Computer-aided design of non sulphonyl COX-2 inhibitors: an improved comparative molecular field analysis incorporating additional descriptors and comparative molecular similarity indices analysis of 1,3-diarylisoindole derivatives

Increased catalytic activity through ZnMo7O24/g-C3N4 heterostructured assemblies for greener indole condensation reaction at room temperature

As an economical conjugated polymer, graphitic carbon nitride (g-C₃N₄) has recently attracted much attention due to its exciting chemical and thermal stability and easy availability. Herein, we constructed a metal-coordinated graphitic carbon nitride (M–g-C₃N₄) catalyst through simple impregnation and calcination methods and used it as a new heterogeneous catalyst for the efficient synthesis of bis (indolyl) methanes and trisindolines under mild conditions. This reaction is performed efficiently in water as an environmentally friendly solvent at ambient conditions. The ZnMo₇O₂₄/g-C₃N₄ nanocomposite was synthesized by a simple method by immobilizing Mo₇O₂₄(NH₄)₆·4H₂O and ZnCl₂ on the surface of g-C₃N₄ under hydrothermal conditions. It was characterized by FT-IR, EDS, and electronic scanning microscopy (SEM). The metal doping of Mo and Zn on the surface of graphitic carbon nitride leads to the formation of a green catalyst that gives good to excellent yields of products in short reaction times with an easy working procedure. In addition, the ZnMo₇O₂₄/g-C₃N₄ catalyst could be reused at least five runs without apparent loss of efficiency.

Copper-catalyzed asymmetric cyclization of alkenyl diynes: method development and new mechanistic insights

Metal carbenes have proven to be one of the most important and useful intermediates in organic synthesis, but catalytic asymmetric reactions involving metal carbenes are still scarce and remain a challenge. Particularly, the mechanistic pathway and chiral induction model in these asymmetric transformations are far from clear. Described herein is a copper-catalyzed asymmetric cyclization of alkenyl diynes involving a vinylic C(sp²)–H functionalization, which constitutes the first asymmetric vinylic C(sp²)–H functionalization through cyclopentannulation. Significantly, based on extensive mechanistic studies including control experiments and theoretical calculations, a revised mechanism involving a novel type of endocyclic copper carbene via remote-stereocontrol is proposed, thus providing new mechanistic insight into the copper-catalyzed asymmetric diyne cyclization and representing a new chiral control pattern in asymmetric catalysis based on remote-stereocontrol and vinyl cations. This method enables the practical and atom-economical construction of an array of valuable chiral polycyclic-pyrroles in high yields and enantioselectivities.

A copper-catalyzed asymmetric cyclization of alkenyl diynes involving a vinylic C(sp²)–H functionalization is reported, enabling the construction of various valuable chiral polycyclic-pyrroles in high yields and enantioselectivities.

Virtual Screening Approach of Bacterial Peptide Deformylase Inhibitors Results in New Antibiotics

The increasing resistance of bacteria to antibacterial therapy poses an enormous health problem, it renders the development of new antibacterial agents with novel mechanism of action an urgent need. Peptide deformylase, a metalloenzyme which catalytically removes N-formyl group from N-terminal methionine of newly synthesized polypeptides, is an important target in antibacterial drug discovery. In this study, we report the structure-based virtual screening of ZINC database in order to discover potential hits as bacterial peptide deformylase enzyme inhibitors with more affinity as compared to GSK1322322, previously known inhibitor. After virtual screening, fifteen compounds of the top hits predicted were purchased and evaluated in vitro for their antibacterial activities against one Gram positive (Staphylococcus aureus) and three Gram negative (Escherichia coli, Pseudomonas aeruginosa and Klebsiella. pneumoniae) bacteria in different concentrations by disc diffusion method. Out of these, three compounds, ZINC00039650, ZINC03872971 and ZINC00126407, exhibited significant zone of inhibition. The results obtained were confirmed using the dilution method. Thus, these proposed compounds may aid the development of more efficient antibacterial agents.

Computer-aided design of negative allosteric modulators of metabotropic glutamate receptor 5 (mGluR5): Comparative molecular field analysis of aryl ether derivatives

The metabotropic glutamate receptors (mGlu receptors) have emerged as attractive targets for number of neurological and psychiatric disorders. Recently, mGluR5 negative allosteric modulators (NAMs) have gained considerable attention in pharmacological research. Comparative molecular field analysis (CoMFA) was performed on 73 analogs of aryl ether which were reported as mGluR5 NAMs. The study produced a statistically significant model with high correlation coefficient and good predictive abilities.

α-Aminophosphonates as novel anti-leishmanial chemotypes: synthesis, biological evaluation, and CoMFA studies

α-Aminophosphonates have been identified as novel anti-leishmanial chemotypes against theL. donovanipromastigote with low μM range activity.

A ligand's-eye view of protein binding

Docking tools created for structure-based design and virtual screening have also been used to automate ligand alignment for comparative molecular field analysis (CoMFA). Models based on such alignments have been compared with those obtained based solely on shared ligand substructures, but such comparisons have generally failed to distinguish between conformational specification (alignment in the internal coordinate space) and embedding in a shared external frame of reference (Cartesian alignment). Here, large sets of inhibitors were docked into two cyclooxygenase and two reverse transcriptase crystal structures, and the poses generated were evaluated in terms of the CoMFA models they produced. Realigning the conformers obtained by docking by rigid-body rotation and translation to overlay their common substructures improved model statistics and interpretability, provided the protein structure used for docking was reasonably appropriate to the ligands being considered.

Phenylsulphonyl urenyl chalcone derivatives as dual inhibitors of cyclo-oxygenase-2 and 5-lipoxygenase

Two series of phenylsulphonyl urenyl chalcone derivatives (UCH) with various patterns of substitution were tested for their effects on nitric oxide (NO) and prostaglandin E2 (PGE2) overproduction in RAW 264.7 macrophages. None of the tested compounds reduced NO production more than 50% at 10 microM but most of them inhibited the generation of PGE2 with IC50 values under the micromolar range. Me-UCH 1, Me-UCH 5, Me-UCH 9, Cl-UCH 1, and Cl-UCH 9 were selected to evaluate their influence on human leukocyte functions and eicosanoids generation. These derivatives selectively inhibited cyclo-oxygenase-2 (COX-2) activity in human monocytes being Me-UCH 5 the most potent (IC50 0.06 microM). Selected compounds also reduced leukotriene B4 synthesis in human neutrophils by a direct inhibition of 5-lipoxygenase (5-LO) activity, with IC50 values from 0.5 to 0.8 microM. In addition, lysosomal enzyme secretion, such as elastase or myeloperoxidase as well as superoxide generation in human neutrophils were also reduced in a similar range. Our findings indicate that UCH derivatives exert a dual inhibitory effect on COX-2/5-LO activity. The profile and potency of these compounds may have relevance for the modulation of the inflammatory and nociceptive responses with reduction of undesirable side-effects associated with NSAIDs.

Design, synthesis, biological evaluation and molecular docking of curcumin analogues as antioxidant, cyclooxygenase inhibitory and anti-inflammatory agents

Curcuminoids were isolated from Curcuma longa and their pyrazole and isoxazole analogues were synthesized and evaluated for antioxidant, COX-1/COX-2 inhibitory and anti-inflammatory activities. The designed analogues significantly enhance COX-2/COX-1 selectivity and possess significant anti-inflammatory activity in carrageenan induced rat paw edema assay. Pyrazole, isoxazole analogues of curcumin (4 and 7) exhibited higher antioxidant activity than trolox. Molecular docking study revealed the binding orientations of curcumin analogues in the active sites of COX and thereby helps to design novel potent inhibitors.

Investigation of structure-activity relationships in a series of glibenclamide analogues

In this study, the synthesis of 15 new glibenclamide analogues is described. The conformational trends of these analogues were investigated using Monte Carlo conformational analysis. The conformational analysis results resolved the discrepancy between previous molecular modelling simulations of glibenclamide and allowed rationalizing the effect of aqueous environment on the overall conformation. The 3D-QSAR study was carried out with respect to the compounds' ability to antagonize the [(3)H]-glibenclamide binging in rat cerebral cortex. Superimposition of the antagonists was performed using the conformations derived from atom-by-atom fit to the glibenclamide crystal structure and this alignment was used to develop CoMFA models. CoMFA provided a good predictability: number of PLS components = 2, q(2) = 0.876, R(2) = 0.921, SEE = 0.455 and F = 70. Best CoMFA models showed the steric and lipophilic properties as the major interacting forces whilst the electrostatic property contribution was a minor factor.

Three-dimensional quantitative structure (3-D QSAR) activity relationship studies on imidazolyl and N-pyrrolyl heptenoates as 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) inhibitors by comparative molecular similarity indices analysis (CoMSIA)

A comparative molecular similarity indices analysis (CoMSIA) of a set of 29 imidazolyl and N-pyrrolyl heptenoates have been performed to find out the structural requirements for 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) inhibitory activity. The HMG like side chain, a common moiety of statins, was used to align the molecules. The results guide to design new chemical entities with high potency.

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

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