An appraisal of the Suzuki cross-coupling reaction for the synthesis of novel fluorescent coumarin derivatives

We report the chemical design and development of 3-aryl-substituted 7-alkoxy-4-methylcoumarins with enhanced fluorogenic properties. The 3-aryl substituents are installed via an optimized Suzuki–Miyaura cross-coupling (SMC) reaction between a 7-alkoxy-3-bromo-4-methylcoumarin and aryl boronic MIDA esters using Pd(OAc)₂/XPhos in a catalytic system with K₂CO₃ in aqueous THF. Under these conditions, an exocyclic ester functionality is found to be unaffected. Subsequent saponification revealed a carboxylic acid functionality that is suitable for conjugation reactions. Evaluation of their fluorescence properties indicated that the installed 3-heteroaryl substituent, particularly benzofuran-2-yl, resulted in a significant red shift of both the excitation and emission wavelengths.     

Investigation and comparison of biological effects of regioselectively synthesized thiazole derivatives

In this study, anticancer, antibacterial (against hospital-isolated antibiotic-resistant Escherichia coli strains), antifungal, and antioxidant effects of synthesized heterocyclic compounds 5 and 7 containing thiazole core were examined. Cytotoxicity testing was utilized against MCF-7 breast cancer cells via MTT cell viability assay. Antibacterial and antifungal activities were checked out according to Clinical and Laboratory Standards Institute (CLSI) guidelines, and antioxidant properties were evaluated through scavenging 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radicals. Results showed the viability of breast cancer cell lines was reliant on concentration of heterocycles and time of incubation. Synthetic compounds exhibited excellent antibacterial and antifungal properties base on their minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and minimum fungicidal concentration (MFC) values as well as high antioxidant activities according to their IC₅₀ values. Higher anticancer and antibacterial properties were observed with compound 7; on the contrary, thiazole 5 had better antioxidant effects. They can be introduced as potent antimicrobial, antioxidant, and anticancer agents.     

Synthesis and bioactivity evaluation of some novel sulfonamide derivatives

A simple and convenient method for the synthesis of biologically active sulfonamide derivatives was achieved. All the title compounds were characterized by spectral and elemental analysis. They were further screened in vitro for their abilities towards antibacterial, antifungal and antioxidant activities. The compound N,N'-(3,3′-dimethoxybiphenyl-4,4′-diyl)bis(4-fluorobenzenesulfonamide) (5b) and N-(3-(9H-carbazol-4-yloxy)-2-hydroxypropyl)-4-fluoro-N-isopropylbenzenesulfonamide (5e) exhibited good activity when compared to the standard bactericide, Chloramphenicol and fungicide, Ketoconazole respectively. The compounds (2S)-N-((2S,4S)-5-(4-Chloro-phenylsulfonamido)-4-hydroxy-1, 6-diphenylhexan-2-yl)-3-methyl-2-(2-oxotetrahydropyrim-idin-1(2H)-yl)butan-amide (4f) and (2S)-N-((2S,4S)-5-(4-fluorophenylsulfonamido)-4-hydroxy-1,6-diphenyl-hexan-2-yl)-3-methyl-2-(2-oxotetrahydropyrimidin-1(2H)-yl)bu-tana-mide (5f) exhibited good antioxidant activity when compared with standard antioxidant, Ascorbic acid.     

Synthesis and antifungal activities of novel trifluoroethane derivatives with coumarin,indole and thiophene

A series of novel 1-(β-coumarinyl)-1-(β-indolyl)-1-(α-thiophenyl)trifluoroethane derivatives 5aaa-5hdb were prepared by one-pot reaction from 3-(trifluoroacetyl)coumarin with indole and α-substituted thiophene. Their structures were confirmed by ¹H NMR, ¹³C NMR, ¹⁹F NMR, HRMS and X-ray single crystal diffraction, and their antifungal activities against F. moniliforme, F. graminearum, F. oxysporum, R. solani and P. nicotianae were evaluated. The title compounds displayed significant to moderate in vitro antifungal activity when compared to the standard drug triadimefon. Among the synthesized compounds, compound 5bfa showed the highest inhibitor rate of 83.5 % at 0.500 mg/mL against R. solani, while compound 5ada displayed the highest inhibitor rate of 73.3 % at 0.500 mg/mL against F. graminearum.     

Synthesis and biological activities of benzothiazole derivatives bearing a 1,3,4-thiadiazole moiety

A series of benzothiazole derivatives bearing a 1,3,4-thiadiazole moiety were designed, synthesized and evaluated for their antibacterial, antifungal and antiviral activities. The bioassay results indicated that most of target compounds showed good antiviral activities against tobacco mosaic virus (TMV) and antibacterial activities against Xanthomonas oryzae pv. oryzae (Xoo) and Ralstonia solanacearum (Rs). Especially, the anti-Xoo effect of title compounds 5k (N-(5-methoxybenzo[d]thiazol-2-yl)-2-((5-(2-tolyl)-1,3,4-thiadiazol-2-yl)thio)acetamide) and the anti-Rs effect of title compounds 5a (N-(5-nitrobenzo[d]thiazol-2-yl)-2-((5-(4-(trifluorom ethyl)phenyl)-1,3,4-thiadiazol-2-yl)thio)acetmide) respectively reached 52.4% and 71.6% at 100?µg/mL, which are superior to that of bismerthiazol (32.0% and 52.3%). In addition, the protective and inactivation activities of title compound 5i (N-(5-methoxybenzo [d]thiazol-2-yl)-2-((5-(4-nitrophenyl)-1,3,4-thiadiazol-2-yl)thio)acetamide) against TMV were 79.5% and 88.3%, respectively, which are better than that of ningnanmycin (76.4% and 86.8%). The above research showed that benzothiazole derivatives bearing a 1,3,4-thiadiazole moiety may be used as potential molecular templates in searching for highly-efficient antiviral and antibacterial agents.     

Novel imidazole derivatives as antifungal agents: Synthesis,biological evaluation,ADME prediction and molecular docking studies

Abstract

A series of 2-(substituteddithiocarbamoyl)-N-[4-((1H-imidazol-1-yl)methyl)phenyl]acetamide derivatives was designed and synthesized to combat the increasing incidence of drug-resistant fungal infections. All synthesized compounds were characterized by IR, ¹H-NMR, ¹³C-NMR, and HRMS spectra and elemental analyses. Antifungal activity tests were performed against four different fungal strains. Molecular docking studies were performed to investigate the mode of action towards the fungal lanosterol 14α-demethylase, a cytochrome P450-dependent enzyme. ADME studies were carried out and a connection between activities and physicochemical properties of the target compounds was determined. Most of the final compounds exhibited significant activity against Candida albicans and Candida krusei with MIC₅₀ value 12.5?μg/mL. The results of in vitro anti-Candida activity, a docking study and ADME prediction revealed that the newly synthesized compounds have potential anti-Candida activity and evidenced the most active derivative, 5b (2-Pyrrolidinthiocarbonylthio-N-[4-((1H-imidazol-1-yl)methyl)phenyl]acetamide), which can be further optimized as a lead compound.     

Synthesis and biological activities of thio-triazole derivatives as novel potential antibacterial and antifungal agents

A series of novel thio-triazole derivatives including thiols, thioethers and thiones as well as some corresponding triazolium compounds were conveniently and efficiently synthesized from commercially available halobenzyl halides and thiosemicarbazide. All the new compounds were characterized by 1 H NMR, 13 C NMR, FTIR, MS and HRMS spectra. Their antibacterial and antifungal activities in vitro were evaluated against four Gram-positive bacteria, four Gram-negative bacteria and two fungi by two-fold serial dilution technique. The preliminary bioassay indicated that some prepared triazoles exhibited effective antibacterial and antifungal activities. Especially, 3,4-dichlorobenzyl triazolethione and its triazolium derivatives displayed the most potent activities against all the tested strains.     

Synthesis,molecular docking studies,and absorption,distribution, metabolism,and excretion prediction of novel sulfonamide derivatives as antibacterial agents

A series of novel sulfonamide‐amide derivatives were synthesized from 3‐(2,4 dichlorophenylamino)‐3‐oxopropane‐1‐sulfonylchloride and a variety of amines under solvent‐free conditions at room temperature. 3‐(2,4‐dichlorophenylamino)‐3‐oxopropane‐1 sulfonylchloride was synthesized in four steps starting from 2,4‐dichloroaniline and chloropropanoic acid in good yield and purity. The synthesized compounds were screened for their in vitro antibacterial activity against Escherichia coli (ATCC 25922) and Staphylococcus aureus (ATCC 29213). Molecular docking of sulfonamide derivatives into S. aureus tyrosyl‐tRNA synthetase (TyrRS)‐active site was also performed and among these, 5m and 5g tightly fit the active sites that might be inhibitors of TyrRS for further investigations. Also in the silico metabolism profile, drug‐like properties and absorption, distribution, metabolism, excretion and toxicity (ADMET) of the title compounds were calculated by the preADMET server.     

Computational Characterization of Binding of Small Molecule Inhibitors to HIV‐1 gp41

Developing orally available small molecule inhibitors of HIV‐1 fusion has attracted significant interest over many years. Frey had recently reported several synthetic compounds which are experimentally shown to inhibit cell‐cell fusion in the low micromolar range. We carried out computational study to help identify possible binding modes by docking these compounds onto the hydrophobic pocket on gp41 and to characterize structures of binding complexes. The detailed gp41‐molecule binding interactions and free energies of binding are obtained through molecular dynamics simulation and MM‐PBSA calculation. Specific molecular interactions in the gp41‐inhibitor complexes are identified. The present computational study complements the corresponding experimental investigation and helps establish a good starting point for further refinement of small molecular gp41 inhibitors.     

Design,synthesis, and bioactivity evaluation of novel thiochromanone derivatives containing an oxime or oxime ether moiety

In this study, using botanical active component thiochromanone as the lead compound, a series of novel thiochromanone derivatives containing an oxime or oxime ether moiety were designed and synthesized. The half-maximal effective concentration (EC₅₀) values of compound 4a against Xanthomonas oryzae pv. oryzae (Xoo), Xanthomonas oryzae pv. oryzicolaby (Xoc), and Xanthomonas axonopodis pv. citri (Xac) were 6, 10, and 15 μg/ml, respectively, which were superior to those of Bismerthiazol and Thiodiazole-copper. Meanwhile, compound 4a also revealed better antifungal activity against Botrytis cinerea, with the EC₅₀ value of 18 μg/ml, than that of Carbendazim. To the best of our knowledge, this is the first report on the antibacterial and antifungal activities of this series of novel thiochromanone derivatives containing an oxime or oxime ether moiety.     

Computation of affinity and selectivity: Binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases

Binding energy calculations for complexes of mutant and wild-type human dihydrofolate reductases with 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors are reported. Quantitative insight into binding energetics of these molecules is obtained from calculations based on force field energy evaluation and thermal sampling by molecular dynamics simulations. The calculated affinity of methotrexate for wild-type and mutant enzymes is reasonably well reproduced. Truncation of the methotrexate glutamate tail results in a loss of affinity by several orders of magnitude. No major difference in binding strength is predicted between the pteridines and the quinazolines, while the N-methyl group present in methotrexate appears to confer significantly stronger binding. The recent improvement, which is used here, of our linear interaction energy method for binding affinity prediction, as well as problems with treating charged and flexible ligands are discussed. This approach should be suitable in a drug discovery context for prediction of binding energies of new inhibitors prior to their synthesis, when some information about the binding mode is available.     

Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein‐ligand binding free energies

The performances of Bennett's acceptance ratio method and thermodynamic integration (TI) for the calculation of free energy differences in protein simulations are compared. For the latter, the standard trapezoidal rule, Simpson's rule, and Clenshaw‐Curtis integration are used as numerical integration methods. We evaluate the influence of the number and definition of intermediate states on the precision, accuracy, and efficiency of the free energy calculations. Our results show that non‐equidistantly spaced intermediate states are in some cases beneficial for the TI methods. Using several combinations of softness parameters and the λ power dependence, it is shown that these benefits are strongly dependent on the shape of the integrand. Although TI is more user‐friendly due to its simplicity, it was found that Bennett's acceptance ratio method is the more efficient method. It is also the least dependent on the choice of the intermediate states, making it more robust than TI. © 2013 Wiley Periodicals, Inc.     

Synthesis and biological evaluation of novel cyanuric acid-tethered tris-pyridinium derivatives

1. Download : Download high-res image (74KB)
2. Download : Download full-size image

     

Improved convergence in dual-topology free energy calculations through use of harmonic restraints

When calculating free energy differences between two molecular systems by means of molecular dynamics simulation, accessory potential functions can help eliminate uninteresting configurational entropy contributions, improve convergence, and facilitate reversibility. In this work, we demonstrate that the use of a harmonic potential function to restrain key portions of a molecular system in a free energy perturbation dual-topology molecular dynamics approach dramatically improves convergence and precision of the calculation. Limitations of this technique are illustrated, and its use in conjunction with a fixed bond-length constraint is developed. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1278–1283, 1998     

Synthesis,spectral, stereochemical and biological evaluation of (E)-2-(3-pentyl-2,6-diarylpiperidin-4-ylidene)-N-phenylhydrazinecarbothioamide derivatives

A series of new (E)-2-(3-pentyl-2,6-diarylpiperidin-4-ylidene)-N-phenylhydrazinecarbothioamides (1-6) were synthesized from the corresponding 3-pentyl-2,6-diarylpiperidine-4-ones condensation with phenyl thiosemicarbazide. Their chemical structures were confirmed by means of elemental analysis, FT-IR, ¹H, and ¹³C NMR spectral techniques and for compound 3, HOMOCOSY, HSQC, HMBC, NOESY, and DEPT NMR spectral techniques. From the NMR spectral data the compounds (1-6) are shown to exist in normal chair conformation with equatorial orientation of all the phenyl groups at C-2 and C-6 and pentyl group at C-3. The synthesized compounds were screened for their bacterial activity against Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella typhi, and Escherichia coli and fungal activity against Candida albicans, Rhizopus sp, Aspergillus niger, and Aspergillus flasvus.     

Synthesis and biological evaluation of novel bispyridinium salts containing naphthalene-2,7-diylbis(oxy) spacer

1. Download : Download high-res image (101KB)
2. Download : Download full-size image

     

谷氨酰胺结合蛋白的分子动力学模拟和自由能计算

谷氨酰胺结合蛋白(Glutamine-binding protein, GlnBp)是大肠杆菌透性酶系统中一个细胞外液底物专一性结合蛋白, 对于细胞外液中谷氨酰胺(Gln)的运输和传递至关重要. 本文运用分子动力学(Molecular dynamics, MD)模拟采样, 考察了GlnBp关键残基与底物Gln之间的相互作用和GlnBp两条铰链的功能差别; 并采用MM-PBSA方法计算了GlnBp与底物Gln的结合自由能. 结果表明: Ph13, Phe50, Thr118和Ile69与底物Gln的范德华相互作用和Arg75, Thr70, Asp157, Gly68, Lys115, Ala67, His156与底物Gln的静电相互作用是结合Gln的主要推动力; 复合物的铰链区85～89柔性大, 对构象开合提供了结构基础; 而铰链区181～185柔性小, 其作用更多是在功能上把底物Gln限制在口袋中; 自由能预测值与实验值吻合. 本研究很好地解释了GlnBp结构与功能的关系, 为进一步了解GlnBp的开合及转运Gln的机制提供了重要的结构信息.     

Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9

Free energy calculations are described for the small copper‐containing redox protein Azurin from Pseudomonas aeruginosa. A thermodynamic cycle connecting the reduced and oxidized states at pH 5 and pH 9 is considered, allowing for an assessment of convergence in terms of hysteresis and cycle closure. Previously published thermodynamic integration (TI) data is compared to Hamiltonian replica exchange TI (RE‐TI) simulations using different simulation setups. The effects of varying simulation length, initial structure, position restraints on particular atoms, and the strength of temperature coupling are studied. Although the overall simulation times are too short to observe an experimentally described peptide plane rotation, it is found that RE‐TI simulations do stimulate the distribution of conformational changes over the relevant values of the TI coupling parameter λ. This results in significantly improved values for hysteresis and cycle closure when compared to regular TI. © 2012 Wiley Periodicals, Inc.     

Defining the Role of Isoeugenol from Ocimum tenuiflorum against Diabetes Mellitus-Linked Alzheimer’s Disease through Network Pharmacology and Computational Methods

The present study involves the integrated network pharmacology and phytoinformatics-based investigation of phytocompounds from Ocimum tenuiflorum against diabetes mellitus-linked Alzheimer’s disease. It aims to investigate the mechanism of the Ocimum tenuiflorum phytocompounds in the amelioration of diabetes mellitus-linked Alzheimer’s disease through network pharmacology, druglikeness and pharmacokinetics, molecular docking simulations, GO analysis, molecular dynamics simulations, and binding free energy analyses. A total of 14 predicted genes of the 26 orally bioactive compounds were identified. Among these 14 genes, GAPDH and AKT1 were the most significant. The network analysis revealed the AGE-RAGE signaling pathway to be a prominent pathway linked to GAPDH with 50.53% probability. Upon the molecular docking simulation with GAPDH, isoeugenol was found to possess the most significant binding affinity (−6.0 kcal/mol). The molecular dynamics simulation and binding free energy calculation results also predicted that isoeugenol forms a stable protein–ligand complex with GAPDH, where the phytocompound is predicted to chiefly use van der Waal’s binding energy (−159.277 kj/mol). On the basis of these results, it can be concluded that isoeugenol from Ocimum tenuiflorum could be taken for further in vitro and in vivo analysis, targeting GAPDH inhibition for the amelioration of diabetes mellitus-linked Alzheimer’s disease.