Zhanli Wang

Third Military Medical University, Ch’ung-ch’ing-shih, Chongqing Shi, China

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Publications (18)43.17 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: MicroRNAs (miRNAs) are involved in the regulation of numerous physiological and pathological processes. However, little information is available with regard to miRNAs in the left ventricular myocardium of the renovascular angiotensin-dependent hypertensive rat. In this study, miRNA expression profiles in the left ventricular myocardium of two-kidney one-clip (2K1C) hypertensive rats were analyzed using a microarray. The roles of the differentially expressed miRNAs, their target genes and signaling pathways were analyzed using ingenuity pathway analysis (IPA) for the first time to further elucidate the molecular mechanisms of left ventricular remodeling.
    Molecular Medicine Reports 06/2013; · 1.17 Impact Factor
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    ABSTRACT: Chemical feature based pharmacophore models were generated for Toll-like receptors 7 (TLR7) agonists using HypoGen algorithm, which is implemented in the Discovery Studio software. Several methods tools used in validation of pharmacophore model were presented. The first hypothesis Hypo1 was considered to be the best pharmacophore model, which consists of four features: one hydrogen bond acceptor, one hydrogen bond donor, and two hydrophobic features. In addition, homology modeling and molecular docking studies were employed to probe the intermolecular interactions between TLR7 and its agonists. The results further confirmed the reliability of the pharmacophore model. The obtained pharmacophore model (Hypo1) was then employed as a query to screen the Traditional Chinese Medicine Database (TCMD) for other potential lead compounds. One hit was identified as a potent TLR7 agonist, which has antiviral activity against hepatitis virus in vitro. Therefore, our current work provides confidence for the utility of the selected chemical feature based pharmacophore model to design novel TLR7 agonists with desired biological activity.
    PLoS ONE 01/2013; 8(3):e56514. · 3.73 Impact Factor
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    ABSTRACT: Evodiamine, a naturally occurring indole alkaloid, is one of the main bioactive ingredients of Evodiae fructus. With respect to the pharmacological actions of evodiamine, more attention has been paid to beneficial effects in insults involving cancer, obesity, nociception, inflammation, cardiovascular diseases, Alzheimer's disease, infectious diseases and themoregulative effects. Evodiamine has evolved a superior ability to bind various proteins, so we also argue that it is good starting point for multi-target drugs. This review is primarily addressed to the description of the recent advances in the biological activity studies of evodiamine, with a focus on pharmacological mechanism. The present review also includes the pharmacokinetics and the detailed exploration of target-binding properties of evodiamine in an attempt to provide a direction for further multi-target drug design.
    Molecules 01/2013; 18(2):1826-43. · 2.43 Impact Factor
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    ABSTRACT: Celastrol is a novel inhibitor of the human protein complex Hsp90–Cdc37. It was found that the N-terminal domain of Cdc37 (Cdc37_N) was the molecular target for celastrol binding through covalent bonding. To get insight into the binding mode of celastrol in the active site of Cdc37, herein, the homology models of Cdc37_N and N-terminal/middle domain of Cdc37 (Cdc37_NM) were built. Moreover, a model of Cdc37 complexed with celastrol was obtained using docking and molecular dynamics (MD) approaches. Molecular modelling studies indicated that the middle domain of Cdc37 (Cdc37_M) might be an obbligato part of the binding pocket, which could make the pocket stable for celastrol docking. We also found that the S atom of Cys57 was closest to C6 atom of celastrol among all three cysteine residues (Cys54, Cys57 and Cys64) in the pocket, which implied that celastrol and Cys57 did have a good chance to form covalent bond. The covalent interaction between C6 atom of celastrol and Cys57 of Cdc37 could also explain the potency of celastrol to inhibit the interaction of Cdc37 and Hsp90. These findings can be used to develop novel Cdc37 inhibitors.
    Molecular Simulation 01/2013; 39(4). · 1.06 Impact Factor
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    ABSTRACT: Accurate assessment of the potential binding mode of drugs is crucial to computer-aided drug design paradigms. It has been reported that evodiamine acts as an agonist of the vanilloid receptor Transient receptor potential vanilloid-1 (TRPV1). However, the precise interaction between evodiamine and TRPV1 was still not fully understood. In this perspective, the homology models of TRPV1 were generated using the crystal structure of the voltage-dependent shaker family K(+) channel as a template. We then performed docking and molecular dynamics simulation to gain a better understanding of the probable binding modes of evodiamine within the TRPV1 binding pocket. There are no significant interspecies differences in evodiamine binding in rat, human and rabbit TRPV1 models. Pharmacophore modeling further provided confidence for the validity of the docking studies. This study is the first to shed light on the structural determinants required for the interaction between TRPV1 and evodiamine, and gives new suggestions for the rational design of novel TRPV1 ligands.
    International Journal of Molecular Sciences 01/2012; 13(7):8958-69. · 2.46 Impact Factor
  • Hui Yu, Zhanli Wang, Gang Sun, Yongchun Yu
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    ABSTRACT: Toll-like receptors 7 and 8 (TLR7/8), known as pattern recognition receptors (PRR), are currently viewed as important targets for the development of new therapies for multiple diseases. Therefore, manipulating the immune response by using TLR7/8 agonists or antagonists might be of therapeutic value. Nucleic acid-like structures are well-known TLR7/8 ligands, such as single-stranded RNA (ssRNA), small interfering RNA (siRNA), CpG-oligodeoxynucleotides (ODNs) and nucleoside analogues. However, these nucleic acid TLR7/8 ligands show a variety of pharmacological properties and change of their structures offers a high degree of diversity. Unnatural modified nucleosides have been explored to expand the properties and the applications of nucleic acid. In this regard, chemical modification of nucleosides is very useful for production of specific pharmacological qualities of nucleic acid TLR7/8 ligands. In this review, we will summarize the characteristics of nucleic acid TLR7/8 ligand system and describe the applications of chemical modifications, with a focus on potency and structure-activity relationships (SAR).
    Current Medicinal Chemistry 12/2011; 19(9):1365-77. · 4.07 Impact Factor
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    ABSTRACT: A validated 3D pharmacophore model was generated for a series of ACE inhibitory peptides, which consisted of five features (two hydrophobic functions, two hydrogen bond acceptors, and a negative ionizable function). The built model was able to correctly predict the activity of known ACE inhibitors. The model was then used as query to search 3D databases of peptides. Three novel peptides (I, II and III) were synthesized and biologically evaluated in vitro. It appears that the in vitro activity of peptides I, II and III was consistent with their molecular modeling results. Our results provided confidence for the utility of the pharmacophore model to retrieve novel ACE inhibitory peptides with desired biological activity by virtual screening.
    European journal of medicinal chemistry 08/2011; 46(8):3428-33. · 3.27 Impact Factor
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    ABSTRACT: AMP-activated protein kinase (AMPK) is an important therapeutic target for the potential treatment of metabolic disorders, cardiovascular disease and cancer. Recently, various classes of compounds that activate AMPK by direct or indirect interactions have been reported. The importance of computer-aided drug design approaches in the search for potent activators of AMPK is now established, including structure-based design, ligand-based design, fragment-based design, as well as structural analysis. This review article highlights the computer-aided drug design approaches utilized to discover of activators targeting AMPK. The principles, advantages or limitation of the different methods are also being discussed together with examples of applications taken from the literatures.
    Current Computer - Aided Drug Design 05/2011; 7(3):214-27. · 1.54 Impact Factor
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    ABSTRACT: Evodiamine, the major bioactive alkaloid isolated from Wu-Chu-Yu, has been shown to interact with a wide variety of proteins and modify their expression and activities. In this study, we investigated the interaction between evodiamine and the aryl hydrocarbon receptor (AhR). Molecular modeling results revealed that evodiamine directly interacted with the AhR. Cytosolic receptor binding assay also provided the evidence that evodiamine could interact with the AhR with the K(i) value of 28.4±4.9nM. In addition, we observed that evodiamine suppressed the 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) induced nuclear translocation of the AhR and the expression of CYP1A1 dose-dependently. These results suggested that evodiamine was able to bind to the AhR as ligand and exhibit antagonistic effects.
    Biochemical and Biophysical Research Communications 09/2010; 402(1):94-8. · 2.41 Impact Factor
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    ABSTRACT: It has been observed that bromophenol blue interacted specifically with chicken haemoglobin but not with carp haemoglobin during electrophoresis, but the mechanism of interaction is still not well understood. In this computational study, the binding of bromophenol blue to chicken haemoglobin has been investigated using sequence alignment, homology modelling, electrostatic potential distribution and flexible docking methods. Molecular modelling studies reveal that bromophenol blue-binding site, formed by residues Val1α, Leu2α, Ala131α, Thr134α, Ala138α and Arg141α, is located between two α chains of chicken haemoglobin, and the binding is dominated by hydrophobic interactions. Moreover, comparison of chicken and carp haemoglobin structural models provides a structural rationale for the recognition of bromophenol blue by chicken haemoglobin. These principles can in turn be used to study the molecular recognition mechanism and design a mimic of bromophenol blue for the development of new haemoglobin binders.
    Molecular Physics 01/2010; 108(2):215-220. · 1.67 Impact Factor
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    ABSTRACT: The interaction of vascular endothelial growth factor (VEGF) and its receptors (Flt-1, Flk-1/KDR) is correlated with neovascularization in the eyes. Therefore, blocking the binding of VEGF and the corresponding receptor has become critical for inhibiting corneal neovascularization. In this study, we have expressed the cDNA for sFlk-1 under the control of cytomegalovirus immediate-early promoter (CMV) from an E1/partial E3 deleted replication defective recombinant adenovirus, and Ad.sflk-1 expression was determined by Western blotting. We have shown that conditioned media from Ad.sflk-1-infected ARPE-19 cells significantly reduced VEGF-induced human umbilical vein endothelial cells (HUVEC) and murine endothelial cells (SVEC) proliferation in vitro compared with the control vector. In vivo, adenoviral vectors expressing green fluorescent protein alone (Ad.GFP) were utilized to monitor gene transfer to the cornea. Moreover, in the models of corneal neovascularization, the injection of Ad.sflk-1 (10(8)PFU) into the anterior chamber could significantly inhibit angiogenic changes compared with Ad.null-injected and vehicle-injected models. Immunohistochemical analysis showed that corneal endothelial cells and corneal stroma of cauterized rat eyes were efficiently transduced and expressed sFlk-1. These results not only support that adenoviral vectors are capable of high-level transgene expression but also demonstrate that Ad.sflk-1 gene therapy might be a feasible approach for inhibiting the development of corneal neovascularization.
    Biochemical and Biophysical Research Communications 11/2007; 361(4):946-52. · 2.41 Impact Factor
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    ABSTRACT: Herpes simplex virus type-1 thymidine kinase (HSV-1TK) and Escherichia coli cytosine deaminase (CD) fusion protein was designed using InsightII software. The structural rationality of the fusion proteins incorporating a series of flexible linker peptide was analyzed, and a suitable linker peptide was chosen for further investigated. The recombinant plasmid containing the coding regions of HSV-1TK and CD cDNA connected by this linker peptide coding sequence was generated and subsequently transfected into the human embryonic kidney 293 cells (HEK293). The Western blotting indicated that the recombinant fusion protein existed as a dimer with a molecular weight of approximately 90 kDa. The toxicity of the prodrug on the recombinant plasmid-transfected human lung cancer cell line NCIH460 was evaluated, which showed that TKglyCD-expressing cells conferred upon cells prodrug sensitivities equivalent to that observed for each enzyme independently. Most noteworthy, cytotoxicity could be enhanced by concurrently treating TKglyCD-expressing cells with prodrugs GCV and 5-FC. The results indicate that we have successfully constructed a HSV-1TKglyCD fusion gene which might have a potential application for cancer gene therapy.
    Biochemical and Biophysical Research Communications 09/2007; 360(1):46-50. · 2.41 Impact Factor
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    ABSTRACT: In order to elucidate the essential structural features for KDR kinase inhibitors, three-dimensional pharmacophore hypotheses were built on the basis of a set of known KDR kinase inhibitors selected from the literature with CATALYST program. Several methods tools used in validation of pharmacophore hypothsis were presented, and the first hypothesis (Hypo1) was considered to be the best pharmacophore hypothesis. The model (Hypo1) was then employed as 3D search query to screen the Traditional Chinese Medicine Database (TCMD) for other potential lead compounds. One hit illustrated high binding affinity with KDR kinase measured by the surface plasmon resonance biosensor. Docking studies may help elucidate the mechanisms of KDR kinase receptor-ligand interactions.
    Bioorganic & Medicinal Chemistry Letters 05/2007; 17(8):2126-33. · 2.34 Impact Factor
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    ABSTRACT: We have applied pharmacophore generation, database searching and docking methodologies to discover new structures for the design of vascular endothelial growth factor receptors, the tyrosine kinase insert domain-containing receptor kinase inhibitors. The chemical function based pharmacophore models were built for kinase insert domain-containing receptor kinase inhibitors from a set of 10 known inhibitors using the algorithm HipHop, which is implemented in the CATALYST software. The highest scoring HipHop model consists of four features: one hydrophobic, one hydrogen bond acceptor, one hydrogen bond donor and one ring aromatic function. Using the algorithm CatShape within CATALYST, the bound conformation of 4-amino-furo [2, 3-d] pyrimidine binding to kinase insert domain-containing receptor kinase was used to generate a shape query. A merged shape and hypothesis query that is in an appropriate alignment was then built. The combined shape and hypothesis model was used as a query to search Maybridge database for other potential lead compounds. A total of 39 compounds were retrieved as hits. The hits obtained were docked into kinase insert domain-containing receptor kinase active site. One novel potential lead was proposed based on CATALYST fit value, LigandFit docking scores, and examination of how the hit retain key interactions known to be required for kinase binding. This compound inhibited vascular endothelial growth factor stimulated kinase insert domain-containing receptor phosphorylation in human umbilical vein endothelial cells.
    Chemical Biology &amp Drug Design 04/2007; 69(3):204-11. · 2.47 Impact Factor
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    ABSTRACT: Some structural insights into the conformations of the isonucleosides containing duplexes have been provided. Unrestrained molecular-dynamics simulations on 18-mer duplexes with isonucleosides incorporated at the 3'-end or in the center of one strand have been carried out with explicit solvent under periodic boundary conditions using the AMBER force field and the particle mesh Ewald method. The Watson-Crick hydrogen-bonding patterns of the duplexes studied remained intact throughout the simulation. For the modified duplexes, the changes observed in the inter-base pair parameters and backbone torsional angles were primarily localized at the isonucleoside-inserted area. All five structures studied remained in the B-form family. The decreased stacking abilities indicated by the large changes in inter-base pair parameters and the large changes in backbones made the modified duplexes show a minor thermal destabilization in comparison with native DNA. The MM_PBSA method for estimating binding free energies on two complementary strands was used. The results showed that the binding free energies of isonucleoside-incorporated DNA duplexes were lower than the native DNA duplex, which is in good agreement with experimental observations.
    Journal of Molecular Modeling 10/2006; 12(6):781-91. · 1.98 Impact Factor
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    ABSTRACT: The interaction of ribonuclease inhibitor (RI) with kanamycin was studied by molecular modeling. The preliminary binding model was constructed using the Affinity module of the Insight II molecular modeling program and the key residues involved in the combination of RI binding to kanamycin were determined. Meanwhile, we determined relevant surface characteristics determining the interaction behavior. The modeling results indicated that electrostatic interactions and H-bond forces may work as major factors for the molecular interaction between kanamycin and RI. The above results are useful for elucidating the molecular principles upon which the selectivity of a kanamycin is based. The quartz-crystal microbalance (QCM) is a new method usually used to monitor the binding function of macromolecules with samples online in a flow-injection analysis (FIA) system. The experimental results demonstrate that kanamycin has an extraordinary affinity to the basic protein RI, and our result is consistent with the molecular modeling results. These principles can in turn be used to study the molecular recognition mechanism and design a mimic of kanamycin for the development of new RI binders.
    Journal of Molecular Modeling 03/2005; 11(1):80-6. · 1.98 Impact Factor
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    ABSTRACT: Antisense oligonucleotides are recognized to be very efficient tools for the inhibition of gene expression in a sequence specific way. For the discovery of a novel efficient way to modify oligonucleotides, a series of single isonucleotide-incorporated antisense oligodeoxynucleotides have been synthesized, in which an isonucleotide was introduced at different positions of the sequences. The binding behaviors of modified oligodeoxynucleotides to the complementary sequence were studied by UV, CD, and molecular dynamics simulation. The results showed that although the incorporated isonucleotides at certain positions of the sequence interfere with the binding ability to a different extent, B-form duplexes were maintained and the binding abilities of the 3'-end-modified duplexes were better than the corresponding mismatched duplexes. The digestion of modified oligodeoxynucleotides by snake venom phosphodiesterase showed that an isonucleotide strongly antagonizes hydrolysis. The DNA/RNA hybrid formed by a modified oligodeoxynucleotide and its target RNA could activate RNase H. The 3'-end-modified antisense oligodeoxynucelotides inhibited S-glycoprotein expression of SARS-CoV at the mRNA levels in insect Sf9 cells. This study indicated the possibility of designing a novel and effective antisense oligodeoxynucleotide by incorporating an isonucleotide at the 3'-end of the sequence.
    Bioconjugate Chemistry 01/2005; 16(5):1081-7. · 4.58 Impact Factor
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    ABSTRACT: Chemical feature based pharmacophore models were generated for an angiotensin converting enzyme (ACE) inhibitory peptide using the Discovery Studio 2.0 pharmacophore modeling approach. The pharmacophore hypothesis selected has five features (one negative ionizable region, one hydrogen bond donor, one hydrogen bond acceptor and two hydrophobic functional groups). Additionally, ACE inhibitory hexapeptide previously obtained from silkworm pupae protein was optimized to target the ACE based on the selected pharmacophore. The results suggest that tri-peptide (thr-val-phe) may be structural determinant of ACE activity. Docking studies further provided confidence for the validity of the selected pharmacophore model to perform structure optimization of the ACE inhibitory peptide.
    Science in China Series B Chemistry 51(8):786-793. · 1.20 Impact Factor

Publication Stats

42 Citations
43.17 Total Impact Points

Institutions

  • 2010–2013
    • Third Military Medical University
      Ch’ung-ch’ing-shih, Chongqing Shi, China
    • Zhejiang University of Technology
      Hang-hsien, Zhejiang Sheng, China
  • 2011–2012
    • Baotou Medical College
      Pao-t’ou, Inner Mongolia, China
    • Zhejiang University
      • Department of Food and Nutrition Science
      Hangzhou, Zhejiang Sheng, China
  • 2007
    • First People's Hospital Chenzhou
      Chenchow, Hunan, China
  • 2005–2006
    • Peking University
      • School of Pharmaceutical Sciences
      Beijing, Beijing Shi, China
    • Peking University Health Science Center
      Peping, Beijing, China