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Chemical Biology and Drug Design - Verlag: Wiley
CB & DD ist eine wissenschaftlichen Zeitschrift, die sich der Förderung innovativer Wissenschaft, Technik und Medizin mit dem Schwerpunkt auf den interdisziplinären Gebieten der chemischen Biologie und Entwicklung von Arzneimitteln widmet.
Cellular resistance to chemotherapeutics that alkylate the O-6 position of guanine residues in DNA correlates with their O6-alkylguanine-DNA alkyltransferase activity. In normal cells high [O6-alkylguanine-DNA alkyltransferase] is beneficial, sparing the host from toxicity, whereas in tumor cells high [O6-alkylguanine-DNA alkyltransferase] prevents chemotherapeutic response. Therefore, it is necessary to selectively inactivate O6-alkylguanine-DNA alkyltransferase in tumors. The oxygen-deficient compartment unique to solid tumors is conducive to reduction, and could be utilized to provide this selectivity. Therefore, we synthesized 2-nitro-6-benzyloxypurine, an analog of O6-benzylguanine in which the essential 2-amino group is replaced by a nitro moiety, and 2-nitro-6-benzyloxypurine is >2000-fold weaker than O6-benzylguanine as an O6-alkylguanine-DNA alkyltransferase inhibitor. We demonstrate oxygen concentration sensitive net reduction of 2-nitro-6-benzyloxypurine by cytochrome P450 reductase, xanthine oxidase, and EMT6, DU145, and HL-60 cells to yield O6-benzylguanine. We show that 2-nitro-6-benzyloxypurine treatment depletes O6-alkylguanine-DNA alkyltransferase in intact cells under oxygen-deficient conditions and selectively sensitizes cells to laromustine (an agent that chloroethylates the O-6 position of guanine) under oxygen-deficient but not normoxic conditions. 2-Nitro-6-benzyloxypurine represents a proof of concept lead compound; however, its facile reduction (E1/2– 177 mV versus Ag/AgCl) may result in excessive oxidative stress and/or the generation of O6-alkylguanine-DNA alkyltransferase inhibitors in normoxic regions in vivo.In normal tissues high AGT levels block the toxicity O-6 position of guanine alkylating agents, whereas in tumor cells high AGT levels inhibit chemotherapeutic response. We have synthesized and characterized 2-nitro-6-benzyloxypurine, a prodrug of the potent AGT inhibitor O6-benzylguanine, designed to be selectively activated under the oxygen deficient conditions found only in solid tumors. 2-NBP depletes AGT activity in intact cells, and selectively sensitizes cells to the cytotoxic effects of laromustine strongly under oxygen deficient but not normoxic conditions.
Flavonoids are important constituents of food and beverages and have several neuropharmacological activities. Many of these compounds are ligands for ?-aminobutyric acid type A receptors in the central nervous system. This study aimed to investigate the anticonvulsant effects of intracerebroventricularly administered vitexin (5, 7, 4-trihydroxyflavone-8-glucoside), a flavonoid found in plants, in rats treated with pentylenetetrazole (90 mg/kg, intraperitoneally) and to clarify the underlying mechanism. Vitexin (100 and 200 ?m, i.c.v) affected minimal clonic seizures and generalized tonic–clonic seizures induced by pentylenetetrazole by increasing the seizure onset time. Pretreatment with flumazenil suppressed the anticonvulsant effects of vitexin during the onset of both the seizures. These results indicate that vitexin has anticonvulsant effects in the brain, possibly through interaction at the benzodiazepine site of the ?-aminobutyric acid type A receptor complex.Vitexin (5, 7, 4-trihydroxyflavone-8-glucoside), a flavonoid found in plants. The anticonvulsant effects of vitexin were investigated in rats. Vitexin affected minimal clonic seizures and generalized toni–clonic seizures induced by pentylenetetrazole.
A series of novel 1-(substituted benzylidene)-4-(1-(morpholino/piperidino methyl)-2,3-dioxoindolin-5-yl) semicarbazides 6a–6t was designed and synthesized on the basis of semicarbazide-based pharmacophoric model to meet the structural requirements necessary for anticonvulsant activity. The compounds were subjected to in vivo antiepileptic evaluation using maximal electroshock test and subcutaneous pentylenetetrazole seizure test methods. The neurotoxicity was determined by rotorod test. In the preliminary screening, compounds 6c, 6d, 6g, 6h, and 6m were found active in maximal electroshock test model, while 6g, 6i, 6m, and 6o showed significant antiepileptic activity in subcutaneous pentylenetetrazole seizure test model. Further, the compounds 6c, 6d, 6g, 6h, 6i, and 6m were administered orally to rats, of which 6c and 6g showed better activity than phenytoin. Among the synthesized compounds, 6g revealed excellent protection in both models with lower neurotoxicity.The library of new benzylidene substituted semicarbazide incorporating isatin has been synthesized. The in vivo results showed that majority of compounds were effective in maximal electroshock test (MES).
The chemokines and their receptors play a key role in immune and inflammatory responses by promoting recruitment and activation of different subpopulations of leukocytes. The membrane receptor CXCR3 binds three chemokines, CXCL9, CXCL10, and CXCL11, and its involvement is recognized in many inflammatory diseases and cancers. Therefore, the inhibition of CXCR3 pathway through interactions with three ligands was indicated as putative therapeutic target for the treatment of these diseases, and some inhibitory compounds have already been described in the literature. Recently, we studied the interaction between CXCR3 and its three natural ligands and showed that three CXCR3 ligands bound the receptor mainly by their N-terminal regions using aromatic and electrostatic interactions, and, in particular, CXCL11 had the highest affinity for CXCR3. In light of these results, we focused our attention on what structural region(s) of CXCL11 interacted with CXCR3 and what were the structural features. Therefore, we have synthesized three peptides, corresponding to the N-terminal region of CXCL11, but with different aromatic amino acids, analyzed their conformations by circular dichroism, NMR, and molecular dynamics simulations, simulated their complexes with CXCR3 by docking methods, and validated these data by in vitro studies. The results showed that two peptides were able to bind CXCR3 and to mimic the molecular recognition of CXCL11 and demonstrated that N-terminal region of CXCL11 can be used as template and starting point to obtain new molecules by de novo design approaches.Since the inhibition of CXCR3 pathway was indicated as putative therapeutic target for the disease treatment, it is important to study what structural regions of CXCL11 interact with CXCR3 and what were the structural features. The obtained results indicate that the CXCL-11 N-terminal region can be considered as a good template of CXCR3/ligand recognition. Therefore the possibility of modifying the physico-chemical properties of the peptides can represent a good approach to improve the research for therapeutics of CXCR3-associated diseases.
Accounting for protein flexibility is an essential yet challenging component of structure-based virtual screening. Whereas an ideal approach would account for full protein and ligand flexibility during the virtual screening process, this is currently intractable using available computational resources. An alternative is ensemble docking, where calculations are performed on a set of individual rigid receptor conformations and the results combined. The primary challenge associated with this approach is the choice of receptor structures to use for the docking calculations. In this work, we show that selection of a small set of structures based on clustering on binding site volume overlaps provides an efficient and effective way to account for protein flexibility in virtual screening. We first apply the method to crystal structures of cyclin-dependent kinase 2 and HIV protease and show that virtual screening for ensembles of four cluster representative structures yields consistently high enrichments and diverse actives. We then apply the method to a structural ensemble of the androgen receptor generated with molecular dynamics and obtain results that are in agreement with those from the crystal structures of cyclin-dependent kinase 2 and HIV protease. This work provides a step forward in the incorporation of protein flexibility into structure-based virtual screening.We apply a binding site shape overlap clustering method to crystal structures of CDK2 and HIV protease and show that ensembles of four cluster representative structures yield high enrichments and diverse actives. We then apply the method to an ensemble of androgen receptor generated with molecular dynamics and obtain results that are in agreement with those from the crystal structure ensembles. This work provides a step forward in the incorporation of protein flexibility into structure-based virtual screening.
Pancreatic cancer is very difficult to diagnose in its early stage. Molecular marker and imaging have not proven to be accurate modalities for screening of pancreatic cancer. This study aims to develop p38? as a protein marker for pancreatic cancer and to design peptide inhibitor against the same. The serum p38? level of pancreatic cancer (n = 35; 5.06 ?g/mL) was twofold higher compared to that of the chronic pancreatitis (n = 10; 2.92 ?g/mL) and matched normal control (n = 10; 2.86 ?g/ml) (p < 0.0005). Peptide inhibitors were designed to inhibit the activity of p38? and the kinetic assay had shown the dissociation constant, (KD) to be 3.16 × 10?8 M and IC50, 25 nM by Surface Plasmon Resonance (SPR) and Enzyme -Linked Immunosorbent Assay (ELISA), respectively. The peptide inhibitor also significantly reduced viability and induced cytotoxicity in Human Pancreatic carcinoma epithelial-like cell line (PANC-1) cells.This study focused on development of P38? MAPK as a biological marker of pancreatic cancer, as this is an important component of intracellular signaling pathway that are activated in response to many extracellular stimuli leading to inflammatory response and eventually into cancer and was compared with the pancreatitic patients. In addition, we have designed and analysed the peptide inhibitor on the basis of the structure of ATP binding site of P38? and the known inhibitors.
The hydroxamic acid moiety is an effective metal-binding warhead for a variety of metalloenzyme targets of interest in drug-discovery. For the zinc-containing histone deacetylase enzymes in particular, this chemical group has been widely incorporated and studied in the clinic. An alternative chemical functionality for binding zinc is the ?-aminocarbonyl motif, which has been shown to bind to histone deacetylase enzymes. The current article explores the minimal binding site theoretical approach combined with structural knowledge to explore the ideal chemical substitution pattern of the ?-aminocarbonyl motif within HDAC8. The metal-binding strength of the group is predicted to be highly tunable to chemical substitution at the carbonyl and the ?-amino carbon. A fixed receptor model approach with a dispersion-corrected density functional, clearly discerned the effect of different substituents at both these positions using either a flexible or partially fixed ligand optimized in the presence of a fixed receptor model of the HDAC8 binding site. An electron donating substituent such as methyl at the C? in combination with NMe2 substitution at the carbonyl position, similar to observed crystal structures, result in the optimal energetic profile for binding the zinc atom in the HDAC8 enzyme.A small DFT model was used to predict improved zinc binding of an ?-aminocarbonyl warhead for HDAC8 using structural knowledge and density functionals with an adequate treatment of dispersion interactions. Adding methyl groups increased electron donation to the metal and ligand binding and also increased beneficial desolvation.
Cathepsin D is a major component of lysosomes and plays a major role in catabolism and degenerative diseases. The quantitative structure–activity relationship study was used to explore the critical chemical features of cathepsin D inhibitors. Top 10 hypotheses were built based on 36 known cathepsin D inhibitors using HypoGen/Discovery Studio v2.5. The best hypothesis Hypo1 consists of three hydrophobic, one hydrogen bond acceptor lipid, and one hydrogen bond acceptor features. The selected Hypo1 model was cross-validated using Fischer’s randomization method to identify the strong correlation between experimental and predicted activity value as well as the test set and decoy sets used to validate its predictability. Moreover, the best hypothesis was used as a 3D query in virtual screening of Scaffold database. Subsequently, the screened hit molecules were filtered by applying Lipinski’s rule of five, absorption, distribution, metabolism, and toxicity, and molecular docking studies. Finally, 49 compounds were obtained as potent cathepsin D inhibitors based on the consensus scoring values, critical interactions with protein active site residues, and predicted activity values. Thus, we suggest that the application of Hypo1 could assist in the selection of potent cathepsin D leads from various databases. Hence, this model was used as a valuable tool to design new candidate for cathepsin D inhibitors.(i) Ten quantitative hypotheses were generated and the best hypothesis, Hypo1 was validated using Fischer’s randomization method, test set, and decoy set. (ii) Hypo1 was used in virtual screening and the hit molecules were filtered out by drug-like properties. (iii) Finally, 49 leads were selected as potent candidate for Cathepsin D.
Protein acetylation has early emerged as a major posttranslational modification for histones and was recently found to be involved in a variety of biological events such as enzymatic activation and signal transduction. Traditional notion about the physicochemical effects associated with protein acetylation is mainly because of its presence capable of neutralizing positively charged protein system, while diverse non-covalent interactions arising from the acetylation are largely ignored and have never been investigated systematically. In the current work, we perform a comprehensive examination of the geometrical profile and energetic landscape of such acetylation-related non-covalent interactions in protein context by using a combination of high-level ab initio calculations, crystal structure survey, and hybrid mechanical/molecular mechanical analysis, on the basis of small model complexes and real protein systems. It is all coming together to suggest that the formation of complicated non-covalent networks around the acetylated site of protein is fundamentally important for stabilizing local structure, improving systemic rigidity, and even conducting more sophisticated biological functions such as switching enzymatic activity.The formation of complicated noncovalent networks around the acetylated site of protein is fundamentally important for stabilizing local structure, improving systemic rigidity, and even conducting more sophisticated biological functions such as switching enzymatic activity.
N-Protected cysteines 4a–c each with a free sulfhydryl group were prepared in 70–75% yields by treatment of l-cysteine with 1-(benzyloxycarbonyl) benzotriazole (Cbz-Bt) 1a, N-(tert-butyloxy-carbonyl)benzotriazole (Boc-Bt) 1b, and 1-(9-fluorenylmethoxy-carbonyl)benzotriazole (Fmoc-Bt) 1c, respectively. N-Protected, free sulfhydryl cysteines 4a–c were then converted into the corresponding N-protected, free sulfhydryl cysteinoylbenzotriazoles 7a–c (70–85%), which on treatment with diverse amino acids and dipeptides afforded the corresponding N-protected, free sulfhydryl N-terminal cysteine dipeptides 8a–e and tripeptides 8f–h in 73–80% yields. N-Protected, free sulfhydryl cysteine-containing dipeptides 9a,b were converted into the corresponding N-protected, free sulfhydryl dipeptidoylbenzotriazoles 10a,b (69–81%), which on treatment with amino acids, dipeptides, and a tripeptide afforded internal cysteine tripeptides 11a–c, tetrapeptides 11d,e and pentapeptide 11f, each containing a N-protected, free sulfhydryl groups in 70–90% yields under mild conditions. Treatment of N-protected, free sulfhydryl cysteinoylbenzotriazole 7a with diamines 12a,b afforded directly the cysteine-containing disulfide-bridged cyclic peptides 14a,b in 50% yields.Novel and stable N-protected, free sulfhydryl, cysteine-containing dipeptidoylbenzotriazoles formed internal cysteine containing N-protected free sulfhydryl tripeptides, tetrapeptides, and pentapeptide under mild reaction conditions in good yields that can be useful in the syntheses of other naturally occurring or biologically active cysteine-containing peptides.
Several experiments have been performed to test DNA-binding drugs to cure Leishmania infection. However, there are no details of pharmacoinformatics study. Herein, we have selected a good number of compounds from experimentally verified studies and performed a comparative analysis based on pharmacoinformatics techniques. In silico docking study was performed to observe the molecular level interactions of these known ligands with the DNA receptor by automated computational docking using Glide. A comparison between the calculated interaction energies and in silico ADME/T study was made. In agreement with drug likeness rules, our study suggests that seco-hydroxy-aza-CBI-TMI (compound 4b; GScore, ?12.058) is a potential molecule for targeting the DNA to cure leishmaniasis.A comparative Pharmacoinformatics study including ADME/T was performed for DNA binding’s drugs of Leishmania.
During the past century, several epidemics of human African trypanosomiasis, a deadly disease caused by the protist Trypanosoma brucei, have afflicted sub-Saharan Africa. Over 10 000 new victims are reported each year, with hundreds of thousands more at risk. As current drug treatments are either highly toxic or ineffective, novel trypanocides are urgently needed. The T. brucei galactose synthesis pathway is one potential therapeutic target. Although galactose is essential for T. brucei survival, the parasite lacks the transporters required to intake galactose from the environment. UDP-galactose 4?-epimerase (TbGalE) is responsible for the epimerization of UDP-glucose to UDP-galactose and is therefore of great interest to medicinal chemists. Using molecular dynamics simulations, we investigate the atomistic motions of TbGalE in both the apo and holo states. The sampled conformations and protein dynamics depend not only on the presence of a UDP-sugar ligand, but also on the chirality of the UDP-sugar C4 atom. This dependence provides important insights into TbGalE function and may help guide future computer-aided drug discovery efforts targeting this protein.Using molecular dynamics simulations, we investigate the atomistic motions of TbGalE in both the apo and holo states. The sampled conformations and protein dynamics depend not only on the presence of a UDP-sugar ligand, but also on the chirality of the UDP-sugar C4 atom. This dependence provides important insight into TbGalE function and may help guide future computer-aided drug-discovery efforts targeting this protein.
From the molecular mechanism of antagonist unbinding in the ?1 and ?2 adrenoceptors investigated by steered molecular dynamics, we attempt to provide further possibilities of ligand subtype and subspecies selectivity. We have simulated unbinding of ?1-selective Esmolol and ?2-selective ICI-118551 from both receptors to the extracellular environment and found distinct molecular features of unbinding. By calculating work profiles, we show different preference in antagonist unbinding pathways between the receptors, in particular, perpendicular to the membrane pathway is favourable in the ?1 adrenoceptor, whereas the lateral pathway involving helices 5, 6 and 7 is preferable in the ?2 adrenoceptor. The estimated free energy change of unbinding based on the preferable pathway correlates with the experimental ligand selectivity. We then show that the non-conserved K347 (6.58) appears to facilitate in guiding Esmolol to the extracellular surface via hydrogen bonds in the ?1 adrenoceptor. In contrast, hydrophobic and aromatic interactions dominate in driving ICI-118551 through the easiest pathway in the ?2 adrenoceptor. We show how our study can stimulate design of selective antagonists and discuss other possible molecular reasons of ligand selectivity, involving sequential binding of agonists and glycosylation of the receptor extracellular surface.The straight direction of selective antagonist unbinding, involving K347 as a H-bond translator is preferable in ?1AR and the lateral (helices 5,6 and 7) direction of unbinding with the steering role of F194 and H296 is favourable in ?2AR. Sequential binding of agonists and glycosylation to kinetic basis of ligand selectivity are discussed.
A series of N-nitrourea derivatives bearing various aryl substituents were conveniently obtained via three steps including nitration, carbamic chlorination, and aminolysis reactions. The structures of all newly synthesized compounds were characterized and confirmed by IR, 1H-NMR, MS, and elemental analysis. The preliminary bioassays indicate that five compounds possess sufficient fungicidal activity against Rhizoctonia solani. Structure–activity relationship (SAR) is also discussed based on the experimental data, and the further quantitative structure–activity relationship (QSAR) was analyzed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA).A series of N-nitrourea derivatives bearing various aryl substituents were conveniently obtained as potential fungicidal activity against Rhizoctonia solani. Structure-activity relationship (SAR) is also discussed based on the experimental data, and the quantitative structure-activity relationship (QSAR) were further analyzed using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA).
Accumulation of intra- and/or extracellular misfolded proteins as amyloid fibrils is a key hallmark in more than 20 amyloid-related diseases. In that respect, blocking or reversing amyloid aggregation via the use of small compounds is considered as two useful approaches in hampering the development of these diseases. In this research, we have studied the ability of different manganese–salen derivatives to inhibit amyloid self-assembly as well as to dissolve amyloid aggregates of hen egg-white lysozyme, as an in vitro model system, with the aim of investigating their structure–activity relationships. By coupling several techniques such as thioflavin T and anilinonaphthalene-8-sulfonic acid fluorescence, congo red absorbance, far-UV circular dichroism, and transmission electron microscopy, we demonstrated that all compounds possessed anti-amyloidogenic activities and were capable of dispersing the fibrillar aggregates. In addition, MTT assay of the treated SK-N-MC cells with the preformed fibrils formed in the presence of compounds at a drug-to-protein molar ratio of 5:1, indicated a significant increase in the viability of cells, compared to the fibrils formed in the absence of each of the compounds. Our spectroscopy, electron microscopy, and cellular studies indicated that EUK-15, with a methoxy group at the para position (group R5), had higher activity to either inhibit or disrupt the ?-sheet structures relative to other compounds. On the basis of these results, it can be concluded that in addition to aromatic rings of each of the derivatives, the type and position of the side group(s) contribute to lower lysozyme fibril accumulation.In this research, we have studied the ability of several salen derivatives to inhibit amyloid self-assembly as well as to dissolve amyloid aggregates of hen egg-white lysozyme (HEWL), as an in vitro model system, with the aim of investigating their structure-activity relationships. Our results indicated that the aromatic rings of each salen derivative play the primary role in the aggregation inhibition and the side chain groups are responsible for enhancing or diminishing its behavior.
Cbz-(protected)-tri- and tetrapeptide conjugates with steroids, sugars, terpenes, and heterocycles were prepared using Cbz-(protected)-tri- and tetrapeptidoylbenzotriazoles as active intermediates.Cbz-(protected)-tri- and tetrapeptide conjugates with steroids, sugars, terpenes and heterocycles were prepared using Cbz-(protected)-tri- and tetrapeptidoylbenzotriazoles as active intermediates.
A new class of 1H-benzimidazolecarboxamidines was synthesized and evaluated for in vitro antibacterial and antifungal activities, including drug-resistant bacterial strains. The most potent compound (32) has the same ratio of anti-MRSA activity as Vancomycin (minimal inhibitory concentrations value 0.78 ?g/mL). The mechanism of action for 1H-benzimidazolecarboxamidine appears to be different from existing antibacterial agents. These compounds have potential for development as a new class of potent anti-MRSA agent.A new class of 1H-benzimidazolecarboxamidines were synthesized and evaluated for in vitro antibacterial and antifungal activities, including drug resistant bacterial strains. The most potent compound (32) has the same ratio of antiMRSA activity as Vancomycin (MIC100 = 0.78 ?g/mL).
Six lycorine derivatives were prepared, characterized, and evaluated for their in vitro anti-Trichomonas vaginalis activity. Compounds bearing an acetyl (2), lauroyl (3), benzoyl (4 and 5), and p-nitrobenzoyl (6 and 7) groups were synthesized. The best activity was achieved with lycorine esterified at C-2 position with lauroyl group. Preliminary structure–activity relationship points that unprotected OH group at C-1 and C-2 is not necessary to the antiparasitic activity, and none of the derivative was less active than lycorine. The lycorine structural requisites required to kill this amitochondriate cell seem to be different in comparison with the derivatives most active against other parasites and tumor cell lines, both mitochondriated cells. This result is an important contribution with our ongoing studies regarding the mechanism of action of the Amaryllidaceae alkaloids on T. vaginalis cell death opening a new perspective to optimize this innovative pharmacological potential.The lycorine structural requisites required to kill Trichomonas vaginalis (amitochondriate cell) seem to be different in comparison to the derivatives most active against other parasites and tumor cell lines, both mitochondriated cells.
A theoretical study on the two-dimensional, three-dimensional quantitative structure–activity relationships and docking analysis of a novel series of ethynyl-3-quinolinecarbonitriles acting as Src inhibitors has been carried out. To correlate the c-Src kinase-inhibition activity of these compounds with the two-dimensional and three-dimensional structural properties for 39 known compounds, some excellent quantitative structure–activity relationships models with satisfying internal and external predictive abilities were established. A combined method of the density functional theory, molecular mechanics and statistics as well as the comparative molecular field analysis was applied to develop two-dimensional- and three-dimensional-quantitative structure–activity relationship models. The leave-one-out cross-validation q2 values of two-dimensional-quantitative structure–activity relationship and comparative molecular field analysis models are 0.834 and 0.812, respectively. The predictive abilities of these models were further validated by the test set including 10 compounds, and the predicted IC50 values were in a good agreement with the experimental ones. The appropriate binding orientations and conformations of these compounds interacting with c-Src kinase were also revealed by the docking study. Based on two-dimensional- and three-dimensional-quantitative structure–activity relationship results along with docking analysis, some important factors responsible for inhibitory activity of this series of compounds were discussed in detail. These factors can be summarized as follows: selecting certain large-size substituent R2, increasing the negative charge of the first atom of substituent R1 and the net charge of the C15 atom on ring-C will enhance the activity. Meanwhile, the interaction information between protein and ligand was also revealed in detail. These results help to understand the action mechanism and designing novel potential Src inhibitors. Based on the established models and some designing considerations, three new compounds with rather high predicted Src-inhibitory activity have been theoretically designed and presented to experimenters for reference.The appropriate binding orientations and conformations of these compounds interacting with c-Src kinase have been revealed. The control-regularity affecting the activity was obtained by 2D/3D-QSAR studies. Three new compounds with high activity were theoretically designed.
The present study describes ligand-based pharmacophore modeling of a series of structurally diverse acyl coenzyme A cholesterol acyltransferase inhibitors. Quantitative pharmacophore models were generated using HypoGen module of Discovery Studio 2.1, whereby the best pharmacophore model possessing two hydrophobic, one ring aromatic, and one hydrogen bond acceptor feature for inhibition of acyl coenzyme A cholesterol acyltransferase showed a very good correlation coefficient (r = 0.942) along with satisfactory cost analysis. Hypo1 was also validated by test set and cross-validation methods. Developed models were found to be predictive as indicated by low error values for test set molecules. Virtual screening against Maybridge database using Hypo1 was performed. The two most potent compounds (47 and 48; predicted IC50 = 1 nm) of the retrieved hits were synthesized and biologically evaluated. These compounds showed 86% and 88% inhibition of acyl coenzyme A cholesterol acyltransferase (at 10 ?g/mL) with IC50 value of 3.6 and 2.5 nm, respectively. As evident from the close proximity of biological data to the predicted values, it can be concluded that the generated model (Hypo1) is a reliable and useful tool for lead optimization of novel acyl coenzyme A cholesterol acyltransferase inhibitors.A ligand-based pharmacophore modeling of a series of structurally diverse acyl CoA cholesterol acyltransferase (ACAT) inhibitors was carried out. Two most potent compounds (47 and 48; predicted IC50 = 1 nm) of the retrieved hits from virtual screening were synthesized and biologically evaluated. The results demonstrated that these compounds showed 86% and 88% inhibition of ACAT (at 10 ?g/mL) with IC50 value of 3.6 and 2.5 nm, respectively.
A cholesteryl-functionalized derivative of activity dependent neurotrophic factor-9 peptide (a nine amino acid core peptide of activity-dependent neurotrophic factor, acting against Alzheimer’s disease) was synthesized aiming at the improvement of its bioavailability. Therefore, its uptake was comparatively investigated with that of its parent peptide by employing mouse neuroblastoma Neuro-2a cells. Owing to the hydrophobic character of this cholesteryl-functionalized peptide, it exhibited enhanced permeability and intracellular uptake while it also retained its low cytotoxicity at concentrations up to 1 ?m. FACS analysis also revealed that when Neuro-2a cells were treated with this activity dependent neurotrophic factor-9 derivative, at a concentration of 50 nm, an almost 100% uptake was obtained. In addition, in vitro biological activity experiments showed that the functionalized peptide retained its neurotrophic activity at femtomolar concentration range.Activity dependent neurotrophic factor 9 (ADNF-9), a nine amino acid core peptide of ADNF, was functionalized by the introduction of the cholesteryl moiety at its amine end-group. The intracellular uptake of the FITC-labeled cholesteryl ADNF-9 peptide along with its neuroprotective activity against N-methyl-d-aspartate were comparatively investigated with that of the parent peptide employing mouse neuroblastoma Neuro-2a cells. Hydrophobicity enhancement proved a useful strategy for improving the permeability of the peptide across cells membrane.
Atom-based bilinear indices and linear discriminant analysis are used to discover novel trypanosomicidal compounds. The obtained linear discriminant analysis-based quantitative structure–activity relationship models, using non-stochastic and stochastic indices, provide accuracies of 89.02% (85.11%) and 89.60% (88.30%) of the chemicals in the training (test) sets, respectively. Later, both models were applied to the virtual screening of 18 in-house synthesized compounds to find new pro-lead antitrypanosomal agents. The in vitro antitrypanosomal activity of this set against epimastigote forms of Trypanosoma cruzi is assayed. Predictions agree with experimental results to a great extent (16/18) of the chemicals. Sixteen compounds show more than 70% of epimastigote inhibition at a concentration 100 ?g/mL. In addition, three compounds (CRIS 112, CRIS 140 and CRIS 147) present more than 70% of epimastigote inhibition at a concentration of 10 ?g/mL (79.95%, 73.97% and 78.13%, respectively) with low values of cytotoxicity (19.7%, 7.44% and 20.63%, correspondingly).Taking into account all these results, we could say that these three compounds could be optimized in forthcoming works. Even though none of them resulted more active than nifurtimox, the current results constitute a step forward in the search for efficient ways to discover new lead antitrypanosomals.Two LDA-based QSAR models were developed and validated. A pool of approximately 200 compounds was screened to identify potential antitrypanosomal activity. Eighteen compounds were identifies as antitrypanosomal agents by our models. Sixteen of them shown more than 70% of epimastigote inhibition at a concentration of 100 ?g/mL
Structure–activity relationship (SAR) studies are essential in the generation of peptides with enhanced activity and efficacy as therapeutic agents. In this study, we report a Structure–activity relationship study for a family of mimetic peptides derived from type IV collagen with potent anti-angiogenic properties. The Structure–activity relationship study was conducted using a number of validated in vitro assays including cell proliferation, adhesion, migration, and tubule formation. We report a critical sequence (NINNV) within this peptide series, which is required for the potent anti-angiogenic activity. Detailed amino acid substitutions resulted in peptides with superior efficacy. Specifically, substitutions with isoleucine at positions 12 and 18 along with the substitution of the methionine at position 10 with the non-natural amino acid d-alanine led to an increase in potency by two orders of magnitude over the parent peptide. Several mimetic peptides in this series exhibit a significant improvement of activity over the parent peptide. This improved in vitro activity is expected to correlate with an increase in in vivo activity leading to effective peptides for anti-angiogenic therapy for different disease applications including cancer and age-related macular degeneration.In this study we report a Structure–activity relationship study for a family of mimetic peptides derived from type IV collagen with potent anti-angiogenic properties. We report a critical sequence (NINNV) within this peptide series that is required for the potent anti-angiogenic activity. Detailed amino acid substitutions resulted in peptides with superior efficacy.
A ligand-based drug design study was performed to acetaminophen regioisomers as analgesic candidates employing quantum chemical calculations at the DFT/B3LYP level of theory and the 6-31G* basis set. To do so, many molecular descriptors were used such as highest occupied molecular orbital, ionization potential, H–O bond dissociation energies, and spin densities, which might be related to quench reactivity of the tyrosyl radical to give N-acetyl-p-benzosemiquinone-imine through an initial electron withdrawing or hydrogen atom abstraction. Based on this in silico work, the most promising molecule, orthobenzamol, was synthesized and tested. The results expected from the theoretical prediction were confirmed in vivo using mouse models of nociception such as writhing, paw licking, and hot plate tests. All biological results suggested an antinociceptive activity mediated by opioid receptors. Furthermore, at 90 and 120 min, this new compound had an effect that was comparable to morphine, the standard drug for this test. Finally, the pharmacophore model is discussed according to the electronic properties derived from quantum chemistry calculations.The first drug design of analgesic candidates using DFT methods. The interaction between candidates and prostaglandin endoperoxide synthase were measured by OH bond dissociation energies. Theoretical prediction is confirmed by biological evaluation. Ortho regioisomer, named orthobenzamol (OBZ), has better analgesic activity compared with acetaminophen and can be related with opioid effect of morphine.
Hundred and two binding sites from 91 Protein Data Bank files for protein tyrosine phosphatase 1B with different ligands have been compared. It was found that they can be divided into five clusters. Additional clusters were formed by the unliganded and oxidized enzyme. The centroids of the clusters can be used as starting points for further studies of enzyme-inhibitor interaction by computer simulations. A special software tool has been created for the investigation of protein tyrosine phosphatase 1B and other enzymes. It performs multiple comparisons of selected parts of Protein Data Bank files, as well as further clustering, and determines mobility of separate residues.Hundred and two binding sites from 91 PDB files for protein tyrosine phosphatase 1B (PTP1B) with different ligands have been divided into five clusters by a special software tool that performs multiple comparisons of selected parts of PDB files. Additional clusters were formed by the unliganded and oxidized enzyme. The centroids of the clusters can be used as starting points for further studies of enzyme-inhibitor interaction by computer simulations.
The leader peptide of a recombinant manganese superoxide dismutase (rMnSOD-Lp) acts as a molecular carrier. Clonogenic tests on normal (MRC-5) and endometrial adenocarcinoma cells (HTB-112) were carried out in the presence of rMnSOD-Lp, cisplatin alone (CC) or cisplatin conjugated to the rMnSOD-Lp (rMnSOD-Lp-CC). The platinum delivered into the cells was measured by atomic spectrophotometric absorbance. The treatments on tumor and normal cells were finally evaluated by LM and TM microscopy. Tumor cell death in the case of 0.5 ?m cisplatin on its own was minimal, while in the presence of 0.5 ?m rMnSOD-Lp-CC, no tumor cells survived. Atomic absorbance analysis showed that rMnSOD-Lp-CC delivered approximately four times more cisplatin into HTB-112 cells than the amount delivered using cisplatin alone. By LM observation, the cells treated with rMnSOD-Lp-CC showed signs of nuclear and cytoplasmic fragmentation, that is, apoptosis induced by the treatment. The therapeutic effect of rMnSOD-Lp-CC on endometrial cancer cells was significant, while on the normal cells it showed only a minimal toxicity. We believe that rMnSOD-Lp deserves to be considered as a molecular carrier to deliver cisplatin directly into tumor cells, thus transforming its antireplicative activity into a specific and selective antitumor agent.This is a study of recombinant MnSOD peptide which is used to facilitate delivery of cisplatin into tumor endometrial cancer cells. Treatment of endometrial cancer cells with this construct (rMnSOD Lp-CC) may therefore lead to an especially high accumulation of cisplatin in these neoplastic cells, resulting in their selective killing. Indeed following this treatment no tumor cells survived. On the contrary, by using the same amount of cisplatin alone on tumor cells or normal cells, its cytotoxic effect resulted minimal.
Nucleolar targeting peptides are 14–15 residue-long sequences designed by structural minimization of a snake toxin (J Med Chem 2008;50:7041). Peptides such as NrTP1 (YKQCHKKGGKK GSG) and analogues are capable of penetrating human cervix epithelial carcinoma cells and homing into their nucleoli. We now show that NrTP1 similarly penetrates and localizes in the nucleolus of tumour cells derived from human pancreatic (BxPC-3) and human ductal mammary gland (BT-474) carcinomas. Live cell confocal microscopy imaging, combined with flow cytometry analysis of cells arrested to defined phases of their cycle, confirms that NrTP1 uptake and nucleolar homing are independent of cell cycle phase. Peptide uptake is significantly reduced at low temperature. Also, drugs inhibiting chlatrin-mediated endocytosis severely decrease uptake, pointing to a clathrin-dependent route as the primary NrTP1 internalization mechanism. These results highlight nucleolar targeting peptides not only as a novel and efficient class of cell-penetrating peptides but also for their exceptional ability to target preferentially an essential and dynamic subnuclear structure such as the nucleolus.Nucleolar targeting peptides (NrTPs) are 14–15 residue-long sequences designed by structural minimization of a rattlesnake toxin, capable of penetrating mammalian cells and homing into their nucleoli. One of such developed sequences (NrTP1) penetrates and localizes in the nucleolus of cell lines derived from aggressive types of tumours. Using a combination of confocal microscopy, flow cytometry and pharmacological inhibitors, we demonstrated that peptide uptake is mediated by a chlatrin-dependent endocytosis, but the translocation is not associated to the cell cycle phase.
Inosine 5?-monophosphate dehydrogenase (IMPDH) is a key enzyme in the de novo synthesis of guanosine nucleotides. It is considered as an important target in the quest for drugs in the immunosuppressive, antiviral, antibacterial, and anticancer therapeutic areas. Herein, we report the 3D-QSAR analyses using comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and docking on mycophenolic acid derivates for the first time. We obtained cross-validated q2 value of 0.805 for CoMFA and 0.620 for CoMSIA, while the non-cross-validated r2 values for them were 0.969 and 0.935, respectively. Based on the CoMFA and CoMSIA contour maps and docking analyses, some key structural factors responsible for inhibitory activity were revealed. The results obtained from this study could be used for the rational design of potent inhibitors against IMPDH.3D-QSAR studies were carried out on 73 IMPDH inhibitors by CoMFA, CoMSIA and molecular docking methods. The 3D-QSAR models showed excellent predictive capability
Tuberculosis is the second leading infectious killer with 9 million new cases in 2009. Extensive use of pathogen’s lipid metabolism especially in utilizing the host lipids and virulence highlights the importance of exported lipid-catabolizing enzymes. Current study aims to emphasize the importance of Rv0183, an exported monoacylglycerol lipase, involved in metabolizing the host cell membrane lipids. Sequence analysis and homology modeling shows Rv0183 is highly conserved throughout mycobacterial species even in Mycobacterium leprae and also significantly divergent from mammalian lipases. Additionally, employing virtual screening using NCI diversity set and ZINC database with criteria of molecules with higher predicted free energy of binding toward Rv0183 than human lipase, potential inhibitors have been identified for Rv0183. A tautomer of ZINC13451138, known inhibitor for HIV-1 integrase is the best hit with difference in free energy of binding of 8.72 kcal/mol. The sequence and structure analysis were helpful in identifying the ligand binding sites and molecular function of the mycobacterial specific monoacylglycerol lipase. Rv0183 represents a suitable and promising drug target and is also a step towards understanding dormancy development and reactivation, thereby addressing pathogen’s drug resistance. Experimental studies on the discovered potential inhibitors in this virtual screen should further validate the therapeutic utility of Rv0183.ZINC13451138 from ZINC database, a potential selective inhibitor of Rv0183 a highly conserved and essential protein of Mycobacterium species.
BaP1 is a snake venom metalloproteinase from the venom of Bothrops asper, showing high structural homology with the catalytic domain of human adamalysins and matrix metalloproteinases. It induces the release of cytokines, like interleukin-1 and tumor necrosis factor alpha. Recently, the high-resolution crystal structure of BaP1 with a bound inhibitor became available, representing an interesting model concerning inhibitor design for medicinally important metalloproteinases such as tumor necrosis factor alpha–converting enzyme and MMP13. We here use computational modeling to gain a better understanding about the binding properties of various ligands to BaP1, with a focus on computing ligand binding free energies. The obtained results should be of general significance for future research on medicinally important metalloproteinases. We have investigated the binding of the original inhibitor in detail and calculated its binding strength using MMP/GBSA free energy calculations. Additionally, the binding strengths of alternative ligands have been computed, and two of them are predicted and experimentally verified to strongly inhibit the enzyme. A suggestion for chemical modifications of BaP1 inhibitors could be made to guide future synthesis efforts. Furthermore, a contribution to the proteolytic reaction mechanism of metzincins is given. The pK value of the catalytically active glutamic acid residue 143 has been found to be significantly raised when compared with a free glutamate side chain. Calculations on other matrix metalloproteinases confirmed that this is not confined to BaP1, but seems to be a common feature of metzincins.We have investigated the binding properties of various ligands to BaP1, a medicinally important metalloproteinase. Molecular dynamics simulations and free energy calculations reveal the molecular details of the binding process and allow targeted compound modifications to design better inhibitors.
This article describes the identification of two small molecular inhibitors for ?-secretase by integrating virtual screening with fluorescence resonance energy transfer bioassay. A ligand-based pharmacophore model was developed, and the sequential virtual screening of ZINC database was performed using the acquired pharmacophore model and molecular docking. Biological evaluation of 10 virtual hits led to the identification of two novel inhibitors with IC50 values of 4.76 and 0.31 ?m, respectively. These two moderate inhibitors could represent new potentials for the development of anti-Alzheimer’s disease agents.A ligand-based pharmacophore model was developed. The sequential virtual screening of ZINC database by pharmacophore model and molecular docking have led to the identification of two novel inhibitors with IC50 values of 4.76 and 0.31 ?m, respectively.
Aurora-A has been known as one of the most important targets for cancer therapy, and some Aurora-A inhibitors have entered clinical trails. In this study, combination of the ligand-based and structure-based methods is used to clarify the essential quantitative structure–activity relationship of known Aurora-A inhibitors, and multicomplex-based pharmacophore-guided method has been suggested to generate a comprehensive pharmacophore of Aurora-A kinase based on a collection of crystal structures of Aurora-A–inhibitor complex. This model has been successfully used to identify the bioactive conformation and align 37 structurally diverse N-substituted 2?-(aminoaryl)benzothiazoles derivatives. The quantitative structure–activity relationship analyses have been performed on these Aurora-A inhibitors based on multicomplex-based pharmacophore-guided alignment. These results may provide important information for further design and virtual screening of novel Aurora-A inhibitors.Multicomplex-based pharmacophore(MCBP) guided alignment were used for the 3D-QSAR studies on 37 structurally diverse N-substituted 2?-(aminoaryl)benzothiazoles Aurora-A inhibitors.
Twenty-seven novel chalcone derivatives were synthesized using Claisen-Schmidt condensation and their antimalarial activity against asexual blood stages of Plasmodium falciparum was determined. Antiplasmodial IC50 (half-maximal inhibitory concentration) activity of a compound against malaria parasites in vitro provides a good first screen for identifying the antimalarial potential of the compound. The most active compound was 1-(4-benzimidazol-1-yl-phenyl)-3-(2, 4-dimethoxy-phenyl)-propen-1-one with IC50 of 1.1 ?g/mL, while that of the natural phytochemical, licochalcone A is 1.43 ?g/mL. The presence of methoxy groups at position 2 and 4 in chalcone derivatives appeared to be favorable for antimalarial activity as compared to other methoxy-substituted chalcones. Furthermore, 3, 4, 5-trimethoxy groups on chalcone derivative probably cause steric hindrance in binding to the active site of cysteine protease enzyme, explaining the relative lower inhibitory activity.Two step synthesis protocol was used to prepare twenty-seven chalcone analogs. Compound 9 (1-(4-benzoimidazol-1-yl-phenyl)-3-(2,4-dimethoxy-phenyl)-propen-1-one) was found to be most effective in inhibiting the growth of P. falciparum in vitro.
Trypanosomal (trans-) sialidases are enzymes that catalyze the transfer of sialic acid residues between host and parasite glycoconjugates. Herein, we have used homology modeling to construct the 3D structures of sialidases from Trypanosoma brucei and Trypanosoma evansi. Hybrid quantum mechanical/molecular mechanical molecular dynamics simulations were used to determine the interaction energy between the 2-Deoxy-2,3-didehydro-N-acetylneuraminic acid inhibitor and the three sialidases studied here. Our results suggest that the two constructed enzymes share the same basic fold motive of the Trypanosoma rangeli crystallographic structure. In addition, quantum mechanical/molecular mechanical molecular dynamics simulations show that the 2-Deoxy-2,3-didehydro-N-acetylneuraminic acid inhibitor forms a stronger complex with Trypanosoma rangeli than with Trypanosoma brucei and Trypanosoma evansi sialidases. Finally, the interaction energy by residues shows that the arginine triad plays a decisive role to complex 2-Deoxy-2,3-didehydro-N-acetylneuraminic acid with the enzyme through hydrogen bonding.Trypanosomal sialidases enzymes in complex with DANA inhibitor were investigated using homology modeling. Hybrid QM/MM and molecular dynamics simulations. The results suggest that sialidases share the same basic fold and arginine plays an important role to inhibitor–enzyme affinity.
In this review, the use of automated DNA sequencing techniques to determine the sequence specificity of compounds that interact with DNA is discussed. The sequence specificity of a DNA-damaging agent is an essential element in determining the cellular mechanism of action of a drug. A number of DNA-damaging compounds are mutagenic, carcinogenic, as well as being widely used as cancer chemotherapeutic agents. The distribution of lesions in a sequence of DNA can give vital clues in the determination of the precise mechanism of interaction of the agent with DNA. The DNA sequence specificity of a number of DNA-damaging agents has been delineated using automated DNA sequencing technology, and these studies are discussed in this review. The current state-of-the-art methodology involves capillary electrophoresis with laser-induced fluorescence detection usually on an Applied Biosystems ABI 3730 capillary sequencer. This current technique has higher resolution, greater sensitivity, higher precision, more rapid separation times, is safer and easier to perform than previous methods. The two main methods to determine the DNA sequence selectivity of compounds that interact with DNA are described: end labelling and the polymerase stop assay. The interaction of the antitumour drug, bleomycin, with DNA is utilized to illustrate the recent technological advances.The use of automated DNA sequencing techniques to determine the sequence specificity of compounds that interact with DNA is reviewed. The sequence specificity of a DNA damaging agent is an essential element in determining the cellular mechanism of action of a drug. The current state-of-the-art methodology involves capillary electrophoresis with laser-induced fluorescence detection and has higher resolution, greater sensitivity, higher precision, more rapid separation times, is safer, and easier to perform than previous methods.
Biological evaluation of N-aryl-4-aryl-1,3-thiazole-2-amine derivatives was examined for anti-inflammatory activity in in vitro and in vivo assays. The thiazole compounds showed direct inhibition of 5-lipoxygenase (LOX) that is a key enzyme of leukotrienes synthesis and involved in the inflammation-related diseases, including asthma and rheumatoid arthritis. To optimize biological activity, we synthesized 1,3-thiazole-2-amine derivatives and investigated for structure and activity relationship. Especially, N-(3,5-dimethylphenyl)-4-(4-chlorophenyl)-1,3-thiazole-2-amine was shown to have a potent anti-inflammatory activity as a 5-LOX inhibitor.Highlighted are the synthesis and biological evaluation of N-aryl-4-aryl-1,3-thiazole-2-amine derivatives as a direct 5-lipoxygenase inhibitor in in vitro and in vivo assay.
Five lipophilic analogues 1–5 of the active metabolite of the antitubercular drug isoniazid (INH), selected as inhibitors of Mycobacterium smegmatis and Mycobacterium tuberculosis growth, were evaluated for their activity against Corynebacterium glutamicum (lacking in InhA activity), Escherichia coli (to test mycobacteria selectivity), and Plasmodium falciparum (as possible parasite target). Compound 3 was the only one that did not inhibit C. glutamicum growth. The poor InhA inhibitors 1 and 2 were able to inhibit C. glutamicum and their anti(myco)bacterial mechanisms of action involve targets other than InhA. For the effective InhA inhibitors 4 and 5, also active against C. glutamicum and M. tuberculosis strains, more than one pathway should be envisaged to explain their actions. Pyridine-base ring analogues (1, 2, and 3) have no ability to inhibit the growth of E. coli even at a high concentration. Compound 3 thus exhibited a selective inhibitory action toward M. tuberculosis, while it was inactive on C. glutamicum and on E. coli growth. It presented an activity profile similar to that of INH suggesting InhA inhibition as one of the possible mechanisms of action. Finally, although a homologue of the reductase InhA exists in the FAS-II system of P. falciparum, 3 was unable to display antiplasmodial activity.Evaluation of lipophilic analogs of the active isoniazid metabolite towards Escherichia coli, Corynebacterium glutamicum and Plasmodium falciparum.
Forty-eight chromone derivatives were evaluated for their antioxidant activity using 2,2-diphenyl-1-picrylhydrazyl free radical scavenging assay, ferrous ions (Fe2+) chelating activity test, total antioxidant activity test (Ferric thiocyanate and Thiobarbituric acid methods), and total reductive capability (potassium ferricyanide reduction). 7,8-Dihydroxy-2-(3?-trifluoromethylphenyl)-3-(3?-trifluoromethylbenzoyl) chromone 32 showed stronger radical scavenging and metal chelating activities than butylated hydroxytoluene, vitamin E, and trolox. Chromone derivatives that exhibited good radical scavenging and metal chelating also displayed strong total antioxidant and reductive power activities. The results obtained from this study indicated that the synthesized chromone derivatives have remarkable antioxidant activity.Forty-eight chromone derivatives were evaluated for their antioxidant activity. Most compounds showed stronger activities than BHT, vitamin E and trolox.
Type 2 diabetes mellitus (T2DM) is a metabolic disease and a major challenge to healthcare systems around the world. Dipeptidyl peptidase IV (DPP-4), a serine protease, has been rapidly emerging as an effective therapeutic target for the treatment for T2DM. In this study, a series of novel DPP-4 inhibitors, featuring the pyrazole-3-carbohydrazone scaffold, have been discovered using an integrated approach of structure-based virtual screening, chemical synthesis, and bioassay. Virtual screening of SPECS Database, followed by enzymatic activity assay, resulted in five micromolar or low-to-mid-micromolar inhibitory level compounds (1–5) with different scaffold. Compound 1 was selected for the further structure modifications in considering inhibitory activity, structural variability, and synthetic accessibility. Seventeen new compounds were synthesized and tested with biological assays. Nine compounds (6e, 6g, 6k–l, and 7a–e) were found to show inhibitory effects against DPP-4. Molecular docking models give rational explanation about structure–activity relationships. Based on eight DPP-4 inhibitors (1–5, 6e, 6k, and 7d), the best pharmacophore model hypo1 was obtained, consisting of one hydrogen bond donor (HBD), one hydrogen bond acceptor (HBA), and two hydrophobic (HY) features. Both docking models and pharmacophore mapping results are in agreement with pharmacological results. The present studies give some guiding information for further structural optimization and are helpful for future DPP-4 inhibitors design.Best pharmacophore model hypol was obtained, consisting of one hydrogen bond donar (HBD), one hydrogen bond accept (HBA), and two hydrophobic (HY) features.
Two-component signal transduction (TCST) is the predominant signaling scheme used in bacteria to sense and respond to environmental changes in order to survive and thrive. A typical TCST system consists of a sensor histidine kinase to detect external signals and an effector response regulator to respond to external changes. In the signaling scheme, the histidine kinase phosphorylates and activates the response regulator, which functions as a transcription factor to modulate gene expression. One promising strategy toward antibacterial development is to target TCST regulatory systems, specifically the response regulators to disrupt the expression of genes important for virulence. In Salmonella enterica, the PhoQ/PhoP signal transduction system is used to sense and respond to low magnesium levels and regulates the expression for over 40 genes necessary for growth under these conditions, and more interestingly, genes that are important for virulence. In this study, a hybrid approach coupling computational and experimental methods was applied to identify drug-like compounds to target the PhoP response regulator. A computational approach of structure-based virtual screening combined with a series of biochemical and biophysical assays was used to test the predictability of the computational strategy and to characterize the mode of action of the compounds. Eight compounds from virtual screening inhibit the formation of the PhoP-DNA complex necessary for virulence gene regulation. This investigation served as an initial case study for targeting TCST response regulators to modulate the gene expression of a signal transduction pathway important for bacterial virulence. With the increasing resistance of pathogenic bacteria to current antibiotics, targeting TCST response regulators that control virulence is a viable strategy for the development of antimicrobial therapeutics with novel modes of action.Two-component signal transduction (TCST) is the predominant signaling scheme used in bacteria to sense and respond to environmental changes in order to survive and thrive. Computational and experimental methods were used to identify 8 compounds inhibiting Salmonella enterica PhoP TCST response regulator. This investigation served as an initial case study for targeting TCST response regulators to modulate the gene expression of a signal transduction pathway important for bacterial virulence.
In this study, two novel cationic lipids containing protonated cyclen and quaternary ammonium moieties were designed and synthesized as non-viral gene delivery vectors. The structures of the two lipids differ in their hydrophobic region (cholesterol or diosgenin). Cationic liposomes were easily prepared from the lipids individually or from the mixtures of each cationic lipid and dioleoylphosphatidylethanolamine. Several studies including DLS, gel retardation assay, and ethidium bromide intercalation assay suggest that these amphiphilic molecules are able to bind and compact DNA into nanometer particles which can be used as non-viral gene delivery agents. Our results from in vitro transfection show that in association with dioleoylphosphatidylethanolamine, two cationic lipids can induce effective gene transfection in human embryonic kidney 293 cells, although the gene transfection efficiencies of two cationic lipids were found to be lower than that of lipofectamine 2000TM. Besides, different cytotoxicity was found for two lipoplexes. This study demonstrates that the title cationic lipids have large potential to be efficient non-viral gene vectors.Two novel cationic lipids containing cyclen and ammonium moieties have been designed, synthesized and fully characterized for gene delivery. Liposomes formed from those two cationic lipids could bind and compact DNA into nanometer particles and effectively delivery it into HEK 293 cells with low cytotoxicity.
The inherent morbidity and mortality caused by schistosomiasis is a serious public health problem in developing countries. Praziquantel is the only drug in therapeutic use, leading to a permanent risk of parasite resistance. In search for new schistosomicidal drugs, meclonazepam, the 3-methyl-derivative of clonazepam, is still considered an interesting lead-candidate because it has a proven schistosomicidal effect in humans but adverse effects on the central nervous system did not allow its clinical use. Herein, the synthesis, in vitro biological evaluation, and molecular modeling of clonazepam, meclonazepam, and analogues are reported to establish the first structure–activity relationship for schistosomicidal benzodiazepines. Our findings indicate that the amide moiety [N1H-C2(=O)] is the principal pharmacophoric unit of 1,4-benzodiazepine schistosomicidal compounds and that substitution on the amide nitrogen atom (N1 position) is not tolerated.Schistosomiasis is a serious public health problem in developing countries. Praziquantel is the only drug in therapeutics. Taking into account the schistosomicidal activity of clonazepam and meclonazepam, the objective of present work was to establish a structure-activity relationship for 1,4-benzodiazepine compounds with schistosomicidal activity. Our findings indicate that the amide moiety (N1H-C2(=O)) is the principal pharmacophoric unit and that substitution on the amide nitrogen atom (N1 position) is not tolerated.
Plastrum Testudinis (PT) is often used as an important traditional Chinese medicine to treat bone diseases in China for centuries. To identify active components of PT involved in promoting proliferation of MSCs, PT was extracted with ethyl acetate and separated by silica gel column chromatography with gradient elution. Sixteen (Ts-1 ? 16) components were obtained, which were biologically evaluated by MTT assay and flow cytometry on the proliferation of rat marrow-derived mesenchymal stem cells (rMSCs). Results indicated that Ts-12 could induce the proliferation compared with control group (p < 0.05), while Ts-4 exhibited inhibitive effect. The chemical components of PT which regulated the proliferation of rMSCs were investigated by Gas Chromatography-Mass Spectrometry (GC-MS), HPLC, and nine standard compounds. The experimental results suggested that palmitic acid methyl ester and cholesterol myristate, which identified from Ts-12, possessed proliferative activity while stearic acid found in Ts-4 showed inhibition.Plastrum testudinis was extracted with ethyl acetate and separated by silica gel column chromatography with gradient elution. Sixteen (Ts-1 ? 16) components were obtained, evaluated by MTT assay and flow cytometry on the proliferation of rMSCs. Ts-12 could induce proliferation, while Ts-4 exhibited inhibitive effect. Results suggested that palmitic acid methyl ester and cholesterol myristate, which identified from Ts-12, possessed proliferative activity while stearic acid found in Ts-4 showed inhibition.
In continuation to our efforts in finding potential therapeutic agents, a variety of biologically significant semicarbazones were synthesized by the reaction of different carbonyl compounds with phenyl semicarbazides through microwave irradiation. Initially, 18 semicarbazones were studied for their antimicrobial, antitumor, and antioxidant potential. None of the tested compounds showed any antibacterial activity; however, some compounds showed significant antifungal activity. Interestingly, all compounds showed antitumor activity when tested against tumors grown on potato discs. These compounds were also tested for their effect on OH radical-induced oxidative DNA damage. All the compounds showed DNA protection to varying extent. Based on the promising results of antitumor and antioxidant activities, another set of 24 semicarbazones was synthesized, and all of these semicarbazones were evaluated for their antioxidant potential. The results showed that the semicarbazones derived from 2-nitrobenzaldehyde and acetophenone were the most active 2,2-diphenyl-1-picrylhydrazyl 9 (DPPH) free radical scavengers. The overall results have led to the identification of some interesting compounds which seem to have great potential to be developed into effective anticancer drugs.Biological evaluation of a diverse set of 42 synthesized semicarbazones was carried out by screening them for their potential as antioxidant, antimicrobial and antitumor agents and have been found to have significant potential to develop into antioxidant and anticancerous drugs.
Virus-specific cytotoxic T lymphocytes contribute to the control of virus infections including those caused by influenza viruses. However, during the evolution of influenza A viruses, variations in cytotoxic T lymphocytes epitopes have been observed and it will affect the recognition by virus-specific cytotoxic T lymphocytes and the human virus-specific cytotoxic T lymphocytes response in vitro. Here, to gain further insights into the molecular mechanism of the virus-specific cytotoxic T lymphocytes immunity, the class I major histocompatibility complex-encoded HLA-B*3501 protein with six different NP418-426 antigenic peptides emerging from 1918 to 2009 pandemic influenza A virus were studied by molecular dynamics simulation. Dynamical and structural properties (such as atomic fluctuations, solvent-accessible surface areas, binding free energy), based on the solvated protein-peptide complexes, were compared. Free energy calculations emphasized the important role of the secondary anchors (positions 2 and 9) in influencing the binding of MHC-I with antigenic non-apeptides. Furthermore, major interactions with peptides were gained from HLA-B*3501 residues: Tyr7, Ile66, Lys146, Trp147, and Tyr159. Detailed analysis could help to understand how different NP418-426 mutants effectively bind with the HLA-B*3501.A molecular modeling study for six NP418-426 peptides from 1918 to 2009 pandemic in?uenza A virus complexed with HLA-B*3501 was performed by molecular dynamics simulations and binding free energy calculations, in order to investigate mechanisms of the virus-speci?c CTL immunity. Our work will be useful for the design of novel vaccination regimens that provide a measure of protection against unpredicted pandemic and seasonal in?uenza strains.
Predicting HIV-1 protease/inhibitor binding affinity as the difference between the free energy of the inhibitor bound and unbound state remains difficult as the unbound state exists as an ensemble of conformations with various degrees of flap opening. We improve computational prediction of protease/inhibitor affinity by invoking the hypothesis that the free energy of the unbound state while difficult to predict is less sensitive to mutation. Thereby the HIV-1 protease/inhibitor binding affinity can be approximated with the free energy of the bound state alone. Bound state free energy can be predicted from comparative models of HIV-1 protease mutant/inhibitor complexes. Absolute binding energies are predicted with R = 0.71 and SE = 5.91 kJ/mol. Changes in binding free energy upon mutation can be predicted with R = 0.85 and SE = 4.49 kJ/mol. Resistance mutations that lower inhibitor binding affinity can thereby be recognized early in HIV-1 protease inhibitor development.Unbound HIV-1 protease is highly flexible, but becomes rigid upon inhibitor binding. We improve protease binding affinity prediction through our understanding of HIV-1 PR flexibility and its effect on free energy. Resistance mutations that lead to lower inhibitor binding affinity can thereby be predicted early in HIV-1 protease inhibitor development.
Three-dimensional quantitative structure activity relationship (3D-QSAR) study has been carried out on the Escherichia coli DHFR inhibitors 2,4-diamino-5-(substituted-benzyl)pyrimidine derivatives to understand the structural features responsible for the improved potency. To construct highly predictive 3D-QSAR models, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods were used. The predicted models show statistically significant cross-validated and non-cross-validated correlation coefficient of and , respectively. The final 3D-QSAR models were validated using structurally diverse test set compounds. Analysis of the contour maps generated from CoMFA and CoMSIA methods reveals that the substitution of electronegative groups at the first and second position along with electropositive group at the third position of R2 substitution significantly increases the potency of the derivatives. The results obtained from the CoMFA and CoMSIA study delineate the substituents on the trimethoprim analogues responsible for the enhanced potency and also provide valuable directions for the design of new trimethorpim analogues with improved affinity.Three-dimensional quantitative structure activity relationship (3D-QSAR) study has been carried out on the Escherichia coli DHFR inhibitors 2,4-diamino-5-(substituted-benzyl)pyrimidine derivatives to understand the structural features responsible for the improved potency. Analysis of the contour maps generated from CoMFA and CoMSIA methods reveals that the substitution of electronegative groups at the first and second position along with electropositive group at the third position of R2 substitution significantly increases the potency of the derivatives.
An in silico approach was adopted to identify potential cyclooxygenase-2 inhibitors through molecular docking studies. The in vivo studies indicated that synthetic palmitoyl derivatives of salicylic acid, para amino phenol, para amino benzoic acid, and anthranilic acid possessed significant pharmacological activities like anti-inflammatory, analgesic, and antipyretic activities. None of the tested substances produced any significant gastric lesions in experimental animals. In an attempt to understand the ligand–protein interactions in terms of the binding affinity, the above synthetic molecules were subjected to docking analysis using AutoDock. The palmitoyl derivatives palmitoyl anthranilic acid, palmitoyl para amino benzoic acid, palmitoyl para amino phenol, and palmitoyl salicylic acid showed better binding energy than the known inhibitor diclofenac bound to 1PXX. All the palmitoyl derivatives made similar interactions with the binding site residues of cyclooxygenase-2 as compared to that of the known inhibitor. Thus, structure-based drug discovery approach was successfully employed to identify some promising pro-drugs for the treatment of pain and inflammation.Molecular docking studies of four synthesized compounds on COX-2 protein using AutoDock proved to be successful in identifying them as promising lead compounds for the treatment of pain, fever and inflammation.
In this paper, we investigated the structure–activity relationship of two vasopressin analogues, [Cpa1,(L-1-Nal)2]AVP (I) and [Cpa1,(D-Nal)2]AVP (II) by NMR spectroscopy and molecular modeling. Both peptides exhibit antioxytocic and antipressor potency. Inversion of configuration of the residue at position 2 converted a weak antidiuretic agonist (peptide I) into a highly potent antidiuretic antagonist (peptide II). For this reason, the purpose of our study was to explain the causes of different interactions of the analogues with V2 receptors. The results have shown that both analogues display the tendency to adopt ?-turns in the 1–4 and 2–5 fragments, which is characteristic of OT and V1a receptors antagonists. In addition, the [Cpa1,(L-1-Nal)2]AVP (I) shows the propensity to assume ?-turn at position 7,8, which is believed to enhance antidiuretic activity, although not being crucial for its appearance. Moreover, the C-terminal amide group seems to be crucial for signal transduction. Its high accessibility in [Cpa1,(L-1-Nal)2]AVP (I) in contrast to [Cpa1,(D-1-Nal)2]AVP (II), probably results in V2 receptor activation.We investigated the conformations of two vasopressin analogues, [Cpa1,(L-1-Nal)2]AVP (I) and [Cpa1,(D-Nal)2]AVP (II) by NMR spectroscopy and molecular modelling. Both peptides exhibit antioxytocic and antipressor potency. Inversion of configuration of the residue at position 2 converted a weak antidiuretic agonist (peptide I) into a highly potent antidiuretic antagonist (peptide II). For this reason, the purpose of our study was to explain the causes of different interactions of the analogues with V2 receptors.
Our concept of enzyme-mediated cancer imaging and therapy aims to use radiolabeled compounds to target hydrolases over-expressed on the extracellular surface of solid tumors. A data mining approach identified extracellular sulfatase 1 (SULF1) as an enzyme expressed on the surface of pancreatic cancer cells. We designed, synthesized, and characterized 2-(2?-sulfooxyphenyl)-6-iodo-4-(3H)-quinazolinone (IQ2-S) as well as its radioiodinated form (125IQ2-S) as a prodrug with potential for hydrolysis by SULF1. IQ2-S was successfully docked in silico into three enzymes – homolog of SULF1, alkaline phosphatase, and prostatic acid phosphatase. The incubation of 125IQ2-S and 125IQ2-P with the three enzymes in solution confirms the docking results and enzyme selectivity for the analogs. The hydrolysis of both radioactive compounds produces the water-insoluble, fluorescent product 2-(2?-hydroxyphenyl)-6-[125I]iodo-4-(3H)-quinazolinone (125IQ2-OH). The in vitro incubation of 127IQ2-S and 127IQ2-P with pancreatic, ovarian, and prostate cancer cells expressing studied hydrolases also results in their hydrolysis and the precipitation of 127IQ2-OH fluorescent crystals on the cell surface. To our knowledge, these findings are the first to report the targeting of a radioactive substrate to SULF1 and that this prodrug may be potentially useful in the imaging (123I/124I/131I) and radiotherapy (131I) of pancreatic cancer.We identified extracellular sulfatase 1 as an enzyme that is appropriate for our concept of Enzyme-Mediated Cancer Imaging and Therapy, which aims to use radiolabeled compounds to target hydrolases over-expressed on the extracellular surface of pancreatic tumor cells. Fluorescent products of the hydrolysis of the newly designed and synthesized sulfurylated quinazolinone derivative suggest its potential for use in imaging and radiotherapeutic treatment of pancreatic cancer.
HIV protease is a key enzyme to play a key role in the HIV-1 replication cycle and control the maturation from HIV viruses to an infectious virion. HIV-1 protease has become an important target for anti-HIV-1 drug development. Here, we used molecular dynamics simulation to study the binding mode between mannitol derivatives and HIV-1 protease. The results suggest that the most active compound (M35) has more stable hydrogen bonds and stable native contacts than the less active one (M17). These mannitol derivatives might have similar interaction mode with HIV-1 protease. Then, 3D-QSAR was used to construct quantitative structure–activity models. The cross-validated q2 values are found as 0.728 and 0.611 for CoMFA and CoMSIA, respectively. And the non-cross-validated r2 values are 0.973 and 0.950. Nine test set compounds validate the model. The results show that this model possesses better prediction ability than the previous work. This model can be used to design new chemical entities and make quantitative prediction of the bioactivities for HIV-1 protease inhibitors before resorting to in vitro and in vivo experiment.The binding mode of M17 (in gray) and M35 (in green) at the active site of HIV PR was investigated. Both M35 and M17 can form hydrogen bond with the catalytic residue of Asp25. Both M17 and M35 also have contact with Asp25, Ala28, Ile50, and Ile83.
The diversity-oriented chemistry synthesis together with the random screening approach has permitted the discovery and optimization of novel antiviral lead compounds. In this paper, a series of novel 5-substituted-2-(4-substituted phenyl)-1,3-benzoxazoles was synthesized and evaluated for their in vitro anti-influenza A virus and anti-influenza B virus activity. The activity was monitored by the MTS assay in the Madin–Darby canine kidney cells. Compound 7h showed excellent inhibitory activity and selective index against A/H3N2 (EC50 = 37.03 ?m, SI > 5), which were all higher than that of the reference drug oseltamivir (EC50 > 59.00 ?m, SI > 1). However, no compound displays inhibitory activity against influenza B virus.A series of novel 5-substituted-2-(4-substituted phenyl)-1,3-benzoxazoles was synthesized and evaluated for their in vitro anti-influenza A virus (IFV-A) and anti-influenza B virus (IFV-B) activity. Among them, two compounds 7h and 7t from the series exhibited potent inhibitory effects against IFV-A replication in cell culture. Particularly, Compound 7h showed excellent inhibitory activity and selective index against A/H3N2 (EC50 = 37 ?m, SI > 5), which were all higher than that of the reference drug Oseltamivir (EC50 > 59 ?m, SI > 1).
Synthetic drugs such as allopurinol and benzbroarone are commonly used to treat the complex pathogenesis of gout, a metabolic disease that results from an inflammation of the joints caused by precipitation of uric acid. We seek to discover novel phytochemicals that could treat gout, by targeting the xanthine oxidase (XO) and cyclooxygenase 2 (COX-2) enzymes. In this study, we report the screening of 9 compounds of flavonoids from the ZINC and PubChem databases (containing 2,092 flavonoids) using the iGEMDOCK software tool against the XO and COX-2 3D protein structures. Each compound was also evaluated by an in vitro bioassay testing the inhibition of XO and COX-2. Myricetin and luteolin were found to be the potential dual inhibitors of XO and COX-2 as demonstrated by IC50: 62.7 and 3.29?g/mL (XO) / 70.8 and 16.38?g/mL (COX-2), respectively. In addition, structure activity relationships and other important factors of the flavonoids binding to the active site of XO and COX-2 were discussed, which is expected for further rational drug design.
Posted on 3 October 2011 | 10:42 pm
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