1
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Yan R, Li X, Liu Y, Ye X. Design, Synthesis, and Bioassay of 2′-Modified Kanamycin A. Molecules 2022; 27:molecules27217482. [PMID: 36364310 PMCID: PMC9654810 DOI: 10.3390/molecules27217482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Chemical modification of old drugs is an important way to obtain new ones, and it has been widely used in developing new aminoglycoside antibiotics. However, many of the previous modifying strategies seem arbitrary for their lack of support from structural biological detail. In this paper, based on the structural information of aminoglycoside and its drug target, we firstly analyzed the reason that some 2′-N-acetylated products of aminoglycosides caused by aminoglycoside-modifying enzyme AAC(2′) can partially retain activity, and then we designed, synthesized, and evaluated a series of 2′-modified kanamycin A derivatives. Bioassay results showed our modifying strategy was feasible. Our study provided valuable structure–activity relationship information, which would help researchers to develop new aminoglycoside antibiotics more effectively.
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Affiliation(s)
- Ribai Yan
- National Demonstration Center for Experimental Pharmacy Education, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Correspondence: (R.Y.); (X.Y.)
| | - Xiaonan Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yuheng Liu
- Department of Medical Chemistry, College of Pharmaceutical Science, Hebei Medical University, Shijiazhuang 050017, China
| | - Xinshan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Correspondence: (R.Y.); (X.Y.)
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2
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YAN R, NIU Y, LIU Y, DENG J, YE X. Design, synthesis, and bioassay of 5-epi-aminoglycosides. Chin J Nat Med 2022; 20:854-862. [DOI: 10.1016/s1875-5364(22)60212-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Indexed: 11/23/2022]
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3
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Pennetta C, Bono N, Ponti F, Bellucci MC, Viani F, Candiani G, Volonterio A. Multifunctional Neomycin-Triazine-Based Cationic Lipids for Gene Delivery with Antibacterial Properties. Bioconjug Chem 2021; 32:690-701. [PMID: 33470802 PMCID: PMC8154203 DOI: 10.1021/acs.bioconjchem.0c00616] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
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Cationic
lipids (CLs) have gained significant attention among nonviral
gene delivery vectors due to their ease of synthesis and functionalization
with multivalent moieties. In particular, there is an increasing request
for multifunctional CLs having gene delivery capacity and antibacterial
activity. Herein, we describe the design and synthesis of a novel
class of aminoglycoside (AG)-based multifunctional vectors with high
transfection efficiency and noticeable antibacterial properties. Specifically,
cationic amphiphiles were built on a triazine scaffold, allowing for
an easy derivatization with up to three potentially different substituents,
such as neomycin (Neo) that serves as the polar head and one or two
lipophilic tails, namely stearyl (ST) and oleyl (OL) alkyl chains
and cholesteryl (Chol) tail. With the aim to shed more light on the
effect of different types and numbers of lipophilic moieties on the
ability of CLs to condense and transfect cells, the performance of
Neo–triazine-based derivatives as gene delivery vectors was
evaluated and compared. The ability of Neo–triazine-based derivatives
to act as antimicrobial agents was evaluated as well. Neo–triazine-based
CLs invariably exhibited excellent DNA condensation ability, even
at a low charge ratio (CR, +/−). Besides, each derivative showed
very good transfection performance at its optimal CR on two different
cell lines, along with negligible cytotoxicity. CLs bearing symmetric
two-tailed OL proved to be the most effective in transfection. Interestingly,
Neo–triazine-based derivatives, used as either free lipids
or lipoplexes, exhibited strong antibacterial activity against Gram-negative
bacteria, especially in the case of CLs bearing one or two aliphatic
chains. Altogether, these results highlight the potential of Neo–triazine-based
derivatives as effective multifunctional nonviral gene delivery vectors.
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Affiliation(s)
- Chiara Pennetta
- Department of Chemistry, Materials, and Chemical Engineering "G. Natta", Politecnico di Milano, Via Mancinelli 7, Milan 20131, Italy
| | - Nina Bono
- Department of Chemistry, Materials, and Chemical Engineering "G. Natta", Politecnico di Milano, Via Mancinelli 7, Milan 20131, Italy
| | - Federica Ponti
- Department of Chemistry, Materials, and Chemical Engineering "G. Natta", Politecnico di Milano, Via Mancinelli 7, Milan 20131, Italy.,Laboratory for Biomaterials and Bioengineering, Canada Research Chair I in Biomaterials and Bioengineering for the Innovation in Surgery, Department of Min-Met-Materials Engineering & Research Center of CHU de Quebec, Division of Regenerative Medicine, Laval University, Quebec City, Quebec G1 V 0A6, Canada
| | - Maria Cristina Bellucci
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Via Celoria 2, Milan 20133, Italy
| | - Fiorenza Viani
- Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimiche "G. Natta" (SCITEC), Via Mario Bianco 9, Milan 20131, Italy
| | - Gabriele Candiani
- Department of Chemistry, Materials, and Chemical Engineering "G. Natta", Politecnico di Milano, Via Mancinelli 7, Milan 20131, Italy
| | - Alessandro Volonterio
- Department of Chemistry, Materials, and Chemical Engineering "G. Natta", Politecnico di Milano, Via Mancinelli 7, Milan 20131, Italy.,Consiglio Nazionale delle Ricerche, Istituto di Scienze e Tecnologie Chimiche "G. Natta" (SCITEC), Via Mario Bianco 9, Milan 20131, Italy
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4
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Unveiling the druggable RNA targets and small molecule therapeutics. Bioorg Med Chem 2019; 27:2149-2165. [PMID: 30981606 PMCID: PMC7126819 DOI: 10.1016/j.bmc.2019.03.057] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022]
Abstract
The increasing appreciation for the crucial roles of RNAs in infectious and non-infectious human diseases makes them attractive therapeutic targets. Coding and non-coding RNAs frequently fold into complex conformations which, if effectively targeted, offer opportunities to therapeutically modulate numerous cellular processes, including those linked to undruggable protein targets. Despite the considerable skepticism as to whether RNAs can be targeted with small molecule therapeutics, overwhelming evidence suggests the challenges we are currently facing are not outside the realm of possibility. In this review, we highlight the most recent advances in molecular techniques that have sparked a revolution in understanding the RNA structure-to-function relationship. We bring attention to the application of these modern techniques to identify druggable RNA targets and to assess small molecule binding specificity. Finally, we discuss novel screening methodologies that support RNA drug discovery and present examples of therapeutically valuable RNA targets.
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5
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Bono N, Pennetta C, Sganappa A, Giupponi E, Sansone F, Volonterio A, Candiani G. Design and synthesis of biologically active cationic amphiphiles built on the calix[4]arene scaffold. Int J Pharm 2018; 549:436-445. [DOI: 10.1016/j.ijpharm.2018.08.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 07/27/2018] [Accepted: 08/13/2018] [Indexed: 12/14/2022]
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6
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Thamban Chandrika N, Garneau-Tsodikova S. Comprehensive review of chemical strategies for the preparation of new aminoglycosides and their biological activities. Chem Soc Rev 2018; 47:1189-1249. [PMID: 29296992 PMCID: PMC5818290 DOI: 10.1039/c7cs00407a] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A systematic analysis of all synthetic and chemoenzymatic methodologies for the preparation of aminoglycosides for a variety of applications (therapeutic and agricultural) reported in the scientific literature up to 2017 is presented. This comprehensive analysis of derivatization/generation of novel aminoglycosides and their conjugates is divided based on the types of modifications used to make the new derivatives. Both the chemical strategies utilized and the biological results observed are covered. Structure-activity relationships based on different synthetic modifications along with their implications for activity and ability to avoid resistance against different microorganisms are also presented.
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Affiliation(s)
- Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
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7
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Park JW, Ban YH, Nam SJ, Cha SS, Yoon YJ. Biosynthetic pathways of aminoglycosides and their engineering. Curr Opin Biotechnol 2017; 48:33-41. [PMID: 28365471 DOI: 10.1016/j.copbio.2017.03.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/27/2017] [Accepted: 03/15/2017] [Indexed: 11/30/2022]
Abstract
Despite decades long clinical usage, aminoglycosides still remain a valuable pharmaceutical source for fighting Gram-negative bacterial pathogens, and their newly identified bioactivities are also renewing interest in this old class of antibiotics. As Nature's gift, some aminoglycosides possess natural defensive structural elements that can circumvent drug resistance mechanisms. Thus, a detailed understanding of aminoglycoside biosynthesis will enable us to apply Nature's biosynthetic strategy towards expanding structural diversity in order to produce novel and more robust aminoglycoside analogs. The engineered biosynthesis of novel aminoglycosides is required not only to develop effective therapeutics against the emerging 'superbugs' but also to reinvigorate antibiotic lead discovery in readiness for the emerging post-antibiotic era.
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Affiliation(s)
- Je Won Park
- School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea
| | - Yeon Hee Ban
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
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8
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Lee J, Borovika A, Khomutnyk Y, Nagorny P. Chiral phosphoric acid-catalyzed desymmetrizative glycosylation of 2-deoxystreptamine and its application to aminoglycoside synthesis. Chem Commun (Camb) 2017; 53:8976-8979. [DOI: 10.1039/c7cc05052f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This work describes chiral phosphoric acid (CPA)-catalyzed desymmetrizative glycosylation ofmeso-diol derived from 2-deoxystreptamine.
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Affiliation(s)
- Jeonghyo Lee
- University of Michigan
- Chemistry Department
- Ann Arbor
- USA
| | - Alina Borovika
- Bristol-Myers-Squibb Co. 1 Squibb Dr. New Brunswick
- NJ 08901
- USA
| | | | - Pavel Nagorny
- University of Michigan
- Chemistry Department
- Ann Arbor
- USA
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9
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Paul P, Mati SS, Bhattacharya SC, Kumar GS. Exploring the interaction of phenothiazinium dyes methylene blue, new methylene blue, azure A and azure B with tRNAPhe: spectroscopic, thermodynamic, voltammetric and molecular modeling approach. Phys Chem Chem Phys 2017; 19:6636-6653. [DOI: 10.1039/c6cp07888e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA targeting by small molecules.
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Affiliation(s)
- Puja Paul
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | | | | | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
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10
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Yadav S, Deka SR, Jha D, Gautam HK, Sharma AK. Amphiphilic azobenzene-neomycin conjugate self-assembles into nanostructures and transports plasmid DNA efficiently into the mammalian cells. Colloids Surf B Biointerfaces 2016; 148:481-486. [DOI: 10.1016/j.colsurfb.2016.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 08/17/2016] [Accepted: 09/05/2016] [Indexed: 11/08/2022]
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11
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Zimmermann L, Das I, Désiré J, Sautrey G, Barros R. S. V, El Khoury M, Mingeot-Leclercq MP, Décout JL. New Broad-Spectrum Antibacterial Amphiphilic Aminoglycosides Active against Resistant Bacteria: From Neamine Derivatives to Smaller Neosamine Analogues. J Med Chem 2016; 59:9350-9369. [DOI: 10.1021/acs.jmedchem.6b00818] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Louis Zimmermann
- Département
de Pharmacochimie Moléculaire, ICMG FR 2607, University Grenoble Alpes/CNRS, UMR 5063, 470 Rue de la Chimie, BP 53, F-38041 Grenoble, France
| | - Indrajit Das
- Département
de Pharmacochimie Moléculaire, ICMG FR 2607, University Grenoble Alpes/CNRS, UMR 5063, 470 Rue de la Chimie, BP 53, F-38041 Grenoble, France
| | - Jérôme Désiré
- Département
de Pharmacochimie Moléculaire, ICMG FR 2607, University Grenoble Alpes/CNRS, UMR 5063, 470 Rue de la Chimie, BP 53, F-38041 Grenoble, France
| | - Guillaume Sautrey
- Unité
de Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research
Institute, Université Catholique de Louvain, Avenue E.
Mounier 73, B1.73.05, B-1200 Brussels, Belgium
| | - Vinicius Barros R. S.
- Département
de Pharmacochimie Moléculaire, ICMG FR 2607, University Grenoble Alpes/CNRS, UMR 5063, 470 Rue de la Chimie, BP 53, F-38041 Grenoble, France
| | - Micheline El Khoury
- Unité
de Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research
Institute, Université Catholique de Louvain, Avenue E.
Mounier 73, B1.73.05, B-1200 Brussels, Belgium
| | - Marie-Paule Mingeot-Leclercq
- Unité
de Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research
Institute, Université Catholique de Louvain, Avenue E.
Mounier 73, B1.73.05, B-1200 Brussels, Belgium
| | - Jean-Luc Décout
- Département
de Pharmacochimie Moléculaire, ICMG FR 2607, University Grenoble Alpes/CNRS, UMR 5063, 470 Rue de la Chimie, BP 53, F-38041 Grenoble, France
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12
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Mingeot-Leclercq MP, Décout JL. Bacterial lipid membranes as promising targets to fight antimicrobial resistance, molecular foundations and illustration through the renewal of aminoglycoside antibiotics and emergence of amphiphilic aminoglycosides. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00503e] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Membrane anionic lipids as attractive targets in the design of amphiphilic antibacterial drugs active against resistant bacteria: molecular foundations and examples.
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Affiliation(s)
- Marie-Paule Mingeot-Leclercq
- Louvain Drug Research Institute
- Université catholique de Louvain
- Unité de Pharmacologie Cellulaire et Moléculaire
- Brussels
- Belgium
| | - Jean-Luc Décout
- Département de Pharmacochimie Moléculaire
- Université Grenoble Alpes/CNRS
- UMR 5063
- ICMG FR 2607
- F-38041 Grenoble
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13
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Jäger M, Minnaard AJ. Regioselective modification of unprotected glycosides. Chem Commun (Camb) 2016; 52:656-64. [DOI: 10.1039/c5cc08199h] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The regioselective modification of unprotected glycosides represents shortcuts in carbohydrate chemistry and enables efficient routes to complex derivatives.
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Affiliation(s)
- Manuel Jäger
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Adriaan J. Minnaard
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
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14
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Kudo F, Eguchi T. Aminoglycoside Antibiotics: New Insights into the Biosynthetic Machinery of Old Drugs. CHEM REC 2015; 16:4-18. [PMID: 26455715 DOI: 10.1002/tcr.201500210] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Indexed: 11/07/2022]
Abstract
2-Deoxystreptamine (2DOS) is the unique chemically stable aminocyclitol scaffold of clinically important aminoglycoside antibiotics such as neomycin, kanamycin, and gentamicin, which are produced by Actinomycetes. The 2DOS core can be decorated with various deoxyaminosugars to make structurally diverse pseudo-oligosaccharides. After the discovery of biosynthetic gene clusters for 2DOS-containing aminoglycoside antibiotics, the function of each biosynthetic enzyme has been extensively elucidated. The common biosynthetic intermediates 2DOS, paromamine and ribostamycin are constructed by conserved enzymes encoded in the gene clusters. The biosynthetic intermediates are then converted to characteristic architectures by unique enzymes encoded in each biosynthetic gene cluster. In this Personal Account, we summarize both common biosynthetic pathways and the pathways used for structural diversification.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
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15
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Ramachandran V, Arumugasamy K, Singh SK, Edayadulla N, Ramesh P, Kamaraj SK. Synthesis, antibacterial studies, and molecular modeling studies of 3,4-dihydropyrimidinone compounds. J Chem Biol 2015; 9:31-40. [PMID: 26855679 DOI: 10.1007/s12154-015-0142-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 06/10/2015] [Indexed: 11/30/2022] Open
Abstract
The syntheses of dihydropyrimidinones (DHPMs) using solvent-free grindstone chemistry method. All the synthesized compounds exhibited significant activity against pathogenic bacteria. The current effort has been developed to obtain new DHPM derivatives that focus on the bacterial ribosomal A site RNA as a drug target. Molecular docking simulation analysis was applied to confirm the target specificity of DHPMs. The crystal structure of bacterial 16S rRNA and human 40S rRNA was taken as receptors for docking. Finally, the docking score, binding site interaction analysis revealed that DHPMs exhibit more specificity towards 16S rRNA than known antibiotic amikacin. Accordingly, targeting the bacterial ribosomal A site RNA with potential drug leads promises to overcome the bacterial drug resistance. Even though, anti-neoplastic activities of DHPMs were also predicted through prediction of activity spectra for substances (PASS) tool. Further, the results establish that the DHPMs can serve as perfect leads against bacterial drug resistance.
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Affiliation(s)
- Vanitha Ramachandran
- Department of Natural Products Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, 625021 Tamil Nadu India
| | | | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi, 630 003 Tamil Nadu India
| | - Naushad Edayadulla
- School of Chemical Engineering, Yeungnam University, Gyeongsan, 712-749 Republic of Korea
| | - Penugonda Ramesh
- Department of Natural Products Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, 625021 Tamil Nadu India
| | - Sathish-Kumar Kamaraj
- Ingeniería en Energía, Universidad Politécnica de Aguascalientes, Calle Paseo San Gerardo No. 207. Fracc. San Gerardo, Aguascalientes, AGS Mexico 20342
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16
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Tyagi G, Agarwal S, Mehrotra R. tRNA binding with anti-cancer alkaloids–nature of interaction and comparison with DNA–alkaloids adducts. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 142:250-6. [DOI: 10.1016/j.jphotobiol.2014.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/01/2014] [Accepted: 12/06/2014] [Indexed: 11/26/2022]
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17
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Hong W, Zeng J, Xie J. Antibiotic drugs targeting bacterial RNAs. Acta Pharm Sin B 2014; 4:258-65. [PMID: 26579393 PMCID: PMC4629089 DOI: 10.1016/j.apsb.2014.06.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/04/2014] [Accepted: 06/20/2014] [Indexed: 10/26/2022] Open
Abstract
RNAs have diverse structures that include bulges and internal loops able to form tertiary contacts or serve as ligand binding sites. The recent increase in structural and functional information related to RNAs has put them in the limelight as a drug target for small molecule therapy. In addition, the recognition of the marked difference between prokaryotic and eukaryotic rRNA has led to the development of antibiotics that specifically target bacterial rRNA, reduce protein translation and thereby inhibit bacterial growth. To facilitate the development of new antibiotics targeting RNA, we here review the literature concerning such antibiotics, mRNA, riboswitch and tRNA and the key methodologies used for their screening.
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Affiliation(s)
| | | | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
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18
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Ghilardi A, Pezzoli D, Bellucci MC, Malloggi C, Negri A, Sganappa A, Tedeschi G, Candiani G, Volonterio A. Synthesis of Multifunctional PAMAM–Aminoglycoside Conjugates with Enhanced Transfection Efficiency. Bioconjug Chem 2013; 24:1928-36. [DOI: 10.1021/bc4003635] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Alessandra Ghilardi
- Department
of Chemistry, Materials, and Chemical Engineering “G. Natta”, Politecnico di Milano, via Mancinelli 7, 20131 Milano, Italy
| | - Daniele Pezzoli
- Politecnico
di Milano Research Unit, National Interuniversity Consortium of Materials Science and Technology - INSTM, via Mancinelli 7, 20131 Milano, Italy
| | - Maria Cristina Bellucci
- Department
of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Chiara Malloggi
- Department
of Chemistry, Materials, and Chemical Engineering “G. Natta”, Politecnico di Milano, via Mancinelli 7, 20131 Milano, Italy
| | - Armando Negri
- Department
of Veterinary Science and Public Health, Università degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
| | - Aurora Sganappa
- Department
of Chemistry, Materials, and Chemical Engineering “G. Natta”, Politecnico di Milano, via Mancinelli 7, 20131 Milano, Italy
| | - Gabriella Tedeschi
- Department
of Veterinary Science and Public Health, Università degli Studi di Milano, via Celoria 10, 20133 Milano, Italy
| | - Gabriele Candiani
- Department
of Chemistry, Materials, and Chemical Engineering “G. Natta”, Politecnico di Milano, via Mancinelli 7, 20131 Milano, Italy
- Politecnico
di Milano Research Unit, National Interuniversity Consortium of Materials Science and Technology - INSTM, via Mancinelli 7, 20131 Milano, Italy
| | - Alessandro Volonterio
- Department
of Chemistry, Materials, and Chemical Engineering “G. Natta”, Politecnico di Milano, via Mancinelli 7, 20131 Milano, Italy
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19
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Perigolo de Oliveira M, Constant JF, Peuchmaur M, Pitta I, Décout JL. Antibiotic drugs aminoglycosides cleave DNA at abasic sites: shedding new light on their toxicity? Chem Res Toxicol 2013; 26:1710-9. [PMID: 24127848 DOI: 10.1021/tx4002836] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Abasic sites are probably the most common lesions in DNA resulting from the hydrolytic cleavage of glycosidic bonds that can occur spontaneously and through DNA alkylation by anticancer agents, by radiotherapy, and during the repair processes of damaged nucleic bases. If not repaired, the abasic site can be mutagenic or lethal. Thus, compounds able to specifically bind and react at abasic sites have attracted much attention for therapeutic and diagnostic purposes. Here, we report on the efficient cleavage activity of characteristic antibiotic drugs of the major aminoglycosides (AG) family at abasic sites introduced either by depurination in a plasmidic DNA or site specifically in a synthetic oligonucleotide. Among the antibiotic AG drugs selected for this study, neomycin B is the most efficient (a 0.1 μM concentration induces 50% cleavage of an abasic site containing DNA). This cleavage activity could be related to aminoglycoside toxicity but also find medicinal applications through potentiation of cancer radiotherapy and chemotherapy with alkylating drugs. In the search for antibiotic and antiviral agents, we have previously described the synthesis of derivatives of the small aminoglycoside neamine, which corresponds to rings I and II of neomycin B constituted of four rings. The cleavage activity at abasic sites of four of these neamine derivatives is also reported in the present study. One of them appeared to be much more active than the parent compound neamine with cleavage efficiency close to that of neomycin.
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Affiliation(s)
- Maralise Perigolo de Oliveira
- UMR 5063, Département de Pharmacochimie Moléculaire, ICMG FR 2607, Université de Grenoble I/CNRS , 470 rue de la Chimie, BP 53, F-38041 Grenoble, France
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Kondo J, Westhof E. Aminoglycoside Antibiotics: Structural Decoding of Inhibitors Targeting the Ribosomal Decoding A Site. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Zimmermann L, Bussière A, Ouberai M, Baussanne I, Jolivalt C, Mingeot-Leclercq MP, Décout JL. Tuning the Antibacterial Activity of Amphiphilic Neamine Derivatives and Comparison to Paromamine Homologues. J Med Chem 2013; 56:7691-705. [DOI: 10.1021/jm401148j] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Louis Zimmermann
- Département
de Pharmacochimie Moléculaire, Université de Grenoble I/CNRS, UMR 5063, ICMG FR
2607, 470 rue de la Chimie, BP 53, F-38041 Grenoble, France
| | - Antoine Bussière
- Département
de Pharmacochimie Moléculaire, Université de Grenoble I/CNRS, UMR 5063, ICMG FR
2607, 470 rue de la Chimie, BP 53, F-38041 Grenoble, France
| | - Myriam Ouberai
- Unité de Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université Catholique de Louvain, Avenue E. Mounier 73, B1.73.05, B-1200 Brussels, Belgium
| | - Isabelle Baussanne
- Département
de Pharmacochimie Moléculaire, Université de Grenoble I/CNRS, UMR 5063, ICMG FR
2607, 470 rue de la Chimie, BP 53, F-38041 Grenoble, France
| | - Claude Jolivalt
- Ecole Nationale de Chimie de Paris/CNRS, UMR
7573, 11 rue Pierre et Marie Curie, F-75231 Paris cedex 05, France
| | - Marie-Paule Mingeot-Leclercq
- Unité de Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université Catholique de Louvain, Avenue E. Mounier 73, B1.73.05, B-1200 Brussels, Belgium
| | - Jean-Luc Décout
- Département
de Pharmacochimie Moléculaire, Université de Grenoble I/CNRS, UMR 5063, ICMG FR
2607, 470 rue de la Chimie, BP 53, F-38041 Grenoble, France
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Bastian AA, Warszawik EM, Panduru P, Arenz C, Herrmann A. Regioselective Diazo-Transfer Reaction at the C3-Position of the 2-Desoxystreptamine Ring of Neamine Antibiotics. Chemistry 2013; 19:9151-4. [DOI: 10.1002/chem.201300912] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Indexed: 11/09/2022]
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Schitter G, Wrodnigg TM. Update on carbohydrate-containing antibacterial agents. Expert Opin Drug Discov 2013; 4:315-56. [PMID: 23489128 DOI: 10.1517/17460440902778725] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Since the first known use of antibiotics > 2,500 years ago, a research field with immense importance for the welfare of mankind has been developed. After a decrease in interest in this topic by the end of the 20th century the occurrence of (poly-)resistant strains of bacteria induced a revival of antibiotics research. Health systems have been seeking viable and reliable solutions to this dangerous and expansive threat. OBJECTIVE This review will focus on carbohydrate-containing antibiotics and will give an outline of recently published novel isolated, semisynthetic as well as synthetic structures, their mechanism of action, if known, and the strategies for the design of compounds with potential by improved antibacterial properties. METHODS The literature between 2000 and 2008 was screened with main focus on recent examples of novel structures and strategies for the lead finding of exclusively antibacterial agents. RESULTS/CONCLUSION With the explanation of the role of the carbohydrate moieties in the respective antibacterial agents together with better synthetic strategies in carbohydrate chemistry as well as improvements in assay development for high throughput screening methods, carbohydrate-containing antibiotics can be used for the finding of potential drug leads that contribute to the fight against infections and diseases caused by (resistant) bacterial pathogens.
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Affiliation(s)
- Georg Schitter
- Technical University Graz, Institute of Organic Chemistry, Univ.-Doz. TMW, Dip.-Ing. GS, Glycogroup, A-8010 Graz, Austria +43 316 873 8744 ; +43 316 873 8740 ;
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25
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Watkins D, Norris FA, Kumar S, Arya DP. A fluorescence-based screen for ribosome binding antibiotics. Anal Biochem 2012; 434:300-7. [PMID: 23262284 DOI: 10.1016/j.ab.2012.12.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/30/2012] [Accepted: 12/03/2012] [Indexed: 12/12/2022]
Abstract
The development of new antibacterial agents has become necessary to treat the large number of emerging bacterial strains resistant to current antibiotics. Despite the different methods of resistance developed by these new strains, the A-site of the bacterial ribosome remains an attractive target for new antibiotics. To develop new drugs that target the ribosomal A-site, a high-throughput screen is necessary to identify compounds that bind to the target with high affinity. To this end, we present an assay that uses a novel fluorescein-conjugated neomycin (F-neo) molecule as a binding probe to determine the relative binding affinity of a drug library. We show here that the binding of F-neo to a model Escherichia coli ribosomal A-site results in a large decrease in the fluorescence of the molecule. Furthermore, we have determined that the change in fluorescence is due to the relative change in the pK(a) of the probe resulting from the change in the electrostatic environment that occurs when the probe is taken from the solvent and localized into the negative potential of the A-site major groove. Finally, we demonstrate that F-neo can be used in a robust, highly reproducible assay, determined by a Z'-factor greater than 0.80 for 3 consecutive days. The assay is capable of rapidly determining the relative binding affinity of a compound library in a 96-well plate format using a single channel electronic pipette. The current assay format will be easily adaptable to a high-throughput format with the use of a liquid handling robot for large drug libraries currently available and under development.
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Romanowska J, Reuter N, Trylska J. Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes. Proteins 2012; 81:63-80. [PMID: 22907688 DOI: 10.1002/prot.24163] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 08/02/2012] [Accepted: 08/09/2012] [Indexed: 11/10/2022]
Abstract
Aminoglycoside antibiotics are used against severe bacterial infections. They bind to the bacterial ribosomal RNA and interfere with the translation process. However, bacteria produce aminoglycoside modifying enzymes (AME) to resist aminoglycoside actions. AMEs form a variable group and yet they specifically recognize and efficiently bind aminoglycosides, which are also diverse in terms of total net charge and the number of pseudo-sugar rings. Here, we present the results of 25 molecular dynamics simulations of three AME representatives and aminoglycoside ribosomal RNA binding site, unliganded and complexed with an aminoglycoside, kanamycin A. A comparison of the aminoglycoside binding sites in these different receptors revealed that the enzymes efficiently mimic the nucleic acid environment of the ribosomal RNA binding cleft. Although internal dynamics of AMEs and their interaction patterns with aminoglycosides differ, the energetical analysis showed that the most favorable sites are virtually the same in the enzymes and RNA. The most copied interactions were of electrostatic nature, but stacking was also replicated in one AME:kanamycin complex. In addition, we found that some water-mediated interactions were very stable in the simulations of the complexes. We show that our simulations reproduce well findings from NMR or X-ray structural studies, as well as results from directed mutagenesis. The outcomes of our analyses provide new insight into aminoglycoside resistance mechanism that is related to the enzymatic modification of these drugs.
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Affiliation(s)
- Julia Romanowska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Hoża 69, 00-681 Warsaw, Poland.
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27
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Gironés D, Hanckmann M, Rutjes FPJT, van Delft FL. 2′-Modified Neamine Analogues from Thiomannosides through Glycosidation-Stereoinversion. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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Selective transformations of complex molecules are enabled by aptameric protective groups. Nat Chem 2012; 4:789-93. [PMID: 23000991 DOI: 10.1038/nchem.1402] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 06/06/2012] [Indexed: 11/08/2022]
Abstract
Emerging trends in drug discovery are prompting a renewed interest in natural products as a source of chemical diversity and lead structures. However, owing to the structural complexity of many natural compounds, the synthesis of derivatives is not easily realized. Here, we demonstrate a conceptually new approach using oligonucleotides as aptameric protective groups. These block several functionalities by non-covalent interactions in a complex molecule and enable the highly chemo- and regioselective derivatization (>99%) of natural antibiotics in a single synthetic step with excellent conversions of up to 83%. This technique reveals an important structure-activity relationship in neamine-based antibiotics and should help both to accelerate the discovery of new biologically active structures and to avoid potentially costly and cumbersome synthetic routes.
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Das I, Désiré J, Manvar D, Baussanne I, Pandey VN, Décout JL. A peptide nucleic acid-aminosugar conjugate targeting transactivation response element of HIV-1 RNA genome shows a high bioavailability in human cells and strongly inhibits tat-mediated transactivation of HIV-1 transcription. J Med Chem 2012; 55:6021-32. [PMID: 22698070 PMCID: PMC3400927 DOI: 10.1021/jm300253q] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The 6-aminoglucosamine ring of the aminoglycoside antibiotic neomycin B (ring II) was conjugated to a 16-mer peptide nucleic acid (PNA) targeting HIV-1 TAR RNA. For this purpose, we prepared the aminoglucosamine monomer 15 and attached it to the protected PNA prior to its cleavage from the solid support. We found that the resulting PNA-aminoglucosamine conjugate is stable under acidic conditions, efficiently taken up by the human cells and fairly distributed in both cytosol and nucleus without endosomal entrapment because cotreatment with endosome-disrupting agent had no effect on its cellular distribution. The conjugate displayed very high target specificity in vitro and strongly inhibited Tat mediated transactivation of HIV-1 LTR transcription in a cell culture system. The unique properties of this new class of PNA conjugate suggest it to be a potential candidate for therapeutic application.
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Affiliation(s)
- Indrajit Das
- Université de Grenoble I/CNRS, UMR 5063, Département de Pharmacochimie Moléculaire, ICMG FR 2607, 470 rue de la Chimie BP 53 F-38041 Grenoble, France
| | - Jérôme Désiré
- Université de Grenoble I/CNRS, UMR 5063, Département de Pharmacochimie Moléculaire, ICMG FR 2607, 470 rue de la Chimie BP 53 F-38041 Grenoble, France
| | - Dinesh Manvar
- Center for the Study of Emerging and Re-emerging Pathogens, UMDNJ-New Jersey Medical School, Department of Biochemistry and Molecular Biology, 185 South Orange Avenue, Newark, New Jersey 07103, USA
| | - Isabelle Baussanne
- Université de Grenoble I/CNRS, UMR 5063, Département de Pharmacochimie Moléculaire, ICMG FR 2607, 470 rue de la Chimie BP 53 F-38041 Grenoble, France
| | - Virendra N. Pandey
- Center for the Study of Emerging and Re-emerging Pathogens, UMDNJ-New Jersey Medical School, Department of Biochemistry and Molecular Biology, 185 South Orange Avenue, Newark, New Jersey 07103, USA
| | - Jean-Luc Décout
- Université de Grenoble I/CNRS, UMR 5063, Département de Pharmacochimie Moléculaire, ICMG FR 2607, 470 rue de la Chimie BP 53 F-38041 Grenoble, France
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Chiu CC, Lin YT, Sun SL, Sung KH, Wang LF. Anticancer Activity of Released Doxorubicin from a Folate-Mediated Polyelectrolyte Complex. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2012; 22:1487-507. [DOI: 10.1163/092050610x512414] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Chien Chih Chiu
- a Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yin Tzu Lin
- b Department of Medicinal & Applied Chemistry, College of Life Science, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung City 807, Taiwan
| | - Shuo Li Sun
- c Department of Medicinal & Applied Chemistry, College of Life Science, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung City 807, Taiwan
| | - Kuo Hsun Sung
- d Department of Medicinal & Applied Chemistry, College of Life Science, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung City 807, Taiwan
| | - Li Fang Wang
- e Department of Medicinal & Applied Chemistry, College of Life Science, Kaohsiung Medical University, 100 Shih-Chuan 1st Road, Kaohsiung City 807, Taiwan
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Jackowski O, Bussière A, Vanhaverbeke C, Baussanne I, Peyrin E, Mingeot-Leclercq MP, Décout JL. Major increases of the reactivity and selectivity in aminoglycoside O-alkylation due to the presence of fluoride ions. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.10.102] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Xi H, Davis E, Ranjan N, Xue L, Hyde-Volpe D, Arya DP. Thermodynamics of nucleic acid "shape readout" by an aminosugar. Biochemistry 2011; 50:9088-113. [PMID: 21863895 PMCID: PMC3673541 DOI: 10.1021/bi201077h] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recognition of nucleic acids is important for our understanding of nucleic acid structure as well as for our understanding of nucleic acid-protein interactions. In addition to the direct readout mechanisms of nucleic acids such as H-bonding, shape recognition of nucleic acids is being increasingly recognized as playing an equally important role in DNA recognition. Competition dialysis, UV, flourescent intercalator displacement (FID), computational docking, and calorimetry studies were conducted to study the interaction of neomycin with a variety of nucleic acid conformations (shapes). At pH 5.5, the results suggest the following. (1) Neomycin binds three RNA structures [16S A site rRNA, poly(rA)·poly(rA), and poly(rA)·poly(rU)] with high affinities (K(a) ~ 10(7) M(-1)). (2) The binding of neomycin to A-form GC-rich oligomer d(A(2)G(15)C(15)T(2))(2) has an affinity comparable to those of RNA structures. (3) The binding of neomycin to DNA·RNA hybrids shows a 3-fold variance that can be attributed to their structural differences [for poly(dA)·poly(rU), K(a) = 9.4 × 10(6) M(-1), and for poly(rA)·poly(dT), K(a) = 3.1 × 10(6) M(-1)]. (4) The interaction of neomycin with DNA triplex poly(dA)·2poly(dT) yields a binding affinity (K(a)) of 2.4 × 10(5) M(-1). (5) Poly(dA-dT)(2) shows the lowest association constant for all nucleic acids studied (K(a) < 10(5)). (6) Neomycin binds to G-quadruplexes with K(a) values of ~10(4)-10(5) M(-1). (7) Computational studies show that the decrease in major groove width in the B to A transition correlates with increasing neomycin affinity. Neomycin's affinity for various nucleic acid structures can be ranked as follows: RNAs and GC-rich d(A(2)G(15)C(15)T(2))(2) structures > poly(dA)·poly(rU) > poly(rA)·poly(dT) > T·A-T triplex, G-quadruplex, B-form AT-rich, or GC-rich DNA sequences. The results illustrate the first example of a small molecule-based "shape readout" of different nucleic acid conformations.
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Affiliation(s)
- Hongjuan Xi
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Erik Davis
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Liang Xue
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - David Hyde-Volpe
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
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Rational design and synthesis of potent aminoglycoside antibiotics against resistant bacterial strains. Bioorg Med Chem 2011; 19:30-40. [DOI: 10.1016/j.bmc.2010.11.065] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Revised: 11/27/2010] [Accepted: 11/30/2010] [Indexed: 11/20/2022]
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34
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McCoy LS, Xie Y, Tor Y. Antibiotics that target protein synthesis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:209-32. [DOI: 10.1002/wrna.60] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Pfrengle F, Reissig H. Internally Protected Amino Sugar Equivalents from Enantiopure 1,2‐Oxazines: Synthesis of Variably Configured Carbohydrates with C‐Branched Amino Sugar Units. Chemistry 2010; 16:11915-25. [DOI: 10.1002/chem.201001060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fabian Pfrengle
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin (Germany), Fax: (+49) 30‐83855367
| | - Hans‐Ulrich Reissig
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin (Germany), Fax: (+49) 30‐83855367
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Kurumbang NP, Park JW, Yoon YJ, Liou K, Sohng JK. Heterologous production of ribostamycin derivatives in engineered Escherichia coli. Res Microbiol 2010; 161:526-33. [PMID: 20561584 DOI: 10.1016/j.resmic.2010.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 02/25/2010] [Accepted: 04/29/2010] [Indexed: 11/18/2022]
Abstract
Aminoglycosides are a class of important antibiotic compounds used for various therapeutic indications. In recent times, their efficacy has been curtailed due to the rapid development of bacterial resistance. There is a need to develop novel derivatives with an improved spectrum of activity and higher sensitivity against pathogenic bacteria. Although efforts have been focused on the development of newer therapeutic agents by chemical synthesis, to our knowledge, there has been no attempt to harness the potential of microorganisms for this purpose. Escherichia coli affords a widely studied cellular system that could be utilized not only for understanding but also for attempting to engineer the biosynthetic pathway of secondary metabolites. The primary metabolic pathway of E. coli can be engineered to divert the precursor pool required for the biosynthesis of secondary metabolites. Utilizing this approach previously, we engineered E. coli host and generated E. coli M1. Here, we produced a ribostamycin derivative in the engineered host by heterologous expression of the recombinants constructed from the genes encoding the biosynthetic pathway in aminoglycoside-producing strains. The products obtained from the transformants were isolated, analyzed and verified to be ribostamycin derivatives. The study further demonstrated the importance of E. coli as surrogate antibiotic producer and also offered future possibility for the production of other aminoglycoside derivatives through genetic engineering and expression in a heterologous background.
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Affiliation(s)
- Nagendra Prasad Kurumbang
- Institute of Biomolecule Reconstruction, Department of Pharmaceutical Engineering, Sun Moon University, 100, Kalsan-ri, Tangjeonmyun, Asansi, Chungnam 336-708, Republic of Korea
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Wu S, Fu Y, Yan R, Wu Y, Lei X, Ye XS. Synthesis of neamine–carboline conjugates for RNA binding and their antibacterial activities. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.03.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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38
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Baussanne I, Bussière A, Halder S, Ganem-Elbaz C, Ouberai M, Riou M, Paris JM, Ennifar E, Mingeot-Leclercq MP, Décout JL. Synthesis and antimicrobial evaluation of amphiphilic neamine derivatives. J Med Chem 2010; 53:119-27. [PMID: 20000576 DOI: 10.1021/jm900615h] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aminoglycoside antibiotics bind to the 16S bacterial rRNA and disturb the protein synthesis. One to four hydroxyl functions of the small aminoglycoside neamine were capped with phenyl, naphthyl, pyridyl, or quinolyl rings. The 3',4'- (6), 3',6- (7a), and the 3',4',6- (10a) 2-naphthylmethylene derivatives appeared to be active against sensitive and resistant Staphylococcus aureus strains. 10a also showed marked antibacterial activities against Gram (-) bacteria, including strains expressing enzymes modifying aminoglycosides, efflux pumps, or rRNA methylases. 7a and 10a revealed a weak and aspecific binding to a model bacterial 16S rRNA. Moreover, as compared to neomycin B, 10a showed a lower ability to decrease (3)H leucine incorporation into proteins in Pseudomonas aeruginosa. All together, our results suggest that the 3',4',6-tri-2-naphthylmethylene neamine derivative 10a should act against Gram (-) bacteria through a mechanism different from inhibition of protein synthesis, probably by membrane destabilization.
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Affiliation(s)
- Isabelle Baussanne
- Universite de Grenoble I/CNRS, UMR 5063, Departement de Pharmacochimie Moleculaire, ICMG FR 2607, France
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Abstract
Bacterial ribosomal RNA is the target of clinically important antibiotics, while biologically important RNAs in viral and eukaryotic genomes present a range of potential drug targets. The physicochemical properties of RNA present difficulties for medicinal chemistry, particularly when oral availability is needed. Peptidic ligands and analysis of their RNA-binding properties are providing insight into RNA recognition. RNA-binding ligands include far more chemical classes than just aminoglycosides. Chemical functionalities from known RNA-binding small molecules are being exploited in fragment- and ligand-based projects. While targeting of RNA for drug design is very challenging, continuing advances in our understanding of the principles of RNA–ligand interaction will be necessary to realize the full potential of this class of targets.
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Pokrovskaya V, Nudelman I, Kandasamy J, Baasov T. Aminoglycosides redesign strategies for improved antibiotics and compounds for treatment of human genetic diseases. Methods Enzymol 2010; 478:437-62. [PMID: 20816493 DOI: 10.1016/s0076-6879(10)78021-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Aminoglycosides are highly potent, broad-spectrum antibiotics that kill bacteria by binding to the ribosomal decoding site and reducing the fidelity of protein synthesis. The emergence of bacterial strains resistant to these drugs, as well as their relative toxicity, have inspired extensive searches toward the goal of obtaining novel molecular designs with improved antibacterial activity and reduced toxicity. In recent years, a new therapeutic approach that employs the ability of certain aminoglycosides to induce mammalian ribosomes to readthrough premature stop codon mutations has emerged. This new and challenging task has introduced fresh research avenues in the field of aminoglycosides research. In this chapter, our recent observations and current challenges in the design of aminoglycosides with improved antibacterial activity and the treatment of human genetic diseases are discussed.
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Affiliation(s)
- Varvara Pokrovskaya
- The Edith and Joseph Fischer Enzyme Inhibitors Laboratory, Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, Israel
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Affiliation(s)
- Fabian Pfrengle
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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Bhattacharya R, Kesharwani MK, Manna C, Ganguly B, Suresh CG, Pathak T. An Experimental and Theoretical Study on the Remarkable Influence of Protecting Groups on the Selectivity of Addition of Amines to Vinyl Sulfone-Modified Hex-2-enopyranosides. J Org Chem 2009; 75:303-14. [DOI: 10.1021/jo902046g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rahul Bhattacharya
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302, India
| | - Manoj K. Kesharwani
- Analytical Science Discipline, Central Salt & Marine Chemicals Research Institute (CSIR), Bhavnagar 364 002, Gujarat, India
| | - Chinmoy Manna
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302, India
| | - Bishwajit Ganguly
- Analytical Science Discipline, Central Salt & Marine Chemicals Research Institute (CSIR), Bhavnagar 364 002, Gujarat, India
| | | | - Tanmaya Pathak
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302, India
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Setny P, Trylska J. Search for novel aminoglycosides by combining fragment-based virtual screening and 3D-QSAR scoring. J Chem Inf Model 2009; 49:390-400. [PMID: 19434840 DOI: 10.1021/ci800361a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aminoglycosides are antibiotics targeting the 16S RNA A site of the bacterial ribosome. There have been many efforts directed toward design of their synthetic derivatives, however with only few successes. As RNA binders, aminoglycosides are also a difficult target for computational drug design, since most of the existing methods were developed for protein ligands. Here, we present an approach that allows for evading the problems related to still poorly developed RNA docking and scoring algorithms. It is aimed at identification of new molecular scaffolds potentially binding to the A site. The considered molecules are based on the neamine core, which is common for all aminoglycosides and provides specificity toward the binding site, linked with diverse molecular fragments via its O5 or O6 oxygen atom. Suitable fragments are selected with the use of 3D searches of molecular fragments library against two distinct pharmacophores designed on the basis of available structural data for aminoglycoside-RNA complexes. The compounds resulting from fragments assembly with neamine are then scored with a 3D-QSAR model developed using the biological data for known aminoglycoside derivatives. Twenty-one new potential ligands are obtained, four of which have predicted activities comparable to less potent aminoglycoside antibiotics.
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Affiliation(s)
- Piotr Setny
- Interdisciplinary Centre for Mathematical and Computational Modelling and Faculty of Physics, University of Warsaw, Warsaw 02-089, Poland.
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Synthesis and evaluation of novel neamine derivatives effectively targeting to RNA. Bioorg Med Chem Lett 2009; 19:2103-6. [DOI: 10.1016/j.bmcl.2009.03.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Revised: 02/18/2009] [Accepted: 03/09/2009] [Indexed: 11/21/2022]
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Pang LJ, Wang D, Zhou J, Zhang LH, Ye XS. Synthesis of neamine-derived pseudodisaccharides by stereo- and regio-selective functional group transformations. Org Biomol Chem 2009; 7:4252-66. [DOI: 10.1039/b907518f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Nudelman I, Chen L, Llewellyn N, Sahraoui EH, Cherniavsky M, Spencer J, Baasov T. Combined Chemical-Enzymatic Assembly of Aminoglycoside Derivatives with N-1-AHB Side Chain. Adv Synth Catal 2008. [DOI: 10.1002/adsc.200800229] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kren V, Rezanka T. Sweet antibiotics - the role of glycosidic residues in antibiotic and antitumor activity and their randomization. FEMS Microbiol Rev 2008; 32:858-89. [PMID: 18647177 DOI: 10.1111/j.1574-6976.2008.00124.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A large number of antibiotics are glycosides. In numerous cases the glycosidic residues are crucial to their activity; sometimes, glycosylation only improves their pharmacokinetic parameters. Recent developments in molecular glycobiology have improved our understanding of aglycone vs. glycoside activities and made it possible to develop new, more active or more effective glycodrugs based on these findings - a very illustrative recent example is vancomycin. The majority of attention has been devoted to glycosidic antibiotics including their past, present, and probably future position in antimicrobial therapy. The role of the glycosidic residue in the biological activity of glycosidic antibiotics, and the attendant targeting and antibiotic selectivity mediated by glycone and aglycone in antibiotics some antitumor agents is discussed here in detail. Chemical and enzymatic modifications of aglycones in antibiotics, including their synthesis, are demonstrated on various examples, with particular emphasis on the role of specific and mutant glycosyltransferases and glycorandomization in the preparation of these compounds. The last section of this review describes and explains the interactions of the glycone moiety of the antibiotics with DNA and especially the design and structure-activity relationship of glycosidic antibiotics, including their classification based on their aglycone and glycosidic moiety. The new enzymatic methodology 'glycorandomization' enabled the preparation of glycoside libraries and opened up new ways to prepare optimized or entirely novel glycoside antibiotics.
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Affiliation(s)
- Vladimír Kren
- Centre of Biocatalysis and Biotransformation, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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