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Chemical Biology & Drug Design

Cover image for Chemical Biology & Drug Design

June 2012

Volume 79, Issue 6

Pages i–iii, 879–1071

  1. Issue Information

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

      Version of Record online: 1 MAY 2012 | DOI: 10.1111/j.1747-0285.2012.01388.x

  2. Research Articles

    1. Top of page
    2. Issue Information
    3. Research Articles
    4. Research Letters
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      Cationic Lipids Containing Cyclen and Ammonium Moieties as Gene Delivery Vectors (pages 879–887)

      Qing-Dong Huang, Jiang Ren, Wen-Jing Ou, Yun Fu, Mao-Qiang Cai, Ji Zhang, Wen Zhu and Xiao-Qi Yu

      Version of Record online: 19 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01355.x

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      Two novel cationic lipids containing cyclen and ammonium moieties have been designed, synthesized and fully characterized for gene delivery. Liposomes formed from those two cationic lipids could bind and compact DNA into nanometer particles and effectively delivery it into HEK 293 cells with low cytotoxicity.

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      Prediction of HIV-1 Protease/Inhibitor Affinity using RosettaLigand (pages 888–896)

      Gordon Lemmon, Kristian Kaufmann and Jens Meiler

      Version of Record online: 19 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01356.x

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      Unbound HIV-1 protease is highly flexible, but becomes rigid upon inhibitor binding. We improve protease binding affinity prediction through our understanding of HIV-1 PR flexibility and its effect on free energy. Resistance mutations that lead to lower inhibitor binding affinity can thereby be predicted early in HIV-1 protease inhibitor development.

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      Synthesis, Structure–Activity Relationship, and Pharmacophore Modeling Studies of Pyrazole-3-Carbohydrazone Derivatives as Dipeptidyl Peptidase IV Inhibitors (pages 897–906)

      Deyan Wu, Fangfang Jin, Weiqiang Lu, Jin Zhu, Cui Li, Wei Wang, Yun Tang, Hualiang Jiang, Jin Huang, Guixia Liu and Jian Li

      Version of Record online: 21 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01365.x

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      Best pharmacophore model hypol was obtained, consisting of one hydrogen bond donar (HBD), one hydrogen bond accept (HBA), and two hydrophobic (HY) features.

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      Insights into the Uptake Mechanism of NrTP, A Cell-Penetrating Peptide Preferentially Targeting the Nucleolus of Tumour Cells (pages 907–915)

      Gandhi Rádis-Baptista, Beatriz G. de la Torre and David Andreu

      Version of Record online: 17 APR 2012 | DOI: 10.1111/j.1747-0285.2012.01377.x

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      Nucleolar targeting peptides (NrTPs) are 14–15 residue-long sequences designed by structural minimization of a rattlesnake toxin, capable of penetrating mammalian cells and homing into their nucleoli. One of such developed sequences (NrTP1) penetrates and localizes in the nucleolus of cell lines derived from aggressive types of tumours. Using a combination of confocal microscopy, flow cytometry and pharmacological inhibitors, we demonstrated that peptide uptake is mediated by a chlatrin-dependent endocytosis, but the translocation is not associated to the cell cycle phase.

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      Revealing Interaction Mode between HIV-1 Protease and Mannitol Analog Inhibitor (pages 916–925)

      Guan-Wen Yan, Yue Chen, Yixue Li and Hai-Feng Chen

      Version of Record online: 20 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01348.x

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      The binding mode of M17 (in gray) and M35 (in green) at the active site of HIV PR was investigated. Both M35 and M17 can form hydrogen bond with the catalytic residue of Asp25. Both M17 and M35 also have contact with Asp25, Ala28, Ile50, and Ile83.

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      Computational and Biological Evaluation of Quinazolinone Prodrug for Targeting Pancreatic Cancer (pages 926–934)

      Pavel Pospisil, Houari Korideck, Ketai Wang, Yongliang Yang, Lakshmanan K. Iyer and Amin I. Kassis

      Version of Record online: 16 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01350.x

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      We identified extracellular sulfatase 1 as an enzyme that is appropriate for our concept of Enzyme-Mediated Cancer Imaging and Therapy, which aims to use radiolabeled compounds to target hydrolases over-expressed on the extracellular surface of pancreatic tumor cells. Fluorescent products of the hydrolysis of the newly designed and synthesized sulfurylated quinazolinone derivative suggest its potential for use in imaging and radiotherapeutic treatment of pancreatic cancer.

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      3D-QSAR Studies on the Inhibitory Activity of Trimethoprim Analogues against Escherichia coli Dihydrofolate Reductase (pages 935–942)

      Ramadoss Vijayaraj, Mekapothula Lakshmi Vasavi Devi, Venkatesan Subramanian and Pratim Kumar Chattaraj

      Version of Record online: 19 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01351.x

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      Three-dimensional quantitative structure activity relationship (3D-QSAR) study has been carried out on the Escherichia coli DHFR inhibitors 2,4-diamino-5-(substituted-benzyl)pyrimidine derivatives to understand the structural features responsible for the improved potency. Analysis of the contour maps generated from CoMFA and CoMSIA methods reveals that the substitution of electronegative groups at the first and second position along with electropositive group at the third position of R2 substitution significantly increases the potency of the derivatives.

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      Synthesis, Biological Evaluation, and Structure–activity Relationship of Clonazepam, Meclonazepam, and 1,4-Benzodiazepine Compounds with Schistosomicidal Activity (pages 943–949)

      Carla M. S. Menezes, Gildardo Rivera, Marina A. Alves, Daniel N. do Amaral, Jean Pierre B. Thibaut, François Noël, Eliezer J. Barreiro and Lídia M. Lima

      Version of Record online: 19 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01354.x

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      Schistosomiasis is a serious public health problem in developing countries. Praziquantel is the only drug in therapeutics. Taking into account the schistosomicidal activity of clonazepam and meclonazepam, the objective of present work was to establish a structure-activity relationship for 1,4-benzodiazepine compounds with schistosomicidal activity. Our findings indicate that the amide moiety (N1H-C2(=O)) is the principal pharmacophoric unit and that substitution on the amide nitrogen atom (N1 position) is not tolerated.

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      Microwave-assisted Synthesis and Bioevaluation of Some Semicarbazones (pages 950–959)

      Laila Jafri, Farzana L. Ansari, Maryam Jamil, Saima Kalsoom, Sana Qureishi and Bushra Mirza

      Version of Record online: 19 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01360.x

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      Biological evaluation of a diverse set of 42 synthesized semicarbazones was carried out by screening them for their potential as antioxidant, antimicrobial and antitumor agents and have been found to have significant potential to develop into antioxidant and anticancerous drugs.

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      Multicomplex-Based Pharmacophore-Guided 3D-QSAR Studies of N-Substituted 2′-(Aminoaryl)Benzothiazoles as Aurora-A Inhibitors (pages 960–971)

      Gu He, Minghua Qiu, Rui Li, Liang Ouyang, Fengbo Wu, Xiangrong Song, Li Cheng, Mingli Xiang and Luoting Yu

      Version of Record online: 17 APR 2012 | DOI: 10.1111/j.1747-0285.2012.01366.x

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      Multicomplex-based pharmacophore(MCBP) guided alignment were used for the 3D-QSAR studies on 37 structurally diverse N-substituted 2′-(aminoaryl)benzothiazoles Aurora-A inhibitors.

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      The Discovery of Novel β-Secretase Inhibitors: Pharmacophore Modeling, Virtual Screening, and Docking Studies (pages 972–980)

      Yan Niu, Chao Ma, Hongwei Jin, Fengrong Xu, Haifei Gao, Peng Liu, Yongjian Li, Chao Wang, Guanyu Yang and Ping Xu

      Version of Record online: 17 APR 2012 | DOI: 10.1111/j.1747-0285.2012.01367.x

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      A ligand-based pharmacophore model was developed. The sequential virtual screening of ZINC database by pharmacophore model and molecular docking have led to the identification of two novel inhibitors with IC50 values of 4.76 and 0.31 μm, respectively.

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      In Vitro Antioxidant Activity Study of Novel Chromone Derivatives (pages 981–989)

      Narumol Phosrithong, Weerasak Samee, Patcharawee Nunthanavanit and Jiraporn Ungwitayatorn

      Version of Record online: 21 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01368.x

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      Forty-eight chromone derivatives were evaluated for their antioxidant activity. Most compounds showed stronger activities than BHT, vitamin E and trolox.

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      Free Energy Calculations on Snake Venom Metalloproteinase BaP1 (pages 990–1000)

      Torsten Lingott, Irmgard Merfort and Thomas Steinbrecher

      Version of Record online: 17 APR 2012 | DOI: 10.1111/j.1747-0285.2012.01369.x

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      We have investigated the binding properties of various ligands to BaP1, a medicinally important metalloproteinase. Molecular dynamics simulations and free energy calculations reveal the molecular details of the binding process and allow targeted compound modifications to design better inhibitors.

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      Preliminary Investigations of the Effect of Lipophilic Analogues of the Active Metabolite of Isoniazid Toward Bacterial and Plasmodial Strains (pages 1001–1006)

      Tamara Delaine, Vania Bernardes-Génisson, Annaïk Quémard, Patricia Constant, Frédéric Cosledan, Bernard Meunier and Jean Bernadou

      Version of Record online: 10 APR 2012 | DOI: 10.1111/j.1747-0285.2012.01374.x

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      Evaluation of lipophilic analogs of the active isoniazid metabolite towards Escherichia coli, Corynebacterium glutamicum and Plasmodium falciparum.

  3. Research Letters

    1. Top of page
    2. Issue Information
    3. Research Articles
    4. Research Letters
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      Inhibition of Bacterial Virulence: Drug-Like Molecules Targeting the Salmonella enterica PhoP Response Regulator (pages 1007–1017)

      Yat T. Tang, Rong Gao, James J. Havranek, Eduardo A. Groisman, Ann M. Stock and Garland R. Marshall

      Version of Record online: 21 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01362.x

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      Two-component signal transduction (TCST) is the predominant signaling scheme used in bacteria to sense and respond to environmental changes in order to survive and thrive. Computational and experimental methods were used to identify 8 compounds inhibiting Salmonella enterica PhoP TCST response regulator. This investigation served as an initial case study for targeting TCST response regulators to modulate the gene expression of a signal transduction pathway important for bacterial virulence.

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      Synthesis and Preliminary Biologic Evaluation of 5-Substituted-2-(4-substituted phenyl)-1,3-Benzoxazoles as A Novel Class of Influenza Virus A Inhibitors (pages 1018–1024)

      Zhenyu Li, Peng Zhan, Lieve Naesens, Evelien Vanderlinden, Ailin Liu, Guanhua Du, Erik De Clercq and Xinyong Liu

      Version of Record online: 20 FEB 2012 | DOI: 10.1111/j.1747-0285.2012.01344.x

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      A series of novel 5-substituted-2-(4-substituted phenyl)-1,3-benzoxazoles was synthesized and evaluated for their in vitro anti-influenza A virus (IFV-A) and anti-influenza B virus (IFV-B) activity. Among them, two compounds 7h and 7t from the series exhibited potent inhibitory effects against IFV-A replication in cell culture. Particularly, Compound 7h showed excellent inhibitory activity and selective index against A/H3N2 (EC50 = 37 μm, SI > 5), which were all higher than that of the reference drug Oseltamivir (EC50 > 59 μm, SI > 1).

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      The Evolution of HLA-B*3501 Binding Affinity to Variable Immunodominant NP418-426 Peptides from 1918 to 2009 Pandemic Influenza A Virus: A Molecular Dynamics Simulation and Free Energy Calculation Study (pages 1025–1032)

      Jingjing Guo, Xiaoting Wang, Huijun Sun, Huanxiang Liu, Yulin Shen and Xiaojun Yao

      Version of Record online: 19 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01357.x

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      A molecular modeling study for six NP418-426 peptides from 1918 to 2009 pandemic influenza A virus complexed with HLA-B*3501 was performed by molecular dynamics simulations and binding free energy calculations, in order to investigate mechanisms of the virus-specific CTL immunity. Our work will be useful for the design of novel vaccination regimens that provide a measure of protection against unpredicted pandemic and seasonal influenza strains.

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      Highly Potent Antidiuretic Antagonists: Conformational Studies of Vasopressin Analogues Modified with 1-Naphthylalanine Enantiomers at Position 2 (pages 1033–1042)

      Emilia A. Lubecka, Jerzy Ciarkowski, Adam Prahl and Emilia Sikorska

      Version of Record online: 16 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01358.x

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      We investigated the conformations of two vasopressin analogues, [Cpa1,(L-1-Nal)2]AVP (I) and [Cpa1,(D-Nal)2]AVP (II) by NMR spectroscopy and molecular modelling. Both peptides exhibit antioxytocic and antipressor potency. Inversion of configuration of the residue at position 2 converted a weak antidiuretic agonist (peptide I) into a highly potent antidiuretic antagonist (peptide II). For this reason, the purpose of our study was to explain the causes of different interactions of the analogues with V2 receptors.

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      Molecular Docking Studies of Novel Palmitoyl-ligands for Cyclooxygenase-2 (pages 1043–1048)

      Raghu Bhagavat, Asma Saqib and Chandrakant Karigar

      Version of Record online: 16 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01359.x

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      Molecular docking studies of four synthesized compounds on COX-2 protein using AutoDock proved to be successful in identifying them as promising lead compounds for the treatment of pain, fever and inflammation.

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      Chemical Components in Extracts from Plastrum Testudinis with Proliferation-Promoting Effects on Rat Mesenchymal Stem Cells (pages 1049–1055)

      Ting-Ting Wang, Wei Chen, He-Ping Zeng and Dong-Feng Chen

      Version of Record online: 19 MAR 2012 | DOI: 10.1111/j.1747-0285.2012.01361.x

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      Plastrum testudinis was extracted with ethyl acetate and separated by silica gel column chromatography with gradient elution. Sixteen (Ts-1 ∼ 16) components were obtained, evaluated by MTT assay and flow cytometry on the proliferation of rMSCs. Ts-12 could induce proliferation, while Ts-4 exhibited inhibitive effect. Results suggested that palmitic acid methyl ester and cholesterol myristate, which identified from Ts-12, possessed proliferative activity while stearic acid found in Ts-4 showed inhibition.

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      Potential Selective Inhibitors against Rv0183 of Mycobacterium tuberculosis Targeting Host Lipid Metabolism (pages 1056–1062)

      Parameswaran Saravanan, Vikash Kumar Dubey and Sanjukta Patra

      Version of Record online: 17 APR 2012 | DOI: 10.1111/j.1747-0285.2012.01373.x

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      ZINC13451138 from ZINC database, a potential selective inhibitor of Rv0183 a highly conserved and essential protein of Mycobacterium species.

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      Computational Insights into the Inhibition of Inosine 5′-Monophosphate Dehydrogenase by Mycophenolic Acid Analogs: Three-Dimensional Quantitative Structure–Activity Relationship and Molecular Docking Studies (pages 1063–1071)

      Na Yang, Jian Wang, Zhi-Wei Wang, Qing-He Wang, Hong-Guang Yang, Xiu-Jun Wang and Mao-Sheng Cheng

      Version of Record online: 17 APR 2012 | DOI: 10.1111/j.1747-0285.2012.01375.x

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      3D-QSAR studies were carried out on 73 IMPDH inhibitors by CoMFA, CoMSIA and molecular docking methods. The 3D-QSAR models showed excellent predictive capability

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