Homology modeling of wild-type, D516V, and H526L Mycobacterium tuberculosis RNA polymerase and their molecular docking study with inhibitors

Rifamicyns (Rifs) are antibiotic widely used for the treatment of tuberculosis (TB); nevertheless, their efficacy has been limited by a high percentage of mutations, principally in the rpoB gene. In this work, the first three-dimensional molecular model of the hypothetical structures for the wild-type and D516V and H526L mutants of Mycobacterium tuberculosis (mtRNAP) were elucidated by a homology modeling method. In addition, the orientations and binding affinities of some Rifs with those new structures were investigated. Our findings could be helpful for the design of new more potent rifamycin analogs.     

New lanostane-type triterpenoids, inonotsutriols D, and E, from Inonotus obliquus

Two new lanostane-type triterpenoids, inonotsutriols D (1) and E (2), were isolated from the sclerotia of Inonotus obliquus (Pers.: Fr.) Pil. (Japanese name: kabanoanatake; Russian name: chaga). Their structures were determined to be lanost-8-ene-3β,22R,24R-triol (1) and lanost-8-ene-3β,22R,24S-triol (2) on the basis of spectral data, including 2D NMR analysis. In addition, major compounds, inotodiol (3), trametenolic acid (4), 3β-hydroxylanosta-8,24-dien-21-al (5), 21-hydroxylanosterol (6), inonotsuoxide A (7) and inonotsuoxide B (8) were identified, and all compounds, except 2, were evaluated for their cancer cell growth inhibitory activity against P388, HL-60, L1210 and KB cell lines.     

New phenylspirodrimane metabolites MBJ-0030, MBJ-0031, and MBJ-0032 isolated from the soil fungal strain Stachybotrys sp. f23793

ABSTRACT

Chemical screening of culture medium from the soil fungus Stachybotrys sp. resulted in the isolation of the three new phenylspirodrimanes MBJ-0030 (1), MBJ-0031 (2) and MBJ-0032 (3). Their structures were determined by detailed analysis of spectroscopic data. The absolute configurations of 1–3 were determined by modified Mosher’s and Marfey’s methods. In addition, cytotoxic and antimicrobial evaluations of the compounds were conducted.     

Structures of Gibberellins A39, A48, A49 and a New Kaurenolide in Cucurbita pepo L.

The structures of three new gibberellins A₃₀, A₄₈ and A₄₉ and a new kaurenolide, isolated from seeds of Cucurbita pepo L., were elucidated. The structures of GA₃₉, GA₄₈ and GA₄₉ were shown to be ent-3α,12β-dihydroxygibberell-16-ene-7,19,20-trioic acid (1), ent-2α,3α,10,12α-tetrahydroxy-20-norgibberell-16-ene-7,19-dioic acid 19,10-lactone (5) and the epimer at C–12 of GA₄₈ (8), respectively. The kaurenolide was shown to have the structure: ent-6β,7α,12β-trihydroxykaur-16-en-19-oic acid 19,6-lactone (14).     

A Novel Lepidopteran Sex Pheromone Produced by Females of a Lithosiinae Species,Lyclene dharma dharma,in the Family of Arctiidae

Female moths of Lyclene dharma dharma (Arctiidae, Lithosiinae) produced three pheromone components (I–III), which strongly stimulated male antennae. Using GC–MS analysis and chemical derivatizations, the following structures were estimated: 6-methyl-2-octadecanone (I), 14-methyl-2-octadecanone (II), and 6,14-dimethyl-2-octadecanone (III). While the stereochemistry of the chiral centers could not be determined because it was difficult to collect a sufficient amount of the natural pheromone, the plain structures of I and II were confirmed by synthesis of the racemic mixtures starting from diols. These methyl-branched ketones have not been identified as a natural product, indicating that they constitute a new chemical group of lepidopteran female sex pheromones.     

Molecular Modeling of Mycobacterium Tuberculosis DNA Gyrase and its Molecular Docking Study with Gatifloxacin Inhibitors

Abstract

Mycobacterium tuberculosis (Mt) is a leading cause of infectious disease in the world today. This outlook is aggravated by a growing number of Mt infections in individuals who are immunocompromised as a result of HIV infections. Thus, new and more potent anti-tuberculosis agents are necessary. Therefore, DNA gyrase was selected as a target enzyme to combat Mt. In this work, the first three-dimensional molecular model of the hypothetical structures for the Mycobacterium tuberculosis DNA gyrase (mtDNAg) was elucidated by a homology modeling method. In addition, the orientations and binding affinities of some gatifloxacin analogs with those new structures were investigated. Our findings could be helpful for the design of new more potent gatifloxacin analogs.     

New semicarbazones as gorge-spanning ligands of acetylcholinesterase and potential new drugs against Alzheimer’s disease: Synthesis,molecular modeling,NMR, and biological evaluation

Two new compounds (E)-2-(5,7-dibromo-3,3-dimethyl-3,4-dihydroacridin-1(2H)-ylidene)hydrazinecarbothiomide (3) and (E)-2-(5,7-dibromo-3,3-dimethyl-3,4-dhihydroacridin-1(2H)-ylidene)hydrazinecarboxamide (4) were synthesized and evaluated for their anticholinesterase activities. In vitro tests performed by NMR and Ellman’s tests, pointed to a mixed kinetic mechanism for the inhibition of acetylcholinesterase (AChE). This result was corroborated through further docking and molecular dynamics studies, suggesting that the new compounds can work as gorge-spanning ligands by interacting with two different binding sites inside AChE. Also, in silico toxicity evaluation suggested that these new compounds can be less toxic than tacrine.     

Coumarins from Magydaris pastinacea as inhibitors of the tumour-associated carbonic anhydrases IX and XII: isolation,biological studies and in silico evaluation

Abstract

In an in vitro screening for human carbonic anhydrase (hCA) inhibiting agents from higher plants, the petroleum ether and ethyl acetate extracts of Magydaris pastinacea seeds selectively inhibited hCA IX and hCA XII isoforms. The phytochemical investigation of the extracts led to the isolation of ten linear furocoumarins (1–10), four simple coumarins (12–15) and a new angular dihydrofurocoumarin (11). The structures of the isolated compounds were elucidated based on 1?D and 2?D NMR, MS, and ECD data analysis. All isolated compounds were inactive towards the ubiquitous cytosolic isoform hCA I and II (K _i?>?10,000?nM) while they were significantly active against the tumour-associated isoforms hCA IX and XII. Umbelliprenin was the most potent coumarin inhibiting hCA XII isoform with a K _i of 5.7?nM. The cytotoxicity of the most interesting compounds on HeLa cancer cells was also investigated.     

Chaetominine, (+)-alantrypinone,questin, isorhodoptilometrin,and 4-hydroxybenzaldehyde produced by the endophytic fungus Aspergillus sp. YL-6 inhibit wheat (Triticum aestivum) and radish (Raphanus sativus) germination

Five phytotoxic substances with allelopathic activity were isolated from endophytic fungi Aspergillus sp. YL-6 habited in Pleioblastus amarus. The chemical structures of these substances were determined as chaetominine (1), (+)-alantrypinone (2), questin (3), isorhodoptilometrin (4), and 4-hydroxybenzaldehyde (5) by nuclear magnetic resonance and mass spectrometry data. The potential allelopathic effects of compounds 1–5 were evaluated on wheat (Triticum aestivum) and radish (Raphanus sativus). Under lab condition, at concentrations of 10 and 20 ppm, compounds 1–5 inhibit the germination and growth of the two tested seeds completely. An idole-3-acetic acid (IAA) derivative, (+)-alantrypinone (2) displayed the best inhibitory effects on radish seeds among these tested compounds with the similar activity as the positive control glyphosate, a broad-spectrum systemic herbicide. In the further evaluation of compounds 1–5, Questin (3), an anthraquinone derivative, can inhibit shoot and root elongation of wheat, the inhibitory effects assessed were similar to the positive control glyphosate.     

Stereochemistry of Female-Specific Normonoterpenes,Sex Pheromone Candidates from the Acarid Mite,Tyreophagus sp. (Astigmata: Acaridae)

Two normonoterpenes were detected from an unidentified Tyreophagus sp. as new female-specific components. Both planar structures were identified to be 2,6-dimethyl-5-heptenal (1) and 2,6-dimethyl-5-hepten-1-ol (2) by GC/MS co-chromatography with synthetic 1 and 2. The stereochemistry of 2 was determined to be R by a GC analysis with a chiral column, while that of 1 was presumed to be similar to 2 based on the biosynthetic aspects.     

Design,synthesis and anticancer activity of novel pyrimidine and pyrimidine-thiadiazole hybrid glycosides

Abstract

New 1,3,4-thiadiazole thioglycosides linked to substituted pyrimidines were synthesized via glycosylation of 1,3,4-thiadiazole thiol compounds. Also, novel 1,2,3-triazole derivatives linked to carbohydrate units were prepared using the standard click chemistry conditions employing the Cu(I)-catalyzed azide-alkyne cycloaddition of substituted-aryl-azides with a selection of alkyne-functionalized sugars. The chemical structures of the new derivatives were verified using various spectroscopic techniques, such as IR, ¹H NMR, ¹³C NMR and elemental analyses. The cytotoxic activities of the prepared compounds were investigated in vitro against human liver cancer (HepG-2) and human breast adenocarcinoma (MCF7) cell lines. In addition, the biological evaluation of the new compounds involved the investigation of their effects on a human normal retinal pigmented epithelial cell line (RPE1) using the MTT assay.     

Repraesentins D,E and F,New Plant Growth Promoters from Lactarius repraesentaneus

Three new plant growth regulatory sesquiterpenes were isolated from the Lactarius repraesentaneus fungus. Their structures were elucidated to be lactarane sesquiterpenes, namely repraesentins D (1) and E (2), and a protoilludane-related sesquiterpene, namely repraesentin F (3). Repraesentin E (2) showed the strongest promotion activity, 164% at 3.6 μM, of the three compounds toward the radicle elongation of lettuce seedlings.     

Design,green synthesis and pharmacological evaluation of novel 5,6-diaryl-1,2,4-triazines bearing 3-morpholinoethylamine moiety as potential antithrombotic agents*

The aim of this research work was to investigate a series of novel 5,6-diaryl-1,2,4-triazines (3a–3q) containing 3-morpholinoethylamine side chain, and to address their antiplatelet activity by in vitro, ex vivo and in vivo methods. All compounds were synthesized by environment benign route and their structures were unambiguously confirmed by spectral data. Compounds (3l) and (3m) were confirmed by their single crystal X-ray structures. Out of all the synthesized compounds, 10 were found to be more potent in vitro than aspirin; six of them were found to be prominent in ex vivo assays and one compound (3d) was found to have the most promising antithrombotic profile in vivo. Moreover, compound (3d) demonstrated less ulcerogenicity in rats as compared to aspirin. The selectivity of the most promising compound (3d) for COX-1 and COX-2 enzymes was determined with the help of molecular docking studies and the results were correlated with the biological activity.     

The chemical constituents of Piper kadsura and their cytotoxic and anti-neuroinflammtaory activities

The n-hexane and CHCl₃ soluble fractions of the MeOH extract of the aerial parts of Piper kadsura were found to potently inhibit nitric oxide (NO) production in LPS-activated BV-2 cells, a microglial cell line. From the active fractions, a new stereoisomer of guaiane sesquiterpene, 1α,5β-guai-4(15)-ene-6β,10β-diol, kadsuguain A (1) and a new cyclohexadienone, kadsuketanone A (2), together with twelve known compounds (3–14) were isolated. The structures of these compounds were elucidated by extensive NMR spectral studies. The absolute configuration of 2 was determined by circular dichroism (CD) spectra. Compounds 2, 6, and 11–14 significantly inhibited both nitric oxide (NO) and prostaglandin E₂ (PGE₂) production in the LPS-activated microglia cells. In addition, compounds 4, 6, and 11–14 exhibited cytotoxicity against the A549, SK-OV-3, SK-MEL-2, and HCT15 human tumour cells.     

Design,synthesis of novel pyranotriazolopyrimidines and evaluation of their anti-soybean lipoxygenase,anti-xanthine oxidase,and cytotoxic activities

The synthesis of 14-(aryl)-14H-naphto[2,1-b]pyrano[3,2-e][1,2,4]triazolo[1,5-c]pyrimidine-2-yl) acetamidoximes 2a–e has been accomplished by reaction of 2-acetonitrile derivatives 1a–e with hydroxylamine. Cyclocondensation reaction of precursors 2a–e with some elctrophilic species such as ethylorthoformate, acetic anhydride, and methyl-acetoacetate provided the new oxadiazole derivatives 3a–e, 4a–e, and 5a–e, respectively. On the other hand, the reaction of precursors 2a–e with 2-chloropropanoyl chloride afforded the new acetimidamides 6a–e which evolve under reflux of toluene to the new oxadiazoles 7a–e. The synthetic compounds were screened for their anti-xanthine oxidase, anti-soybean lipoxygenase, and cytotoxic activities. Moderate to weak xanthine oxidase and soybean lipoxygenase inhibitions were obtained but significant cytotoxic activities were noted. The most cytotoxic activities were recorded mainly (i) 5a was the most active (IC_50?=_?4.0?μM) and selective against MCF-7 and (ii) 2a was cytotoxic against the four cell lines with selectivity for MCF-7 and OVCAR-3 (IC_50?=_?17 and 12?μM, respectively) while 2e is highly selective against OVCAR-3 (IC_50?=_?10?μM).     

Structure and Dynamics of Elastin Building Blocks. Boc-LG-OEt,Boc-VG-OEt,Boc-VGG-OH

Abstract

Short di- and tripeptides such as Boc-LG-OEt, Boc-VG-OEt and Boc-VGG-OH, corresponding to abundant repetitive sequences in elastin, have been extensively studied both in solid state, by X-ray diffraction, and in solution by circular dicroism and nuclear magnetic resonance. Furthermore, theoretical procedures such as simulated annealing and molecular dynamics were also performed on these peptides.

In general, the results indicate that no one single structure (be folded or extended) could be representative for these sequences in the protein, but rather that a multiplicity of interconverting conformers, ranging from folded to extended structures, should be considered. In any case, these structures, e.g. β-turns, polyglycine II and β-conformations, are those previously suggested to participate to conformational equilibria of elastin.     

Synthesis and anticandidal evaluation of new benzothiazole derivatives with hydrazone moiety

In this study, we have performed the synthesis of new N′-(arylidene)-4-[(benzothiazol-2-yl)thio]butanoylhydrazide derivatives (3a–s) bearing azole moiety and hydrazone group in a lipophilic structural framework. The target compounds were prepared by a three step synthetic procedure starting from 2-mercaptobenzothiazole. The structures of the target compounds were elucidated by IR, ¹H NMR, ¹³C NMR spectra and elemental analysis. The antifungal activity of the obtained compounds has been determined against a number of clinic and fluconazole-resistant Candida strains by using microdilution method. Compounds (3a–3s) exhibited anticandidal activity in different ratios varying between the range of MIC: 50 and 200?µg/mL.     

链霉菌CB02959中四霉素及四烯菌素的鉴定及培养基优化

【背景】四霉素(Tetramycin)和四烯菌素(Tetrin)是具有广谱抗真菌活性的四烯大环内酯类抗生素。链霉菌CB02959是一株雷纳霉素(Leinamycin)类化合物的潜在产生菌株,利用antiSMASH分析其基因组发现该菌株含有一个纳他霉素(Natamycin)类四烯大环内酯化合物的生物合成基因簇。【目的】对Streptomyces sp. CB02959中次级代谢产物进行研究,确定其是否可以产生四烯大环内酯化合物,对其发酵产物进行分离和结构鉴定,并进行初步的发酵优化以提高产量。【方法】基于生物信息学预测和高分辨质谱数据,推测CB02959中多烯化合物的结构;在不同发酵培养基中培养CB02959,确定适合大规模发酵的培养基;敲除tetrA基因以确定目标基因簇和四烯大环内酯化合物产生的相关性;分离和鉴定CB02959产生的主要代谢物的结构;通过改变培养基中葡萄糖、麦芽提取物和胰蛋白胨的含量,提高四烯大环内酯化合物的产量。【结果】通过对CB02959中纳他霉素类化合物生物合成基因簇的分析及16S rRNA基因序列的进化树分析,推测CB02959可能是一株新的四霉素和四烯菌素产生菌;在YEME发酵培养基中对CB02959进行大规模发酵,分离得到4个化合物,鉴定为四霉素A (1)、四霉素B (2)、四烯菌素A (3)、四烯菌素B (4);最后通过培养基的初步优化,将化合物1–4的产量分别提高至208.1、100.0、1 315.6、109.9 mg/L。【结论】通过基因组挖掘策略发现了一株新的四霉素和四烯菌素产生菌链霉菌CB02959,并通过培养基优化提升了其四烯大环内酯化合物的产量,此发现为这类抗真菌天然产物的后续开发奠定了基础。     

Novel tetrazole and cyanamide derivatives as inhibitors of cyclooxygenase-2 enzyme: design,synthesis, anti-inflammatory evaluation,ulcerogenic liability and docking study

Nineteen new compounds containing tetrazole and/or cyanamide moiety have been designed and synthesised. Their structures were confirmed using spectroscopic methods and elemental analyses. Anti-inflammatory activity for all the synthesised compounds was evaluated in vivo. The most active compounds 4c, 5a, 5d–f, 8a and b and 9a and b were further investigated for their ulcerogenic liability and analgesic activity. Pyrazoline derivatives 9b and 8b bearing trimethoxyphenyl part and SO₂NH₂ or SO₂Me pharmacophore showed equal or nearly the same ulcerogenic liability (UI: 0.5, 0.75, respectively), to celecoxib (UI: 0.50). Most of tested compounds showed potent central and/or peripheral analgesic activities. Histopathological investigations were done to evaluate test compounds effect on rat's gastric tissue. The obtained results were in consistent with the in vitro data on COX evaluation. Docking study was also done for all the target compounds inside COX-2-active site.     

Novel DPPH Radical Scavengers,Demethylbisorbibutenolide and Trichopyrone,from a Fungus

In our screening program for antioxidants with 1,1-diphenyl-2-picrylhydrazyl (DPPH)-radical scavenging activity, two novel compounds, demethylbisorbibutenolide (1) and trichopyrone (2), were isolated from the fermentation broth of the fungus of USF-4860 strain isolated from a soil sample. The structures of these compounds were determined from spectroscopic evidence. The biosynthetic origin of the carbon atoms of 2 was unambiguously determined by feeding experiments using ¹³C-labeled precursors and elucidation of the ¹³C-NMR spectrum of ¹³C-labeled 2. These studies showed that 2 was derived from five acetates and a methyl group of methionine. In the DPPH-radical scavenging assay, 1 and 2 gave ED₅₀ values of 149 and 167 μM after standing for 2.0 hr. Compound 2 reacted with the DPPH radical to form reaction product 3 which was determined to be 1-[4-(3,4-dihydro-3-methyl-6-{1,3-pentadienyl}-2,4-dioxo-2H-pyran-3-yl)-phenyl]-1-phenyl-2-picrylhydrazine from spectroscopic evidence.