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Chemical Biology & Drug Design

Cover image for Vol. 79 Issue 5

May 2012

Volume 79, Issue 5

Pages i–iii, 617–877

  1. Issue Information

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

      Article first published online: 3 APR 2012 | DOI: 10.1111/j.1747-0285.2012.01386.x

  2. Review Article

    1. Top of page
    2. Issue Information
    3. Review Article
    4. Research Articles
    5. Research Letters
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      The Nucleotide, Inhibitor, and Cation Binding Sites of P-type II ATPases (pages 617–627)

      Mukesh Chourasia and G. Narahari Sastry

      Article first published online: 23 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01334.x

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      P-Type ATPases constitute a ubiquitous superfamilly of cation transport enzymes, responsible for carrying out actions of paramount importance in biology such as ion transport, and expulsion of toxic ions from cells etc. The harmonized toggling of gates in the extra and intracellular domains explains the phenomenon of specific cation binding in selective physiological states. The current review delineates the importance of cation, nucleotide and inhibitor binding domains, with a focus on the therapeutic potential and biological relevance of the three P-Type II ATPases.

  3. Research Articles

    1. Top of page
    2. Issue Information
    3. Review Article
    4. Research Articles
    5. Research Letters
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      Synthesis, Molecular Docking, and Biofilm Formation Inhibitory Activity of 5-Substituted 3,4-Dihalo-5H-furan-2-one Derivatives on Pseudomonas aeruginosa (pages 628–638)

      Guo-Yong Liu, Bao-Qin Guo, Wan-Na Chen, Chao Cheng, Qian-Lan Zhang, Mi-Bei Dai, Jun-Rong Sun, Ping-Hua Sun and Wei-Min Chen

      Article first published online: 15 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01342.x

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      A set of 5-(aryl-1′-hydroxy-methyl)- or 5-(aryl-2-methylene)-3,4-dihalo-5H-furan-2-ones were designed and synthesized. Several compounds exhibited remarkable biofilm inhibitory activities. Key structural features of these compounds were preliminarily identified by molecular docking studies.

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      Discovery of Small Molecule Inhibitors that Interact with γ-Tubulin (pages 639–652)

      Douglas E. Friesen, Khaled H. Barakat, Valentyna Semenchenko, Rolando Perez-Pineiro, Bruce W. Fenske, Jonathan Mane, David S. Wishart and Jack A. Tuszynski

      Article first published online: 15 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01340.x

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      We present experimental evidence that colchicine and combretastatin A-4 bind to γ-tubulin, which are to our knowledge the first drug-like compounds known to interact with γ-tubulin, a protein key to nucleating microtubules. Molecular dynamics (MD) simulations and docking studies were used to analyze the hypothesized γ-tubulin binding domain of these compounds. This discovery is a significant first step in the rational drug design of an effective small molecule inhibitor of γ-tubulin.

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      Design of Potent, Non-Toxic Antimicrobial Agents Based upon the Structure of the Frog Skin Peptide, Temporin-1CEb from Chinese Brown Frog, Rana chensinensis (pages 653–662)

      Dejing Shang, Xiaofan Li, Yue Sun, Che Wang, Li Sun, Shi Wei and Meng Gou

      Article first published online: 16 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01363.x

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      Eight analogues of temporin-1CEb are designed to understand the relationship of structure-activity by modifications of the cationicity and hydrophobicity. l-K6 may find use as a new drug candidate because it displayed the most improved antimicrobial activity against Gram-positive and -negative bacteria and showed greatly decreased haemolytic activity. l-K6 affected the integrity of the plasma membrane of E. coli and S. aureus by inducing membrane depolarization in <1 min.

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      3′-Axial CH2OH Substitution on Glucopyranose does not Increase Glycogen Phosphorylase Inhibitory Potency. QM/MM-PBSA Calculations Suggest Why (pages 663–673)

      Stella Manta, Andromachi Xipnitou, Christos Kiritsis, Anastassia L. Kantsadi, Joseph M. Hayes, Vicky T. Skamnaki, Christos Lamprakis, Maria Kontou, Panagiotis Zoumpoulakis, Spyridon E. Zographos, Demetres D. Leonidas and Dimitri Komiotis

      Article first published online: 7 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01349.x

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      1-[3′-C-(hydroxymethyl)-β-d-glucopyranosyl)]5-fluorouracil has been synthesized and has been identified as an inhibitor of muscle glycogen phosphorylase b. The parent ligand 1-(β-d-glucopyranosyl)5-fluorouracil is 2.9 times more potent. Modeling calculations and X-ray structural studies were performed to identify the source of the greater binding affinity compared to its 3′-substituted glucose derivative.

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      Molecular Modeling Evaluation of Non-Steroidal Aromatase Inhibitors (pages 674–682)

      Bheemanapalli Lakshmi Narayana, Deb Pran Kishore, Chadrasekaran Balakumar, Kaki Venkata Rao, Rajwinder Kaur, Akkinepally Raghuram Rao, Javali Narashima Murthy and Muttineni Ravikumar

      Article first published online: 23 FEB 2012 | DOI: 10.1111/j.1747-0285.2011.01277.x

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      A recent discovery of aromatase crystal structure triggered the efforts to design novel aromatase inhibitors for breast cancer therapy. Quantitative structure activity relationships were developed between the aromatase inhibitory activity (pIC50) of flavonoidal derivatives (= 39) and docking scores and docking descriptors, validated externally. Results confirm the potential of our methodology for the design of new potent non-steroidal AIs.

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      Effects of the TAT Peptide Orientation and Relative Location on the Protein Transduction Efficiency (pages 683–690)

      Qingguo Guo, Guojie Zhao, Fengjin Hao and Yifu Guan

      Article first published online: 20 FEB 2012 | DOI: 10.1111/j.1747-0285.2011.01315.x

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      Four TAT-EGFP conjugates with different TAT sequence orientations and relative locations with respect to the cargo protein have been constructed. They have demonstrated almost identical cellular transduction efficiency in vitro. They can traverse into different tissues of mice in vivo study.

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      QSAR Models for isoindolinone-based p53–MDM2 Interaction Inhibitors Using Linear and Non-linear Statistical Methods (pages 691–702)

      Xiaowu Dong, Jingying Yan, Dong Lu, Peng Wu, Jiadi Gao, Tao Liu, Bo Yang and Yongzhou Hu

      Article first published online: 9 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01322.x

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      Linear and non-linear QSAR models were developed and validated using FS-MLR, ERM-MLR and SVMR methods for isoindolinone-based p53-MDM2 interaction inhibitors.

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      Molecular Dynamics in Drug Design: New Generations of Compstatin Analogs (pages 703–718)

      Phanourios Tamamis, Aliana López de Victoria, Ronald D. Gorham Jr, Meghan L. Bellows-Peterson, Panayiota Pierou, Christodoulos A. Floudas, Dimitrios Morikis and Georgios Archontis

      Article first published online: 9 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01324.x

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      The use of molecular dynamics in drug design is demonstrated, using compstatin family peptides as a paradigm. Analogs with novel properties are presented using the following design criteria: (i) optimization for high binding affinity and for the balance between hydrophobicity and polarity to improve solubility, compared to known compstatin analogs; and (ii) development of dual specificity antihuman-rat/mouse C3 analogs, which is important for use in animal models for disease, given the species specificity of known compstatin analogs.

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      Synthesis of 5- and 6-N-heterocyclic Methylenebisphosphonate Derivatives and Evaluation of their Cytogenetic Activity in Normal Human Lymphocyte Cultures (pages 719–730)

      Wafaa M. Abdou, Azza A. Kamel, Rizk E. Khidre, Athina Geronikaki and Maria T. Ekonomopoulou

      Article first published online: 15 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01327.x

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      Methods for the preparation of varios aminomethylene-bisphosphonates (BPs) were developed. The sister chromatid exchanges (SCE) frequency and proliferation rate index (PRI) values of human lymphocyte cultures were estimated.

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      Ligustrazine Derivatives. Part 4: Design, Synthesis, and Biological Evaluation of Novel Ligustrazine-based Stilbene Derivatives as Potential Cardiovascular Agents (pages 731–739)

      Lijuan Deng, Xiuli Guo, Li Zhai, Yuning Song, Hongfei Chen, Peng Zhan, Jingde Wu and Xinyong Liu

      Article first published online: 15 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01332.x

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      A series of novel stilbene derivatives containing ligustrazinyl moiety was designed, synthesized, and assayed for their protective effects on damaged endothelial cells. Compound A27 displayed EC50 0.0249 μm, which is 30 000 times higher than that of Ligustrazine, presenting a most promising lead for further investigation.

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      Receptor-Dependent 4D-QSAR Analysis of Peptidemimetic Inhibitors of Trypanosoma cruzi Trypanothione Reductase with Receptor-Based Alignment (pages 740–748)

      Samuel Silva da Rocha Pita, Magaly Girão Albuquerque, Carlos Rangel Rodrigues, Helena Carla Castro and Anton J. Hopfinger

      Article first published online: 20 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01338.x

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      Trypanothione Reductase is a valuable target in the discovery and development of new drugs for Chagas disease. Twenty-one peptides that had previously inhibited TR are studied for their mechanism of action applying RD-4D-QSAR method. The best equations generated by the RD-4D-QSAR method resulted in good models (q2 > 0.72, inline image > 0.78 and r2 > 0.81) that revealed regions of particular interest in drug discovery process: the catalytic cysteines, the Z-site, and, the FAD region.

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      A Bioinformatics Search for Selective Histamine H4 Receptor Antagonists Through Structure-Based Virtual Screening Strategies (pages 749–759)

      Fenila Christopher, Elden Berla Thangam and Muthaiyan Xavier Suresh

      Article first published online: 7 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01336.x

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      Histamine H4 receptor modeled based on human B2-adrenergic G protein-coupled receptor was docked with structurally similar compounds of the three known antagonists JNJ777120, Thioperamide and Vuf6002. Six compounds with high docking scores have been identified showing interactions with Asp94, a key amino acid residue at the binding site of the receptor.

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      Pharmacophore and QSAR Studies to Design Novel Histone Deacetylase 2 Inhibitors (pages 760–770)

      Yuhong Xiang, Zhaoyan Hou and Zhuoyong Zhang

      Article first published online: 15 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01341.x

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      The hit compound (NSC204640) has a good interaction with HDAC2 (PDB ID: 3MAX). The similarity between NSC204640 and the reference molecule extracted from 3MAX is 0.793 and the docking score value is 13.7125.

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      Synthesis and Anticonvulsant Activity of 1-(2-(8-(benzyloxy)quinolin-2-yl)-1-butyrylcyclopropyl)-3-Substituted Urea Derivatives (pages 771–779)

      Xianran He, Min Zhong, Jin Yang, Zhongyuan Wu, Yuling Xiao, Hao Guo and Xianming Hu

      Article first published online: 16 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01352.x

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      A series of 1-(2-(8-(benzyloxy)quinolin-2-yl)-1-butyrylcyclopropyl)-3-substituted urea derivatives were synthesized. Two models have been used for determining the anticonvulsant activity of candidate compounds. Compound 7e showed ED50 value of 14.3 mg/kg and PI of 30.3 in the MES test.

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      Natural Products as Sources of New Fungicides: Synthesis and Antifungal Activity of Zopfiellin Analogues (pages 780–789)

      Loana Musso, Sabrina Dallavalle, Gandolfina Farina and Elio Burrone

      Article first published online: 20 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01343.x

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      A series of cyclooctadiene anhydrides, analogues of zopfiellin, were synthesised and their in vitro antifungal activity on a set of plant pathogenic fungi was assayed. Most of the compounds possessed a broad spectrum of activity. Preliminary in vivo evaluation of their protectant activity was also carried out.

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      Synthesis and Antimalarial Activity of Dihydroperoxides and Tetraoxanes Conjugated with Bis(benzyl)acetone Derivatives (pages 790–797)

      Lucas Lopardi Franco, Mauro Vieira de Almeida, Luiz Francisco Rocha e Silva, Pedro Paulo Ribeiro Vieira, Adrian Martin Pohlit and Marcelo Siqueira Valle

      Article first published online: 16 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01345.x

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      Dihydroperoxides and tetraoxanes derived from symmetrically substituted bis(arylmethyl)acetones were synthesized in modest to good yields using several methods. Three of these compounds exhibit important in vitro antimalarial activity (1.0 μm ≤ IC50 ≤ 5.0 μm) against blood forms of the human malaria parasite Plasmodium falciparum.

  4. Research Letters

    1. Top of page
    2. Issue Information
    3. Review Article
    4. Research Articles
    5. Research Letters
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      New Active HIV-1 Protease Inhibitors Derived from 3-Hexanol: Conformation Study of the Free Inhibitors in Crystalline State and in Complex with the Enzyme (pages 798–809)

      Natasza E. Ziółkowska, Anna Bujacz, Ramnarayan S. Randad, John W. Erickson, Tereza Skálová, Jindřich Hašek and Grzegorz Bujacz

      Article first published online: 7 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01328.x

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      Four novel linear non-peptidic HIV-1 protease inhibitors derived from 2,5-diamino-1,6-diphenyl-3-hexanol were synthesized and characterized. The investigated inhibitors were crystallized and their crystal structures were determined by X-ray diffraction. In all cases, the conformations found in the crystalline state differ significantly from the conformations obtained by computational docking of the inhibitor in the binding cleft of native HIV-1 protease.

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      Design and Synthesis of 3,5-Disubstituted-1,2,4-Oxadiazoles as Potent Inhibitors of Phosphodiesterase4B2 (pages 810–818)

      Dalip Kumar, Gautam Patel, Lalitha Vijayakrishnan, Sunanda G. Dastidar and Abhijit Ray

      Article first published online: 9 FEB 2012 | DOI: 10.1111/j.1747-0285.2011.01304.x

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      The 3,5-disubstituted-1,2,4-oxadiazoles have been identified as potent inhibitors of PDE4B2.

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      Prodrugs of Acyclovir – A Computational Approach (pages 819–834)

      Rafik Karaman, Khuloud K. Dajani, Alaa Qtait and Mustafa Khamis

      Article first published online: 15 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01335.x

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      Intramolecular acid-catalyzed hydrolysis of acyclovir prodrug to acyclovir. k is dependent on the nature of R1 and R2.

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      Identification of Novel HIV-1 Integrase Inhibitors Using Shape-Based Screening, QSAR, and Docking Approach (pages 835–849)

      Pawan Gupta, Prabha Garg and Nilanjan Roy

      Article first published online: 9 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01326.x

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      Shape based screening was performed using best docked conformation of highly active benzodithiazine derivatives to identify new hits against HIV-1 IN. The screened molecules were subjected to QSAR models to predict inhibitory activity. The best predicted molecules were docked for binding mode analysis.

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      Structure-Based Rationale Design and Synthesis of Aurantiamide Acetate Analogues – Towards a New Class of Potent Analgesic and Anti-inflammatory Agents (pages 850–862)

      Ramesh Suhas and Dase Channe Gowda

      Article first published online: 13 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01331.x

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      The present work reports the synthesis and characterization of a new class of aurantiamide acetate analogues as potent analgesic and anti-inflammatory agents with no ulcerogenic liability.

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      Docking and 3D-QSAR investigations of pyrrolidine derivatives as potent neuraminidase inhibitors (pages 863–868)

      Jiaying Sun and Hu Mei

      Article first published online: 15 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01330.x

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      Docking and 3D-QSAR of 87 pyrrolidine derivatives were investigated. Moreover, the QSAR modeling results were unanimous in the docking results. So, the obtained 3D-QSAR models can design and screen new compounds.

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      Synthesis and Evaluation of Antioxidant Properties of Novel 2-[2-(4-chlorophenyl) benzimidazole-1-yl]-N-(2-arylmethylene amino) acetamides and 2-[2-(4-chlorophenyl) benzimidazole-1-yl]-N-(4-oxo-2-aryl-thiazolidine-3-yl) acetamides-I (pages 869–877)

      Gülgün Ayhan-Kılcıgil, Selen Gürkan, Tülay Çoban, Elçin Deniz Özdamar and Benay Can-Eke

      Article first published online: 23 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01347.x

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      In this study some new 2-[2-(4-chlorophenyl)benzimidazole-1-yl]-N-(2-arylmethyleneamino) acetamide (1–18) and 2-[2-(4-chlorophenyl)benzimidazole-1-yl]-N-(4-oxo-2-aryl-thiazolidine-3-yl)acetamide (1t–18t) derivatives were synthesized and their in vitro effects on rat liver microsomal NADPH-dependent lipid peroxidation levels (LP assay) and microsomal ethoxyresorufin O-deethylase activities (EROD assay) were determined. The free radical scavenging properties of the compounds were also examined in vitro determining the interaction of 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical. The compounds showed significant effects in the above tests.

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