用分子对接方法预测HIV-1整合酶与金精三羧酸抑制剂的相互作用

用分子对接方法(Docking)研究了HIV-1整合酶与其抑制剂金精三羧酸的结合过程.为弄清金属离子在结合中所起的作用,选择含有一个Mg+2或不含Mg+2的两种不同的整合酶受体分别与金精三羧酸对接.结果表明, Mg+2对稳定配体与受体的结合起了重要作用. 金精三羧酸配体与含有一个金属Mg+2的整合酶受体对接,最优结合自由能为-45.19 kJ/mol. 当Mg+2失去后,整合酶的活性中心构象将发生变化,使金精三羧酸抑制剂与整合酶的结合自由能(-24.35 kJ/mol)明显增加. 预测了未知的HIV-1整合酶与其抑制剂金精三羧酸的复合物结构, 并可对基于结构的抗HIV-1整合酶的药物设计提供重要信息.     

Synthesis,in vitro lipoxygenase inhibition,docking study and thermal stability analyses of novel indole derivatives

A series of indole derivatives has been synthesized and biologically evaluated to identify potent new lipoxygenase (LOX) inhibitors. All selected indole derivatives were screened for their LOX inhibition studies. Most of compounds showed good in vitro LOX inhibition properties exhibiting IC₅₀ values in the range of 53.61 ± 0.14 to 198.61 ± 0.11 μM (mean ± SEM), as compared to the standard inhibitor baicalein with IC₅₀ value 22.4 ± 1.3 μM. Structure activity relationship has been discussed and docking stimulation of most active compound 4f has also performed. Thermal stability and melting point of indole derivatives have been performed by thermal gravimetric analysis and differential scanning calorimetry analysis under nitrogen atmosphere at heating rate of 20 °C min^?1. Compound 4f bearing bis-phenyl moiety has been found to be the most potent (IC₅₀ 53.61 ± 0.14 μM) and thermally most stable among the tested compounds. Imine (C=N) was found to be the key moiety for increasing the thermal stabilities of indole derivatives. FT-IR, NMR and elemental analysis techniques were performed for structural characterization.     

Virtual screening of the SAMPL4 blinded HIV integrase inhibitors dataset

Several combinations of docking software and scoring functions were evaluated for their ability to predict the binding of a dataset of potential HIV integrase inhibitors. We found that different docking software were appropriate for each one of the three binding sites considered (LEDGF, Y3 and fragment sites), and the most suitable two docking protocols, involving Glide SP and Gold ChemScore, were selected using a training set of compounds identified from the structural data available. These protocols could successfully predict respectively 20.0 and 23.6 % of the HIV integrase binders, all of them being present in the LEDGF site. When a different analysis of the results was carried out by removing all alternate isomers of binders from the set, our predictions were dramatically improved, with an overall ROC AUC of 0.73 and enrichment factor at 10 % of 2.89 for the prediction obtained using Gold ChemScore. This study highlighted the ability of the selected docking protocols to correctly position in most cases the ortho-alkoxy-carboxylate core functional group of the ligands in the corresponding binding site, but also their difficulties to correctly rank the docking poses.     

Novel and versatile methodology for synthesis of β-aryl-β-mercapto ketone derivatives as potential urease inhibitors

The objective was to obtain new scaffold of compounds possessing anti-urease activity. For this new and simple method for the synthesis of β-aryl-β-mercapto ketone derivatives based on Michael addition of thiophenol to chalcones in an ionic liquid as a solvent was improved. The products were obtained in good to moderate yields with high purity and characterized by spectral and elemental analyses. The activities of synthesized compounds were investigated as new inhibitors of jack bean urease. Among 22 synthesized compounds, all of them have shown inhibitory effect in micromolar range, and the most potent one has IC₅₀ = 6 μM compared to hydroxyurea IC₅₀ = 100 μM as a reference inhibitor. A docking study was performed using Autodock 4.2 in parallel to in vitro experiments to illustrate the corresponded binding affinities as well as binding site, and involved residues in interaction. These computational results complimented the experimental inhibition activity and enabled us to report a potent urease inhibitors based on β-aryl-β-mercapto ketone scaffold.     

Activity-guided investigation of Carissa carandas (L.) roots for anti-inflammatory constituents

The present study was structured to investigate the anti-inflammatory potential of the extracts, fractions and compounds isolated from Carissa carandas (L.) roots. Bioassay guided fractionation of methanol extract based on inhibitory potential towards proinflammatory mediators (TNF-α, IL-1β and nitric oxide (NO)) led to the identification of stigmasterol (1), lupeol (2), oleanolic acid (3), carissone (4) and scopoletin (5) as potential anti-inflammatory agents. Carissone (4) (IC₅₀ = 20.1 ± 2.69 μg/mL) and scopoletin (5) (IC₅₀ = 24.6 ± 1.36 μg/mL) exhibited significant inhibition of NO production comparable to specific NO inhibitor (L-NAME; IC₅₀ = 19.82 ± 1.64 μg/mL) without affecting the cell viability. Also, 4 and 5 at a concentration of 30 μM were found to inhibit 41.88–53.44% of TNF-α and IL-1β. To the best of our knowledge, this is the first report displaying the anti-inflammatory effects of C. carandas (L.) roots, partially mediated by inhibition of TNF-α, IL-1β and NO.     

Synthesis of Novel 3-(5-(Alkyl/arylthio)-1,3,4-Oxadiazol-2-yl)-8-Phenylquinolin-4(1H)-One Derivatives as Anti-HIV Agents

Novel quinolone derivatives featuring an 1,3,4-oxadiazole ring as a metal-chelating component and a benzyl group base on HIV-1 integrase inhibitors pharmacophore were designed and synthesized. An antiviral assay revealed that most analogues inhibited HIV-1 replication in the cell culture. Our results showed that compounds bearing small alkyl groups as R group were inactive in anti-HIV-1 assay, whereas compounds possessing benzyl or substituted benzyl at the same position showed good anti-HIV activity with the range of 20–57% at 100 μM concentration. Among them, 3-(5-((2-fluorobenzyl)thio)-1,3,4-oxadiazol-2-yl)-8-phenylquinolin-4-(1H)-one (compound 13) showed reasonable cell-based antiviral activity (EC₅₀ = 50 μM) with no considerable cytotoxicity (CC₅₀ > 100 μM) in the cell viability assay, suggesting that it may be amenable to further development for identifying new anti-HIV-1 agents. Docking studies using the later crystallographic data available for PFV integrase corroborate favorable binding to the active site of HIV integrase, providing a basis for the design of more potent analogues.     

Design of new secreted phospholipase A<Subscript>2</Subscript> inhibitors based on docking calculations by modifying the pharmacophore segments of the FPL67047XX inhibitor

Docking calculations that allow the estimation of the binding energy of small ligands in the GIIA sPLA₂ active site were used in a structure-based design protocol. Four GIIA sPLA₂ inhibitors co-crystallised with the enzyme, were used for examining the enzyme active site and for testing the FlexX in SYBYL 6.8 molecular docking program to reproduce the crystallographic experimental data. The FPL67047XX inhibitor was chosen as a prototype structure for applying free energy perturbation (FEP) studies. Structural modifications of the initial structure of the FPL67047XX inhibitor (IC₅₀ 0.013 μM) were performed in an effort to optimise the interactions in the GIIA sPLA₂ active site. The structural modifications were based on: (1) the exploration of absolute configuration (i.e. comparison of the binding score of (R)- and (S)-enantiomers); (2) bioisosterism (i.e. replacement of the carboxylate group with the bioisosteric sulphonate and phosphonate groups); (3) insertion of substituents that fit better in the active site. The generated new structures exhibited higher binding energy. Such structures may spark off the interest of medicinal chemists for synthesizing potentially more active GIIA sPLA₂ inhibitors.     

The redox couple avarol/avarone in the fight with malignant gliomas: the case study of U-251 MG cells

This study aimed to screen in vitro antitumour activity of the redox couple avarol/avarone against the human malignant glioma cell line U-251 MG for the first time. Compared both with avarol and positive controls used (temozolomide and doxorubicin), avarone was found to be the most active compound with IC₅₀ value below 1 μM (IC₅₀ 0.68 ± 0.04 μM, 96 h). Considerable less DNA damage in the cells treated with avarol and avarone vs. doxorubicin (105 & 123% vs. 299%, respectively; untreated U-251 MG cells were used as a control, 100%), coupled with no sign of cytotoxicity against the normal human foetal lung fibroblast MRC-5 cells (IC₅₀ > 100 μM), has actually pointed out the importance of this marine sesquiterpenoid quinone structure as a promising lead compound in development of novel brain chemotherapeutics.     

Experimental and computational approaches to reveal the potential of Ficus deltoidea leaves extract as α-amylase inhibitor

Ficus deltoidea leaves extract are known to have good therapeutic properties such as antioxidant, anti-inflammatory and anti-diabetic. We showed that 50% ethanol-water extract of F. deltoidea leaves and its pungent compounds vitexin and isovitexin exhibited significant (p < 0.05) α-amylase inhibition with IC₅₀ (vitexin: 4.6 μM [0.02 μg/mL]; isovitexin: 0.06 μg/mL [13.8 μM] and DPPH scavenging with IC₅₀ (vitexin: 92.5 μM [0.4 μg/mL]; isovitexin: 0.5 μg/mL [115.4 μM]). Additionally, molecular docking analysis confirmed that vitexin has a higher binding affinity (-7.54 kcal/mol) towards α-amylase compared to isovitexin (?5.61 kcal/mol). On the other hand, the molecular dynamics findings showed that vitexin-α-amylase complex is more stable during the simulation of 20 ns when compared to the isovitexin-α-amylase complex. Our results suggest that vitexin is more potent and stable against α-amylase enzyme, thus it could develop as a therapeutic drug for the treatment of diabetes.     

Synthesis,solid-state structures,and urease inhibition activities of new copper(II) complexes based on O,N,O-tridentate Schiff bases

Six new complexes of copper(II) coordinated with O,N,O-tridentate Schiff base dianions were synthesized and structurally characterized. The solid-state structures of 1–6 contain four-coordinate mononuclear copper(II) units with a slightly distorted square planar geometry. Complexes 1 and 4 derived from d-tyrosine have an infinite 1-D, right-handed helical chain, while 5 derived from l-tyrosine has an infinite 1-D, left-handed helical chain. Inhibitions of jack bean urease by 1–6 have been investigated, and potent inhibitory activities with IC₅₀ range of 2.15 ± 0.11–32.12 ± 0.65 μM have been observed for these copper(II) complexes. A docking analysis using a DOCK program was conducted to position 4 into the jack bean urease active site to determine the probable binding conformation.     

Novel 4-azaandrostenes as prostate cancer cell growth inhibitors: Synthesis,antiproliferative effects,and molecular docking studies

In this study, synthesis, structural characterization, molecular docking studies, and antiproliferative effects in four different cell lines of several novel 16-arylidene-4-azaandrost-5-ene compounds are reported. These compounds were prepared by oxidative cleavage of the enone system of androstenedione followed by an azacyclization reaction and an aldol condensation with various aldehydes at C16. In the androgen-dependent LNCaP cells, the most relevant antiproliferative effects were observed with the 16-phenyl, 16-p-tolyl, and 16-p-nitrophenyl derivatives. Compound 16E-[(4-methylphenyl)methylidene]-4-azaandrost-5-ene-3,17-dione was the most potent in these cells (IC₅₀ = 28.28 μM), having lower antiproliferative effects in the androgen-independent PC-3 cells (IC₅₀ = 45.31 μM). In addition, an interesting selectivity toward cancer cell lines was found for all compounds because a generally low cytotoxicity was detected in healthy human fibroblasts. Furthermore, the 16-p-tolylazaandrostene steroid induced a reduction of viability in LNCaP cells similar to that observed with finasteride, a clinically used 5α-reductase inhibitor. Moreover, molecular docking studies predicted that these 4-azaandrostene derivatives can interact with 5β-reductase, which has a high level of similarity to 5α-reductase enzyme, and with other common targets of steroidal drugs, particularly the enzyme 17α-hydroxylase/17,20-lyase.     

Marcanine G,a new cytotoxic 1-azaanthraquinone from the stem bark of Goniothalamus marcanii Craib

The ethanolic extract from the stem bark of Goniothalamus marcanii Craib was shown in preliminary brine shrimp lethality data having good cytotoxic activity. Further bioassay guided isolation was done by means of solvent partition, chromatography and precipitation to provide four isolated compounds: a novel compound 1 with the core structure of 1-azaanthraquinone moiety referred as marcanine G; as well as compounds 2–4 with known aristolactam structures namely, piperolactam C, cepharanone B and taliscanine. These compounds were characterised by spectroscopic techniques. The assessment of cytotoxicity was established on an SRB assay using doxorubicin as a positive control. Marcanine G (1) was considered the most active compound indicating the IC₅₀ values of 14.87 and 15.18 μM against human lung cancer cells (A549) and human breast cancer cells (MCF7), respectively. However, 2 showed mild activity with the IC₅₀ values of 83.72 and 82.32 μM against A549 and MCF7 cells, respectively.     

Synthesis and biological evaluation of coumarin derivatives containing oxime ester as α-glucosidase inhibitors

In this study, potent coumarin derivatives containing oxime ester 1 ～ 28 as α-glucosidase inhibitors were developed through a stepwise structure optimization, and the structure activity relationship was uncovered. Among them, compound 20 exhibited outstanding α-glucosidase inhibitory activity with IC₅₀ of 2.54 ± 0.04 μM compared to 640.57 ± 1.13 μM of Acarbose. Kinetic study ascertained that compound 20 was a reversible and uncompetitive α-glucosidase inhibitor. 3D fluorescence results showed that the interaction of compound 20 with α-glucosidase caused the changes of microenvironments and polypeptide backbone structure of α-glucosidase. CD spectra results revealed that compound 20 decreased the α-helix content and increased the β-sheet content. Molecular docking analysis indicated that compound 20 well located into the active site and mainly bind with Phe157, His239, His279, Tyr71, and Arg312 to reduce the catalytic activity of α-glucosidase.     

Design,synthesis and biological evaluation of isoxazole-naphthalene derivatives as anti-tubulin agents

In this study, a novel series of isoxazole-naphthalene derivatives as tubulin polymerization inhibitors were designed, synthesized and evaluated for their anti-proliferative activities against human breast cancer cell line MCF-7. Most of the synthesized compounds exhibited moderate to potent antiproliferative activity (IC₅₀ < 10.0 μM), as compared to cisplatin (15.24 ± 1.27 μM). Among them, compound 5j containing 4-ethoxy substitution at phenyl ring was found to be the most active compound with IC₅₀ value of 1.23 ± 0.16 μM. Mechanistic studies revealed that compound 5j arrested cell cycle at G2/M phase and induces apoptosis. Furthermore, in vitro tubulin polymerization assay showed that compound 5j displayed better inhibition activity on tubulin polymerization (IC₅₀ = 3.4 μM) than colchicine (IC₅₀ = 7.5 μM). Molecular docking study also revealed that compound 5j binds to the colchicine binding site of tubulin.     

C-methyl flavonoid from the leaves of Cleistocalyx conspersipunctatus: α-glucosidase inhibitory,molecular docking simulation and biosynthetic pathway

We extracted one new C-methyl flavonoid, farrerol 7-O-β-d-(6-O-galloyl)glucopyranoside (1), along with 11 known flavonoids, from the Cleistocalyx (C.) conspersipunctatus leaves. Elucidation of these flavonoid structures was accomplished through spectroscopic investigation and electronic circular dichroism (ECD) computation. Compared to corosolic acid (IC₅₀: 15.5 ± 0.9 μM), an established inhibitor, the compound 1 (IC₅₀: 6.9 ± 1.2 μM) was found more active in suppressing α-glucosidase. These findings imply the potential of compound 1 as a valid α-glucosidase inhibitor, which also offer evidence for future animal experiments and clinical trials. Besides, molecular docking was employed to explore the probable mechanism for α-glucosidase–compound 1 interaction. The biosynthetic pathway of these flavonoids in C. conspersipunctatus were proposed.     

Discovery of potent and selective acetylcholinesterase (AChE) inhibitors: acacetin 7-O-methyl ether Mannich base derivatives synthesised from easy access natural product naringin

Naringin, as a component universal existing in the peel of some fruits or medicinal plants, was usually selected as the material to synthesise bioactive derivates since it was easy to gain with low cost. In present investigation, eight new acacetin-7-O-methyl ether Mannich base derivatives (1–8) were synthesised from naringin. The bioactivity evaluation revealed that most of them exhibited moderate or potent acetylcholinesterase (AChE) inhibitory activity. Among them, compound 7 (IC₅₀ for AChE = 0.82 ± 0.08 μmol?L^?1, IC₅₀ for BuChE = 46.30 ± 3.26 μmol?L^?1) showed a potent activity and high selectivity compared with the positive control Rivastigmine (IC₅₀ for AChE = 10.54 ± 0.86 μmol?L^?1, IC₅₀ for BuChE = 0.26 ± 0.08 μmol?L^?1). The kinetic study suggested that compound 7 bind to AChE with mix-type inhibitory profile. Molecular docking study revealed that compound 7 could combine both catalytic active site (CAS) and peripheral active site (PAS) of AChE with four points (Trp84, Trp279, Tyr70 and Phe330), while it could bind with BuChE via only His 20.     

Synthesis of novel 3-substituted-5H-benzo[5,6][1, 4]thiazino[3,2-e][1,2,4]triazines and their 15-lipoxygenase inhibitory activity

A new group of 3-substituted-5H-benzo[5,6][1,4]thiazino[3,2-e][1,2,4]triazines was designed, synthesized and evaluated as inhibitors of 15-lipoxygenase (15-LO), and the results were compared with those of standard ligand 4-methyl-2-(4-methylpiperazin-1-yl)pyrimido[4,5-b][1,4]benzothiazine (4-MMPB). Among the newly designed ligands, compound 9e showed the best IC₅₀ of 15-LO inhibition (IC₅₀ = 38 µM). The docking calculations were performed in MOE software based on the function of force-field scoring, in order to study the interaction of these new compounds and standard ligand with 15-LO. The docking study implied that these ligands have hydrogen bond interaction with the residue of active site of 15-LO.     

New α-glucosidase inhibiting anthracenone from the barks of Harungana madagascariensis Lam

Two new 10-hydroxy-9(10H)-anthracenone, madagascenone A (1) and B (2), were isolated from the barks of Harungana madagascariensis Lam. The structures of the compounds were determined using 1D- and 2D-NMR and mass spectroscopic techniques. Both of the compounds showed an in vitro α-glucosidase inhibition with IC₅₀ = 69.9 ± 4.21 and 122.3 ± 1.13 μM, respectively, more potent than the standard acarbose (IC₅₀ = 840 ± 1.23 μM).     

Synthesis and Evaluation of Substituted Pyrazoles: Potential Antimalarials Targeting the Enoyl‐ACP Reductase of Plasmodium Falciparum

A series of 1,5‐ and 1,3‐diarylsubstituted pyrazoles were designed, synthesized, and evaluated for their ability to inhibit enoyl‐ACP reductase of Plasmodium falciparum. The inhibitory activity of these synthesized compounds was evaluated in a continuous spectrophotometric assay. Of all the compounds analyzed, NAS‐81 and NAS‐39 inhibited the enzyme with IC₅₀ values of 30 µM and 50 µM, respectively. The mode of ligand binding was investigated by docking the synthetic inhibitors at the active site of the crystal structure of the enzyme.     

Anticancer activity of Ophiobolin A,isolated from the endophytic fungus Bipolaris setariae

The present work describes the anticancer activity of Ophiobolin A isolated from the endophytic fungus Bipolaris setariae. Ophiobolin A was isolated using preparative HPLC and its structure was confirmed by HRMS, ¹H NMR, ¹³C NMR, COSY, DEPT, HSQC and HMBC. It inhibited solid and haematological cancer cell proliferation with IC₅₀ of 0.4–4.3 μM. In comparison, IC₅₀ against normal cells was 20.9 μM. It was found to inhibit the phosphorylation of S6 (IC₅₀ = 1.9 ± 0.2 μM), ERK (IC₅₀ = 0.28 ± 0.02 μM) and RB (IC₅₀ = 1.42 ± 0.1 μM), the effector proteins of PI3K/mTOR, Ras/Raf/ERK and CDK/RB pathways, respectively. It induced apoptosis and inhibited cell cycle progression in MDA-MB-231 cancer cells with concomitant inhibition of signalling proteins. Thus, this study reveals that anticancer activity of Ophiobolin A is associated with simultaneous inhibition of multiple oncogenic signalling pathways namely PI3K/mTOR, Ras/Raf/ERK and CDK/RB.