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Chemical Biology & Drug Design

Cover image for Vol. 80 Issue 5

November 2012

Volume 80, Issue 5

Pages i–iii, 639–786

  1. Issue Information

    1. Top of page
    2. Issue Information
    3. Reviews
    4. Research Articles
    5. Research Letters
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      Issue Information (pages i–iii)

      Version of Record online: 5 OCT 2012 | DOI: 10.1111/cbdd.12061

  2. Reviews

    1. Top of page
    2. Issue Information
    3. Reviews
    4. Research Articles
    5. Research Letters
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      Cell-penetrating Peptides as a Novel Transdermal Drug Delivery System (pages 639–646)

      Saman A. Nasrollahi, Changiz Taghibiglou, Ebrahim Azizi and Effat S. Farboud

      Version of Record online: 31 AUG 2012 | DOI: 10.1111/cbdd.12008

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      Different CPPs can be succesfully used for the delivery of high molecular weight drugs into cells with high efficiency and relatively low toxicity.

  3. Research Articles

    1. Top of page
    2. Issue Information
    3. Reviews
    4. Research Articles
    5. Research Letters
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      Novel Targeted Liposomes Deliver siRNA to Hepatocellular Carcinoma Cells in vitro (pages 647–656)

      Shantal Dorasamy, Nicolisha Narainpersad, Moganavelli Singh and Mario Ariatti

      Version of Record online: 3 SEP 2012 | DOI: 10.1111/j.1747-0285.2012.01446.x

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      The d-galactopyranosyl ring in direct β-glycosidic link to cholesterol, when formulated into cationic liposomes with the cytofectin 3β[N-(N′,N′,N′,-trimethylammoniumpropane) carbamoyl] cholesterol iodide promotes efficient targeted delivery of a cytotoxic siRNA to the human hepatoblastoma cell line HepG2 via the asialoglycoprotein receptor (ASGP-R). However the receptor-negative human embryonic kidney cell line HEK293 is resistant to transfection under the same conditions.

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      Identification of Type-II Inhibitors Using Kinase Structures (pages 657–664)

      Frank Lovering, Joseph McDonald, Gavin A. Whitlock, Paul A. Glossop, Chris Phillips, Andrew Bent, Yogesh Sabnis, Mark Ryan, Lori Fitz, Julie Lee, Jeanne S. Chang, Seungil Han, Ravi Kurumbail and Atli Thorarensen

      Version of Record online: 3 SEP 2012 | DOI: 10.1111/j.1747-0285.2012.01443.x

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      A protein structure/ligand based approach has been successfully utilized to identify ligands that bind to novel conformations of Spleen Tyrosine Kinase (Syk). Kinase protein crystal structure databases have been applied to the discovery of the first Syk type-II ligands, including a DFG-out inhibitor and a rare deep pocket c-helix out inhibitor.

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      Identification of Purple Acid Phosphatase Inhibitors by Fragment-Based Screening: Promising New Leads for Osteoporosis Therapeutics (pages 665–674)

      Daniel Feder, Waleed M. Hussein, Daniel J. Clayton, Meng-Wei Kan, Gerhard Schenk, Ross P. McGeary and Luke W. Guddat

      Version of Record online: 3 SEP 2012 | DOI: 10.1111/cbdd.12001

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      Fragment-based screening has been used to identify three inhibitors of purple acid phosphatase with Ki values in 30–60 μm range. X-ray crystal structures of these compounds in complex with a plant purple acid phosphatase (2.3–2.7 Å resolution) have been determined and docking studies with mammalian purple acid phosphatase undertaken.

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      Evaluation of Perylenediimide Derivatives for Potential Therapeutic Benefits on Cancer Chemotherapy (pages 675–681)

      Taner Keskin, Belgin S. Isgor, Yasemin G. Isgor and Funda Yukruk

      Version of Record online: 31 AUG 2012 | DOI: 10.1111/cbdd.12004

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      The analysis of novel N,N′-disubstituted perylenediimides with amino acid functional groups and their 1,7-dibromo derivatives revealed their GST and PTK inhibitory activity at nanomolar to micromolar range. The inhibition profiles were investigated through their effects on central signaling component Src, and on cytosolic GSTs from liver homogenates. As the GSTs are highly overexpressed in cancer cells, their inhibition by perylenediimides might offer new clues on their mechanism of action and open interesting perspectives for future tumor therapies.

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      Design, Synthesis and Fungicidal Activity of Novel Sclerotiorin Derivatives (pages 682–692)

      Long Lin, Nick Mulholland, Shao-Wei Huang, David Beattie, Dianne Irwin, Yu-Cheng Gu, John Clough, Qiong-You Wu and Guang-Fu Yang

      Version of Record online: 31 AUG 2012 | DOI: 10.1111/cbdd.12005

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      Sclerotiorin analogues were designed and synthesized with an aim of discovering novel agrochemical. The antifungal activity of the synthesized compounds was evaluated against seven phytopathogenic species. Several compounds were found to have a broad spectrum of fungicidal activity, and these structurally simpler products can be recognized as lead compounds for further optimization.

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      Unraveling the Energetics and Mode of the Recognition of Antibiotics Tetracycline and Rolitetracycline by Bovine Serum Albumin (pages 693–705)

      Sinjan Choudhary and Nand Kishore

      Version of Record online: 31 AUG 2012 | DOI: 10.1111/cbdd.12009

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      Tetracycline and rolitetracycline bind to BSA in a sequential manner via a mix of hydrophobic, ionic and hydrogen bonding interactions. The calorimetry in combination with spectroscopy suggest the binding of these drugs at site-2 on BSA. Quantitative and qualitative aspects of the binding interactions and stabilization of the protein in presence of drugs have been discussed

      .

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      Structural Basis of the Allosteric Inhibitor Interaction on the HIV-1 Reverse Transcriptase RNase H Domain (pages 706–716)

      Martin T. Christen, Lakshmi Menon, Nataliya S. Myshakina, Jinwoo Ahn, Michael A. Parniak and Rieko Ishima

      Version of Record online: 31 AUG 2012 | DOI: 10.1111/cbdd.12010

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      Currently, there is no clinically approved inhibitor of the RNH activity in HIV-1 reverse transcriptase (RT). Little structural information about the interactions between RT RNH and inhibitors is available. Here, we identify an allosteric interaction site for an acylhydrazone inhibitor, BHMP07, on the HIV-1 RNH fragment.

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      Molecular Scaffold Analysis of Natural Products Databases in the Public Domain (pages 717–724)

      Austin B. Yongye, Jacob Waddell and José L. Medina-Franco

      Version of Record online: 31 AUG 2012 | DOI: 10.1111/cbdd.12011

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      Publicly available natural products databases were compiled and compared to each other using complementary measures of scaffold diversity including, cumulative scaffold recovery curves and Shannon entropy. The most and least diverse collections were identified. In addition to benzene and acyclic compounds, flavones, coumarins, and flavanones were found as the most frequent molecular scaffolds across the different natural products collections.

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      Design of a Novel Antimicrobial Peptide Activated by Virulent Proteases (pages 725–733)

      Wataru Aoki, Nao Kitahara, Natsuko Miura, Hironobu Morisaka, Kouichi Kuroda and Mitsuyoshi Ueda

      Version of Record online: 10 SEP 2012 | DOI: 10.1111/cbdd.12012

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      Antimicrobial peptides (AMPs) are promising antibiotics, but administration of an antibiotic with a very broad spectrum of activity increases the risks of other fatal infections. To solve the problem, we designed a novel AMP that is activated by virulent proteases of pathogenic organisms. A designed peptide like the one may protect normal microflora, resulting in enhanced safety as a therapeutic.

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      Genome-wide Inference of Transcription Factor–DNA Binding Specificity in Cell Regeneration Using a Combination Strategy (pages 734–744)

      Xiaofeng Wang, Aiqun Zhang, Weizheng Ren, Caiyu Chen and Jiahong Dong

      Version of Record online: 10 SEP 2012 | DOI: 10.1111/cbdd.12013

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      A combination strategy is used to predict the binding affinity and infer the binding specificity of transcription factor–DNA interactions at the genomic level. It is revealed that the interactives and conformational effects contribute significantly to the sequence-specific recognition.

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      Effect of 3-Alkylpyridine Marine Alkaloid Analogues in Leishmania Species Related to American Cutaneous Leishmaniasis (pages 745–751)

      Patrícia A. Machado, Flaviane F. Hilário, Lidiane O. Carvalho, Mariana L. T. Silveira, Rosemeire B. Alves, Rossimiriam P. Freitas and Elaine S. Coimbra

      Version of Record online: 10 SEP 2012 | DOI: 10.1111/cbdd.12017

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      The 3-alkylpyridine marine alkaloid analogues 11, 14, 15 and 16, exhibited IC50 below 3.0 μm against amastigotes of L. amazonensis.

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      CASE Plots for the Chemotype-Based Activity and Selectivity Analysis: A CASE Study of Cyclooxygenase Inhibitors (pages 752–762)

      Jaime Pérez-Villanueva, José L. Medina-Franco, Oscar Méndez-Lucio, Jakyung Yoo, Olivia Soria-Arteche, Teresa Izquierdo, M. Concepción Lozada and Rafael Castillo

      Version of Record online: 10 SEP 2012 | DOI: 10.1111/cbdd.12019

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      Chemotype Activity and Selectivity Enrichment (CASE) plots are presented in this work as a novel graphical representation of the chemical structure, activity and selectivity of a molecular database with activity against two biological endpoints. Compounds with selected chemotypes (most active and selective) were further characterized using Dual Activity Difference (DAD) maps. The application of both methodologies leads to a comprehensive SAR analysis comprising scaffolds and side chains for a set of cyclooxygenase inhibitors.

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      Modulation of Opioid Receptor Ligand Affinity and Efficacy Using Active and Inactive State Receptor Models (pages 763–770)

      Jessica P. Anand, Lauren C. Purington, Irina D. Pogozheva, John R. Traynor and Henry I. Mosberg

      Version of Record online: 12 SEP 2012 | DOI: 10.1111/cbdd.12014

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      Mixed efficacy opioid peptides displaying mu agonist/delta antagonist properties were developed using opioid receptor models of active and inactive states to guide design. This bifunctional pharmacological profile holds great promise for pain treatment with limited tolerance development.

  4. Research Letters

    1. Top of page
    2. Issue Information
    3. Reviews
    4. Research Articles
    5. Research Letters
    1. You have free access to this content
      Superior Analgesic Effect of H-Dmt-D-Arg-Phe-Lys-NH2 ([Dmt1]DALDA), a Multifunctional Opioid Peptide, Compared to Morphine in a Rat Model of Neuropathic Pain (pages 771–774)

      Megumi Shimoyama, Peter W. Schiller, Naohito Shimoyama, Satoshi Toyama and Hazel H. Szeto

      Version of Record online: 3 SEP 2012 | DOI: 10.1111/cbdd.12003

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      The effect of [Dmt1]DALDA, a synthetic multifunctional opioid peptide, was compared with morphine in a model of experimental neuropathic pain. Systemic [Dmt1]DALDA was more effective than morphine in increasing thermal pain threshold in thermal hyperalgesia due to neuropathic pain produced by spinal nerve ligation in rats.

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      Synthesis, in vitro Biological Evaluation and Molecular Docking Studies of Benzimidamides as Potential BACE1 Inhibitors (pages 775–780)

      Yan Niu, Haifei Gao, Fengrong Xu, Chao Wang, Peng Liu, Guanyu Yang, Qi Sun and Ping Xu

      Version of Record online: 10 SEP 2012 | DOI: 10.1111/cbdd.12016

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      A series of 3, 5-disubstituted benzimidamides were synthesized and biologically evaluated as potential BACE1 inhibitors in a cell free FRET assay. All the targeted benzimidamides, and some of the synthetic intermediates (benzonitriles) were found active, with compound 6d generating the lowest IC50 of 3.35 μm. Molecular docking study proposed that the benzimidamides could bind rationally in the active site and the predicted logBB values suggested that they were BBB penetrable.

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      6-Hydrogen-8-Methylquinolones Active Against Replicating and Non-replicating Mycobacterium tuberculosis (pages 781–786)

      Oriana Tabarrini, Stefano Sabatini, Serena Massari, Marco Pieroni, Scott G. Franzblau and Violetta Cecchetti

      Version of Record online: 10 SEP 2012 | DOI: 10.1111/cbdd.12022

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      The screening of an in-house quinolones library against Mycobacterium tuberculosis H37Rv, followed by a first cycle of optimization, yielded 6-hydrogen-8-methyl derivatives endowed with good potency also against the bacteria in a non-replicating state with MIC values lower than those of the reference agent, moxifloxacin.

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