1
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Liu Y, Zhou Q, Huo Y, Sun X, Hu J. Recent advances in developing modified C14 side chain pleuromutilins as novel antibacterial agents. Eur J Med Chem 2024; 269:116313. [PMID: 38503168 DOI: 10.1016/j.ejmech.2024.116313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024]
Abstract
Owing to the increasing resistance to most existing antimicrobial drugs, research has shifted towards developing novel antimicrobial agents with mechanisms of action distinct from those of current clinical options. Pleuromutilins are antibiotics known for their distinct mechanism of action, inhibiting bacterial protein synthesis by binding to the peptidyl transferase center of the ribosome. Recent studies have revealed that pleuromutilin derivatives can disrupt bacterial cell membranes, thereby enhancing antibacterial efficacy. Both marketed pleuromutilin derivatives and those in clinical trials have been developed by structurally modifying the pleuromutilin C14 side chain to improve their antimicrobial activity. Therefore, this review aims to review advancement in the chemical structural characteristics, antibacterial activities, and structure-activity relationship studies of pleuromutilins, specifically focusing on modifications made to the C14 side chain in recent years. These findings provide a valuable reference for future research and development of pleuromutilins.
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Affiliation(s)
- Yue Liu
- Shandong Second Medical University, No.7166 Baotong Road, Weifang, 261053, PR China
| | - Qinjiang Zhou
- Shandong Second Medical University, No.7166 Baotong Road, Weifang, 261053, PR China
| | - Yiwen Huo
- Shandong Second Medical University, No.7166 Baotong Road, Weifang, 261053, PR China
| | - Xiujuan Sun
- Shandong Second Medical University, No.7166 Baotong Road, Weifang, 261053, PR China
| | - Jinxing Hu
- Shandong Second Medical University, No.7166 Baotong Road, Weifang, 261053, PR China.
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Ren J, Zhang QW, He XJ, Chen XY, Zhou ZD, Zeng ZL, Jin Z, Tang YZ. Design, synthesis, biological evaluation and molecular docking study of novel pleuromutilin derivatives containing substituted benzoxazole as antibacterial agents. J Enzyme Inhib Med Chem 2023; 38:2251712. [PMID: 37664987 PMCID: PMC10478630 DOI: 10.1080/14756366.2023.2251712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/21/2023] [Accepted: 08/20/2023] [Indexed: 09/05/2023] Open
Abstract
A series of pleuromutilin analogs containing substituted benzoxazole were designed, synthesised, and assessed for their antibacterial activity both in vivo and in vitro. The MIC of the synthesised derivatives was initially assessed using the broth dilution method against four strains of Staphylococcus aureus (MRSA ATCC 43300, S. aureus ATCC 29213, clinical isolation of S. aureus AD3 and S. aureus 144). Most of the synthesised derivatives displayed prominent in vitro activity (MIC ≤ 0.5 µg/mL). Compounds 50 and 57 exhibited the most effective antibacterial effect against MRSA (MIC = 0.125 µg/mL). Furthermore, the time-kill curves showed that compounds 50 and 57 had a certain inhibitory effect against MRSA in vitro. The in vivo antibacterial activity of compound 50 was evaluated further using a murine thigh model infected with MRSA (-1.24 log10CFU/mL). Compound 50 exhibited superior antibacterial efficacy to tiamulin. It was also found that compound 50 did not display significant inhibitory effect on the proliferation of RAW 264.7 cells. Molecular docking study revealed that compound 50 can effectively bind to the active site of the 50S ribosome (the binding free energy -7.50 kcal/mol).
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Affiliation(s)
- Jie Ren
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Qi-Wen Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xian-Jin He
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao-Ying Chen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zi-Dan Zhou
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhen-Ling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhen Jin
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - You-Zhi Tang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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da Silva JF, Corrêa DS, Campos ÉL, Leite GZ, de Oliveira JDM, Fachini J, da Silva J, Obach ES, Campo LF, Grivicich I, de Amorim HLN, Picada JN. Evaluation of toxicological aspects of three new benzoxazole compounds with sunscreen photophysical properties using in silico and in vitro methods. Toxicol In Vitro 2021; 79:105300. [PMID: 34933087 DOI: 10.1016/j.tiv.2021.105300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/23/2021] [Accepted: 12/11/2021] [Indexed: 11/18/2022]
Abstract
Sunscreening chemicals protect against damage caused by sunlight most absorbing UVA or UVB radiations. In this sense, 2-(2'-hydroxyphenyl)benzoxazole derivatives with amino substituents in the 4' and 5' positions have an outstandingly high Sun Protection Factor and adequate photostability, but their toxicity is not yet known. This study aimed to evaluate the toxicity of three synthetic 2-(2'-hydroxyphenyl)benzoxazole derivatives for their possible application as sunscreens. In silico tools were used in order to assess potential risks regarding mutagenic, carcinogenic, and skin sensitizing potential. Bioassays were performed in L929 cells to assess cytotoxicity in MTT assay and genotoxic activities in the Comet assay and micronucleus test. Also, the Salmonella/microsome assay was performed to evaluate gene mutations. The in silico predictions indicate a low risk of mutagenicity and carcinogenicity of the compounds while the skin sensitizing potential was low or inconclusive. The 2-(4'-amino-2'-hydroxyphenyl)benzoxazol compound was the most cytotoxic and genotoxic among the compounds evaluated in L929 cells, but none induced mutations in the Salmonella/microsome assay. The amino substituted at the 4' position of the phenyl ring appears to have greater toxicological risks than substituents at the 5' position of 2-(phenyl)benzoxazole. The findings warrant further studies of these compounds in cosmetic formulations.
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Affiliation(s)
- Jâmeson Ferreira da Silva
- Laboratório de Genética Toxicológica, Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, CEP: 92425-900 Canoas, RS, Brazil; Centro de Pesquisa em Produto e Desenvolvimento (CEPPED), Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, CEP: 92425-900 Canoas, RS, Brazil
| | - Dione Silva Corrêa
- Centro de Pesquisa em Produto e Desenvolvimento (CEPPED), Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, CEP: 92425-900 Canoas, RS, Brazil
| | - Érico Leite Campos
- Laboratório de Genética Toxicológica, Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, CEP: 92425-900 Canoas, RS, Brazil; Centro de Pesquisa em Produto e Desenvolvimento (CEPPED), Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, CEP: 92425-900 Canoas, RS, Brazil
| | - Giovana Zamprônio Leite
- Laboratório de Genética Toxicológica, Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, CEP: 92425-900 Canoas, RS, Brazil; Centro de Pesquisa em Produto e Desenvolvimento (CEPPED), Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, CEP: 92425-900 Canoas, RS, Brazil
| | - João Denis Medeiros de Oliveira
- Laboratório de Genética Toxicológica, Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, CEP: 92425-900 Canoas, RS, Brazil
| | - Jean Fachini
- Laboratório de Genética Toxicológica, Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, CEP: 92425-900 Canoas, RS, Brazil
| | - Juliana da Silva
- Laboratório de Genética Toxicológica, Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, CEP: 92425-900 Canoas, RS, Brazil; Laboratório de Genetica Toxicológica, Universidade La Salle, Av. Victor Barreto, 2288, CEP: 92010-000 Canoas, RS, Brazil
| | - Eliane Sempé Obach
- Laboratório de Tecnologia Farmacêutica, Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, CEP: 92425-900 Canoas, RS, Brazil
| | - Leandra Franciscato Campo
- Laboratório de Novos Materiais Orgânicos e Quimica Forense, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, CEP: 90650-001 Porto Alegre, RS, Brazil
| | - Ivana Grivicich
- Laboratório de Biologia do Câncer, Universidade Luterana do Brasil (ULBRA), Farroupilha Avenue 8001, CEP: 92425-900 Canoas, RS, Brazil
| | | | - Jaqueline Nascimento Picada
- Laboratório de Genética Toxicológica, Universidade Luterana do Brasil (ULBRA), Av. Farroupilha, 8001, CEP: 92425-900 Canoas, RS, Brazil; Laboratório de Novos Materiais Orgânicos e Quimica Forense, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, CEP: 90650-001 Porto Alegre, RS, Brazil.
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Temiz-Arpaci O, Zeyrek CT, Arisoy M, Erol M, Celik I, Kaynak-Onurdag F. Synthesis, quantum mechanical calculations, antimicrobial activities and molecular docking studies of five novel 2,5-disubstituted benzoxazole derivatives. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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5
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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6
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Zeyrek CT, Arpacı ÖT, Arısoy M, Onurdağ FK. Synthesis, antimicrobial activity, density functional modelling and molecular docking with COVID-19 main protease studies of benzoxazole derivative: 2-(p-chloro-benzyl)-5-[3-(4-ethly-1-piperazynl) propionamido]-benzoxazole. J Mol Struct 2021; 1237:130413. [PMID: 33846658 PMCID: PMC8026219 DOI: 10.1016/j.molstruc.2021.130413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/20/2021] [Accepted: 03/30/2021] [Indexed: 12/28/2022]
Abstract
This study contains synthesis, antimicrobial activity, density functional modelling and molecular docking studies of benzoxazole derivative: 2-(p-chloro-benzyl)-5-[3-(4-ethly-1-piperazynl) propionamido]-benzoxazole. The synthetic procedure of investigated compound is given in detail. The newly synthesized benzoxazole compound and standard drugs were evaluated for their antimicrobial activity against some Gram-positive, Gram-negative bacteria and fungus C. albicans and their drug-resistant isolates. The benzoxazole compound has been characterized by using 1H-NMR, IR and MASS spectrometry and elemental analysis techniques. The molecular structure of the compound in the ground state has been modelling using density functional theory (DFT) with B3LYP/6-311++g(d,p) level. The molecular docking of 2-(p-chloro-benzyl)-5-[3-(4-ethly-1-piperazynl) propionamido]-benzoxazole with COVID-19 main protease has been also performed by using optimized geometry and the experimentally determined dimensional structure of the main protease (M-pro) of COVID-19.
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Affiliation(s)
- Celal Tuğrul Zeyrek
- Department of Academy and Publications, Turkish Energy, Nuclear and Mining Research Instution, TR-06100, Beşevler, Ankara, Turkey
| | - Özlem Temiz Arpacı
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, TR-06100, Beşevler, Ankara, Turkey
| | - Mustafa Arısoy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ankara University, TR-06100, Beşevler, Ankara, Turkey
| | - Fatma Kaynak Onurdağ
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Trakya University, TR-22030, Edirne, Turkey
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7
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Erol M, Celik I, Kuyucuklu G. Synthesis, Molecular Docking, Molecular Dynamics, DFT and Antimicrobial Activity Studies of 5-substituted-2-(p-methylphenyl)benzoxazole Derivatives. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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8
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Theoretical and experimental verification of molecular properties of novel benzamide derivatives using computational platforms and in vitro antibacterial activity. Med Chem Res 2021. [DOI: 10.1007/s00044-020-02671-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Celik I, Erol M, Kuyucuklu G. Molecular modeling, density functional theory, ADME prediction and antimicrobial activity studies of 2-(substituted)oxazolo[4,5- b]pyridine derivatives. NEW J CHEM 2021. [DOI: 10.1039/d1nj00701g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Molecular docking, molecular dynamics, DFT, ADME prediction, and antimicrobial activity studies of some 2-(substituted)oxazolo[4,5-b]pyridine derivatives were carried out.
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Affiliation(s)
- Ismail Celik
- Erciyes University
- Faculty of Pharmacy
- Department of Pharmaceutical Chemistry
- Kayseri
- Turkey
| | - Meryem Erol
- Erciyes University
- Faculty of Pharmacy
- Department of Pharmaceutical Chemistry
- Kayseri
- Turkey
| | - Gulcan Kuyucuklu
- Department of Medical Microbiology
- Faculty of Medicine
- Trakya University
- Edirne
- Turkey
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10
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Synthesis, molecular docking and ADME prediction of some new benzimidazole carboxamidines derivatives as antimicrobial agents. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02621-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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11
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Erol M, Celik I, Uzunhisarcikli E, Kuyucuklu G. Synthesis, Molecular Docking, and DFT Studies of Some New 2,5-Disubstituted Benzoxazoles as Potential Antimicrobial and Cytotoxic Agents. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1802305] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Meryem Erol
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Erciyes University, Kayseri, Turkey
| | - Ismail Celik
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Erciyes University, Kayseri, Turkey
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Ankara University, Ankara, Turkey
| | - Ebru Uzunhisarcikli
- Faculty of Pharmacy, Department of Pharmacology, Erciyes University, Kayseri, Turkey
| | - Gulcan Kuyucuklu
- Faculty of Medicine, Department of Medical Microbiology, Trakya University, Edirne, Turkey
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12
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Erol M, Celik I, Temiz-Arpaci O, Kaynak-Onurdag F, Okten S. Design, synthesis, molecular docking, density functional theory and antimicrobial studies of some novel benzoxazole derivatives as structural bioisosteres of nucleotides. J Biomol Struct Dyn 2020; 39:3080-3091. [PMID: 32323628 DOI: 10.1080/07391102.2020.1760134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A series of some novel 2-(p-tert-butylphenyl)-5-(3-substituted-propionamido)benzoxazole derivatives have been designed, synthesized, evaluated for antimicrobial activity and have performed molecular docking studies against penicillin-binding protein 4 (PBP4) and active and allosteric site of PBP2a; were calculated some theoretical quantum parameters and absorption, distribution, metabolism and excretion (ADME) descriptors. B9 acted at minimum inhibitory concentration (MIC) = 8 µg/mL against S. aureus, E. faecalis and their drug-resistant isolates and also formed with GLU145 (1.74 Å) and ILE144 (1.89 Å) two hydrogen bonds at allosteric site of PBP2a with Glide emodel score: -42.168. ΔE of compound B9 had moderate value of all compounds with 0.14742.[Formula: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Meryem Erol
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Erciyes University, Kayseri, Turkey
| | - Ismail Celik
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Erciyes University, Kayseri, Turkey.,Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Ankara University, Ankara, Turkey
| | - Ozlem Temiz-Arpaci
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Ankara University, Ankara, Turkey
| | - Fatma Kaynak-Onurdag
- Faculty of Pharmacy, Department of Pharmaceutical Microbiology, Trakya University, Edirne, Turkey
| | - Suzan Okten
- Faculty of Pharmacy, Department of Pharmaceutical Microbiology, Trakya University, Edirne, Turkey
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13
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Nguyen GTH, Leung WY, Tran TN, Wang H, Murray V, Donald WA. Mechanism for the Binding of Netropsin to Hairpin DNA Revealed Using Nanoscale Ion Emitters in Native Mass Spectrometry. Anal Chem 2019; 92:1130-1137. [PMID: 31778608 DOI: 10.1021/acs.analchem.9b04209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Netropsin is one of the first ligands to be discovered that selectively binds to the minor groove of DNA and is actively used as a scaffold for developing potential anticancer and antibiotic agents. The mechanism by which netropsin binds to hairpin DNA remains controversial with two competing mechanisms having been proposed. In one mechanism, netropsin binding induces a hairpin-to-duplex DNA transition. Alternatively, netropsin binds in two thermodynamically different modes at a single duplexed AATT site. Here, results from native mass spectrometry (MS) with nanoscale ion emitters indicate that netropsin can simultaneously and sequentially bind to both hairpin and duplex DNA. Duplex DNA was not detected using conventional MS with larger emitters because nanoscale emitters significantly reduce the extent of salt adduction to ligand-DNA complex ions, including in the presence of relatively high concentrations of nonvolatile salts. Based on native MS and polyacrylamide gel electrophoresis results, the abundances of hairpin and duplex DNA are unaffected by the addition of netropsin. By native MS, the binding affinities for five ligand-DNA and DNA-DNA interactions can be rapidly obtained simultaneously. This research indicates a "simultaneous binding mechanism" for the interactions of netropsin with DNA.
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Affiliation(s)
- Giang T H Nguyen
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Wai Yu Leung
- School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Thinh N Tran
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Huixin Wang
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia.,Mark Wainwright Analytical Centre , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Vincent Murray
- School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - William A Donald
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia
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14
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Paston SV, Nikolaev AI, Ushkov PA. EDTA, thymidine, and Cu2+ ion complexes from mass spectrometry data. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617020251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Mary YS, Alzoman NZ, Menon VV, Al-Abdullah ES, El-Emam AA, Panicker CY, Temiz-Arpaci O, Armaković S, Armaković SJ, Van Alsenoy C. Reactive, spectroscopic and antimicrobial assessments of 5-[(4-methylphenyl) acetamido]-2-(4-tert-butylphenyl)benzoxazole: Combined experimental and computational study. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.09.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Nayab PS, Pulaganti M, Chitta SK, Abid M, Uddin R. Evaluation of DNA Binding, Radicals Scavenging and Antimicrobial Studies of Newly Synthesized N-Substituted Naphthalimides: Spectroscopic and Molecular Docking Investigations. J Fluoresc 2015; 25:1905-20. [DOI: 10.1007/s10895-015-1683-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/28/2015] [Indexed: 11/28/2022]
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17
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Synthesis and antimycobacterial and photosynthesis-inhibiting evaluation of 2-[(E)-2-substituted-ethenyl]-1,3-benzoxazoles. ScientificWorldJournal 2014; 2014:705973. [PMID: 25197708 PMCID: PMC4146477 DOI: 10.1155/2014/705973] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 07/15/2014] [Indexed: 11/18/2022] Open
Abstract
A series of twelve 2-[(E)-2-substituted-ethenyl]-1,3-benzoxazoles was designed. All the synthesized compounds were tested against three mycobacterial strains. The compounds were also evaluated for their ability to inhibit photosynthetic electron transport (PET) in spinach (Spinacia oleracea L.) chloroplasts. 2-[(E)-2-(4-Methoxyphenyl)ethenyl]-1,3-benzoxazole, 2-[(E)-2-(2,3-dihydro-1-benzofuran-5-yl)ethenyl]-1,3-benzoxazole and 2-{(E)-2-[4-(methylsulfanyl)phenyl]ethenyl}-1,3-benzoxazole showed the highest activity against M. tuberculosis, M. kansasii, and M. avium, and they demonstrated significantly higher activity against M. avium and M. kansasii than isoniazid. The PET-inhibiting activity of the most active ortho-substituted compound 2-[(E)-2-(2-methoxyphenyl)ethenyl]-1,3-benzoxazole was IC₅₀ = 76.3 μmol/L, while the PET-inhibiting activity of para-substituted compounds was significantly lower. The site of inhibitory action of tested compounds is situated on the donor side of photosystem II. The structure-activity relationships are discussed.
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Ma Y, Zhang G, Pan J. Spectroscopic studies of DNA interactions with food colorant indigo carmine with the use of ethidium bromide as a fluorescence probe. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:10867-10875. [PMID: 23057637 DOI: 10.1021/jf303698k] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The interaction of indigo carmine (IC) with calf thymus DNA in physiological buffer (pH 7.4), using ethidium bromide (EB) dye as a fluorescence probe, was investigated by ultraviolet-visible absorption, fluorescence, and circular dichroism (CD) spectroscopy, coupled with viscosity measurements and DNA-melting studies. Hypochromicity of the absorption spectra of IC and enhancement in fluorescence polarization of IC were observed with the addition of DNA. Moreover, the binding of IC to DNA was able to decrease iodide and single-stranded DNA (ssDNA) quenching effects, increase the melting temperature and relative viscosity of DNA, and induce the changes in CD spectra of DNA. All of the evidence indicated that IC interacted with DNA in the mode of intercalative binding. Furthermore, the three-way synchronous fluorescence spectra data obtained from the interaction between IC and DNA-EB were resolved by parallel factor analysis (PARAFAC), and the results provided simultaneously the concentration information and the pure spectra for the three reaction components (IC, EB, and DNA-EB) of the system at equilibrium. This PARAFAC demonstrated that the intercalation of IC molecules into DNA proceeded by substituting for EB in the DNA-EB complex. The calculated thermodynamic parameters, ΔH° and ΔS°, suggested that both hydrophobic interactions and hydrogen bonds played a predominant role in the binding of IC to DNA.
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Affiliation(s)
- Yadi Ma
- State Key Laboratory of Food Science and Technology, Nanchang University, Number 235, Nanjing East Road, Nanchang 330047, Jiangxi, People's Republic of China
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19
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Ramos CI, Graça Santana-Marques M. Electrospray mass spectrometry for the study of the non-covalent interactions of porphyrins and duplex desoxyribonucleotides. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424609000590] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
An overview of the use of electrospray mass spectrometry for the study of non-covalent interactions of cationic porphyrins and small DNA duplexes, highlighting the work developed in the Mass Spectrometry Laboratory of the University of Aveiro, is presented here.
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20
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Smith SI, Brodbelt JS. Rapid characterization of cross-links, mono-adducts, and non-covalent binding of psoralens to deoxyoligonucleotides by LC-UV/ESI-MS and IRMPD mass spectrometry. Analyst 2010; 135:943-52. [PMID: 20419242 PMCID: PMC2890229 DOI: 10.1039/b924023c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Upon UV photoactivation, psoralen analogs form covalent mono-adducts and cross-links with DNA at thymine residues. Electrospray ionization mass spectrometric analysis allowed rapid and efficient determination of the reaction percentages of each psoralen analog with DNA duplexes containing different binding sites after exposure to UV irradiation. The distribution of cross-linked products and mono-adducts was monitored by both LC-UV and IRMPD-MS methods with the highest ratio of cross-linked products to mono-adducts obtained for 8-methoxypsoralen (8-MOP), psoralen (P), and 5-methoxypsoralen (5-MOP). Reactions at 5'-TA sites were favored over 5'-AT sites, and duplexes containing two and three binding sites showed extensive binding by the psoralens. 4'-Aminomethyl-4,5',8-trimethylpsoralen (AMP) bound non-selectively via non-covalent interactions and was the only psoralen analog to show significant binding in the absence of UV irradiation. 8-MOP binding displayed the greatest sequence selectivity among the psoralen analogs. The sites of interstrand cross-linking were determined by fragmentation of the duplex/psoralen complexes by infrared multiphoton dissociation (IRMPD), which produced cross-linked product ions containing an intact single strand, the psoralen analog, and either a w(n) or a(n)-B portion of the complementary strand. IRMPD of DNA/AMP complexes after UV irradiation also produced high abundances of the intact single strands with the AMP ligand attached, products indicative of a significant population of mono-adducts.
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Affiliation(s)
- Suncerae I Smith
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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21
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Brodbelt JS. Evaluation of DNA/Ligand interactions by electrospray ionization mass spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2010; 3:67-87. [PMID: 20636034 DOI: 10.1146/annurev.anchem.111808.073627] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) has enabled the detection and characterization of DNA/ligand complexes, including evaluation of both relative binding affinities and selectivities of DNA-interactive ligands. The noncovalent complexes that are transferred from the solution to the gas phase retain the signature of the native species, thus allowing the use of MS to screen DNA/ligand complexes, reveal the stoichiometries of the complexes, and provide insight into the nature of the interactions. Ligands that bind to DNA via metal-mediated modes and those that bind to unusual DNA structures, such as quadruplexes, are amenable to ESI. Chemical probe methods applied to DNA/ligand complexes with ESI-MS detection afford information about ligand-binding sites and conformational changes of DNA that occur upon ligand binding.
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry and Biochemistry, University of Texas, Austin, 78712, USA.
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22
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Oberacher H. Frontiers of mass spectrometry in nucleic acids analysis. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:351-365. [PMID: 20530841 DOI: 10.1255/ejms.1045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Nucleic acids research is a highly competitive field of research. A number of well established methods are available. The current output of high throughput ("next generation") sequencing technologies is impressive, and still technologies are continuing to make progress regarding read lengths, bp per second, accuracy and costs. Although in the 1990s MS was considered as an analytical platform for sequencing, it was soon realized that MS will never be competitive. Thus, the focus shifted from de novo sequencing towards other areas of application where MS has proven to be a powerful analytical tool. Potential niches for the application of MS in nucleic acids research include genotyping of genetic markers (single nucleotide polymorphisms, short tandem repeats, and combinations thereof), quality control of synthetic oligonucleotides, metabolic profiling of therapeutics, characterization of modified nucleobases in DNA and RNA molecules, and the study of non covalent interactions among nucleic acids as well as interactions of nucleic acids with drugs and proteins. The diversity of possible applications for MS highlights its significance for nucleic acid research.
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Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
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23
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Smith S, Guziec FS, Guziec L, Brodbelt JS. Interactions of sulfur-containing acridine ligands with DNA by ESI-MS. Analyst 2009; 134:2058-66. [PMID: 19768213 PMCID: PMC2892893 DOI: 10.1039/b905071j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The alkylating proficiency of sulfur-containing mustards may be increased by using an acridine moiety to guide the sulfur mustard to its cellular target. In this study, the interactions of a new series of sulfur-containing acridine ligands, some that also function as alkylating mustards, with DNA were evaluated by electrospray ionization mass spectrometry (ESI-MS). Relative binding affinities were estimated from the ESI-MS data based on the fraction of bound DNA for DNA/acridine mixtures. The extent of binding observed for the series of sulfur-containing acridines was similar, presumably because the intercalating acridine moiety was identical. Upon infrared multi-photon dissociation (IRMPD) of the resulting oligonucleotide/sulfur-containing acridine complexes, ejection of the ligand was the dominant pathway for most of the complexes. However, for AS4, an acridine sulfide mustard, and AN1, an acridine nitrogen mustard, strand separation with the ligand remaining on one of the single strands was observed. At higher irradiation times, a variety of sequence ions were observed, some retaining the AS4/AN1 ligand, which was indicative of covalent binding.
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Affiliation(s)
- Suncerae Smith
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
| | - Frank S. Guziec
- Department of Chemistry, Southwestern University, Georgetown, TX 79626
| | - Lynn Guziec
- Department of Chemistry, Southwestern University, Georgetown, TX 79626
| | - Jennifer S. Brodbelt
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
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24
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Buchmann W, Boutorine A, Halby L, Tortajada J, De Pauw E. A new method for the determination of the relative affinity of a ligand against various DNA sequences by electrospray ionization mass spectrometry. Application to a polyamide minor groove binder. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:1171-1181. [PMID: 19408249 DOI: 10.1002/jms.1592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A new method for the determination of the relative affinity of a ligand against various dsDNA sequences is presented by using electrospray ionization time-of-flight mass spectrometry (ESI-QTOF) mass spectrometry. The principle is described here through the complexation of double-stranded DNA by a polyamide ligand including twelve N-methylpyrrole rings. However this method could be applied to other ligands especially when dissociation constants (Kd) are in nanomolar range. This method does not require knowing the ligand concentration accurately. It allows determination of the relative affinity of a ligand against various dsDNA sequences for 1 : 1 complex stoichiometries in a quick manner without labeling.
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Affiliation(s)
- William Buchmann
- Université d'Evry val d'Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, (CNRS UMR 8587/CEA), Bâtiment Maupertuis, Bd. François Mitterrand, 91025 Evry, France.
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25
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Anichina J, Bohme DK. Mass-spectrometric studies of the interactions of selected metalloantibiotics and drugs with deprotonated hexadeoxynucleotide GCATGC. J Phys Chem B 2009; 113:328-35. [PMID: 19072169 DOI: 10.1021/jp807034v] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
ESI tandem mass spectrometry is employed in a detailed study of the interactions of a hexameric duplex d(5'GCATGC) with three types of ligated first-row transition metal dications M(2+): metallated bleomycins, singly, doubly, and triply ligated metallophenanthrolines and [M(triethylenetetramine)](2+). The singly, doubly, and triply metallated species were found to dissociate by noncovalent separation into two strands with metal ions attached either to one or to both. Relative gas-phase stabilities of the double-stranded oligodeoxynucleotide (ODN)-M(2+) complexes were found to follow the order Mn(II) > Fe(II) > Co(II) > Ni(II) > Zn(II) > Cu(II). Overall, the presence of metal dications is found to increase the gas-phase stability of the duplex against noncovalent dissociation with the exception of one and three copper dications. An analysis of the dissociation pathways and relative gas-phase stabilities of the species that were investigated provided a basis for the assessment of the possible binding modes between duplex oligonucleotides and metallocomplexes.
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Affiliation(s)
- Janna Anichina
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
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26
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Xu Y, Afonso C, Wen R, Tabet JC. Investigation of double-stranded DNA/drug interaction by ESI/FT ICR: orientation of dissociations relates to stabilizing salt bridges. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:1531-1544. [PMID: 18521852 DOI: 10.1002/jms.1430] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Noncovalent complexes of DNA and Hoechst 33258 were investigated by ESI-FT/ICR MS in various activation modes (collision-induced dissociation (CID), sustained off-resonance irradiation collision-induced dissociation (SORI-CID), infrared multiphoton dissociation (IRMPD) and electron detachment dissociation (EDD)). The binding selectivity of Hoechst 33258 was confirmed by the comparative study of its noncovalent association with different DNA sequences. The CID spectra of [ds + HO - 5H](5-) obtained with a linear hexapole ion trap resulted in unzipping of the strands. This outcome is a clue to the drug-binding mode, shading light on the localization of the binding sites of Hoechst 33258 to the DNA sequence. The IRMPD and SORI-CID experiments mainly gave DNA backbone cleavages and internal fragment ions. From this result, information on the localization of the binding sites of Hoechst 33258 in the DNA sequence was obtained. No sodium cationization was observed on the DNA sequence ions although they were present on fragmentation of the duplex, indicating that the backbone cleavages were generated from the single strand associated with the Hoechst 33258 where the number of alkali cation is restricted. Under electron detachment (ED) conditions, multiple EDs were achieved for the [ds + HO - 5H](5-) ion without any significant dissociation. The presence of drug appears to enhance the stability of the multiply charged system. It was proposed that the studied noncovalent complex involved the formation of zwitterions and consequently strong salt-bridge interactions between DNA and drug.
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Affiliation(s)
- Ying Xu
- Université Pierre et Marie Curie-Paris 6, UMR 7613 Synthèse, Structure et Fonction de Molécules Bioactives, Paris, F-75005, France
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27
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Feil SW, Koyanagi GK, Anichina J, Bohme DK. Chemical stability and reactivity of deprotonated oligonucleotides (DNA) in the gas phase: protonation and solvation with hydrogen bromide. J Phys Chem B 2008; 112:10375-81. [PMID: 18651764 DOI: 10.1021/jp804193u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selected deprotonated oligodeoxynucleotides generated by electrospray ionization were exposed to a variety of neutral molecules in the gas phase at room temperature in flowing helium gas at 0.35 Torr. Single-stranded [AGTCTG-nH]n- and single- and double-stranded [GCATGC-nH]n- anions were found to be remarkably unreactive with strong oxidants (O3, O2, N2O) and potential intercalators (benzene, pyridine, toluene, and quinoxaline). Hydration also was observed to be inefficient. However, [AGTCTG-nH]n- anions with n=2, 3, 4, and 5 were seen to be sequentially protonated and/or hydrobrominated with HBr (but not damaged) and displayed an interesting "end effect" against protonation. Measurements are provided for the rate coefficients of reaction and the efficiencies of protonation. These experimental results point toward the exciting prospect of measuring the intrinsic chemistry of other bare DNA-like anions, including double-stranded oligonucleotide anions in the gas phase at room temperature.
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Affiliation(s)
- Stefan W Feil
- Department of Chemistry, Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
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28
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Wang Z, Cui M, Song F, Lu L, Liu Z, Liu S. Evaluation of flavonoids binding to DNA duplexes by electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:914-922. [PMID: 18467117 DOI: 10.1016/j.jasms.2008.04.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 04/01/2008] [Accepted: 04/02/2008] [Indexed: 05/26/2023]
Abstract
In this study, electrospray ionization mass spectrometry (ESI-MS) was used to investigate the binding interactions of ten flavonoid aglycones and ten flavonoid glycosides with DNA duplexes. Relative binding affinities of the flavonoids toward DNA duplexes were estimated based on the fraction of bound DNA. The results revealed that the 4'-OH group of flavonoid aglycones was essential for their DNA-binding properties. Flavonoid glycosides with sugar chain linked on ring A or ring B showed enhanced binding toward the duplexes over their aglycone counterparts, whereas glycosylation of the flavonol quercetin on ring C exhibited a less pronounced effect. The aglycone skeletons and other hydroxyl substitutions on the aglycone also have an effect on the fractions of bound DNA. Upon collision-induced dissociation, the complexes containing flavonoid aglycones underwent the predominant ejection of a neutral ligand molecule, suggesting an intercalative DNA-binding mode. However, for complexes containing flavonoid glycosides, the loss of nucleobase increased to different extents, indicating a stronger binding or different binding mode. The results may provide not only a deeper insight into the DNA-binding properties of flavonoids but also a useful guideline for the design of efficient DNA-binding agents for chemotherapy.
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Affiliation(s)
- Zhaofu Wang
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun Center of Mass Spectrometry, Changchun, 130022, PR China
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29
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Pierce SE, Sherman CL, Jayawickramarajah J, Lawrence CM, Sessler JL, Brodbelt JS. ESI-MS characterization of a novel pyrrole-inosine nucleoside that interacts with guanine bases. Anal Chim Acta 2008; 627:129-35. [PMID: 18790136 DOI: 10.1016/j.aca.2008.04.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 04/03/2008] [Accepted: 04/08/2008] [Indexed: 11/27/2022]
Abstract
Based on binding studies undertaken by electrospray ionization-mass spectrometry, a synthetic pyrrole-inosine nucleoside, 1, capable of forming an extended three-point Hoogsteen-type hydrogen-bonding interaction with guanine, is shown to form specific complexes with two different quadruplex DNA structures [dTG(4)T](4) and d(T(2)G(4))(4) as well as guanine-rich duplex DNA. The binding interactions of two other analogs were evaluated in order to unravel the structural features that contribute to specific DNA recognition. The importance of the Hoogsteen interactions was confirmed through the absence of specific binding when the pyrrole NH hydrogen-bonding site was blocked or removed. While 2, with a large blocking group, was not found to interact with virtually any form of DNA, 3, with the pyrrole functionality missing, was found to interact non-specifically with several types of DNA. The specific binding of 1 to guanine-rich DNA emphasizes the necessity of careful ligand design for specific sequence recognition.
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Affiliation(s)
- Sarah E Pierce
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712-1167, United States
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30
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Wang Z, Guo X, Liu Z, Cui M, Song F, Liu S. Studies on alkaloids binding to GC-rich human survivin promoter DNA using positive and negative ion electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:327-335. [PMID: 17968851 DOI: 10.1002/jms.1320] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) was used to investigate the binding of 13 alkaloids to two GC-rich DNA duplexes which are critical sequences in human survivin promoter. Negative ion ESI-MS was first applied to screen the binding of the alkaloids to the duplexes. Six alkaloids (including berberine, jatrorrhizine, palmatine, reserpine, berbamine, and tetrandrine) show complexation with the target DNA sequences. Relative binding affinities were estimated from the negative ion ESI data, and the alkaloids show a binding preference to the duplex with higher GC content. Positive ion ESI mass spectra of the complexes were also recorded and compared with those obtained in negative ion mode. Only the 1 : 1 complex with berbamine was observed with lower abundance in the positive ion mass spectrum while complexes with the other alkaloids were absolutely absent. Collision-induced dissociation (CID) experiments indicate that the complexes with the protoberberine alkaloids (berberine, jatrorrhizine, and palmatine) dissociate via base loss and covalent cleavage. In contrast, product ion spectra of the complexes with the alkaloids reserpine, berbamine, and tetrandrine show the predominant loss of a neutral alkaloid molecule, accompanied by base loss and covalent cleavage to a lesser extent. A comparison of the gas-phase behaviors of complexes with the alkaloids to those with the traditional DNA binders has suggested an intercalative binding mode of these alkaloids to the target DNA duplexes.
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Affiliation(s)
- Zhaofu Wang
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun Center of Mass Spectrometry, Changchun, 130022, P R China
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31
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McKee ML, Kerwin SM. Synthesis, metal ion binding, and biological evaluation of new anticancer 2-(2'-hydroxyphenyl)benzoxazole analogs of UK-1. Bioorg Med Chem 2008; 16:1775-83. [PMID: 18037301 PMCID: PMC2268758 DOI: 10.1016/j.bmc.2007.11.019] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 11/02/2007] [Accepted: 11/05/2007] [Indexed: 11/18/2022]
Abstract
UK-1 is a bis(benzoxazole) natural product displaying activity against a wide range of human cancer cell lines. A simplified analog of UK-1, 4-carbomethoxy-2-(2'-hydroxyphenyl)benzoxazole, was previously found to be almost as active as UK-1 against cancer cell lines, and similar to the natural product, formed complexes with a variety of metal ions such as Mg2+ and Zn2+. A series of 4-substituted-2-(2'-hydroxyphenyl)benzoxazole analogs of this 'minimal pharmacophore' of UK-1 were prepared. The anti-cancer activity of these analogs was examined in breast and lung cancer cell lines. Spectrophotometric titrations in methanol were carried out in order to assess the ability of UK-1 and these analogs to coordinate with Mg2+ and Cu2+ ions. Although none of the new analogs were more cytotoxic than 4-carbomethoxy-2-(2'-hydroxyphenyl)benzoxazole, some analogs were identified that display similar cytotoxicity to this simplified UK-1 analog with improved water solubility. UK-1 and all of these new analogs bind Cu2+ ions better than Mg2+ ions, and the nature of the 4-substituent is important for the Mg2+ ion binding ability of these 2-(2'-hydroxyphenyl)benzoxazoles. Previous studies of a limited number of UK-1 analogs demonstrated a correlation between Mg2+ ion binding ability and cytotoxicity; however, within this series of 4-substituted-2-(2'-hydroxyphenyl)benzoxazoles the variations in cytotoxicity do not correlate with either Mg2+ or Cu2+ ion binding ability. These results, together with recent ESI-MS studies of Cu2+-mediated DNA binding by UK-1 and analogs, indicate that UK-1 and analogs may exert their cytotoxic effects by interaction with Cu2+ or other transition metal ions, rather than Mg2+, and that metal ion-mediated DNA binding, rather than metal ion binding affinity, is important for the cytotoxic effect of these compounds. The potential role of Cu2+ ions in the cytotoxic action of UK-1 is further supported by the observation that UK-1 in the presence of Cu2+ displays enhanced cytotoxicity to MCF-7 and A549 cells when compared to UK-1 alone.
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Affiliation(s)
- Mireya L. McKee
- Department of Chemistry and Biochemistry, Division of Medicinal Chemistry, and Institute of Cellular and Molecular Biology, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712
| | - Sean M. Kerwin
- Department of Chemistry and Biochemistry, Division of Medicinal Chemistry, and Institute of Cellular and Molecular Biology, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712
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32
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Mazzitelli CL, Rodriguez M, Kerwin SM, Brodbelt JS. Evaluation of metal-mediated DNA binding of benzoxazole ligands by electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:209-18. [PMID: 17583529 PMCID: PMC2277474 DOI: 10.1016/j.jasms.2007.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 05/04/2007] [Accepted: 05/16/2007] [Indexed: 05/15/2023]
Abstract
The binding of a series of benzoxazole analogs with different amide- and ester-linked side chains to duplex DNA in the absence and presence of divalent metal cations is examined. All ligands were found to form complexes with Ni2+, Cu2+, and Zn2+, with 2:1 ligand/metal cation binding stoichiometries dominating for ligands containing shorter side chains (2, 6, 7, and 8), while 1:1 complexes were the most abundant for ligands with long side chains (9, 10, and 11). Ligand binding with duplex DNA in the absence of metal cations was assessed, and the long side-chain ligands were found to form low abundance complexes with 1:1 ligand/DNA binding stoichiometries. The ligands with the shorter side chains only formed DNA complexes in the presence of metal cations, most notably for 7 and 8 binding to DNA in the presence of Cu2+. The binding of long side-chain ligands was enhanced by Cu2+ and to a lesser degree by Ni2+ and Zn2+. The cytotoxicities of all of the ligands against the A549 lung cancer and MCF7 breast cancer cell lines were also examined. The ligands exhibiting the most dramatic metal-enhanced DNA binding also demonstrated the greatest cytotoxic activity. Both 7 and 8 were found to be the most cytotoxic against the A549 lung cancer cell line and 8 demonstrated moderate cytotoxicity against MCF7 breast cancer cells. Metal ions also enhanced the DNA binding of the ligands with the long side chains, especially for 9, which also exhibited the highest level of cytotoxicity of the long side-chain compounds.
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Affiliation(s)
- Carolyn L Mazzitelli
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
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33
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Mazzitelli CL, Brodbelt JS. Probing ligand binding to duplex DNA using KMnO4 reactions and electrospray ionization tandem mass spectrometry. Anal Chem 2007; 79:4636-47. [PMID: 17508717 PMCID: PMC2531255 DOI: 10.1021/ac070145p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An electrospray ionization tandem mass spectrometry (ESI-MS/MS) strategy employing the thymine-selective KMnO4 oxidation reaction to detect conformational changes and ligand binding sites in noncovalent DNA/drug complexes is reported. ESI-MS/MS is used to detect specific mass shifts of the DNA ions that are associated with the oxidation of thymines. This KMnO4 oxidation/ESI-MS/MS approach is an alternative to conventional gel-based oxidation methods and affords excellent sensitivity while eliminating the reliance on radiolabeled DNA. Comparison of single-strand versus duplex DNA indicates that the duplexes exhibit a significant resistance to the reaction, thus confirming that the oxidation process is favored for unwound or single-strand regions of DNA. DNA complexes containing different drugs including echinomycin, actinomycin-D, ethidium bromide, Hoechst 33342, and cis-C1 were subjected to the oxidation reaction. Echinomycin, a ligand with a bisintercalative binding mode, was found to induce the greatest KMnO4 reactivity, while Hoechst 33342, a minor groove binder, caused no increase in the oxidation of DNA. The oxidation of echinomycin/DNA complexes containing duplexes with different sequences and lengths was also assessed. Duplexes with thymines closer to the terminal ends of the duplex demonstrated a greater increase in the degree of oxidation than those with thymines in the middle of the sequence. Collisional activated dissociation (CAD) and infrared multiphoton dissociation (IRMPD) experiments were used to determine the site of oxidation based on oligonucleotide fragmentation patterns.
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Affiliation(s)
- Carolyn L Mazzitelli
- Department of Chemistry and Biochemistry, 1 University Station A5300, University of Texas at Austin, Austin, Texas 78712, USA
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34
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Smith SI, Guziec LJ, Guziec FS, Hasinoff BB, Brodbelt JS. Evaluation of relative DNA binding affinities of anthrapyrazoles by electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:681-8. [PMID: 17405184 DOI: 10.1002/jms.1205] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Binding interactions of a new series of anthrapyrazoles (APs) with DNA were evaluated by electrospray ionization mass spectrometry (ESI-MS). Relative binding affinities were estimated from the ESI-MS data based on the fraction of bound DNA for DNA/anthrapyrazole mixtures, and they show a correlation to the shift in melting point of the DNA measured from a previous study. Minimal sequence specificity was observed for the series of anthrapyrazoles. Upon collisionally activated dissociation of the duplex/anthrapyrazole complexes, typically ejection of the ligand was the dominant pathway for most of the complexes. However, for complexes containing AP2 or mitoxantrone, strand separation with the ligand remaining on one of the single strands was observed, indicative of a different binding mode or stronger binding.
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Affiliation(s)
- Suncerae I Smith
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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Wilson JJ, Brodbelt JS. Infrared multiphoton dissociation of duplex DNA/drug complexes in a quadrupole ion trap. Anal Chem 2007; 79:2067-77. [PMID: 17249688 PMCID: PMC2518938 DOI: 10.1021/ac061946f] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Noncovalent duplex DNA/drug complexes formed between one of three 14-base pair non-self-complementary duplexes with variable GC content and one of eight different DNA-interactive drugs are characterized by infrared multiphoton dissociation (IRMPD), and the resulting spectra are compared to conventional collisionally activated dissociation (CAD) mass spectra in a quadrupole ion trap mass spectrometer. IRMPD yielded comparable information to previously reported CAD results in which strand separation pathways dominate for complexes containing the more AT-rich sequences and/or minor groove binding drugs, whereas drug ejection pathways are prominent for complexes containing intercalating drugs and/or duplexes with higher GC base content. The large photoabsorptive cross section of the phosphate backbone at 10.6 mum promotes highly efficient dissociation within short irradiation times (<2 ms at 50 W) or using lower laser powers and longer irradiation times (<15 W at 15 ms), activation times on par with or shorter than standard CAD experiments. This large photoabsorptivity leads to a controllable ion activation method which can be used to produce qualitatively similar spectra to CAD while minimizing uninformative base loss dissociation pathways or instead be tuned to yield a high degree of secondary fragmentation. Additionally, the low-mass cutoff associated with conventional CAD plays no role in IRMPD, resulting in richer MS/MS information in the low m/z region. IRMPD is also used for multiadduct dissociation in order to increase MS/MS sensitivity, and a two-stage IRMPD/IRMPD method is demonstrated as a means to give specific DNA sequence information that would be useful when screening drug binding by mixtures of duplexes.
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Affiliation(s)
- Jeffrey J Wilson
- Department of Chemistry and Biochemistry, 1 University Station A5300, University of Texas at Austin, Austin, Texas 78712, USA
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Hofstadler SA, Sannes-Lowery KA. Applications of ESI-MS in drug discovery: interrogation of noncovalent complexes. Nat Rev Drug Discov 2006; 5:585-95. [PMID: 16816839 DOI: 10.1038/nrd2083] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For many years, analytical mass spectrometry has had numerous supporting roles in the drug development process, including the assessment of compound purity; quantitation of absorption, distribution, metabolism and excretion; and compound-specific pharmacokinetic analyses. More recently, mass spectrometry has emerged as an effective technique for identifying lead compounds on the basis of the characterization of noncovalent ligand-macromolecular target interactions. This approach offers several attractive properties for screening applications in drug discovery compared with other strategies, including the small quantities of target and ligands required, and the capacity to study ligands or targets without having to label them. Here, we review the application of electrospray ionization mass spectrometry to the interrogation of noncovalent complexes, highlighting examples from drug discovery efforts aimed at a range of target classes.
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Affiliation(s)
- Steven A Hofstadler
- Ibis Therapeutics, A Division of ISIS Pharmaceuticals, 1891 Rutherford Road, Carlsbad, California 92008, USA.
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Ramos CIV, Barros CM, Fernandes AM, Santana-Marques MG, Correia AJF, Tomé JPC, Carrilho MDCT, Faustino MAF, Tomé AC, Neves MGPMS, Cavaleiro JAS. Interactions of cationic porphyrins with double-stranded oligodeoxynucleotides: a study by electrospray ionisation mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:1439-47. [PMID: 16261648 DOI: 10.1002/jms.936] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Electrospray ionisation mass spectrometry (ESI-MS), electrospray ionisation tandem mass spectrometry (ESI-MS/MS) and Ultraviolet-visible (UV-vis) spectroscopy were used to investigate the non-covalent interactions between small oligonucleotide duplexes with the GC motif and a group of cationic meso(N-methylpyridynium-4-yl)porphyrins (four free bases with one to four positive charges, and the zinc complex of the tetracationic free base). The results obtained point to outside binding of the porphyrins, with the binding strength increasing with the number of positive charges. Fragmentations involving losses from both chains were observed for the porphyrins with N-methylpyridinium-4-yl groups in opposite meso positions.
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Affiliation(s)
- Catarina I V Ramos
- Mass Spectrometry Laboratory, Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:973-84. [PMID: 16034836 DOI: 10.1002/jms.808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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