Ding Li

Sun Yat-Sen University, Shengcheng, Guangdong, China

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Publications (104)336.57 Total impact

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    ABSTRACT: Ferrocene (Fc) tagged peptide nanowires (Fc-PNWs) were synthesized via the self-assemble of Fc coupled diphenylalanine (Phe-Phe, FF) and then utilized as supporting matrix for the immobilization of glucose oxidase (GOx). Scanning electron microscopy (SEM) characterization indicates the Fc-PNWs were twisted together with diameter around 50 nm. The GOx functionalized Fc-PNWs contains both mediator Fc and GOx that necessary for the electrochemical detection of glucose. So, with simply dropping the biocomposite onto electrode surface in one step, the resulting biosensor displays high sensitivity, wide linear range and good stability towards glucose detection. The good performance of the biosensor was originated from the great amount of Fc moieties contained in the nanowire and the facile electron transfer between Fc and GOx. For real sample analysis, the glucose contents in blood samples determined by the biosensor was in good agreement with those obtained using the glucose detection kit. The simplicity of the biosensor preparation process enables mass production of the biosensor with wide potential commercial applications. The synthesized Fc-PNWs can also be used in different sensing and biosensing fields.
    Analytical methods 07/2014; · 1.86 Impact Factor
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    ABSTRACT: Accelerated proliferation of solid tumor and hematologic cancer cells is related to accelerated transcription of ribosomal DNA by the RNA polymerase I to produce elevated level of ribosomal RNA. Therefore, down-regulation of RNA polymerase I transcription in cancer cells is an important anticancer therapeutic strategy.
    Biochimica et biophysica acta. 07/2014;
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    ABSTRACT: In the present study, we found that three enzymes, MVK, MDD and FPPS, in the mevalonate pathway (MVP) of cholesterol biosynthesis, can be simultaneously inhibited by two green tea polyphenols ((-)-epicatechin-3-gallate, ECG; (-)-epigallocatechin-3-gallate, EGCG). Molecular dynamics simulations and pharmacophore studies were carried out to elucidate the tri-targeted inhibition mechanisms. Our results indicate that similar triangular binding pockets exist in all three enzymes, which is essential for their binding with polyphenols. Two distinct binding poses for ECG and EGCG were observed in our MD simulations. These results shed light on the potential for further selective and multi-targeted inhibitor design for the treatment of hyperlipidemia.
    Organic & Biomolecular Chemistry 05/2014; · 3.57 Impact Factor
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    ABSTRACT: A tailor-made colorimetric and red-emitting fluorescent dual probe for G-quadruplex nucleic acids was developed by incorporating a coumarin-hemicyanine fluorophore into an isaindigotone framework. The significant and distinct changes in both the color and fluorescence of this probe enable the label-free and visual detection of G-quadruplex structures.
    Chemical communications (Cambridge, England). 05/2014;
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    ABSTRACT: Alzheimer's disease (AD) is a progressive neurodegenerative brain disorder that is characterized by dementia, cognitive impairment, and memory loss. Diverse factors are related to the development of AD, such as increased level of β-amyloid (Aβ), acetylcholine, metal ion deregulation, hyperphosphorylated tau protein, and oxidative stress. The following methods were used: organic syntheses of 1H-phenanthro[9,10-d]imidazole derivatives, inhibition of self-mediated and metal-induced Aβ1-42 aggregation, inhibition studies for acetylcholinesterase and butyrylcholinesterase, anti-oxidation activity studies, CD, MTT assay, transmission electron microscopy, dot plot assay, gel electrophoresis, Western blot, and molecular docking studies. We synthesized and characterized a new type of 1H-phenanthro[9,10-d]imidazole derivatives as multifunctional agents for AD treatment. Our results showed that most of these derivatives exhibited strong Aβ aggregation inhibitory activity. Compound 9g had 74% Aβ1-42 aggregation inhibitory effect at 10 μM concentration with its IC50 value of 6.5 μM for self-induced Aβ1-42 aggregation. This compound also showed good inhibition of metal-mediated (Cu(2+) and Fe(2+)) and acetylcholinesterase-induced Aβ1-42 aggregation, as indicated by using thioflavin T assay, transmission electron microscopy, gel electrophoresis, and Western blot. Besides, compound 9g exhibited cholinesterase inhibitory activity, with its IC50 values of 0.86 μM and 0.51 μM for acetylcholinesterase and butyrylcholinesterase, respectively. In addition, compound 9g showed good anti-oxidation effect with oxygen radical absorbance capacity (ORAC) value of 2.29. Compound 9g was found to be a potent multi-target-directed agent for Alzheimer's disease. Compound 9g could become a lead compound for further development as a multi-target-directed agent for AD treatment.
    Biochimica et Biophysica Acta 05/2014; · 4.66 Impact Factor
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    ABSTRACT: Cyanobacterial fructose-1, 6-/sedoheptulose-1, 7-bisphoshatase (cy-FBP/SBPase) is a potential enzymatic target for screening novel inhibitors that can combat harmful algal blooms (HABs). In the present study, we targeted the substrate binding pocket of cy-FBP/SBPase. A series of novel hit compounds from SPECs database were selected by using a pharmacophore-based virtual screening strategy. Most of the compounds tested exhibited moderate inhibitory activities (IC50 = 20.7 -176.9.8 μM) against cy-FBP/SBPase. The compound 2 and its analogues, compounds 10 and 11 exhibited strong inhibitory activities, with IC50 values of 20.7, 13.4, and 19.0 μM against cy-FBP/SBPase in vitro, and with EC50 values of 12.3, 10.9, and 2.9 ppm against cyanobacteria Synechocystis PCC6803 in vivo, respectively. The compound 10 was selected in order to perform the refined docking study to investigate the rational binding mode of inhibitors with cy-FBP/SBPase. Furthermore, the possible interaction of the residues with inhibitors was examined by site-directed mutagenesis, enzymatic assays, and fluorescence spectral analyses. The results provide insight into the binding-mode between the inhibitors and substrate binding pocket. The observed theoretical and experimental results are in concert, indicating that modeling strategies and screening methods employed are appropriate for searching novel lead compounds having both structural diversity and high inhibitory activity against cy-FBP/SBPase.
    Journal of Chemical Information and Modeling 02/2014; · 4.30 Impact Factor
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    ABSTRACT: In insects, cholesterol is one of the membrane components in cells and a precursor of ecdysteroid biosynthesis. Because insects lack two key enzymes, squalene synthase and lanosterol synthase, in the cholesterol biosynthesis pathway, they cannot autonomously synthesize cholesterol de novo from simple compounds and therefore have to obtain sterols from their diet. Sterol carrier protein (SCP) is a cholesterol-binding protein responsible for cholesterol absorption and transport. In this study, a model of the three-dimensional structure of SlSCPx-2 in Spodoptera litura, a destructive polyphagous agricultural pest insect in tropical and subtropical areas, was constructed. Docking of sterol and fatty acid ligands to SlSCPx-2 and ANS fluorescent replacement assay showed that SlSCPx-2 was able to bind with relatively high affinities to cholesterol, stearic acid, linoleic acid, stigmasterol, oleic acid, palmitic acid and arachidonate, implying that SlSCPx may play an important role in absorption and transport of these cholesterol and fatty acids from host plants. Site-directed mutation assay of SlSCPx-2 suggests that amino acid residues F53, W66, F89, F110, I115, T128 and Q131 are critical for the ligand-binding activity of the SlSCPx-2 protein. Virtual ligand screening resulted in identification of several lead compounds which are potential inhibitors of SlSCPx-2. Bioassay for inhibitory effect of five selected compounds showed that AH-487/41731687, AG-664/14117324, AG-205/36813059 and AG-205/07775053 inhibited the growth of S. litura larvae. Compounds AH-487/41731687, AG-664/14117324, AG-205/36813059 and AG-205/07775053 selected based on structural modeling showed binding affinity to SlSCPx-2 protein and inhibitory effect on the growth of S. litura larvae.
    PLoS ONE 01/2014; 9(1):e81542. · 3.73 Impact Factor
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    ABSTRACT: Cellular nucleic acid binding protein (CNBP) has been implicated in vertebrate craniofacial development and in myotonic dystrophy type 2 (DM2) and sporadic inclusion body myositis (sIBM) human diseases by controlling cell proliferation and survival to mediate neural crest expansion. CNBP has been found to bind single-stranded nucleic acid and promote rearrangements of nucleic acid secondary structure in an ATP-independent manner, acting as a nucleic acid chaperone. A variety of methods were used, including cell viability assays, wound-scratch assays, chemotaxis assays, invasion assays, circular dichroic (CD) spectroscopy, NMR spectroscopy, chromatin immunoprecipitation, expression and purification of recombinant human CNBP, electrophoretic mobility shift assay (EMSA), surface plasmon resonance (SPR), fluorescence resonance energy transfer (FRET) analyses, Luciferase reporter assay, Western blotting, isothermal titration calorimetry (ITC). Up-regulation of CNBP induced human fibrosarcoma cell death and suppressed fibrosarcoma cells motility and invasiveness. It was found that CNBP transcriptionally down-regulated expression of heterogeneous ribonucleoprotein K (hnRNP K) through its conversion of a G-rich sequence into G-quadruplex in the promoter of hnRNP K. G-Quadruplex stabilizing ligand tetra-(N-methyl-4-pyridyl) porphyrin (TMPyP4) could interact with and stabilize the G-quadruplex, resulting in downregulation of hnRNP K transcription. CNBP overexpression caused increase of cell death and suppression of cell metastasis through its induction of G-quadruplex formation in the promoter of hnRNP K resulting in hnRNP K down-regulation. The present result provided a new solution for controlling hnRNP K expression, which should shed light on new anticancer drug design and development.
    Biochimica et Biophysica Acta (BBA) - General Subjects 01/2014; · 3.85 Impact Factor
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    ABSTRACT: Background Telomere is protected by its G-quadruplex, T-loop structure, telomerase, and binding protein complex. Protein POT1 (protection of telomeres 1) is one subunit of telomere binding protein complex Shelterin. POT1 acts as a regulator of telomerase-dependent telomere length, and it can help telomere to form D-loop structure to stabilize telomere. POT1 protects telomere ends from ATR-dependent DNA damage response as well. Methods Extensive methods were used, including CD, EMSA, ITC, PCR stop assay, luciferase reporter assay, quantitative real-time PCR, Western blot, chromatin immunoprecipitation (Ch-IP), cloning, expression and purification of proteins. Results We found a new G-rich 30-base-pair long sequence (P-pot1 G18) located from -165 to -136 base pairs upstream of the translation starting site of protein POT1. This sequence in the promoter region of pot1 gene formed G-quadruplex resulting in down-regulation of pot1 gene transcription. This G-rich sequence is close to a binding site “TCCC” for transcription factor hnRNP K (heterogeneous nuclear ribonucleoprotein K), and its conversion to G-quadruplex prevented the access of hnRNP K to this binding site. The binding of hnRNP K could up-regulate pot1 gene transcription. TMPyP4 (meso-tetra(N-methyl-4-pyridyl)porphine) has been widely used as G-quadruplex binding ligand, which stabilized the G-quadruplex in vitro and in cellulo, resulting in down-regulation of pot1 gene transcription. Conclusions This G-quadruplex might become a potentially new drug target for antitumor agents. General significance Our results first demonstrated that G-quadruplex formation can affect the binding of transcription factor to its nearby binding site, and thus making additional influence to gene transcription.
    Biochimica et Biophysica Acta (BBA) - General Subjects 01/2014; · 3.85 Impact Factor
  • Dyes and Pigments 01/2014; 107:97–105. · 3.53 Impact Factor
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    ABSTRACT: Cyanobacterial fructose-1,6/sedoheptulose-1,7-bisphosphatase (cy-FBP/SBPase) plays a vital role in gluconeogenesis and in photosynthetic carbon reduction pathway and is thus a potential enzymatic target for inhibition of harmful cyanobacterial blooms. Here, we describe the crystal structure of cy-FBP/SBPase in complex with adenosine monophosphate (AMP) and fructose-1,6-bisphosphate (FBP). The allosteric inhibitor AMP and the substrate FBP exhibit an unusual binding mode when in complex with cy-FBP/SBPase. The binding mode analysis suggests that AMP bound to the allosteric sites near the interface across the up-down subunit pairs C1C4 and C2C3 assembled in the center of the tetramer, while FBP binds opposite to the interface between the horizontal subunit pairs C1C2 or C3C4. We identified a series of residues important for FBP and AMP binding and suggest the formation of a disulfide linkage between Cys 75 and Cys 99. Further analysis indicates that cy-FBP/SBPase may be regulated through ligand binding and changing of the structure of the enzyme complex. The interactions between ligands and cy-FBP/SBPase are different from those of scaffold ligand-bound structures of other FBPase family members and thus provide new insight into the molecular mechanisms of structure and catalysis of cy-FBP/SBPase. Our studies provide novel insight into the evolution of this enzyme family, and may help in the design of inhibitors aimed at preventing toxic cyanobacterial blooms. cy-FBP/SBPase and cy-FBP/SBPase bind by x-ray crystallography (View interaction) This article is protected by copyright. All rights reserved.
    FEBS Journal 11/2013; · 4.25 Impact Factor
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    ABSTRACT: Farnesyl pyrophosphate synthase (FPPS) is a key regulatory enzyme in the biosynthesis of cholesterol and in the post-translational modification of signaling proteins. It has been reported that non-bisphosphonate FPPS inhibitors targeting its allosteric binding pocket are potentially important for the development of promising anti-cancer drugs. The following methods were used: organic syntheses of non-bisphophonate quinoline derivatives, enzyme inhibition studies, fluorescence titration assays, synergistic effect studies of quinoline derivatives with zoledronate, ITC studies for the binding of FPPS with quinoline derivatives, NMR-based HAP binding assays, molecular modeling studies, fluorescence imaging assay and MTT assays. We report our syntheses of a series of quinoline derivatives as new FPPS inhibitors possibly targeting the allosteric site of the enzyme. Compound 6b showed potent inhibition to FPPS without significant hydroxyapatite binding affinity. The compound showed synergistic inhibitory effect with active-site inhibitor zoledronate. ITC experiment confirmed the good binding effect of compound 6b to FPPS, and further indicated the binding ratio of 1:1. Molecular modeling studies showed that 6b could possibly bind to the allosteric binding pocket of the enzyme. The fluorescence microscopy indicated that these compounds could get into cancer cells. The traditional FPPS active-site inhibitors bisphosphonates show poor membrane permeability to tumor cells, due to their strong polarity. The development of new non-bisphophonate FPPS inhibitors with good cell membrane permeability is potentially important. Our results showed that quinoline derivative 6b could become a new lead compound for further optimization for cancer treatment.
    Biochimica et Biophysica Acta 11/2013; · 4.66 Impact Factor
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    ABSTRACT: A series of pyridophenazine derivatives were synthesized and characterized as DNA intercalating fluorophores. These pyridophenazines showed absorption maxima at ca. 450 nm, and some compounds exhibited strong fluorescence at ca. 530 nm with excellent quantum yields in ethyl acetate solution. DNA binding properties of these pyridophenazines to calf thymus DNA (CT DNA) were studied in phosphate buffered saline at pH 7.4 by means of fluorescence titration. All compounds showed high binding affinity toward CT DNA with binding constant values in the range of 106 M−1, with fluorescence enhancement upon their binding to CT DNA. The fluorescent aminoethylpiperidine substituted pyridophenazine was employed as a sensitive agent for DNA determination with a limit of detection of 65 nM over a linear range of 100–1000 nM. The fluorescence titration and Top1 mediated DNA unwinding assay showed that this derivative exhibited DNA intercalation.
    Dyes and Pigments 10/2013; 99(1):82–89. · 3.53 Impact Factor
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    ABSTRACT: Two series of novel C-9 chloro- and bromo-substituted mansonone E derivatives with triazole moieties at the C-3 position were prepared by using copper-catalysed azide-alkyne cycloaddition click chemistry. These compounds were found as potent inhibitors of topoisomerase II (Topo II) and topoisomerase I (Topo I). The Topo II-mediated pBR322 DNA relaxation and cleavage assay showed that the derivatives might act as catalytic inhibitors. Their cytotoxic activities against A549, HL-60, K562 and HeLa cells were evaluated, indicating that these compounds were potent antitumour agents. Their structure activity relationships and molecular docking study revealed that the substituents of the triazole were particularly important for cytotoxicity.
    European journal of medicinal chemistry 08/2013; 68C:58-71. · 3.27 Impact Factor
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    ABSTRACT: Cyanobacteria class II fructose-1,6-bisphoshate aldolase (Cy-FBA-II) and cyanobacteria fructose-1,6-bisphosphatase (Cy-FBPase) are two neighboring key regulatory enzymes in the Calvin cycle of the cyanobacteria photosynthesis system. Each of them might be taken as a potential target for designing novel inhibitors to chemically control harmful algal blooms (HABs). In the present paper, a series of novel inhibitors were rationally designed, synthesized, and optimized based upon the structural and interactional information of both Cy-FBA-II and Cy-FBPase, and their inhibitory activities were examined in vitro and in vivo. The experimental results showed that compounds L19e-L19g exhibited moderate inhibitory activities (IC50 = 28.1-103.2 μM) against both Cy-FBA-II and Cy-FBPase; compounds L19a-L19d, L19h, L20a-L20d exhibited high Cy-FBA-II inhibitory activities (IC50 = 2.3-16.9 μM) and moderate Cy-FBPase inhibitory activities (IC50 = 31.5-141.2 μM); however, compounds L20e-L20h could potently inhibit both Cy-FBA-II and Cy-FBPase with IC50 values less than 30 μM, which demonstrated more or less dual-target inhibitor's feature. Moreover, most of them exhibited potent algicide activity (EC50 = 0.8-22.3 ppm) against cyanobacteria Synechocystis sp. PCC 6803.
    Journal of Agricultural and Food Chemistry 07/2013; · 2.91 Impact Factor
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    ABSTRACT: G-quadruplexes are promising therapeutic targets for small molecules. In general, the introduction of steady positive charges through the in situ alkylation of nitrogen atoms within potential G-quadruplex ligands can significantly improve their quadruplex binding and stabilization abilities. However, our previous studies on bisaryldiketene derivatives showed that the derivative M4, whose central piperidone moiety is quaternized, exhibits a poor G-quadruplex stabilization ability. To clarify this unusual finding, CD, ITC, UV and NMR analyses were performed to determine the binding behaviors of M4 and its non-quaternized analog M2 to G-quadruplex DNA [d(TGGGT)]4. Molecular modeling approaches were also employed to help illustrate ligand-quadruplex DNA interactions. The CD melting and ITC analyses revealed that M2 exhibited much stronger stabilization and binding abilities to [d(TGGGT)]4 compared to M4. Moreover, the CD and ITC analyses in combination with UV, NMR and MD simulations revealed that M2 tended to be end-stacked on the G-quartet, whereas M4 tended to be bound in the groove region. Analysis of the electrostatic potential showed that the charged surface of M4 was more positive than that of M2 and other reported ligands that bind to the G-quadruplex via end-stacking interactions. The results indicated that the different positively charged surfaces of M2 and M4 might be the key reason for their different binding modes. These different binding modes also lead to different binding affinities and stabilization abilities for [d(TGGGT)]4. These results provide new clues for the rational design of G-quadruplex-binding small molecules with steady positive charges.
    Biochimica et Biophysica Acta 07/2013; · 4.66 Impact Factor
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    ABSTRACT: G-Quadruplex is a highly polymorphic structure, and its behavior in acidic condition has not been well studied. Circular dichroism (CD) spectra were used to study the conformational change of G-quadruplex. The thermal stabilities of the G-quadruplex were measured with CD melting. Interconversion kinetics profiles were investigated by using CD kinetics. The fluorescence of the inserted 2-Aminopurine (Ap) was monitored during pH change and acrylamide quenching, indicating the status of the loop. Proton NMR was adopted to help illustrate the change of the conformation. G-Quadruplex of specific loop was found to be able to transform upon pH variation. The transformation was resulted from the loop rearrangement. After screening of a library of diverse G-quadruplex, a sequence exhibiting the best transformation property was found. A pH-driven nanoswitch with three gears was obtained based on this transition cycle. Certain G-quadruplex was found to go through conformational change at low pH. Loop was the decisive factor controlling the interconversion upon pH variation. G-Quadruplex with TT central loop could be converted in a much milder condition than the one with TTA loop. It can be used to design pH-driven nanodevices such as a nanoswitch. These results provide more insights into G-quadruplex polymorphism, and also contribute to the design of DNA-based nanomachines and logic gates.
    Biochimica et Biophysica Acta 06/2013; · 4.66 Impact Factor
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    ABSTRACT: A series of disubstituted bis(vinylquinolinium)benzene derivatives were designed, which were prepared through a facile three-component one-pot reaction in good yield. FRET results showed that 1,3-disubstituted benzene derivatives had much stronger stabilization effect on G-quadruplex DNA than that of 1,4-disubstituted benzene derivatives. The introduction of substituted amine side chain at quinolinium obviously increased the binding affinity of compounds to G-quadruplex DNA. It was also found that 1,3-disubstituted benzene derivatives and 1,4-disubstituted benzene derivatives had different effects on the conformation of G-quadruplex DNA by CD spectroscopy analysis. The differences for the interactions of these two classes of compounds with G-quadruplex were further studied and elaborated through molecular modeling experiments.
    Tetrahedron. 06/2013; 69(24):4922–4932.
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    ABSTRACT: BACKGROUND: Guanine-rich sequence of c-myc nucleic hypersensitive element (NHE) III1 is known to fold in G-quadruplex and subsequently serves as transcriptional silencer. Cellular nucleic-acid-binding protein (CNBP), a highly conserved zinc-finger protein with multiple biological functions, could bind to c-myc NHE III1 region, specifically to the single strand G-rich sequence. METHODS: Cloning, expression and purification of protein, EMSA, CD, FRET, Ch-IP, RNA Interference, Luciferase Reporter Assay, SPR, Co-Immunoprecipitation, and Co-transfection. RESULTS AND CONCLUSIONS: We found that human CNBP specifically bound to the G-rich sequence of c-myc NHE III1 region both in vitro and in cellulo, and subsequently promoted the formation of G-quadruplex. CNBP could induce a transient decrease followed by an increase in c-myc transcription in vivo. The interaction of CNBP with NM23-H2 was responsible for the increase of c-myc transcription. Based on above experimental results, a new mechanism, involving G-quadruplex related CNBP/NM23-H2 interaction, for the regulation of c-myc transcription was proposed. GENERAL SIGNIFICANCE: These findings indicated that the regulation of c-myc transcription through NHE III1 region might be governed by mechanisms involving complex protein-protein interactions, and suggested a new possibility of CNBP as a potential anti-cancer target based on CNBP's biological function in c-myc transcription.
    Biochimica et Biophysica Acta 06/2013; · 4.66 Impact Factor
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    ABSTRACT: A series of new isoliquiritigenin (ISL) derivatives were synthesized and evaluated as dual inhibitors for amyloid-beta (Aβ) aggregation and 5-lipoxygenase (5-LO). It was found that all these synthetic compounds inhibited Aβ (1-42) aggregation effectively with their IC50 values ranged from 2.2 ± 1.5 μM to 23.8 ± 2.0 μM. These derivatives also showed inhibitory activity to 5-LO with their IC50 values ranged from 6.1 ± 0.1 μM to 35.9 ± 0.3 μM. Their structure-activity relationships (SAR) and mechanisms of inhibitions were studied. This study provided potentially important information for further development of ISL derivatives as multifunctional agents for Alzheimer's disease (AD) treatment.
    European journal of medicinal chemistry 05/2013; 66C:22-31. · 3.27 Impact Factor

Publication Stats

335 Citations
336.57 Total Impact Points

Institutions

  • 2010–2014
    • Sun Yat-Sen University
      • • School of Pharmaceutical Science
      • • Department of Chemical Engineering
      Shengcheng, Guangdong, China
  • 2002–2013
    • City University of Hong Kong
      • Department of Biology and Chemistry
      Kowloon, Hong Kong
  • 2012
    • Huazhong (Central China) Normal University
      • College of Chemistry
      Wuhan, Hubei, China
  • 2003–2011
    • The University of Hong Kong
      • Department of Biochemistry
      Hong Kong, Hong Kong