CoFe2O4/TMU‐17‐NH2 as a hybrid magnetic nanocomposite catalyst for multicomponent synthesis of dihydropyrimidines

A new magnetic metal–organic framework nanocomposite (CoFe₂O₄/TMU‐17‐NH₂) was prepared via an embedding approach by synthesis of the metal–organic framework crystals in the presence of magnetic cobalt ferrite nanoparticles. We demonstrated that the resulting magnetic nanocomposite can serve as a recyclable nanocatalyst for one‐pot synthesis of bis‐3,4‐dihydropyrimidin‐2(1H)‐one and 3,4‐dihydropyrimidin‐2(1H)‐one derivatives via three‐component reaction of 1,3‐diketone, urea or thiourea and aromatic aldehyde under solvent‐free conditions. CoFe₂O₄/TMU‐17‐NH₂ was characterized using various techniques. The recovery of the nanocomposite was achieved by a simple magnetic decantation and it was reused at least seven times without significant degradation in catalytic activity.     

Synthesis and Fungicidal Activity of (E)‐5‐[1‐(2‐Oxo‐1‐oxaspiro[4,5]dec/non‐3‐en‐3‐yl)ethylidene]‐2‐aminoimidazolin‐4‐one Derivatives

The novel fungicidal agents, (E )‐5‐[1‐(2‐oxo‐1‐oxaspiro[4,5]dec/non‐3‐en‐3‐yl)ethylidene]‐2‐aminoimidazolin‐ 4‐one derivatives, were designed and synthesized in moderate to excellent yields in four steps using α ‐hydroxyketone and diketene as raw materials and characterized by HR‐ESI‐MS , ¹H NMR and X‐ray diffraction. The preliminary bioassay showed that some of these compounds, such as 5e , 6a , 6e , and 7 h exhibit 87.8%, 91.3%, 89.9% and 87.8% inhibition rates against Sclerotinia scleotiorum , 3b , 3c , 4c and 7 h exhibit 96.4%, 92.5%, 90.3% and 76.9% inhibition rates against Phytophthora capsici at the concentration of 50 µg/mL , respectively. These compounds exhibited significant fungicidal activities against S. scleotiorum and P. capsici with EC₅₀ values of 2.56–11.60 µg/mL , and compounds 6e and 7 h exhibited weak inhibition against the spore germination of S. scleotiorum , while the spore germination of P. capsici was strongly inhibited by compound 7 h solution. Scanning electron microscopy (SEM ) and transmission electron microscopy (TEM ) observation indicated that compound 7 h had a significant impact on the structure and function of the hyphal cell wall of P. capsici mycelium.     

Synthesis and Antimicrobial Activity of Novel Quinoxaline Derivatives

In this study, certain 3‐substituted styrylquinoxalin‐2(1H)‐ones ( 2a‐d ) and their 2‐chloro ( 3a‐d ) and 2‐piperazinyl derivatives ( 4a‐g ) were synthesized from 3‐methylquinoxalin‐2(1H)‐one ( 1 ). In addition, a series of 1‐alkyl‐3‐substituted styrylquinoxalin‐2(1H)‐ones ( 5a‐d ) was also prepared. Moreover, 3‐(N²‐arylidenehydrazinocarbonyl)quinoxalin‐2(1H)‐ones ( 8a‐c ) as well as their cyclized oxadiazolinyl derivatives ( 9a‐c ) were prepared from 3‐hydrazinocarbonylquinoxalin‐2(1H)‐one ( 7 ). Furthermore, 3‐(5‐substituted thio‐1,3,4‐oxadiazol‐2‐yl)quinoxalin‐2(1H)‐ones ( 11a‐c ) and ( 12a‐c ) were obtained from the intermediate compound ( 10 ) ‐ previously obtained via cyclization of ( 7 ) with CS₂. Likewise, 3‐(5‐oxo‐4,5‐dihydro‐(1,3,4‐oxadiazol‐2‐yl)quinoxalin‐2(1H)‐one ( 13 ), 3‐[5‐(4‐nitrophenyl)‐1,3,4‐oxadiazol‐2‐yl]‐quinoxalin‐2(1H)‐one ( 14 ) and its 2‐chloro derivative ( 15 ) were prepared from 3‐hydrazinocarbonylquinoxalin‐2(1H)‐one ( 7 ). Some of these derivatives were evaluated for antimicrobial activity in vitro and some of the tested compounds showed antibacterial or antifungal activity.     

Effect of the Brush Structure on the Degradation Mechanism of Polystyrene–Clay Nanocomposites

Summary: Pyrolysis‐GC‐MS and TGA‐FT‐IR methods have been used to perform a comparative degradation study of polystyrene and a polystyrene–clay composite. An abnormally high yield of α‐methylstyrene has been detected for the composite. This and other differences in degradation products have been explained by enhanced intermolecular interaction of the grafted PS chains, forming a brush structure. A conceptual model of the process has been suggested.

GC pyrograms of virgin PS (A) and PS–clay composite (B) pyrolyzed at 500 °C (1: styrene; 2: 2,4‐diphenylbut‐1‐ene; 2′: dimer derivatives; 3: 2,4,6‐triphenylhex‐1‐ene; 3′: trimer derivatives; 4: α‐methylstyrene).     

Structural and energetic insight into the interactions between the benzolactam inhibitors and tumor marker HSP90α

The heat shock protein 90α (HSP90α) provides a promising molecular target for cancer therapy. A series of novel benzolactam inhibitors exhibited distinct inhibitory activity for HSP90α. However, the structural basis for the impact of distinct R₁ substituent groups of nine benzolactam inhibitors on HSP90α binding affinities remains unknown. In this study, we carried out molecular docking, molecular dynamics (MD) simulations, and molecular mechanics and generalized Born/surface area (MM–GBSA) binding free energy calculations to address the differences. Molecular docking studies indicated that all nine compounds presented one conformation in the ATP-binding site of HSP90α N-terminal domain. MD simulations and subsequent MM–GBSA calculations revealed that the hydrophobic interactions between all compounds and HSP90α contributed the most to the binding affinity and a good linear correlation was obtained between the calculated and the experimental binding free energies (R = 0.88). The per residue decomposition revealed that the most remarkable differences of residue contributions were found in the residues Ala55, Ile96, and Leu107 defining a hydrophobic pocket for the R₁ group, consistent with the analysis of binding modes. This study may be helpful for the future design of novel HSP90α inhibitors.     

Synthesis of 4‐Arylisocoumarins (=4‐Aryl‐1H‐2‐benzopyran‐1‐ones) through Acidic Hydrolysis of (Z)‐2‐(1‐Aryl‐2‐methoxyethenyl)benzaldehydes,Followed by Oxidation

4‐Arylisocoumarins (=4‐aryl‐1H‐2‐benzopyran‐1‐ones) 6 were prepared from 2‐(1‐aryl‐2‐methoxyethenyl)‐1‐bromobenzenes 1 . Successive treatment of these bromo styrenes with BuLi and 1‐formylpiperidine gave a mixture of (E)‐ and (Z)‐2‐(1‐aryl‐2‐methoxyethenyl)benzaldehydes 2 . Hydrolysis of (Z)‐isomers with conc. HBr, followed by pyridinium chlorochromate (PCC) oxidation of the resulting 1H‐2‐benzopyran‐1‐ol derivatives 4 (and 5 ), afforded the desired products.     

Synthesis of α‐(Fluorophenyl)pyridine by Palladium‐Catalyzed Cross‐Coupling Reaction

A series of α‐(fluoro‐substituted phenyl)pyridines have been synthesized by means of a palladium‐catalyzed cross‐coupling reaction between fluoro‐substituted phenylboronic acid and 2‐bromopyridine or its derivatives. The reactivities of the phenylboronic acids containing di‐ and tri‐fluoro substituents with α‐pyridyl bromide were investigated in different catalyst systems. Unsuccessful results were observed in the Pd/C and PPh₃ catalyst system due to phenylboronic acid containing electron‐withdrawing F atom(s). For the catalyst system of Pd(OAc)₂/PPh₃, the reactions gave moderate yields of 55% –80%, meanwhile, affording 10% –20% of dimerisation (self‐coupling) by‐products, but trace products were obtained in coupling with 2,4‐difluorophenylboronic acids because of steric hinderance. Pd(PPh₃)₄ was more reactive for boronic acids with sterically hindering F atom(s), and the coupling reactions gave good yields of 90% and 91% without any self‐coupling by‐product.     

In silico fragment-mapping method: a new tool for fragment-based/structure-based drug discovery

Here, we propose an in silico fragment-mapping method as a potential tool for fragment-based/structure-based drug discovery (FBDD/SBDD). For this method, we created a database named Canonical Subsite–Fragment DataBase (CSFDB) and developed a knowledge-based fragment-mapping program, Fsubsite. CSFDB consists of various pairs of subsite–fragments derived from X-ray crystal structures of known protein–ligand complexes. Using three-dimensional similarity-matching between subsites on one protein and another, Fsubsite compares the surface of a target protein with all subsites in CSFDB. When a local topography similar to the subsite is found on the surface, Fsubsite places a fragment combined with the subsite in CSFDB on the target protein. For validation purposes, we applied the method to the apo-structure of cyclin-dependent kinase 2 (CDK2) and identified four compounds containing three mapped fragments that existed in the list of known inhibitors of CDK2. Next, the utility of our fragment-mapping method for fragment-growing was examined on the complex structure of tRNA-guanine transglycosylase with a small ligand. Fsubsite mapped appropriate fragments on the same position as the binding ligand or in the vicinity of the ligand. Finally, a 3D-pharmacophore model was constructed from the fragments mapped on the apo-structure of heat shock protein 90-α (HSP90α). Then, 3D pharmacophore-based virtual screening was carried out using a commercially available compound database. The resultant hit compounds were very similar to a known ligand of HSP90α. As a result of these findings, this in silico fragment-mapping method seems to be a useful tool for computational FBDD and SBDD.     

High‐performance liquid chromatographic enantioseparation of isoxazoline‐fused 2‐aminocyclopentanecarboxylic acids on a chiral ligand‐exchange stationary phase

The application of a chiral ligand‐exchange column for the direct high‐performance liquid chromatographic enantioseparation of unusual β‐amino acids with a sodium N‐((R)‐2‐hydroxy‐1‐phenylethyl)‐N‐undecylaminoacetate‐Cu(II) complex as chiral selector is reported. The investigated amino acids were isoxazoline‐fused 2‐aminocyclopentanecarboxylic acid analogs. The chromatographic conditions were varied to achieve optimal separation. The effects of temperature were studied at constant mobile phase compositions in the temperature range 5–45°C, and thermodynamic parameters were calculated from plots of lnk or lnα versus 1/T. Δ(ΔH°) ranged from –2.3 to 2.2 kJ/mol, Δ(ΔS°) from –3.0 to 7.8 J mol^?1 K^?1 and –Δ(ΔG°) from 0.1 to 1.7 kJ/mol, and both enthalpy‐ and entropy‐controlled enantioseparations were observed. The latter was advantageous with regard to the shorter retention and greater selectivity at high temperature. Some mechanistic aspects of the chiral recognition process are discussed with respect to the structures of the analytes. The sequence of elution of the enantiomers was determined in all cases.     

PPA-SiO2 Catalyzed Multi-component Synthesis of N-[α-(β-Hydroxy-α-naphthyl)(benzyl)] O-Alkyl Carbamate Derivatives

Silica-supported polyphosphoric acid (PPA-SiO2) was found to be an efficient catalyst for the multi-component condensation reaction of benzaldehydes, 2-naphthol, and methyl/benzyl carbamate to afford the corresponding N-[α-(β-hydroxy-α-naphthyl)(benzyl)] O-alkyl carbamate derivatives in good to excellent yields. This new approach consistently has the advantage of short reaction time, high conversions, clean reaction profiles, and simple experimental and work-up procedures.     

Synthesis and Bioactivity of Some New 2-(Alkoxy carbonyl alkyl)-6-bromo-3,4-dihydro-3-(α-methyl benzyl)-2-oxo- benzo[e] [2H-1,3,2-oxazaphosphinine] Derivatives

Synthesis of some new 2-(alkoxy carbonyl alkyl)-6-bromo-3,4-dihydro-3-(α-methyl benzyl)-2-oxo-3-benzo- [e][2H-1,3,2-oxazaphosphinine] derivatives was accomplished through a two step process, which involves the condensation of 2-[(α-methylbenzyl amino)methyl]-4-bromophenol (1) with phosphorus oxychloride in equimolar quantities in the presence of triethylamine in dry toluene in 50—55 ℃ producing the corresponding intermediate (2), and subsequent reaction with the amino acid alkyl ester in dry tetrahydrofuran in the presence of triethylamine at different temperatures. They exhibited significant antibacterial and fungal activity.     

Synthesis of Some Quinazoline‐2(1H),4(3H)‐dione Derivatives

Several quinazoline‐2(1H),4(3H)‐dione derivatives were synthesized from pyrimidine‐2(1H),4(3H)‐dione derivative.     

Synthesis of 2‐Substituted 3‐Alkylidene‐2,3‐dihydro‐1H‐isoindol‐1‐imines through Cyclization of [1‐(2‐Cyanophenyl)alkylidene]aminide Intermediates Generated from the Reaction of 2‐(1‐Azidoalkyl)benzonitriles with NaH

A convenient sequence for the preparation of 3‐alkylidene‐2,3‐dihydro‐1H‐isoindol‐1‐imine derivatives 6 has been developed. Thus, 2‐(1‐azidoalkyl)benzonitriles 2 , readily accessible from 2‐alkylbenzonitriles, are allowed to react with NaH in DMF at 0° to room temperature to generate [1‐(2‐cyanophenyl)alkylidene]aminide intermediates 3 , of which cyclization and the subsequent rearrangement, followed by alkylation with alkyl halides, affords 2‐substituted 1‐alkylidene‐2,3‐dihydro‐1H‐isoindol‐2‐imines 6 in generally moderate yields.     

Gallium(III) Iodide‐catalyzed Biginelli‐type Reaction Under Solvent‐free Conditions: Efficient Synthesis of Dihydropyrimidine‐2(1H)‐one Derivatives

The Biginelli‐type condensation of ethyl acetoacetate/cycloketone, aldehyde and urea/thiourea under solvent‐free condition catalyzed by 10% gallium(III) iodide to form dihydropyrimidine‐2(1H)‐one derivatives was described. This process offered one way to constructing dihydropyrimidine‐2(1H)‐ones in good to excellent yields with simple procedure and short reaction time.     

Ring Opening of 2‐(Benzylamino)‐2H‐1,4‐benzoxazin‐3(4H)‐ones and 2‐Bromo‐2H‐1,4‐benzoxazin‐3(4H)‐ones

Substituted 2‐(benzylamino)‐2H‐1,4‐benzoxazin‐3(4H)‐ones are unstable under alkaline and acidic conditions, undergoing opening of the benzoxazinone ring. 2‐Bromo‐2H‐1,4‐benzoxazin‐3(4H)‐ones show similar degradation under alkaline conditions, while replacement of Br at C(2) to give 2‐hydroxy‐2H‐1,4‐benzoxazin‐3(4H)‐ones was observed only under mild alkaline conditions. Mechanisms of ring opening and degradation to 2‐aminophenol derivatives are proposed.     

Synthesis and Reactions of 2‐[1‐Methyl‐1‐(pyrrolidin‐2‐yl)ethyl]‐1H‐pyrrole and Some Derivatives with Aldehydes: Chiral Structures Combining a Secondary‐Amine Group with an 1H‐Pyrrole Moiety as Excellent H‐Bond Donor

The synthesis of compound 2 and its derivatives 6 and 8 combining a pyrrolidine ring with an 1H‐pyrrole unit is described (Scheme 2). Their attempted usability as organocatalysts was not successful. Reacting these simple pyrrolidine derivatives with cinnamaldehyde led to the tricyclic products 3b, 9b , and 10b first (Scheme 1, Fig. 2). The final, major products were the pyrrolo‐indolizidine tricycles 3a, 9a , and 10a obtained via the iminium ion reacting intramolecularly with the nucleophilic β‐position of the 1H‐pyrrole moiety (cf. Scheme 1).     

Docking pose selection by interaction pattern graph similarity: application to the D3R grand challenge 2015

High affinity ligands for a given target tend to share key molecular interactions with important anchoring amino acids and therefore often present quite conserved interaction patterns. This simple concept was formalized in a topological knowledge-based scoring function (GRIM) for selecting the most appropriate docking poses from previously X-rayed interaction patterns. GRIM first converts protein–ligand atomic coordinates (docking poses) into a simple 3D graph describing the corresponding interaction pattern. In a second step, proposed graphs are compared to that found from template structures in the Protein Data Bank. Last, all docking poses are rescored according to an empirical score (GRIMscore) accounting for overlap of maximum common subgraphs. Taking the opportunity of the public D3R Grand Challenge 2015, GRIM was used to rescore docking poses for 36 ligands (6 HSP90α inhibitors, 30 MAP4K4 inhibitors) prior to the release of the corresponding protein–ligand X-ray structures. When applied to the HSP90α dataset, for which many protein–ligand X-ray structures are already available, GRIM provided very high quality solutions (mean rmsd = 1.06 Å, n = 6) as top-ranked poses, and significantly outperformed a state-of-the-art scoring function. In the case of MAP4K4 inhibitors, for which preexisting 3D knowledge is scarce and chemical diversity is much larger, the accuracy of GRIM poses decays (mean rmsd = 3.18 Å, n = 30) although GRIM still outperforms an energy-based scoring function. GRIM rescoring appears to be quite robust with comparison to the other approaches competing for the same challenge (42 submissions for the HSP90 dataset, 27 for the MAP4K4 dataset) as it ranked 3rd and 2nd respectively, for the two investigated datasets. The rescoring method is quite simple to implement, independent on a docking engine, and applicable to any target for which at least one holo X-ray structure is available.     

Pesticidal and antifertility activities of triorganogermanium(IV) complexes synthesized using a green chemical approach

Microwave chemistry is a green chemical method that improves reaction conditions and product yields while reducing solvent amounts and reaction times. This paper deals with the synthesis, spectral and biological studies of germanium(IV) complexes with chelating hydrazones derived from 1‐(pyridine‐2‐yl)ethanone (F₁) and 1‐(furan‐2‐yl)ethanone (F₂) with isonicotinohydrazide (INH). The complexes have been synthesized under a microwave–green chemical approach and investigated using a combination of microanalytical analysis, melting point, IR spectra, ¹H NMR spectra and ¹³C NMR spectra. Trimethylgermanium(IV)chloride and triphenylgermanium(IV)chloride interact with the hydrazones in a 1:1 molar ratio (metal:ligand), resulting in the formation of coloured products. On the basis of conductance and spectral evidence, a pentacoordinated structure for germanium(IV) complexes has been assigned for these products. The ligand is coordinated to the germanium(IV) via the azomethine nitrogen atom and the enolic oxygen atom. The free ligands and their metal complexes have been tested in male rats in order to assess their antifertility properties. Ligands and their metal complexes have also been tested in vitro against a number of pathogenic microorganisms in order to assess their antimicrobial and pesticidal properties. Both the ligands and their complexes were found to possess appreciable antifertility activity and other activities, which have been discussed in brief. Copyright © 2013 John Wiley & Sons, Ltd.     

New Flavonoids from Lysimachia christinae Hance

A chemical investigation of Lysimachia christinae, a traditional Chinese medicine used as an effective conservative treatment for gall stones, hepatolithiasis, and urinary calculi, resulted in the isolation of two new flavonoids, myricetin 3,3′‐di‐α‐L ‐rhamnopyranoside ( 1 ) and quercetin 3,3′‐di‐α‐L ‐rhamnopyranoside ( 2 ), along with the five known flavonoids quercetin 3‐[O‐α‐L ‐rhamnopyranosyl‐(1→2)‐β‐D ‐galactopyranoside], amentoflavone, hyperin, quercetin 3‐β‐D ‐glucopyranoside, and kaempferol 3‐α‐L ‐rhamnopyranoside. Amentoflavone was reported for the first time from the genus Lysimachia, and quercetin 3‐[O‐α‐L ‐rhamopyranosyl‐(1→2)‐β‐D ‐galactopyranoside] was isolated from this plant for the first time. The structures of the new compounds were elucidated on the basis of their chemical reactions and extensive spectroscopic analyses, including UV, mass, and NMR spectra.     

Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.