Bioactivity-guided isolation of chemical constituents against H2O2-induced neurotoxicity on PC12 from Cimicifuga dahurica (Turcz.) Maxim.

Three new compounds (1, 6, 9), with six known compounds (2–5, 7–8) were obtained from water-soluble extract of Cimicifuga dahurica (Turcz.) Maxim. by bioactivity-guided isolation. Their structures were elucidated by chemical and spectral analysis, including 1D, 2D NMR data and HRESIMS. H₂O₂-induced neurotoxicity on PC12 cells model were conducted to evaluate the neuro-protective capability of these compounds. The piscidic acid derivatives compounds 4–7 showed marked neuro-protective effect at certain concentration.     

Drug repurposing for chronic myeloid leukemia: in silico and in vitro investigation of DrugBank database for allosteric Bcr-Abl inhibitors

Chronic myeloid leukemia (CML) is caused by chromosomal rearrangement resulting in the expression of Bcr-Abl fusion protein with deregulated Abl tyrosine kinase activity. Approved drugs – imatinib, dasatinib, nilotinib, and ponatinib – target the ATP-binding site of Abl kinase. Even though these drugs are initially effective, long-term usefulness is limited by the development of resistance. To overcome this problem, targeting the allosteric site of Abl kinase, which is remote from the ATP-binding site is found to be a useful strategy. In this study, structure-based and ligand-based virtual screening methods were applied to narrow down possible drugs (from DrugBank database) that could target the allosteric site of Abl kinase. Detailed investigations of the selected drugs in the allosteric site of Abl kinase, using molecular dynamics and steered molecular dynamics simulation shows that gefitinib, an EGFR inhibitor approved for the treatment of lung cancer, could bind effectively to the allosteric site of Bcr-Abl. More interestingly, gefitinib was found to enhance the ability of imatinib to bind at the ATP-binding site of Bcr-Abl kinase. Based on the in silico findings, gefitinib was tested in combination with imatinib in K562 CML cell line using MTT cell proliferation assay and found to have a synergistic antiproliferative activity. Further detailed mechanistic study could help to unravel the full potential of imatinib – gefitinib combination for the treatment of CML.     

Chemical composition and antioxidant activities of different polysaccharides from the roots of Angelica dahurica

The total crude polysaccharides (CADPs), isolated from the roots of Angelica dahurica by H(2) O extraction, EtOH precipitation, and dialysis, and the four fractions ADP1, ADP2, ADP3, and ADP4, obtained by gel filtration of the CADPs, were analyzed to characterize their composition and evaluated for their antioxidant activity using different in vitro tests such as the malondialdehyde (MDA)-production, the ferrous ion (Fe(2+) )-chelating, and the HO(.) radical-scavenging assays. The predominant neutral monosaccharides in the four fractions were identified as arabinose, galactose, and glucose, while the composition and ratio of the monosaccharides were different between the fractions. The CADPs and its fractions were found to significantly inhibit lipid peroxidation, chelate Fe(2+) , and scavenge HO(.) radicals, indicating that these polysaccharides possessed antioxidant activity. Among the four fractions, ADP4 exhibited the strongest antioxidant activity, which was stronger than that of the control antioxidant vitamin E (Vit E). Taken together, the chemical composition of these polysaccharides might affect their antioxidant activity, and ADP4 could be explored as a source of potential novel natural antioxidants for food and pharmaceutical purposes.     

Structural basis of fullerene derivatives as novel potent inhibitors of protein acetylcholinesterase without catalytic active site interaction: insight into the inhibitory mechanism through molecular modeling studies

Abstract

Acetylcholinesterase (AChE) is an important kind of esterase that plays a key biological role in the central and peripheral nervous systems. Recent research has demonstrated that some fullerene derivatives serve as a new nanoscale class of potent inhibitors of AChE, but the specific inhibition mechanism remains unclear. In the present article, several molecular modeling methods, such as molecular docking, molecular dynamics simulations and molecular mechanics/generalized Born surface area calculations, were used for the investigation of the binding mode and inhibition mechanism of fullerene inhibitions for AChE. Results revealed that fullerene inhibitors block the entrance of substrates by binding with the peripheral anionic site (PAS) region. Thus, fullerene derivatives might mainly serve as competitive inhibitors. The interactions of a fullerene backbone with AChE are at the same level in different single side chain systems and seem to be related to the length or aromaticity of the side chain. The inhibitor with multihydroxyl side chains shows an obviously large electrostatic interaction as it forms additional hydrogen bonds with AChE. Moreover, fullerene derivatives might exhibit noncompetitive inhibition partly by affecting some secondary structures around them. Thus, the destructions of these secondary structures can lead to conformational changes in some important regions, such as the catalytic triad and acyl pocket. The investigation is of great importance to the discovery of good fullerene inhibitors.

Communicated by Ramaswamy H. Sarma     

国产毛茛科升麻属四种植物的核形态研究，并略论升麻的细胞地理

本文研究了国产四种升麻属植物(小升麻、单穗升麻、云南升麻、升麻及其变种毛叶升麻)的核 形态。除发现升麻在云南西北部地区有二倍体和四倍体两种细胞型存在外,其他类群都为二倍体。云南升麻和毛叶升麻的染色体数目和核型为首次报道。     

Karyomorphology of four species in Cimicifuga (Ranunculaceae) from China,with some cytogeographical notes on C. foetida

In this paper, four species of the genus Cimicifuga L. from China(C. acerina, C. simplex, C. yunnanensis, C. foetida var. foetida and C. foetida var. velutina ) were karyomorphologically investigated. All the taxa studied had the same chromosome number of 2n= 16 except for C. foetida var. foetida, in which a tetraploid cytotype was found to occur in northwestern Yunnan. Their karyotypes are all presented. The chromosomecounts in C. yunnanensis and C. foetida var. velutina are reported here for the first time.     

Phytochemical and chemotaxonomic investigation from the roots of Anemone vitifolia Buch.-Ham. (Ranunculaceae)

Phytochemical investigation from the roots of Anemone vitifolia Buch.-Ham. led to the isolation of eight compounds, including one triterpenoid saponin, two sugars, one coumarin, one amide, one saturated alkane, one olefin and one fatty acid. The structures of these metabolites were elucidated by spectroscopic data and comparisons with the data available in the literature. Among them, compound 7 ((6Z,9Z,12Z)-6,9,12-Eicosatriene) was isolated for the first time as a natural product. Furthermore, compounds 2 (D-(+)-raffinose), 3 (mixture of β-D-fructopyranose and β-D-fructofuranose) and 5 (bonaroside) were obtained from the Ranunculaceae family for the first time. Compounds 4 (siderin) and 6 (n-hexadecane) were isolated from A. vitifolia for the first time. The chemotaxonomic significance of the isolated compounds was discussed.     

In vitro and in silico studies on cell adhesion protein peroxinectin from Fenneropenaeus indicus and screening of heme blockers against activity

In invertebrates, the prophenoloxidase (proPO) pathway is involved in the phenol‐like antioxidant production against invading pathogens. Overproduction of melanin and phenolic substances leads to the disruption of hemocytes (own host cells); therefore, there is a prerequisite to regulate the antioxidant production, which is performed by the proteases and proPO‐associated cell adhesion protein peroxinectin (PX). PX is a macromolecular structure consisting of protein involved in the proPO pathway, which is a potential target in the regulatory mechanism in crustaceans. In the proPO cascade, pattern recognition proteins initiate the proPO cascade by the consequent reaction, and PX is involved in the key step in the regulatory mechanism of phenoloxidase enzyme synthesis. In the present study, Indian white shrimp Fenneropenaeus indicus PX (Fein‐PX) gene sequence was used. Upregulation of Fein‐PX was determined using immunostimulants β‐glucan (agonists) and examined its expression by quantitative RT‐PCR. To find the downregulation or negative regulation of Fein‐PX, inhibitors were screened, and its 3D model provides molecular insights into the rationale inhibitor design for developing an effective molecule against Fein‐PX. Copyright © 2015 John Wiley & Sons, Ltd.     

In vitro and in silico evaluation of new thiazole compounds as monoamine oxidase inhibitors

New twenty compounds bearing thiazole ring (3a-3t) were designed and synthesized as monoamine oxidase (MAO) inhibitors. The fluorometric enzyme inhibition assay was used to determine the biological effects of synthesized compounds. Most of them showed remarkable inhibitory activity against both MAO-A and MAO-B. By comparing their IC₅₀ values, it can be seen that active derivatives displayed generally selectivity on MAO-B enzyme. Compounds 3j and 3t, which bear dihydroxy moiety at the 3rd and 4th position of phenyl ring, were the most active derivatives in the series against both isoenzymes. Compounds 3j and 3t showed significant inhibition profile on MAO-A with the IC₅₀ values of 0.134 ± 0.004 µM and 0.123 ± 0.005 µM, respectively, while they performed selectivity against MAO-B with the IC₅₀ values of 0.027 ± 0.001 µM and 0.025 ± 0.001 µM, respectively. Also, docking studies about these compounds were carried out to evaluate their binding modes on the active regions of MAO-A and MAO-B.     

Kinetic and in silico studies of hydroxy-based inhibitors of carbonic anhydrase isoforms I and II

A series of hydroxy and phenolic compounds have been assayed for the inhibition of two physiologically relevant carbonic anhydrase (CA, EC 4.2.1.1) isozymes, the cytosolic human isozymes I and II. The investigated molecules showed inhibition constants in the range of 1.07–4003 and 0.09–31.5?μM at the hCA I and hCA II enzymes, respectively. In order to investigate the binding mechanisms of these inhibitors, in silico studies were also applied. Molecular docking scores of the studied compounds are compared using three different scoring algorithms, namely Glide/SP, Glide/XP and Glide/IFD. In addition, different ADME (absorption, distribution, metabolism and excretion) analysis was performed. All the examined compounds were found within the acceptable range of pharmacokinetic profiles.     

Partial purification and some properties of a cholinesterase from bush bean (Phaseolus vulgaris L.) roots.

A cholinesterase was partially purified from bush bean (Phaseolus vulgaris L.) roots by using acridinium-based ligand affinity chromatography. The procedure gave a 78-fold increase in specific activity, although at least three inactive contaminants remained. The enzyme activity was maximal against acetyl esters of choline and was inhibited by neostigmine. Di-isopropyl phosphorofluoridate completely inhibited activity at concentrations greater than 0.1 mM. The catalytic centre activity was 2 X 10(-4) times that of electric eel acetylcholinesterase. Cholinesterase activity appeared as a peak (s = 4.2 +/- 0.1 S) after isokinetic sedimentation. The Stokes radius was 4.00 nm and the apparent molecular weight was 72700 +/- 1900. The smallest active and native form of the enzyme appeared to be a monomer. This contrasts with animal acetylcholinesterases, in which the smallest active and native forms are multimeric.     

In vitro and in silico studies of bis (indol-3-yl) methane derivatives as potential α-glucosidase and α-amylase inhibitors

In this paper, bis (indol-3-yl) methanes (BIMs) were synthesised and evaluated for their inhibitory activity against α-glucosidase and α-amylase. All synthesised compounds showed potential α-glucosidase and α-amylase inhibitory activities. Compounds 5 g (IC₅₀: 7.54 ± 1.10 μM), 5e (IC₅₀: 9.00 ± 0.97 μM), and 5 h (IC₅₀: 9.57 ± 0.62 μM) presented strongest inhibitory activities against α-glucosidase, that were ∼ 30 times stronger than acarbose. Compounds 5 g (IC₅₀: 32.18 ± 1.66 µM), 5 h (IC₅₀: 31.47 ± 1.42 µM), and 5 s (IC₅₀: 30.91 ± 0.86 µM) showed strongest inhibitory activities towards α-amylase, ∼ 2.5 times stronger than acarbose. The mechanisms and docking simulation of the compounds were also studied. Compounds 5 g and 5 h exhibited bifunctional inhibitory activity against these two enzymes. Furthermore, compounds showed no toxicity against 3T3-L1 cells and HepG2 cells.

Highlights

1. A series of bis (indol-3-yl) methanes (BIMs) were synthesised and evaluated inhibitory activities against α-glucosidase and α-amylase.
2. Compound 5g exhibited promising activity (IC₅₀ = 7.54 ± 1.10 μM) against α-glucosidase.
3. Compound 5s exhibited promising activity (IC₅₀ = 30.91 ± 0.86 μM) against α-amylase.
4. In silico studies were performed to confirm the binding interactions of synthetic compounds with the enzyme active site.

     

Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: combination of in silico and in vitro studies

Poly(ADP-ribose) polymerase-1 (PARP-1) enzyme has critical roles in DNA replication repair and recombination. Thus, PARP-1 inhibitors play an important role in the cancer therapy. In the current study, we have performed combination of in silico and in vitro studies in order to discover novel inhibitors against PARP-1 target. Structure-based virtual screening was carried out for an available small molecules database. A total of 257,951 ligands from Otava database were screened at the binding pocket of PARP-1 using high-throughput virtual screening techniques. Filtered structures based on predicted binding energy results were then used in more sophisticated molecular docking simulations (i.e. Glide/standard precision, Glide/XP, induced fit docking – IFD, and quantum mechanics polarized ligand docking – QPLD). Potential high binding affinity compounds that are predicted by molecular simulations were then tested by in vitro methods. Computationally proposed compounds as PARP-1 inhibitors (Otava Compound Codes: 7111620047 and 7119980926) were confirmed by in vitro studies. In vitro results showed that compounds 7111620047 and 7119980926 have IC₅₀ values of 0.56 and 63 μM against PARP-1 target, respectively. The molecular mechanism analysis, free energy perturbation calculations using long multiple molecular dynamics simulations for the discovered compounds which showed high binding affinity against PARP-1 enzyme, as well as structure-based pharmacophore development (E-pharmacophore) studies were also studied.     

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.     

A study on the development of stigma and megagametophyte,and embryogeny in Cimicifuga simplex Wormsk

This is one of a series of studies on the reproductive features in Cimicifuga nanchuanensis Hsiao, an endangered plant endemic to China, and C. simplex Wormsk, a closely related and widely spread species as a control. The present paper deals with the results of cyto-morphological observations on the megasporogenesis, the development of female gametophytes, and the embryogeny in C. simplex. Its anatropous ovules are bitegminous and crassinucellate. A megaspore mother cell undergoes meiosis to form a linear or T-shaped megaspore tetrad. The embryo sac is of Polygonum type. The three antipodal cells persist up to the globular stage of embryo development.Two polar nuclei fuse to form a secondary nucleus close to the chalazal end of the embryo sac and connect with antipodal cells before fertilization. The development of endosperm is of Nuclear type. Cellularization of nuclear endosperm initiates since early globular stage of the embryo development. Development of the embryo in C. simplex is of Onagrad type. C. simplex is dichogamous. Stigmatic papillae emerge on the 1st∽2nd day and they elongate into stigmatic hairs on the 3rd∽5th day after stamens withering. The great impact of the differences of the receptible period of stigmas and pollen viabilitybetween the two species on effective pollination and seed-setting rate is discussed.     

单穗升麻的柱头和雌配子体发育及胚胎发生

单穗升麻的雌蕊群由1～5枚离生心皮组成。子房单室,4～9枚倒生胚珠,双珠被,厚珠心;大孢子四分体呈线形或T形排列,合点端一个具功能。胚囊发育为蓼型。成熟胚囊中3个单核反足细胞,胞质浓密,在球形胚时期尚能观察到其退化痕迹。极核融合早,次生核位于合点端。胚胎发生为柳叶菜型;核型胚乳。雄蕊凋谢后1～2天花柱顶端腹缝线周围出现乳突细胞,雄蕊凋谢后3～5天延长成柱头毛。讨论了单穗升麻与南川升麻柱头可授期与花粉生活力的差异对传粉效果和结籽率的显著影响。     

Docking and molecular dynamics studies of peptide inhibitors of ornithine decarboxylase: a rate-limiting enzyme for the metabolism of Fusarium solani

Fusarium solani causes a wide variety of diseases in plants. Polyamine biosynthesis is responsible for the growth and pathogenicity of the fungus. The initial step of this pathway involves the decarboxylation of ornithine to putrescine, and is catalyzed by the enzyme ornithine decarboxylase (ODC). Inhibiting this process may be a promising approach for the management of fungal disease in various crops. Therefore, there is a need to develop inhibitors of ODC that have higher binding capacity than ornithine. Fifteen peptides were designed and modeled based on physicochemical properties of residues in the active site of ODC. The peptide GLIWGNGPF showed the highest dock score. It is assumed that the de novo design of peptides could be a potential approach to inhibit polyamine biosynthesis. Molecular dynamics studies make an important contribution to understanding the effect of the binding of peptides and the stability of an ODC-peptide complex system.

An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:8.     

Ligand- and structure-based in silico studies to identify kinesin spindle protein (KSP) inhibitors as potential anticancer agents

Kinesin spindle protein (KSP) belongs to the kinesin superfamily of microtubule-based motor proteins. KSP is responsible for the establishment of the bipolar mitotic spindle which mediates cell division. Inhibition of KSP expedites the blockade of the normal cell cycle during mitosis through the generation of monoastral MT arrays that finally cause apoptotic cell death. As KSP is highly expressed in proliferating/cancer cells, it has gained considerable attention as a potential drug target for cancer chemotherapy. Therefore, this study envisaged to design novel KSP inhibitors by employing computational techniques/tools such as pharmacophore modelling, virtual database screening, molecular docking and molecular dynamics. Initially, the pharmacophore models were generated from the data-set of highly potent KSP inhibitors and the pharmacophore models were validated against in house test set ligands. The validated pharmacophore model was then taken for database screening (Maybridge and ChemBridge) to yield hits, which were further filtered for their drug-likeliness. The potential hits retrieved from virtual database screening were docked using CDOCKER to identify the ligand binding landscape. The top-ranked hits obtained from molecular docking were progressed to molecular dynamics (AMBER) simulations to deduce the ligand binding affinity. This study identified MB-41570 and CB-10358 as potential hits and evaluated these experimentally using in vitro KSP ATPase inhibition assays.