Virtual screening using the ligand ZINC database for novel lipoxygenase-3 inhibitors

The leukotrienes constitute a group of arachidonic acid-derived compounds with biologic activities suggesting important roles in inflammation and immediate hypersensitivity. Epidermis-type lipoxygenase-3 (ALOXE3), a distinct subclass within the multigene family of mammalian lipoxygenases, is a novel isoenzyme involved in the metabolism of leukotrienes and plays a very important role in skin barrier functions. Lipoxygenase selective inhibitors such as azelastine and zileuton are currently used to reduce inflammatory response. Nausea, pharyngolaryngeal pain, headache, nasal burning and somnolence are the most frequently reported adverse effects of these drugs. Therefore, there is still a need to develop more potent lipoxygenase inhibitors. In this paper, we report the screening of various compounds from the ZINC database (contains over 21 million compounds) using the Molegro Virtual Docker software against the ALOXE3 protein. Screening was performed using molecular constraints tool to filter compounds with physico-chemical properties similar to the 1N8Q bound ligand protocatechuic acid. The analysis resulted in 4319 Lipinski compliant hits which are docked and scored to identify structurally novel ligands that make similar interactions to those of known ligands or may have different interactions with other parts of the binding site. Our screening approach identified four molecules ZINC84299674; ZINC76643455; ZINC84299122 & ZINC75626957 with MolDock score of -128.901, -120.22, -116.873 & - 102.116 kcal/mol, respectively. Their energy scores were better than the 1N8Q bound co-crystallized ligand protocatechuic acid (with MolDock score of -77.225 kcal/mol). All the ligands were docked within the binding pocket forming interactions with amino acid residues.     

Ligand based virtual screening to find novel inhibitors against plant toxin Ricin by using the ZINC database

Ricin is known as a potent toxin against animals. It consists of two chains, Ricin Toxin A (RTA) and Ricin Toxin B (RTB). The toxic effect is known to be caused by RTA. Inhibitors for RTA with less efficiency have been reported. Hence, it is of interest to identify new inhibitors. Virtual screening methods (computer aided drug designing) to find similar molecules in drug database were used for screening new inhibitors against RTA. We used the structure of RTA in complex with Pteroic acid (PDB code: 1BR6) as target molecule. Ligand based virtual screening approach was used in which the known inhibitory molecule Pteroic acid (PTA) served as a template to identify similar ligands from the ZINC database. These ligands were docked inside the binding pocket of RTA by using the MVD (Molegro Virtual Docker). This approach successfully identified six novel compounds. These docked ligands interacted with Asn78, Ala79, Val81, Gly121 and Ser176 amino acids, which are key residues of the RTA active site. Three compounds in particular, ZINC05156321 (6, 7 diphenylpteridin-4-ol), ZINC05156324 (6, 7-bis (3-fluorophenyl) pteridin-4-ol) and ZINC08555900 (6, 7-bis (4-fluorophenyl)-1H-pteridin-4-one), showed higher binding affinity in comparison to PTA, with high interaction energy, better space fitting and electrostatic interactions. These molecules should be tested for in vitro and in vivo activities in future for consideration as effective inhibitors.     

Potency and pharmacokinetics of broad spectrum and isoform-specific p110γ and δ inhibitors in cancers

Emerging data on cancer suggesting that target-based therapy is promising strategy in cancer treatment. PI3K-AKT pathway is extensively studied in many cancers; several inhibitors target this pathway in different levels. Recent finding on this pathway uncovered the therapeutic applications of PI3K-specific inhibitors; PI3K, AKT, and mTORC broad spectrum inhibitors. Noticeably, class I PI3K isoforms, p110γ and p110δ catalytic subunits have rational therapeutic application than other isoforms. Therefore, three classes of inhibitors: isoform-specific, dual-specific and broad spectrum were selected for molecular docking and dynamics. First, p110δ structure was modelled; active site was analyzed. Then, molecular docking of each class of inhibitors were studied; the docked complexes were further used in 1.2?ns molecular dynamics simulation to report the potency of each class of inhibitor. Remarkably, both the studies retained the similar kind of protein ligand interactions. GDC-0941, XL-147 (broad spectrum); TG100-115 (dual-specific); and AS-252424, PIK-294 (isoform-specific) were found to be potential inhibitors of p110γ and p110δ, respectively. In addition to that pharmacokinetic properties are within recommended ranges. Finally, molecular phylogeny revealed that p110γ and p110δ are evolutionarily divergent; they probably need separate strategies for drug development.     

Anion-exchange high-performance liquid chromatographic assay of plasma lipoproteins of rabbits, rats and mice

A fast, accurate and precise high-performance liquid chromatographic assay method has been developed for plasma lipoproteins of experimental animals, rabbits, rats and mice. The method includes complete separation of high, low and very low density lipoproteins from one another within 20 min by a DEAE–glucomannan gel using stepwise elution, and determination by postcolumn reaction with an enzymatic cholesterol reagent as the total cholesterol level. The relative standard deviation of each lipoprotein assay was highly reproducible, being less than 2.0 and 2.4% for repeatability and intermediate precision, respectively. The method was successfully applied to the assays of plasma lipoproteins in three species of normolipidemic and hyperlipidemic animals.     

Detection of phytochrome-like genes from Rhazya stricta (Apocynaceae) using de novo genome assembly

Phytochrome-like genes in the wild plant species Rhazya stricta Decne were characterized using a de novo genome assembly of next generation sequence data. Rhazya stricta contains more than 100 alkaloids with multiple pharmacological properties, and leaf extracts have been used to cure chronic rheumatism, to treat tumors, and in the treatment of several other diseases. Phytochromes are known to be involved in the light-regulated biosynthesis of some alkaloids. Phytochromes are soluble chromoproteins that function in the absorption of red and far-red light and the transduction of intracellular signals during light-regulated plant development. De novo assembly of the nuclear genome of R. stricta recovered 45,641 contigs greater than 1000 bp long, which were used in constructing a local database. Five sequences belonging to Arabidopsis thaliana phytochrome gene family (i.e., AtphyABCDE) were used to identify R. stricta contigs with phytochrome-like sequences using BLAST. This led to the identification of three contigs with phytochrome-like sequences covering AtphyA-, AtphyC- and AtphyE-like full-length genes. Annotation of the three sequences showed that each contig consists of one phytochrome-like gene with three exons and two introns. BLASTn and BLASTp results indicated that RsphyA mRNA and protein sequences had homologues in Wrightia coccinea and and Solanum tuberosum, respectively. RsphyC-like mRNA and protein sequence were homologous to Vitis vinifera and Vitis riparia. RsphyE-like mRNA coding and protein sequences were homologous to Ipomoea nil. Multiple-sequence alignment of phytochrome proteins indicated a homology with 30 sequences from 23 different species of flowering plants. Phylogenetic analysis confirmed that each R. stricta phytochrome gene is related to the same phytochrome gene of other flowering plants. It is proposed that the absence of phyB gene in R. stricta is due to RsphyA gene taking over the role of phyB.     

Two Stemona alkaloids from Stemona sessilifolia (Miq.) Miq.

Two new alkaloids, named dehydrostenine A (1) and B (2), were isolated from the roots of Stemona sessilifolia (Miq.) Miq. Their structures were elucidated by comprehensive NMR spectroscopy and X-ray single-crystal diffraction experiment. Anti-acetylcholinesterase activities of compounds 1 and 2 were also tested, but did not show significant activity.     

Penicillivinacine,antimigratory diketopiperazine alkaloid from the marine-derived fungus Penicillium vinaceum

In the course of our ongoing search for biologically active compounds from marine-derived fungi, the organic extract of the marine-derived fungus Penicillium vinaceum species was investigated. Seven compounds including a new alkaloid with an unprecedented carbon skeleton, penicillivinacine (1) together with six previously reported ones were isolated. The known compounds were identified as indol-3-carbaldehyde (2), α-cyclopiazonic acid (3), terretrione A (4), brevianamide F (5), cyclo-d-Trp-l-pro (6) and citreoisocoumarin (7). Their structures were established by different spectroscopic data including 1D (¹H NMR and ¹³C NMR) and 2D NMR (COSY, HSQC, HMBC and NOESY) studies as well as high-resolution mass spectral data. The isolated compounds were evaluated for their antimigratory activity against the human breast cancer cell line MDA-MB-231 as well as antimicrobial activities against different pathogens. Compounds 1 and 4 displayed potent antimigratory activities against the highly metastatic triple negative human breast cancer cells MDA-MB-231 with IC₅₀ of 18.4 and 17.7 μM, respectively. Furthermore, compounds 1–7 showed different antimicrobial activities.     

Experiments Towards the Synthesis of the Ergot Alkaloids and Related Structures. Part 8.17 The Total Synthesis of 4-Methyl-2,3,4,4a,5,6-hexahydro-benzo[f]quinoline-2-carbonitrile Hydrochloride Hemihydrate,an Immediate Precursor of the Despyrrole Analogues of Lysergic Acid and Its Amides

Exposure of the N -methoxycarbonyl-bicyclic-keto-acid 5 (improved preparation) to the Barnick β -keto-acid synthesis 1 yielded an aqueous solution of the sodium salts of the β -keto-acids 26 and 27 which on heating at 60-65°C furnished the N -methoxycarbonyl-tricyclic-ketone 9 (55%) plus the hydroxy-ketone 28 which on acid treatment raised the yield of 9 to 68%. Reduction (NaBH 4) of 9 yielded the alcohol 32 (94%) which was treated with thionyl chloride followed by copper (I) cyanide and sodium iodide in acetonitrile to give the tricyclic- N -methoxycarbonyl nitrile 35 whose relative configuration was obtained by X-ray analysis. Attempts to remove the N -methoxycarbonyl group from 35 were unsuccessful. Conversion of the alcohol 32 to its methoxypropyl ether 41 followed by reaction with ethereal MeLi-LiBr yielded the amino-alcohol 39 (75%) converted to the N -formyl-tricyclic alcohol 42 with formic-acetic anhydride (70%). The alcohol 42 was then converted into the N -formyl nitrile 44 via the chloride 43 as employed in the earlier synthesis of the nitrile 35. Removal of the N -formyl group from the nitrile 44 was achieved by refluxing methanolic hydrochloric acid to give the required amino-nitrile hydrochloride 46 (91%) whose structure was confirmed by X-ray analysis. Reaction of the free base with methyl iodide in ethyl acetate in the presence of calcium carbonate furnished the N -methyl base 48 isolated as its hydrochloride, hemihydrate 49 (59%). The overall yield of 49 via this eleven-step synthesis was 3.4%.     

三种乌头中生物碱的含量测定

本文采用薄层光密度法对金阳乌头、雷波乌头,丽江乌头中所含的滇乌碱、光翠雀碱、展花乌头碱进行了含量测定。生药用乙醚冷浸提取,GF_(234)板,展开剂:环已烷—乙酸乙酯—二乙胺(8:1:1),反射法直线扫描,本法灵敏度高,重现性好。