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MS methods to study macromolecule-ligand interaction: Applications in drug discovery. Methods 2018; 144:152-174. [PMID: 29890284 DOI: 10.1016/j.ymeth.2018.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 12/12/2022] Open
Abstract
The interaction of small compounds (i.e. ligands) with macromolecules or macromolecule assemblies (i.e. targets) is the mechanism of action of most of the drugs available today. Mass spectrometry is a popular technique for the interrogation of macromolecule-ligand interactions and therefore is also widely used in drug discovery and development. Thanks to its versatility, mass spectrometry is used for multiple purposes such as biomarker screening, identification of the mechanism of action, ligand structure optimization or toxicity assessment. The evolution and automation of the instruments now allows the development of high throughput methods with high sensitivity and a minimized false discovery rate. Herein, all these approaches are described with a focus on the methods for studying macromolecule-ligand interaction aimed at defining the structure-activity relationships of drug candidates, along with their mechanism of action, metabolism and toxicity.
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Widjaja F, Max JP, Jin Z, Nash JJ, Kenttämaa HI. Gas-phase Reactivity of meta-Benzyne Analogs Toward Small Oligonucleotides of Differing Lengths. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1392-1405. [PMID: 28456883 DOI: 10.1007/s13361-017-1655-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/05/2017] [Accepted: 03/06/2017] [Indexed: 06/07/2023]
Abstract
The gas-phase reactivity of two aromatic carbon-centered σ,σ-biradicals (meta-benzyne analogs) and a related monoradical towards small oligonucleotides of differing lengths was investigated in a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer coupled with laser-induced acoustic desorption (LIAD). The mono- and biradicals were positively charged to allow for manipulation in the mass spectrometer. The oligonucleotides were evaporated into the gas phase as intact neutral molecules by using LIAD. One of the biradicals was found to be unreactive. The reactive biradical reacts with dinucleoside phosphates and trinucleoside diphosphates mainly by addition to a nucleobase moiety followed by cleavage of the glycosidic bond, leading to a nucleobase radical (e.g., base-H) abstraction. In some instances, after the initial cleavage, the unquenched radical site of the biradical abstracts a hydrogen atom from the neutral fragment, which results in a net nucleobase abstraction. In sharp contrast, the related monoradical mainly undergoes facile hydrogen atom abstraction from the sugar moiety. As the size of the oligonucleotides increases, the rate of hydrogen atom abstraction from the sugar moiety by the monoradical was found to increase due to the presence of more hydrogen atom donor sites, and it is the only reaction observed for tetranucleoside triphosphates. Hence, the monoradical only attacks sugar moieties in these substrates. The biradical also shows significant attack at the sugar moiety for tetranucleoside triphosphates. This drastic change in reactivity indicates that the size of the oligonucleotides plays a key role in the outcome of these reactions. This finding is attributed to more compact conformations in the gas phase for the tetranucleoside triphosphates than for the smaller oligonucleotides, which result from stronger stabilizing interactions between the nucleobases. Graphical Abstract ᅟ.
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Affiliation(s)
- Fanny Widjaja
- Department of Chemistry, Purdue University, West Lafayette, IN, 47906, USA
- , 1 Makeway Ave #15-03, Singapore, 228598, Singapore
| | - Joann P Max
- Department of Chemistry, Purdue University, West Lafayette, IN, 47906, USA
| | - Zhicheng Jin
- Department of Chemistry, Purdue University, West Lafayette, IN, 47906, USA
- Northeast Ohio Medical University, 4209 OH-44, Rootstown, OH, 44272, USA
| | - John J Nash
- Department of Chemistry, Purdue University, West Lafayette, IN, 47906, USA
| | - Hilkka I Kenttämaa
- Department of Chemistry, Purdue University, West Lafayette, IN, 47906, USA.
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Williams PE, Jankiewicz BJ, Yang L, Kenttämaa HI. Properties and reactivity of gaseous distonic radical ions with aryl radical sites. Chem Rev 2013; 113:6949-85. [PMID: 23987564 PMCID: PMC3889672 DOI: 10.1021/cr400121w] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Peggy E. Williams
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906
| | | | - Linan Yang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906
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Silvestri C, Brodbelt JS. Tandem mass spectrometry for characterization of covalent adducts of DNA with anticancer therapeutics. MASS SPECTROMETRY REVIEWS 2013; 32:247-66. [PMID: 23150278 PMCID: PMC3578003 DOI: 10.1002/mas.21363] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 08/17/2012] [Accepted: 08/18/2012] [Indexed: 05/17/2023]
Abstract
The chemotherapeutic activities of many anticancer and antibacterial drugs arise from their interactions with nucleic acid substrates. Some of these ligands interact with DNA in a way that causes conformational changes or damage to the nucleic acid targets, ultimately altering recognition by key DNA-specific enzymes, interfering with DNA transcription or prohibiting replication, and terminating cell growth and proliferation. The design and synthesis of ligands that bind to nucleic acids remains a dynamic field in medicinal chemistry and pharmaceutical research. The quest for more selective and efficacious DNA-interactive anticancer chemotherapeutics has likewise catalyzed the need for sensitive analytical methods that can provide structural information about the nature of the resulting DNA adducts and provide insight into the mechanistic pathways of the DNA/drug interactions and the impact on the cellular processes in biological systems. This review focuses on the array of tandem mass spectrometric strategies developed and applied for characterization of covalent adducts formed between DNA and anticancer ligands.
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Affiliation(s)
- Catherine Silvestri
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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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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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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Chan W, Yue H, Wong RNS, Cai Z. Characterization of the DNA adducts induced by aristolochic acids in oligonucleotides by electrospray ionization tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:3735-3742. [PMID: 18973202 DOI: 10.1002/rcm.3791] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Metabolic activation of carcinogenic aristolochic acids (AA) produces reactive aristolactam-nitrenium ion intermediates. Electrophilic attack of the aristolactam-nitrenium ion via its C7 position to the exocyclic amino group in the purine bases leads to the formation of DNA adducts. DNA-binding assays have demonstrated that carcinogens show site- and sequence-specificity and the biological consequence is defined by the nature of binding as well as their position in the genome. In this study, electrospray ionization tandem mass spectrometry was applied for the identification and position mapping of DNA adducts in oligonucleotides (ODNs). The developed method was successfully applied for the analysis of unmodified and AA-modified ODNs (5'-TTTATT-3', 5'-TTTGTT-3' and 5'-TACATGTGT-3'). The observation of the modified bases (modified adenine and guanine) together with the complementary product ions ([a(n)-B*(n)](-), w(-)) from the cleavage of the 3' C--O bond adjacent to the modified base in MS/MS analyses readily enabled the identification of the AA-binding site in ODNs.
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Affiliation(s)
- Wan Chan
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, China
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Yang L, Nash JJ, Yurkovich MJ, Jin Z, Vinueza NR, Kenttämaa HI. Gas-phase reactivity of aromatic sigma,sigma-biradicals toward dinucleoside phosphates. Org Lett 2008; 10:1889-92. [PMID: 18429617 DOI: 10.1021/ol800312g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In order to improve the understanding of the interactions of aromatic sigma,sigma-biradicals with DNA, the reactivity of three isomeric sigma,sigma-biradicals toward four dinucleoside phosphates was studied in a mass spectrometer. The dinucleoside phosphates were evaporated into the mass spectrometer by using laser-induced acoustic desorption (LIAD). The results demonstrate that the structure of the sigma,sigma-biradical and the base sequence of the dinucleoside phosphate can have a major influence on these reactions.
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Affiliation(s)
- Linan Yang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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