3D-QSAR studies on PU3 analogues by comparative molecular field analysis

A comparative molecular field analysis (CoMFA) of PU3 derivatives of Hsp90 (Heat shock protein 90) inhibitors has been performed to determine the factors contributing the corresponding activities. The energy minimized conformations were obtained by molecular mechanics using SYBYL package. The developed model, with r(2) value of 0.947, was verified by performing leave-one out (LOO) cross-validation, which showed q(2) value of 0.513. The calculated model not only elucidates the relationship between compound structures and biological activities but, more importantly, facilitates design of new Hsp90 inhibitors with calculated antiproliferative activity.     

3D-QSAR studies on sildenafil analogues, selective phosphodiesterase 5 inhibitors

Sildenafil, one of selective phosphodiesterase 5 (PDE5) inhibitors, is a widely used oral agent for the treatment of erectile dysfunction. To develop new PDE5 inhibitors with improved therapeutic efficacy, a series of sildenafil analogues have been prepared and their in vitro PDE5 inhibitory activities were evaluated. Their IC(50) values ranged from 423 to 0.05 nM. Herein, the results of 3D-QSAR (CoMFA and CoMSIA) analyses on these inhibitors are reported. Both CoMFA and CoMSIA gave reliable models with q(2) values >0.75 and r(2) values >0.99. The resulting CoMFA and CoMSIA models reveal a good correlation between the contour maps and the active site residues critical for the interaction with inhibitor, and nicely predict the key structural features of new analogues with improved activity and selectivity.     

3D-QSAR CoMFA studies on bis-coumarine analogues as urease inhibitors: a strategic design in anti-urease agents

A 3D-QSAR study has been performed on thirty (30) bis-coumarine derivatives to correlate their chemical structures with their observed urease inhibitory activity. Due to the absence of information on their active mechanism, comparative molecular field analysis (CoMFA) was used in the study. Two different properties: steric, electrostatic, assumed to cover the major contributions to ligand binding, were used to generate the 3D-QSAR model. Significant cross-validated correlation coefficients q(2) (0.558) and r(2) (0.992) for CoMFA were obtained, indicating the statistical significance of this class of compounds. The red electrostatic contour map highlighting those portion of compounds which may be interacting with nickel metal center in the active site of urease; while the blue contour map indicates positively charged groups in the ligands have improved biological activity and thus lower the IC(50)s. The steric contour map shows that bulkier substitutions at the 'R' position are detrimental to ligand receptor interaction. Actual urease inhibitory activities of this class and the predicted values were in good agreement with the experimental results. Moreover, from the contour maps, the key features vital to ligand binding have been identified, which are important for us to trace the important properties and gain insight into the potential mechanisms of intermolecular interactions between the ligand and receptor.     

3D-QSAR studies on malonyl coenzyme A decarboxylase inhibitors

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a series of Malonyl Co-A decarboxylase (MCD) inhibitors (Cheng et al. J. Med. Chem.2006, 49, 1517-1525 and Cheng et al. Bioorg. Med. Chem. Lett.2006, 16, 695-700). These inhibitors have shown protective action on the ischemic heart by inhibiting fatty acid oxidation. The CoMFA model produced statistically significant results, with the cross-validated and conventional correlation coefficients being 0.544 and 0.986, respectively. The best results were obtained by combining steric, electrostatic, hydrophobic, and H-bond acceptor fields in CoMSIA, in which case the respective cross-validated and conventional correlation coefficients were 0.551 and 0.918. The predictive ability of CoMFA and CoMSIA, determined using a test set of 24 compounds, gave predictive correlation coefficients of 0.718 and 0.725, respectively. The information obtained from CoMFA and CoMSIA 3D contour maps may be of utility in the design of more potent MCD inhibitors.     

Pharmacophore generation,atom-based 3D-QSAR,molecular docking and molecular dynamics simulation studies on benzamide analogues as FtsZ inhibitors

FtsZ is an appealing target for the design of antimicrobial agent that can be used to defeat the multidrug-resistant bacterial pathogens. Pharmacophore modelling, molecular docking and molecular dynamics (MD) simulation studies were performed on a series of three-substituted benzamide derivatives. In the present study a five-featured pharmacophore model with one hydrogen bond acceptors, one hydrogen bond donors, one hydrophobic and two aromatic rings was developed using 97 molecules having MIC values ranging from .07 to 957 μM. A statistically significant 3D-QSAR model was obtained using this pharmacophore hypothesis with a good correlation coefficient (R² = .8319), cross validated coefficient (Q² = .6213) and a high Fisher ratio (F = 103.9) with three component PLS factor. A good correlation between experimental and predicted activity of the training (R² = .83) and test set (R² = .67) molecules were displayed by ADHRR.1682 model. The generated model was further validated by enrichment studies using the decoy test and MAE-based criteria to measure the efficiency of the model. The docking studies of all selected inhibitors in the active site of FtsZ protein showed crucial hydrogen bond interactions with Val 207, Asn 263, Leu 209, Gly 205 and Asn-299 residues. The binding free energies of these inhibitors were calculated by the molecular mechanics/generalized born surface area VSGB 2.0 method. Finally, a 15 ns MD simulation was done to confirm the stability of the 4DXD–ligand complex. On a wider scope, the prospect of present work provides insight in designing molecules with better selective FtsZ inhibitory potential.     

3D-QSAR studies on fluroquinolones derivatives as inhibitors for tuberculosis

A quantitative structure activity relationship (QSAR) study was performed on the fluroquinolones known to have anti-tuberculosis activity. The 3D-QSAR models were generated using stepwise variable selection of the four methods - multiple regression (MR), partial least square regression (PLSR), principal component regression (PCR) and artificial neural networks (kNN-MFA). The statistical result showed a significant correlation coefficient q(2) (90%) for MR model and an external test set of (pred_r(2)) -1.7535, though the external predictivity showed to improve using kNN-MFA method with pred_r(2) of -0.4644. Contour maps showed that steric effects dominantly determine the binding affinities. The QSAR models may lead to a better understanding of the structural requirements of anti-tuberculosis compounds and also help in the design of novel molecules.     

3D-QSAR, homology modeling, and molecular docking studies on spiropiperidines analogues as agonists of nociceptin/orphanin FQ receptor

The nociceptin/orphanin FQ receptor (NOP) has been implicated in a wide range of biological functions, including pain, anxiety, depression and drug abuse. Especially, its agonists have a great potential to be developed into anxiolytics. However, the crystal structure of NOP is still not available. In the present work, both structure-based and ligand-based modeling methods have been used to achieve a comprehensive understanding on 67N-substituted spiropiperidine analogues as NOP agonists. The comparative molecular-field analysis method was performed to formulate a reasonable 3D-QSAR model (cross-validated coefficient q(2)=0.819 and conventional r(2)=0.950), whose robustness and predictability were further verified by leave-eight-out, Y-randomization, and external test-set validations. The excellent performance of CoMFA to the affinity differences among these compounds was attributed to the contributions of electrostatic/hydrogen-bonding and steric/hydrophobic interactions, which was supported by the Surflex-Dock and CDOCKER molecular-docking simulations based on the 3D model of NOP built by the homology modeling method. The CoMFA contour maps and the molecular docking simulations were integrated to propose a binding mode for the spiropiperidine analogues at the binding site of NOP.     

Enhanced JNK activation by NESK without kinase activity upon caspase-mediated cleavage during apoptosis

Nck-interacting kinase-like embryo-specific kinase (NESK) is a protein kinase that is predominantly expressed in skeletal muscle during the late stages of mouse embryogenesis. NESK belongs to the germinal center kinase (GCK) family and selectively activates the c-Jun N-terminal kinase (JNK) pathway when overexpressed in cultured cells. Some members of the GCK family have been shown to be proteolytically cleaved and activated during apoptosis. Here, we report that NESK is also proteolytically cleaved during apoptosis. Treatment of NESK-transfected HeLa cells with TNF-alpha in the presence of cycloheximide or with staurosporine induced proteolytic cleavage of NESK. The cleavage of NESK occurred at two sites, generating three fragments: an N-terminal fragment containing a kinase domain, an intermediate fragment and a C-terminal fragment containing a regulatory CNH domain. These two cleavages occurred in a stepwise manner and were dependent on a caspase activity. The cleavage sites were identified as aspartic acid residues at 868 and 1091. The N-terminal fragment had less kinase activity than the full-length NESK and did not activate the JNK pathway. In contrast, the C-terminal fragment activated the JNK pathway more strongly than the full-length NESK and promoted TNF-alpha-induced apoptotic cell death. These results implicate NESK in the JNK pathway-mediated promotion of apoptosis through its C-terminal regulatory domain generated by proteolytic cleavage during apoptosis, in a unique manner different from other GCK family kinases.     

Molecular modeling studies of atorvastatin analogues as HMGR inhibitors using 3D-QSAR,molecular docking and molecular dynamics simulations

3-Hydroxy-3-methylglutaryl coenzyme-A reductase (HMGR) is generally regarded as targets for the treatment of hypercholesterolemia. HMGR inhibitors (more commonly known as statins) are discovered as plasma cholesterol lowering molecules. In this work, 120 atorvastatin analogues were studied using a combination of molecular modeling techniques including three-dimensional quantitative structure–activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulation. The results show that the best CoMFA (comparative molecular field analysis) model has q² = 0.558 and r² = 0.977, and the best CoMSIA (comparative molecular similarity indices analysis) model has q² = 0.582 and r² = 0.919. Molecular docking and MD simulation explored the binding relationship of the ligand and the receptor protein. The calculation results indicated that the hydrophobic and electrostatic fields play key roles in QSAR model. After MD simulation, we found four vital residues (Lys735, Arg590, Asp690 and Asn686) and three hydrophobic regions in HMGR binding site. The calculation results show that atorvastatin analogues obtained by introduction of F atoms or gem-difluoro groups could obviously improve the inhibitory activity. The new HMGR inhibitor analogues design in this Letter had been submitted which is being currently synthesized by our laboratories.     

3D-QSAR studies of heterocyclic quinones with inhibitory activity on vascular smooth muscle cell proliferation using pharmacophore-based alignment

The abnormal proliferation and migration of vascular smooth muscle cells (SMCs) play an important role in the pathology of coronary artery atherosclerosis and restenosis following angioplasty. It was reported that some heterocyclic quinone derivatives such as 6-arylamino-quinoxaline-5,8-diones and 6-arylamino-1H-benzo[d]imidazole-4,7-diones have inhibitory activity on rat aortic smooth muscle cell (RAoSMC) proliferation. To understand the structural basis for antiproliferative activity to design more potent agents, we generated pharmacophore models of representative molecules with high activity using Genetic Algorithm with Linear Assignment of Hypermolecular Alignment of Database (GALAHAD) and aligned a series of compounds to the selected pharmacophore model, then performed three-dimensional quantitative structure-activity relationship (3D-QSAR) studies using Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA). Good cross-validated correlations were obtained with CoMFA (resulting in q(2) of 0.734 and r(2) of 0.947) and CoMSIA (resulting in q(2) of 0.736 and r(2) of 0.913). The IC(50) values of the heterocyclic quinone derivatives on RAoSMC exhibited a strong correlation with steric and hydrophobic fields of the 3D structure of the molecules, resulting in the reliable prediction of inhibitory activity of the series of compounds.     

Requirement of caspase-mediated cleavage of c-Abl during stress-induced apoptosis

c-Abl protein tyrosine kinase plays an important role in cell cycle control and apoptosis. Furthermore, induction of apoptosis correlates with the activation of c-Abl. Here, we demonstrate the cleavage of c-Abl by caspases during apoptosis. Caspases separate c-Abl into functional domains including a Src-kinase, a fragment containing nuclear import sequences, a fragment with an actin-binding domain and nuclear export sequence. Caspase cleavage increases the kinase activity of c-Abl as demonstrated by in vitro kinase assays as well as by auto- and substrate phosphorylation. Cells in which c-Abl expression was knocked down by RNA interference resisted cisplatin- but not TNFalpha-induced apoptosis. A similar selective resistance against cisplatin-induced apoptosis was observed when cleavage resistant c-Abl was overexpressed in treated cells. Our data suggest the selective requirement of c-Abl cleavage by caspases for stress-induced, but not for TNFalpha-induced apoptosis.     

Synthesis and anticancer activity studies of indolylisoxazoline analogues

A new library of thirteen indolylisoxazolines 6a–m has been synthesized by the treatment of indolylchalcones with hydroxylamine hydrochloride. Evaluation of anticancer activity of indolylisoxazolines 6a–m led to the identification of potent compounds 6c–d, 6i and 6l, with IC₅₀ ranging 2.5–5.0?µM against the tested cancer cell lines. Using a number of complementary techniques such as acridine orange/ethidium bromide staining, PARP1 cleavage and DNA strand breaks assay, we show that the compounds 6c and 6i induce apoptosis in highly aggressive C4-2 cells. Our data further revealed that 6c and 6i inhibited C4-2 cells proliferation without inducing reactive oxygen species (ROS). Finally, we show that compounds 6c and 6i also potently inhibit cell migration, indicating these compounds have the potential to serve as effective anti-cancer agents.     

Molecular docking and 3D-QSAR studies of HIV-1 protease inhibitors

HIV-1 protease is an obligatory enzyme in the replication process of the HIV virus. The abundance of structural information on HIV-1PR has made the enzyme an attractive target for computer-aided drug design strategies. The daunting ability of the virus to rapidly generate resistant mutants suggests that there is an ongoing need for new HIV-1PR inhibitors with better efficacy profiles and reduced toxicity. In the present investigation, molecular modeling studies were performed on a series of 54 cyclic urea analogs with symmetric P2/P2′ substituents. The binding modes of these inhibitors were determined by docking. The docking results also provided a reliable conformational superimposition scheme for the 3D-QSAR studies. To gain insight into the steric, electrostatic, hydrophobic and hydrogen-bonding properties of these molecules and their influence on the inhibitory activity, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed. Two different alignment schemes viz. receptor-based and atom-fit alignment, were used in this study to build the QSAR models. The derived 3D-QSAR models were found to be robust with statistically significant r ² and r ² _pred values and have led to the identification of regions important for steric, hydrophobic and electronic interactions. The predictive ability of the models was assessed on a set of molecules that were not included in the training set. Superimposition of the 3D-contour maps generated from these models onto the active site of enzyme provided additional insight into the structural requirements of these inhibitors. The CoMFA and CoMSIA models were used to design some new inhibitors with improved binding affinity. Pharmacokinetic and toxicity predictions were also carried out for these molecules to gauge their ADME and safety profile. The computational results may open up new avenues for synthesis of potent HIV-1 protease inhibitors.     

Computational studies of COX-2 inhibitors: 3D-QSAR and docking

The 3D-QSAR (three-dimensional quantitative structure-activity relationships) studies for 88 selective COX-2 (cyclooxygenase-2) inhibitors belonging to three chemical classes (triaryl rings, diaryl cycloalkanopyrazoles, and diphenyl hydrazides) were conducted using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Partial least squares analysis produced statistically significant models with q(2) values of 0.84 and 0.79 for CoMFA and CoMSIA, respectively. The binding energies calculated from flexible docking were correlated with inhibitory activities by the least-squares fit method. The three chemical classes of inhibitors showed reasonable internal predictability (r(2)=0.51, 0.49, and 0.54), but the sulfonyl-containing inhibitors demonstrated distinctively low binding energy compared to the others. The electrostatic interaction energy between the Arg513 of the COX-2 active site and sulfonyl group of the triaryl rings seemed to have the responsibility for difference in binding energy. Comparative binding energy (COMBINE) analyses gave q(2) values of 0.64, 0.63, and 0.50 for triaryl rings, diaryl cycloalkanopyrazoles, and diphenyl hydrazides, respectively. In this COMBINE model, some protein residues were highlighted as particularly important for inhibitory activity. The combination of ligand-based and structure-based models provided an improved understanding in the interaction between the three chemical classes and the COX-2.     

Cell-penetrating autoantibody induces caspase-mediated apoptosis through catalytic hydrolysis of DNA

In the present study, we investigated the substrate specificity of catalytic activity of a cytotoxic anti-DNA monoclonal autoantibody, G1-5, which was obtained from an MRL-lpr/lpr mouse by hybridoma technology. The antibody catalyzed hydrolysis of single- and double-stranded DNA with a higher substrate specificity for thymine than adenine by either beta-glycosidic or phosphodiester bond cleavage. The hydrolysis rate (kcat) showed maximum at acidic pH conditions, suggesting that the catalytic site of the antibody contains essential carboxylic group(s). Treatment of cells with the antibody promoted cell death and induced the activation of caspases. The cell death induced by the antibody was inhibited by the pan-caspase inhibitor. Furthermore, the antibody binds to cell membrane and penetrates into the cells. Our results suggest that the cell death is initiated by antibodies penetrating to cells and nucleus, hydrolyzing considerable amount of DNA, and mediating the caspase-dependent apoptotic pathway.     

3D-QSAR studies on antitubercular thymidine monophosphate kinase inhibitors based on different alignment methods

Three dimensional quantitative structure-activity relationship (3D-QSAR) studies were carried out on deoxythymidine monophosphate (dTMP) derivatives inhibiting thymidine monophosphate kinase (TMPK) in Mycobacterium tuberculosis. Molecular field analysis (MFA) models with three different alignment techniques, namely, least squares, pharmacophore based and receptor based methods were developed. Receptor based MFA model showed better results when compared with least squares and pharmacophore based models. The results help us to understand the nature of substituents required for activity and thereby provide guidelines to design novel and potent inhibitors as antitubercular agents.     

Structure-function studies on neurohormone D: activity of naturally-occurring hormone analogues

Summary The relative potencies of 11 naturally-occurring peptides of the adipokinetic hormone/red pigmentconcentrating hormone family (AKH/RPCH-family) have been assessed with respect to increase in heart rate in adult, female American cockroaches,Periplaneta americana, in in vitro and in vivo bioassays. In addition, analogues that lacked the N-terminal pyroglutamate residue or had a free threonine acid at the C-terminus were also investigated. In both bioassays the N- or C-terminal-modified analogues give no or little response suggesting that blocked termini are essential for receptor-binding. In both bioassays the naturally-occurring peptide from the cockroach corpus cardiacum Pea-CAH-I (neurohormone D) is more potent than the second endogenous peptide, Pea-CAH-II. On the basis of this result and previous data it is proposed that neurohormone D is the only physiologically important true cardioactive peptide. The dose-response curves of the other peptides indicate that in octapeptides, amino acid residues at positions 2, 6, and 7 are important for receptor-recognition, and that decapeptides are not as effective as octapeptides (exception: the peptide Rom-CC-I isolated from the grasshopperRomalea microptera).     

Further studies on the antiviral activity of alloferon and its analogues

The subject of our studies was the synthesis, biological evaluation, and conformational studies of insect tridecapeptide alloferon (H‐His‐Gly‐Val‐Ser‐Gly‐His‐Gly‐Gln‐His‐Gly‐Val‐His‐Gly‐OH) and its analogues such as: [des‐His¹]‐, [Lys¹]‐, [Arg¹]‐, and [Ala¹]‐alloferon. These peptides were synthesized to check the influence of the His residue at position 1 of the alloferon chain on its antiviral activity. Two aspects of the biological effects of these peptides were determined: (i) the cytotoxicity in vitro in the Vero, LLC‐MK2, and HEp‐2 cell lines, and (ii) the antiviral activity in vitro in respect to DNA and RNA viruses. We found that alloferon inhibited the herpes virus multiplication and failed to affect the coxsackie virus replication, whereas [Lys¹]‐alloferon exhibited a high inhibitory action towards both viruses. Moreover, the peptides did not show any cytotoxic activity against the Vero, LLC‐MK2, and HEp‐2 cells. The preliminary circular dichroism conformational studies showed that the peptides investigated seem to prefer an unordered conformation. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.