidal inhibitor (3). From a number of CoMFA models built with different characteristics, one was recognized as the most statistically relevant; this one is discussed in detail. The features of the 3D QSAR model are consistent with those of other 3D and QSAR models of aromatase and its inhibitors.     

Antitumor agents. I. DNA topoisomerase II inhibitory activity and the structural relationship of podophyllotoxin derivatives as antitumor agents.

Various podophyllotoxin derivatives from desoxypodophyllotoxin (DPT) were synthesized to examine the structural relationships between the biological significance (cytotoxic effect, effects on DNA topoisomerase II and tubulin polymerization) in vitro and antitumor activity in vivo (L 1210). An intact 6,7-methylenedioxy group of DPT is necessary to inhibit tubulin polymerization and topoisomerase II. 4'-Phenolic hydroxyl group of DPT is essential to inhibit DNA topoisomerase II and the inhibitory effect on DNA topoisomerase II contributes to a high cytotoxicity. The introduction of an aminoalkoxy group at 1-position of DPT enhances the inhibitory activity against DNA topoisomerase II and cytotoxic effect, causing the inhibitory activity against tubulin polymerization to disappear. The results of antitumor test in mice bearing L 1210 on podophyllotoxin derivatives suggest the following: 1) the strong cytotoxic effect itself is not a good indication of antitumor activity in vivo as long as it is associated with inhibition of tubulin polymerization. DNA topoisomerase II inhibitory effect contributes to an antitumor activity in vivo; 2) detailed measurements of cytotoxicity and inhibition on DNA topoisomerase II and tubulin polymerization in vitro are necessary to evaluate podophyllotoxin derivatives.     

Synthesis,pharmacological evaluation,and molecular modeling studies of novel isatin hybrids as potential anticancer agents

A novel series of isatin hybrids 5a-g was designed, synthesized, and characterized spectroscopically. The synthesized compounds were evaluated for their cytotoxic activity against the human breast cancer cell line (MCF-7) by in vitro MTT assay. Amongst the tested compounds, 5e compound bearing benzyl moiety at N₄ piperazine was found to be the most active with the promising IC₅₀ (12.47 µM). Moreover, the active compounds 5e and 5g were subjected to antitumor evaluation (in vivo) against Dalton’s ascitic lymphoma (DAL) cell line and the results suggested that the best active compound 5e can normalize the blood picture in comparison to the standard drug. An in silico molecular docking study using the crystal structure of Hsp90 protein described the role of significant protein–ligand interactions and revealed more insights into the binding mode. The drug-likeliness of the compounds was predicted based on Lipinski's rule of five and pharmacokinetic ADME parameters. Hence, the synthesized isatin hybrids could be novel starting point anticancer lead compounds demonstrating drug-like properties which can be explored further for anticancer drug discovery.     

Molecular modeling of the intestinal bile acid carrier: A comparative molecular field analysis study

A structure–binding activity relationship for the intestinal bile acidtransporter has been developed using data from a series of bile acid analogsin a comparative molecular field analysis (CoMFA). The studied compoundsconsisted of a series of bile acid–peptide conjugates, withmodifications at the 24 position of the cholic acid sterol nucleus, andcompounds with slight modifications at the 3, 7, and 12 positions. For theCoMFA study, these compounds were divided into a training set and a test set,comprising 25 and 5 molecules, respectively. The best three-dimensionalquantitative structure–activity relationship model found rationalizesthe steric and electrostatic factors which modulate affinity to the bile acidcarrier with a cross-validated, conventional and predictive r²of 0.63, 0.96, and 0.69, respectively, indicating a good predictive model forcarrier affinity. Binding is facilitated by positioning an electronegativemoiety at the 24–27 position, and also by steric bulk at the end of theside chain. The model suggests substitutions at positions 3, 7, 12, and 24that could lead to new substrates with reasonable affinity for the carrier.     

Facile synthesis and cytotoxicity of 5-C-alkylates of 20（S）- camptothecins

A series of 5-C-alkylating camptothecins have been synthesized by one-step method, and their in vitro antitumor activity was evaluated against six human cancer cell lines. The results showed that all 5-C-alkylates of camptothecins possessed poor cytotoxicity on six human cancer cell lines.