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Rahman M, Marzullo B, Holman SW, Barrow M, Ray AD, O’Connor PB. Advancing PROTAC Characterization: Structural Insights through Adducts and Multimodal Tandem-MS Strategies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:285-299. [PMID: 38197777 PMCID: PMC10853971 DOI: 10.1021/jasms.3c00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/21/2023] [Accepted: 12/25/2023] [Indexed: 01/11/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) are specialized molecules that bind to a target protein and a ubiquitin ligase to facilitate protein degradation. Despite their significance, native PROTACs have not undergone tandem mass spectrometry (MS) analysis. To address this gap, we conducted a pioneering investigation on the fragmentation patterns of two PROTACs in development, dBET1 and VZ185. Employing diverse cations (sodium, lithium, and silver) and multiple tandem-MS techniques, we enhanced their structural characterization. Notably, lithium cations facilitated comprehensive positive-mode coverage for dBET1, while negative polarity mode offered richer insights. Employing de novo structure determination on 2DMS data from degradation studies yielded crucial insights. In the case of VZ185, various charge states were observed, with [M + 2H]2+ revealing fewer moieties than [M + H]+ due to charge-related factors. Augmenting structural details through silver adducts suggested both charge-directed and charge-remote fragmentation. This comprehensive investigation identifies frequently dissociated bonds across multiple fragmentation techniques, pinpointing optimal approaches for elucidating PROTAC structures. The findings contribute to advancing our understanding of PROTACs, pivotal for their continued development as promising therapeutic agents.
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Affiliation(s)
- Mohammed Rahman
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
- Department
of Physics, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Bryan Marzullo
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Stephen W. Holman
- Chemical
Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, SK10 4TF, U.K.
| | - Mark Barrow
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
| | - Andrew D. Ray
- New
Modalities and Parenteral Development, Pharmaceutical Technology &
Development, Operations, AstraZeneca, Macclesfield, SK10 4TF, U.K.
| | - Peter B. O’Connor
- Department
of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K.
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Borges R, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Quantum Chemistry Calculations for Metabolomics. Chem Rev 2021; 121:5633-5670. [PMID: 33979149 PMCID: PMC8161423 DOI: 10.1021/acs.chemrev.0c00901] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 02/07/2023]
Abstract
A primary goal of metabolomics studies is to fully characterize the small-molecule composition of complex biological and environmental samples. However, despite advances in analytical technologies over the past two decades, the majority of small molecules in complex samples are not readily identifiable due to the immense structural and chemical diversity present within the metabolome. Current gold-standard identification methods rely on reference libraries built using authentic chemical materials ("standards"), which are not available for most molecules. Computational quantum chemistry methods, which can be used to calculate chemical properties that are then measured by analytical platforms, offer an alternative route for building reference libraries, i.e., in silico libraries for "standards-free" identification. In this review, we cover the major roadblocks currently facing metabolomics and discuss applications where quantum chemistry calculations offer a solution. Several successful examples for nuclear magnetic resonance spectroscopy, ion mobility spectrometry, infrared spectroscopy, and mass spectrometry methods are reviewed. Finally, we consider current best practices, sources of error, and provide an outlook for quantum chemistry calculations in metabolomics studies. We expect this review will inspire researchers in the field of small-molecule identification to accelerate adoption of in silico methods for generation of reference libraries and to add quantum chemistry calculations as another tool at their disposal to characterize complex samples.
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Affiliation(s)
- Ricardo
M. Borges
- Walter
Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Sean M. Colby
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Susanta Das
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Arthur S. Edison
- Departments
of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate
Research Center and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Tobias Kind
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
| | - Jesi Lee
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Amy T. Merrill
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Kenneth M. Merz
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Thomas O. Metz
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Jamie R. Nunez
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Lee-Ping Wang
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Shunyang Wang
- West
Coast Metabolomics Center for Compound Identification, UC Davis Genome
Center, University of California, Davis, California 95616, United States
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Ryan S. Renslow
- Biological
Science Division, Pacific Northwest National
Laboratory, Richland, Washington 99352, United States
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Yin ZH, Sun CH, Fang HZ. Fragmentation characteristics of hydroxycinnamic acids in ESI-MS n by density functional theory. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:427-433. [PMID: 28482376 DOI: 10.1002/jms.3945] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 04/24/2017] [Accepted: 05/04/2017] [Indexed: 06/07/2023]
Abstract
This work aims to analyze the electrospray ionization multistage mass spectrometry (ESI-MSn ) fragmentation characteristics of hydroxycinnamic acids (HCAs) in negative ion mode. The geometric parameters, energies, natural bond orbitals and frontier orbitals of fragments were calculated by density functional theory (DFT) to investigate mass spectral fragmentation mechanisms. The results showed that proton transfer always occurred during fragmentation of HCAs; their quasi-molecular ions ([M - H]- ) existed in more than one form and were mainly with the lowest energy. The fragmentation characteristics included the followings: (1) according to the different substitution position of phenolic hydroxyl group, the ring contraction reaction by CO elimination from benzene was in an increasingly difficult order: m-phenolic hydroxyl > p-phenolic hydroxyl > o-phenolic hydroxyl; and (2) ortho effect always occurred in o-dihydroxycinnamic acids (o-diHCAs), i.e. one phenolic hydroxyl group offered H+ , which combined with the other one to lose H2 O. In addition, there was a nucleophilic reaction during ring contraction in diHCAs that oxygen atom attacked the carbon atom binding with the other phenolic hydroxyl to lose CO2 . The fragmentation characteristics and mechanism of HCAs could be used for analysis and identification of such compounds quickly and effectively, and as reference for structural analogues by ESI-MS. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Zhi-Hui Yin
- Pharmaceutical College, Jiamusi University, 148 University Street, Jiamusi, Heilongjiang, 154007, China
| | - Chang-Hai Sun
- Pharmaceutical College, Jiamusi University, 148 University Street, Jiamusi, Heilongjiang, 154007, China
| | - Hong-Zhuang Fang
- Pharmaceutical College, Jiamusi University, 148 University Street, Jiamusi, Heilongjiang, 154007, China
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Hong A, Lee HH, Heo CE, Cho Y, Kim S, Kang D, Kim HI. Distinct Fragmentation Pathways of Anticancer Drugs Induced by Charge-Carrying Cations in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:628-637. [PMID: 27981443 DOI: 10.1007/s13361-016-1559-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/24/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
With the growth of the pharmaceutical industry, structural elucidation of drugs and derivatives using tandem mass spectrometry (MS2) has become essential for drug development and pharmacokinetics studies because of its high sensitivity and low sample requirement. Thus, research seeking to understand fundamental relationships between fragmentation patterns and precursor ion structures in the gas phase has gained attention. In this study, we investigate the fragmentation of the widely used anticancer drugs, doxorubicin (DOX), vinblastine (VBL), and vinorelbine (VRL), complexed by a singly charged proton or alkali metal ion (Li+, Na+, K+) in the gas phase. The drug-cation complexes exhibit distinct fragmentation patterns in tandem mass spectra as a function of cation size. The trends in fragmentation patterns are explicable in terms of structures derived from ion mobility mass spectrometry (IM-MS) and theoretical calculations. Graphical Abstract ᅟ.
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Affiliation(s)
- Areum Hong
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul, 02841, Republic of Korea
- Division of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon, 34113, Republic of Korea
| | - Hong Hee Lee
- Division of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon, 34113, Republic of Korea
| | - Chae Eun Heo
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul, 02841, Republic of Korea
| | - Yunju Cho
- Green-Nano Materials Research Center, Daegu, 41566, Republic of Korea
| | - Sunghwan Kim
- Green-Nano Materials Research Center, Daegu, 41566, Republic of Korea
- Department of Chemistry, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dukjin Kang
- Division of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon, 34113, Republic of Korea
| | - Hugh I Kim
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, Seoul, 02841, Republic of Korea.
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Wright P, Alex A, Pullen F. Predicting collision-induced dissociation mass spectra: understanding the role of the mobile proton in small molecule fragmentation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1163-1175. [PMID: 27525343 DOI: 10.1002/rcm.7521] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
RATIONALE Intramolecular proton migration has been reported to be required for fragmentation by collision-induced dissociation (CID). If the collision energy is required to provide energy for proton movement to a ‘dissociative’ site, it may be possible to predict the optimal collision energy for fragmentation using quantum computational chemistry software. A greater understanding of the mechanism(s) of proton migration is necessary. METHODS The product ion spectra of seven compounds were obtained at collision energies stepped in the range from 5 to 50 eV, with precursor ions being generated in positive ion mode by both atmospheric pressure chemical ionization (APCI) and electrospray ionisation (ESI) (using an ESCi ionisation source with or without corona discharge, respectively). The products ions observed at each collision energy were assessed in terms of structure to ascertain if they were formed as a result of protonation at the initial ionisation site or if the proton had migrated to a dissociative site. RESULTS Proton migration was shown to be independent of collision energy, stability of the protonated molecule and the distance that the proton moved. Therefore, proton migration is not a barrier to fragmentation as the proton appears to be fully mobile at 5 eV. As proton migration is independent of collision energy for these compounds, whereas fragmentation is energy dependent, protonation at the dissociative site alone is not sufficient to cause bond cleavage. CONCLUSIONS The role of collision energy in bond cleavage may be to increase the vibrational energy of the bond and/or increase the rate of bond cleavage such that it occurs within the residence time of the ion within the collision cell rather than to supply the energy for proton migration. Therefore, quantum chemistry alone cannot predict the collision energies appropriate for fragmentation on the basis of modelling proton movements.
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Wright PA, Alex A, Pullen FS. Can computational chemistry be used to predict CID fragmentation of anions? RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:2309-2315. [PMID: 26522325 DOI: 10.1002/rcm.7394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/10/2015] [Accepted: 09/10/2015] [Indexed: 06/05/2023]
Affiliation(s)
| | - Alexander Alex
- Evenor Consulting Ltd, The New Barn, Mill Lane, Eastry, UK
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Knolhoff AM, Croley TR. Non-targeted screening approaches for contaminants and adulterants in food using liquid chromatography hyphenated to high resolution mass spectrometry. J Chromatogr A 2015; 1428:86-96. [PMID: 26372444 DOI: 10.1016/j.chroma.2015.08.059] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/14/2015] [Accepted: 08/27/2015] [Indexed: 12/22/2022]
Abstract
The majority of analytical methods for food safety monitor the presence of a specific compound or defined set of compounds. Non-targeted screening methods are complementary to these approaches by detecting and identifying unexpected compounds present in food matrices that may be harmful to public health. However, the development and implementation of generalized non-targeted screening workflows are particularly challenging, especially for food matrices due to inherent sample complexity and diversity and a large analyte concentration range. One approach that can be implemented is liquid chromatography coupled to high-resolution mass spectrometry, which serves to reduce this complexity and is capable of generating molecular formulae for compounds of interest. Current capabilities, strategies, and challenges will be reviewed for sample preparation, mass spectrometry, chromatography, and data processing workflows. Considerations to increase the accuracy and speed of identifying unknown molecular species will also be addressed, including suggestions for achieving sufficient data quality for non-targeted screening applications.
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Affiliation(s)
- Ann M Knolhoff
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5100 Paint Branch Parkway, College Park, MD 20740, United States.
| | - Timothy R Croley
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5100 Paint Branch Parkway, College Park, MD 20740, United States
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Kurka O, Roithová J, Bednář P. Examination of small molecule losses in 5-methylpyranopelargonidin MS/MS CID spectra by DFT calculations. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:1314-1321. [PMID: 25476950 DOI: 10.1002/jms.3466] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 08/12/2014] [Accepted: 08/13/2014] [Indexed: 06/04/2023]
Abstract
Pyranoanthocyanins are formed during food treatment and maturation (e.g. wine, juices), and they can be considered a natural alternative to artificial food colorants. Tandem mass spectrometry (MS/MS) is perhaps the most important technique in analysis of anthocyanin dyes. Knowledge of fragmentation pattern is a key aspect of their successful structural characterization. Polyphenolic compounds are known to lose small molecules during collision-induced dissociation (CID) in MS/MS experiments. However, the specific positions where such losses occur preferentially are unknown. The aim of this communication is to investigate the energetically most preferred places for H2 O and CO losses during the fragmentation of 5-methylpyranopelargonidin molecule by the means of computational chemistry (employing density functional theory) combined with CID MS/MS experiments and infrared multiphoton dissociation spectroscopy. Mechanisms responsible for the fragmentations were investigated, and optimal geometries and transition states were obtained. Cleavage of water as well as carbon monoxide occurs preferentially from the C-ring of flavonoid skeleton. In the most stable structure of 5-methylpyranopelargonidin, B-ring was found to be tilted with respect to the rest of the molecule. Planarization effort of the parent molecule contributes both to its decarbonylation and dehydration.
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Affiliation(s)
- Ondřej Kurka
- Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 771 46, Olomouc, Czech Republic
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Wright P, Alex A, Pullen F. Predicting collision-induced dissociation spectra: semi-empirical calculations as a rapid and effective tool in software-aided mass spectral interpretation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:1127-1143. [PMID: 24711276 DOI: 10.1002/rcm.6870] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 02/07/2014] [Accepted: 02/13/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE Fifteen molecules were modelled using quantum chemistry, prior to interpreting their collision-induced dissociation (CID) product ion spectra, in a 'blind trial' to establish if calculated protonation-induced bond elongation could be used to predict which bonds cleaved during CID. Bond elongation has the potential to be used as a descriptor predicting bond cleavage. METHODS The 15 molecules were modelled with respect to protonation-induced bond length changes using Density Functional Theory (DFT). Significant bond elongations were highlighted to flag potential bond cleavages. CID product ion spectra, obtained using positive ion electrospray ionisation (Waters Synapt G1), were interpreted to establish if observed bond cleavages correlated with calculated bond elongations. Calculations were also undertaken using AM1 (Austin Model 1) to see if this rapid approach gave similar results to the computationally demanding DFT. RESULTS The AM1-calculated bond elongations were found to be similar to those generated by DFT. All the polarised bonds observed to cleave (n = 82) had been calculated to elongate significantly. Protonation, possibly via proton migration, on the most electronegative atom in the bond appeared to initiate cleavage, leading to a 100% success rate in predicting the bonds that broke as a result of protonation on a heteroatom. Cleavage of carbon-carbon bonds was not predicted. CONCLUSIONS Cleavage of the polarised bonds appears to result from protonation on the more electronegative atom of the bond, inducing conformational changes leading to bond weakening. AM1-calculated bond length changes act as a descriptor for predicting bond cleavage. However, the impetus for cleavage of the unpolarised bonds may be product ion stability rather than bond weakening.
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Affiliation(s)
- Patricia Wright
- School of Science, University of Greenwich, Medway Campus, Chatham, ME4 4TB, UK
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