1
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Tao Z, Haiyuan W, Wen M, Zhangyuan L, Panpan H, Nanqian Z, Jianchao H, Ting L, Mingming S, Suping B. Synthesis and Antiproliferative Activity Evaluation of Novel Glaucocalyxin A-1,2,3-Triazole Derivatives. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202205049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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2
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Liu ML, Li WY, Fang HL, Ye YX, Li SY, Song WQ, Xiao ZP, Ouyang H, Zhu HL. Synthesis and Biological Evaluation of Dithiobisacetamides as Novel Urease Inhibitors. ChemMedChem 2021; 17:e202100618. [PMID: 34687265 DOI: 10.1002/cmdc.202100618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Indexed: 12/20/2022]
Abstract
Thirty-eight disulfides containing N-arylacetamide were designed and synthesized in an effort to develop novel urease inhibitors. Biological evaluation revealed that some of the synthetic compounds exhibited strong inhibitory potency against both cell-free urease and urease in intact cell with low cytotoxicity to mammalian cells even at concentration up to 250 μM. Of note, 2,2'-dithiobis(N-(2-fluorophenyl)acetamide) (d7), 2,2'-dithiobis(N-(3,5-difluorophenyl)acetamide) (d24), and 2,2'-dithiobis(N-(3-fluorophenyl)acetamide) (d8) were here identified as the most active inhibitors with IC50 of 0.074, 0.44, and 0.81 μM, showing 32- to 355-fold higher potency than the positive control acetohydroxamic acid. These disulfides were confirmed to bind urease without covalent modification of the cysteine residue and to inhibit urease reversibly with a mixed inhibition mechanism. They also showed very good anti-Helicobacter pylori activities with d8 showing a comparable potency to the clinical used drug amoxicillin. The impressive in vitro biological profile indicated their immense potential as therapeutic agents to tackle H. pylori caused infections.
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Affiliation(s)
- Mei-Ling Liu
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China
| | - Wei-Yi Li
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China
| | - Hai-Lian Fang
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China
| | - Ya-Xi Ye
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Xianlin Road 163, Nanjing, China
| | - Su-Ya Li
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China
| | - Wan-Qing Song
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China
| | - Zhu-Ping Xiao
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Xianlin Road 163, Nanjing, China
| | - Hui Ouyang
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China
| | - Hai-Liang Zhu
- Hunan Provincial Key Laboratory of Research, Resource Mining and High-valued Utilization on Edible & Medicinal Plant, Hunan Engineering Laboratory for Analyse and Drugs Development of Ethnomedicine in Wuling Mountains, National Demonstration Center for Experimental Chemistry Education, Jishou University, The South Section of Renmin Road 120, Jishou, China.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Xianlin Road 163, Nanjing, China
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3
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Ghobadi E, Ghanbarimasir Z, Emami S. A review on the structures and biological activities of anti-Helicobacter pylori agents. Eur J Med Chem 2021; 223:113669. [PMID: 34218084 DOI: 10.1016/j.ejmech.2021.113669] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 12/19/2022]
Abstract
Helicobacter pylori is one of the main causal risk factor in the generation of chronic gastritis, gastroduodenal ulcers and gastric carcinoma. Thus, the eradication of H. pylori infection is an important way for preventing and managing the gastric diseases. Multiple-therapy with several antibacterial agents is used for the eradication of H. pylori infections; however the increase of resistance to H. pylori strains has resulted in unsatisfactory eradication and unsuccessful treatment. Furthermore, the combination therapy with high dosing leads to the disruption of intestinal microbial flora and undesired side effects. Therefore, the search for new therapeutic agents with high selectivity against H. pylori is a field of current interest. In recent years, diverse compounds originating from natural sources or synthetic drug design programs were evaluated and tried to optimize for applying against H. pylori. In this review, we have described various classes of anti-H. pylori compounds, their structure-activity relationship studies, and mechanism of actions, which could be useful for the development of new drugs for the treatment of H. pylori infections.
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Affiliation(s)
- Elham Ghobadi
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zahra Ghanbarimasir
- Department of Organic Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, Iran
| | - Saeed Emami
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran.
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Flavodoxins as Novel Therapeutic Targets against Helicobacter pylori and Other Gastric Pathogens. Int J Mol Sci 2020; 21:ijms21051881. [PMID: 32164177 PMCID: PMC7084853 DOI: 10.3390/ijms21051881] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
Flavodoxins are small soluble electron transfer proteins widely present in bacteria and absent in vertebrates. Flavodoxins participate in different metabolic pathways and, in some bacteria, they have been shown to be essential proteins representing promising therapeutic targets to fight bacterial infections. Using purified flavodoxin and chemical libraries, leads can be identified that block flavodoxin function and act as bactericidal molecules, as it has been demonstrated for Helicobacter pylori (Hp), the most prevalent human gastric pathogen. Increasing antimicrobial resistance by this bacterium has led current therapies to lose effectiveness, so alternative treatments are urgently required. Here, we summarize, with a focus on flavodoxin, opportunities for pharmacological intervention offered by the potential protein targets described for this bacterium and provide information on other gastrointestinal pathogens and also on bacteria from the gut microbiota that contain flavodoxin. The process of discovery and development of novel antimicrobials specific for Hp flavodoxin that is being carried out in our group is explained, as it can be extrapolated to the discovery of inhibitors specific for other gastric pathogens. The high specificity for Hp of the antimicrobials developed may be of help to reduce damage to the gut microbiota and to slow down the development of resistant Hp mutants.
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5
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Pasala C, Katari SK, Nalamolu RM, Bitla AR, Amineni U. In silico probing exercises, bioactive-conformational and dynamic simulations strategies for designing and promoting selective therapeutics against Helicobacter pylori strains. J Mol Graph Model 2019; 92:167-179. [DOI: 10.1016/j.jmgm.2019.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/27/2019] [Accepted: 07/25/2019] [Indexed: 12/25/2022]
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6
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Debraekeleer A, Remaut H. Future perspective for potentialHelicobacter pylorieradication therapies. Future Microbiol 2018; 13:671-687. [PMID: 29798689 DOI: 10.2217/fmb-2017-0115] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Ayla Debraekeleer
- Department of Structural & Molecular Microbiology, VIB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Department of Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Han Remaut
- Department of Structural & Molecular Microbiology, VIB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Department of Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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7
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Peón A, Robles A, Blanco B, Convertino M, Thompson P, Hawkins AR, Caflisch A, González-Bello C. Reducing the Flexibility of Type II Dehydroquinase for Inhibition: A Fragment-Based Approach and Molecular Dynamics Study. ChemMedChem 2017; 12:1512-1524. [DOI: 10.1002/cmdc.201700396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/01/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Antonio Peón
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Adrián Robles
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Beatriz Blanco
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Marino Convertino
- Department of Biochemistry; University of Zurich; 8057 Zurich Switzerland
- Current address: Department of Biochemistry and Biophysics; University of North Carolina, School of Medicine; Chapel Hill NC 27599 USA
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne; Catherine Cookson Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne; Catherine Cookson Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Amedeo Caflisch
- Department of Biochemistry; University of Zurich; 8057 Zurich Switzerland
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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8
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Lee KY, Lee BJ. Solution NMR studies on Helicobacter pylori proteins for antibiotic target discovery. Expert Opin Drug Discov 2016; 11:681-93. [PMID: 27216839 DOI: 10.1080/17460441.2016.1189411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Helicobacter pylori (H. pylori) is a well-known widespread pathogenic bacterium that survives in the extremely acidic conditions of the human gastric mucosa. The global prevalence of H. pylori-resistant antibiotics has become an emerging issue in the 21st century and has necessitated the development of novel antibiotic drugs. Many efforts have aimed to discover antibiotic target proteins of H. pylori based on its genome of more than 1600 genes. AREAS COVERED This article highlights NMR spectroscopy as a valuable tool for determining the structure and dynamics of potential antibiotic-targeted proteins of H. pylori and evaluating their modes of interaction with native or synthetic binding partners. The residue-specific information on binding in solution provides a structural basis to identify and optimize lead compounds. EXPERT OPINION NMR spectroscopy is a powerful method for obtaining details of biomolecular interactions with a broad range of binding affinities. This strength facilitates the identification of the binding interface of the encounter complex that plays an integral role in a variety of biological functions. This low-affinity complex is difficult to crystallize, which impedes structure determination using X-ray crystallography. Additionally, the relative binding affinities can be predicted from the type of spectral change upon binding. High-resolution NMR spectroscopy in combination with advanced computer simulation would provide more confidence in complex structures. The application of NMR to studies of the H. pylori protein could contribute to the development of these targeted novel antibiotics.
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Affiliation(s)
- Ki-Young Lee
- a Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul , Korea
| | - Bong-Jin Lee
- a Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , Seoul , Korea
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9
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González-Bello C, Tizón L, Lence E, Otero JM, van Raaij MJ, Martinez-Guitian M, Beceiro A, Thompson P, Hawkins AR. Chemical Modification of a Dehydratase Enzyme Involved in Bacterial Virulence by an Ammonium Derivative: Evidence of its Active Site Covalent Adduct. J Am Chem Soc 2015; 137:9333-43. [DOI: 10.1021/jacs.5b04080] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | - Mark J. van Raaij
- Departamento
de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CSIC), Campus Cantoblanco, 28049 Madrid, Spain
| | - Marta Martinez-Guitian
- Servicio
de Microbiología-INIBIC, Complejo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Alejandro Beceiro
- Servicio
de Microbiología-INIBIC, Complejo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Paul Thompson
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Alastair R. Hawkins
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
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10
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Sturlese M, Bellanda M, Moro S. NMR-Assisted Molecular Docking Methodologies. Mol Inform 2015; 34:513-25. [DOI: 10.1002/minf.201500012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/24/2015] [Indexed: 11/11/2022]
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11
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Howard NI, Dias MVB, Peyrot F, Chen L, Schmidt MF, Blundell TL, Abell C. Design and Structural Analysis of Aromatic Inhibitors of Type II Dehydroquinase fromMycobacterium tuberculosis. ChemMedChem 2014; 10:116-33. [DOI: 10.1002/cmdc.201402298] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Indexed: 11/09/2022]
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12
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Insights into substrate binding and catalysis in bacterial type I dehydroquinase. Biochem J 2014; 462:415-24. [DOI: 10.1042/bj20140614] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The crystal structure of S. typhi type I dehydroquinase in complex with (2R)-3-methyl-3-dehydroquinic acid is described. A previously unknown key role of several conserved residues and a detailed knowledge of the substrate binding process is detailed.
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13
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Blanco B, Sedes A, Peón A, Otero JM, van Raaij MJ, Thompson P, Hawkins AR, González-Bello C. Exploring the Water-Binding Pocket of the Type II Dehydroquinase Enzyme in the Structure-Based Design of Inhibitors. J Med Chem 2014; 57:3494-510. [DOI: 10.1021/jm500175z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Beatriz Blanco
- Centro
Singular de Investigación en Química Biológica
y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Antía Sedes
- Centro
Singular de Investigación en Química Biológica
y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Antonio Peón
- Centro
Singular de Investigación en Química Biológica
y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José M. Otero
- Departamento
de Bioquímica y Biología Molecular, Centro Singular
de Investigación en Química Biológica y Materiales
Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Mark J. van Raaij
- Departamento
de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CSIC), Campus Cantoblanco, 28049 Madrid, Spain
| | - Paul Thompson
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Alastair R. Hawkins
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Concepción González-Bello
- Centro
Singular de Investigación en Química Biológica
y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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14
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Mechanistic insight into the reaction catalysed by bacterial type II dehydroquinases1. Biochem J 2014; 458:547-57. [DOI: 10.1042/bj20131103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present study identified the residue that deprotonates the essential tyrosine that triggers the catalytic process and provides details of the required motions for the catalytic turnover. A previously unknown key role for the essential arginine and two conserved arginines is also reported.
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15
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Korshin EE, Leitus GM, Bendikov M. Convenient access to readily soluble symmetrical dialkyl-substituted α-oligofurans. Org Biomol Chem 2014; 12:6661-71. [DOI: 10.1039/c4ob00898g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combination of heteroatom directed lithiation/CuCl2-induced homocoupling, Wittig olefination/Pd-catalyzed transfer hydrogenation followed by Suzuki–Miyaura or Stille cross-coupling enables convenient access to dialkyl-substituted α-oligofurans of potential interest for organic electronics.
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Affiliation(s)
- Edward E. Korshin
- Department of Organic Chemistry
- Weizmann Institute of Science
- Rehovot 76100, Israel
| | - Gregory M. Leitus
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 76100, Israel
| | - Michael Bendikov
- Department of Organic Chemistry
- Weizmann Institute of Science
- Rehovot 76100, Israel
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16
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Lence E, Tizón L, Otero JM, Peón A, Prazeres VFV, Llamas-Saiz AL, Fox GC, van Raaij MJ, Lamb H, Hawkins AR, González-Bello C. Mechanistic basis of the inhibition of type II dehydroquinase by (2S)- and (2R)-2-benzyl-3-dehydroquinic acids. ACS Chem Biol 2013. [PMID: 23198883 DOI: 10.1021/cb300493s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural changes caused by the substitution of the aromatic moiety in (2S)-2-benzyl-3-dehydroquinic acids and its epimers in C2 by electron-withdrawing or electron-donating groups in type II dehydroquinase enzyme from M. tuberculosis and H. pylori has been investigated by structural and computational studies. Both compounds are reversible competitive inhibitors of this enzyme, which is essential in these pathogenic bacteria. The crystal structures of M. tuberculosis and H. pylori in complex with (2S)-2-(4-methoxy)benzyl- and (2S)-2-perfluorobenzyl-3-dehydroquinic acids have been solved at 2.0, 2.3, 2.0, and 1.9 Å, respectively. The crystal structure of M. tuberculosis in complex with (2R)-2-(benzothiophen-5-yl)methyl-3-dehydroquinic acid is also reported at 1.55 Å. These crystal structures reveal key differences in the conformation of the flexible loop of the two enzymes, a difference that depends on the presence of electron-withdrawing or electron-donating groups in the aromatic moiety of the inhibitors. This loop closes over the active site after substrate binding, and its flexibility is essential for the function of the enzyme. These differences have also been investigated by molecular dynamics simulations in an effort to understand the significant inhibition potency differences observed between some of these compounds and also to obtain more information about the possible movements of the loop. These computational studies have also allowed us to identify key structural factors of the H. pylori loop that could explain its reduced flexibility in comparison to the M. tuberculosis loop, specifically by the formation of a key salt bridge between the side chains of residues Asp18 and Arg20.
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Affiliation(s)
| | | | | | | | | | | | - Gavin C. Fox
- Proxima 2, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, F-91192
Gif-sur-Yvette, France
| | - Mark J. van Raaij
- Departamento de Estructura de
Macromoléculas, Centro Nacional de Biotecnología (CSIC), Campus Cantoblanco, 28049 Madrid, Spain
| | - Heather Lamb
- Institute of Cell and Molecular
Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Alastair R. Hawkins
- Institute of Cell and Molecular
Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
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Peón A, Coderch C, Gago F, González-Bello C. Comparative binding energy COMBINE analysis for understanding the binding determinants of type II dehydroquinase inhibitors. ChemMedChem 2013; 8:740-7. [PMID: 23450741 DOI: 10.1002/cmdc.201300013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Indexed: 11/08/2022]
Abstract
Herein we report comparative binding energy (COMBINE) analyses to derive quantitative structure-activity relationship (QSAR) models that help rationalize the determinants of binding affinity for inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway. Independent COMBINE models were derived for Helicobacter pylori and Mycobacterium tuberculosis DHQ2, which is an essential enzyme in both these pathogenic bacteria that has no counterpart in human cells. These studies quantify the importance of the hydrogen bonding interactions between the ligands and the water molecule involved in the DHQ2 reaction mechanism. They also highlight important differences in the ligand interactions with the interface pocket close to the active site that could provide guides for future inhibitor design.
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Affiliation(s)
- Antonio Peón
- Centro Singular de Investigación en Química Biológica y Materiales, Moleculares CIQUS, Universidad de Santiago de Compostela calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela Spain
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18
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Jiang M, Xiong B, Shen YM, Yang C. Design, synthesis, and preliminary biological evaluation of novel ketone derivatives of shikimic acid. RSC Adv 2013. [DOI: 10.1039/c3ra43755h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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19
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Vuong KQ, Timerbulatova MG, Peterson MB, Bhadbhade M, Messerle BA. Cationic Rh and Ir complexes containing bidentate imidazolylidene–1,2,3-triazole donor ligands: synthesis and preliminary catalytic studies. Dalton Trans 2013; 42:14298-308. [DOI: 10.1039/c3dt51440d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Blanco B, Sedes A, Peón A, Lamb H, Hawkins AR, Castedo L, González-Bello C. Synthesis of 3-alkyl enol mimics inhibitors of type II dehydroquinase: factors influencing their inhibition potency. Org Biomol Chem 2012; 10:3662-76. [DOI: 10.1039/c2ob07081b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis. Biochem J 2011; 436:729-39. [PMID: 21410435 DOI: 10.1042/bj20110002] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The shikimate pathway is essential in Mycobacterium tuberculosis and its absence from humans makes the enzymes of this pathway potential drug targets. In the present paper, we provide structural insights into ligand and inhibitor binding to 3-dehydroquinate dehydratase (dehydroquinase) from M. tuberculosis (MtDHQase), the third enzyme of the shikimate pathway. The enzyme has been crystallized in complex with its reaction product, 3-dehydroshikimate, and with six different competitive inhibitors. The inhibitor 2,3-anhydroquinate mimics the flattened enol/enolate reaction intermediate and serves as an anchor molecule for four of the inhibitors investigated. MtDHQase also forms a complex with citrazinic acid, a planar analogue of the reaction product. The structure of MtDHQase in complex with a 2,3-anhydroquinate moiety attached to a biaryl group shows that this group extends to an active-site subpocket inducing significant structural rearrangement. The flexible extensions of inhibitors designed to form π-stacking interactions with the catalytic Tyr24 have been investigated. The high-resolution crystal structures of the MtDHQase complexes provide structural evidence for the role of the loop residues 19-24 in MtDHQase ligand binding and catalytic mechanism and provide a rationale for the design and efficacy of inhibitors.
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22
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Tizón L, Otero JM, Prazeres VFV, Llamas-Saiz AL, Fox GC, van Raaij MJ, Lamb H, Hawkins AR, Ainsa JA, Castedo L, González-Bello C. A Prodrug Approach for Improving Antituberculosis Activity of Potent Mycobacterium tuberculosis Type II Dehydroquinase Inhibitors. J Med Chem 2011; 54:6063-84. [DOI: 10.1021/jm2006063] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lorena Tizón
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Universidad de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - José M. Otero
- Laboratoire des Proteines Membranaires, Institut de Biologie Structurale J. P. Ebel, 38027 Grenoble, France
| | - Verónica F. V. Prazeres
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Universidad de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Antonio L. Llamas-Saiz
- Unidad de Rayos X, RIAIDT, Edificio CACTUS, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Gavin C. Fox
- Laboratoire des Proteines Membranaires, Institut de Biologie Structurale J. P. Ebel, 38027 Grenoble, France
| | - Mark J. van Raaij
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CSIC), Campus Cantoblanco, 28049 Madrid, Spain
| | - Heather Lamb
- Institute of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - José A. Ainsa
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública, Facultad de Medicina, 50009 Zaragoza, Spain, and CIBER Enfermedades Respiratorias, Spain
| | - Luis Castedo
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, Avenida de las Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Universidad de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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23
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Paz S, Tizón L, Otero JM, Llamas-Saiz AL, Fox GC, van Raaij MJ, Lamb H, Hawkins AR, Lapthorn AJ, Castedo L, González-Bello C. Tetrahydrobenzothiophene derivatives: conformationally restricted inhibitors of type II dehydroquinase. ChemMedChem 2010; 6:266-72. [PMID: 21275050 DOI: 10.1002/cmdc.201000343] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 10/12/2010] [Indexed: 11/10/2022]
Affiliation(s)
- Sonia Paz
- Departamento de Química Orgánica y Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Universidad de Santiago de Compostela calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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24
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Tran AT, Cergol KM, West NP, Randall EJ, Britton WJ, Bokhari SAI, Ibrahim M, Lapthorn AJ, Payne RJ. Synthesis and evaluation of potent ene-yne inhibitors of type II dehydroquinases as tuberculosis drug leads. ChemMedChem 2010; 6:262-5. [PMID: 21275049 DOI: 10.1002/cmdc.201000399] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Indexed: 11/09/2022]
Affiliation(s)
- Anh Thu Tran
- School of Chemistry F11, The University of Sydney, Sydney, 2006, Australia
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25
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Peón A, Otero JM, Tizón L, Prazeres VFV, Llamas-Saiz AL, Fox GC, van Raaij MJ, Lamb H, Hawkins AR, Gago F, Castedo L, González-Bello C. Understanding the Key Factors that Control the Inhibition of Type II Dehydroquinase by (2R)-2-Benzyl-3-dehydroquinic Acids. ChemMedChem 2010; 5:1726-33. [DOI: 10.1002/cmdc.201000281] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Prazeres VFV, Castedo L, Lamb H, Hawkins AR, González-Bello C. 2-substituted-3-dehydroquinic acids as potent competitive inhibitors of type II dehydroquinase. ChemMedChem 2010; 4:1980-4. [PMID: 19856378 DOI: 10.1002/cmdc.200900319] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Verónica F V Prazeres
- Laboratorio de Química Orgánica (CSIC) y Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, Avenida de las Ciencias s/n, 15782 Santiago de Compostela, Spain
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27
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Tran AT, Cergol KM, Britton WJ, Imran Bokhari SA, Ibrahim M, Lapthorn AJ, Payne RJ. Rapid assembly of potent type II dehydroquinase inhibitorsvia “Click” chemistry. MEDCHEMCOMM 2010. [DOI: 10.1039/c0md00097c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rapid synthesis of a library of potent type II dehydroquinase inhibitors is described. Inhibitors were prepared via a key quinate-derived ene-yne intermediate using Cu(i)-catalysed azide-alkyne cycloaddition (CuAAC) chemistry with a variety of aryl- and heteroaryl-azides.
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Affiliation(s)
- Anh Thu Tran
- School of Chemistry
- The University of Sydney
- Sydney
- Australia
| | | | - Warwick J. Britton
- Faculty of Medicine, Blackburn Building
- The University of Sydney
- NSW 2006
- Australia and Mycobacterial Research Program
- Centenary Institute
| | - Syed Ali Imran Bokhari
- Department of Chemistry and Division of Biochemistry and Life Science
- University of Glasgow
- UK
| | - Musadiq Ibrahim
- Department of Chemistry and Division of Biochemistry and Life Science
- University of Glasgow
- UK
| | - Adrian J. Lapthorn
- Department of Chemistry and Division of Biochemistry and Life Science
- University of Glasgow
- UK
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28
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Duckworth MJ, Okoli AS, Mendz GL. Novel Helicobacter pylori therapeutic targets: the unusual suspects. Expert Rev Anti Infect Ther 2009; 7:835-67. [PMID: 19735225 DOI: 10.1586/eri.09.61] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the current status of the discovery and development of anti-Helicobacter therapies requires an overview of the searches for therapeutic targets performed to date. A summary is given of the very substantial body of work conducted in the quest to find Helicobacter pylori genes that could be suitable candidates for therapeutic intervention. The products of most of these genes perform metabolic functions, and others have roles in growth, cell motility and colonization. The genes identified as potential targets have been organized into three categories according to their degree of characterization. A short description and evaluation is provided of the main candidates in each category. Investigations of potential therapeutic targets have generated a wealth of information about the physiology and genetics of H. pylori, and its interactions with the host, but have yielded little by way of new therapies.
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Affiliation(s)
- Megan J Duckworth
- School of Medicine, Sydney, The University of Notre Dame Australia, 160 Oxford Street, Darlinghurst, NSW 2010, Australia.
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29
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Prazeres VFV, Tizón L, Otero JM, Guardado-Calvo P, Llamas-Saiz AL, van Raaij MJ, Castedo L, Lamb H, Hawkins AR, González-Bello C. Synthesis and Biological Evaluation of New Nanomolar Competitive Inhibitors of Helicobacter pylori Type II Dehydroquinase. Structural Details of the Role of the Aromatic Moieties with Essential Residues. J Med Chem 2009; 53:191-200. [DOI: 10.1021/jm9010466] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Verónica F. V. Prazeres
- Laboratorio de Química Orgánica (CSIC) y Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Lorena Tizón
- Laboratorio de Química Orgánica (CSIC) y Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José M. Otero
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Pablo Guardado-Calvo
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Antonio L. Llamas-Saiz
- Unidad de Rayos X, Edificio CACTUS, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Mark J. van Raaij
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixach 10-12, E-08028 Barcelona, Spain
| | - Luis Castedo
- Laboratorio de Química Orgánica (CSIC) y Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Heather Lamb
- Institute of Cell and Molecular Biosciences, Medical School, University, Newcastle upon Tyne, Catherine Cookson Building, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Medical School, University, Newcastle upon Tyne, Catherine Cookson Building, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K
| | - Concepción González-Bello
- Laboratorio de Química Orgánica (CSIC) y Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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