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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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Zemaitis KJ, Ye H, Nguyen HT, Wood TD. Direct Infusion Metabolomics of the Photosystem and Chlorophyll Related Metabolites within a Drought Tolerant Plant Introduction of Glycine max. Metabolites 2021; 11:metabo11120843. [PMID: 34940601 PMCID: PMC8706224 DOI: 10.3390/metabo11120843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Drought is the most prolific form of abiotic stress that legumes and cereal plants alike can endure, and the planting of an improper cultivar at the beginning of a season can cause unexpected losses up to fifty percent under water deficient conditions. Herein, a plant introduction (PI) of an exotic cultivar of soybean (Glycine max), PI 567731, which demonstrates a slow wilting (SW) canopy phenotype in maturity group III, was profiled under drought conditions in field trials in Missouri against a drought susceptible check cultivar, Pana. Metabolomic profiling was carried out on samples of leaves from each of these cultivars at V5 and R2 growth stages both while irrigated and while under drought stress for three weeks. PI 567731 was observed to have differential phytochemical content, and enhanced levels of chlorophyll (Chl) a/b and pheophytin (Pheo) were profiled by direct infusion electrospray Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Indicating drought induced changes of the photosystem and photosynthetic capabilities alongside water preservation strategies are important within the SW phenotype drought response. Subsequent multivariate analysis was able to form predictive models, encompassing the variance of growth and drought stress of the cultivar. Moreover, the existence of unique Chl-related metabolites (CRM) (m/z > 900) were confirmed through tandem mass spectrometry. The resultant coordination of fatty acids to the core of the porphyrin ring was observed and played an unknown role in the proliferation of the photosynthesis. However, the relative ratio of the most abundant CRM is undisturbed by drought stress in PI 567731, in contrast to the drought susceptible cultivar. These results provide key insights into drought related metabolic mechanisms.
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Affiliation(s)
- Kevin J. Zemaitis
- Department of Chemistry, Natural Sciences Complex, University at Buffalo, State University of New York, Buffalo, NY 14260, USA;
| | - Heng Ye
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA; (H.Y.); (H.T.N.)
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA; (H.Y.); (H.T.N.)
| | - Troy D. Wood
- Department of Chemistry, Natural Sciences Complex, University at Buffalo, State University of New York, Buffalo, NY 14260, USA;
- Correspondence:
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Marzullo BP, Morgan TE, Theisen A, Haris A, Wootton CA, Perry SJ, Saeed M, Barrow MP, O'Connor PB. Combining Ultraviolet Photodissociation and Two-Dimensional Mass Spectrometry: A Contemporary Approach for Characterizing Singly Charged Agrochemicals. Anal Chem 2021; 93:9462-9470. [PMID: 34192872 DOI: 10.1021/acs.analchem.1c01185] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet photodissociation (UVPD) has been shown to produce extensive structurally informative data for a variety of chemically diverse compounds. Herein, we demonstrate the performance of the 193 nm UVPD fragmentation technique on structural/moiety characterization of 14 singly charged agrochemicals. Two-dimensional mass spectrometry (2DMS) using infrared multiphoton dissociation (IRMPD) and electron-induced dissociation (EID) have previously been applied to a select range of singly charged pesticides. The ≥80% moiety coverage achieved for the majority of the species by the UVPD and 2D-UVPD methods was on par with and, in some cases, superior to the data obtained by other fragmentation techniques in previous studies, demonstrating that UVPD is viable for these types of species. A three-dimensional (3D) peak picking method was implemented to extract the data from the 2DMS spectrum, overcoming the limitations of the line extraction method used in previous studies, successfully separating precursor specific fragments with milli-Dalton accuracy. Whole spectrum internal calibration combined with 3D peak picking obtained sub-part-per-million (ppm) to part-per-billion (ppb) mass accuracies across the entire 2DMS spectrum.
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Affiliation(s)
- Bryan P Marzullo
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Tomos E Morgan
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alina Theisen
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Anisha Haris
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - Simon J Perry
- Product Metabolism & Analytical Sciences, Jealott's Hill International Research Centre, Syngenta, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Mansoor Saeed
- Product Metabolism & Analytical Sciences, Jealott's Hill International Research Centre, Syngenta, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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Marzullo BP, Morgan TE, Wootton CA, Perry SJ, Saeed M, Barrow MP, O'Connor PB. Advantages of Two-Dimensional Electron-Induced Dissociation and Infrared Multiphoton Dissociation Mass Spectrometry for the Analysis of Agrochemicals. Anal Chem 2020; 92:11687-11695. [PMID: 32700900 DOI: 10.1021/acs.analchem.0c01585] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Analysis of agrochemicals in an environmental matrix is challenging because these samples contain multiple agrochemicals, their metabolites, degradation products, and endogenous compounds. The analysis of such complex samples is achieved using chromatographic separation techniques coupled to mass spectrometry. Herein, we demonstrate a two-dimensional mass spectrometry (2DMS) technique on a 12 T Fourier transform ion cyclotron resonance mass spectrometer that can analyze a mixture of agrochemicals without using chromatography or quadrupole isolation in a single experiment. The resulting 2DMS contour plot contains abundant tandem MS information for each component in the sample and correlates product ions to their corresponding precursor ions. Two different fragmentation methods are employed, infrared multiphoton dissociation (IRMPD) and electron-induced dissociation (EID), with 2DMS to analyze the mixture of singly charged agrochemicals. The product ions of one of the agrochemicals, pirimiphos-methyl, present in the sample was used to internally calibrate the entire 2DMS spectrum, achieving sub part per million (ppm) to part per billion (ppb) mass accuracies for all species analyzed. The work described in this study will show the advantages of the 2DMS approach, by grouping species with common fragments/core structure and mutual functional groups, using precursor lines and neutral loss lines. In addition, the rich spectral information obtained from IRMPD and EID 2DMS contour plots can accurately identify and characterize agrochemicals.
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Affiliation(s)
- Bryan P Marzullo
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Tomos E Morgan
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | | | - Simon J Perry
- Product Metabolism & Analytical Sciences, Jealott's Hill International Research Centre, Syngenta, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Mansoor Saeed
- Product Metabolism & Analytical Sciences, Jealott's Hill International Research Centre, Syngenta, Bracknell, Berkshire RG42 6EY, United Kingdom
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, United Kingdom
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Harp BP, Scholl PF, Gray PJ, Delmonte P. Quantitation of copper chlorophylls in green table olives by ultra-high-performance liquid chromatography with inductively coupled plasma isotope dilution mass spectrometry. J Chromatogr A 2020; 1620:461008. [PMID: 32252985 DOI: 10.1016/j.chroma.2020.461008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 02/25/2020] [Accepted: 03/02/2020] [Indexed: 10/24/2022]
Abstract
Table olives, a widely consumed delicacy, are often selected by consumers based on the shade of their green color. The appealing coloration of fresh olives fades to brown or pale yellow during the industrial processing necessary for commercialization and storage, as a result of the degradation of chlorophyll a and b to their corresponding pheophytins and other chlorophyll degradation products (CDP). The re-greening of table olives may be achieved by complexation of CDP with Cu2+, to form stable bright green copper CDP (Cu-CDP) complexes. To study this phenomenon, we developed a novel method to separately extract lipophilic and hydrophilic Cu-CDP and quantify Cu-CDP by UHPLC combined with inductively coupled plasma isotope dilution mass spectrometry (UHPLC-ICP-ID-MS) using post-column isotopic dilution with 65Cu. This technique does not require species-specific calibration standards and was applied to survey the Cu-CDP composition of the various types of table olives sold in the US market. The CDP and Cu-CDP extracted from table olives were identified by high resolution full-scan mass spectrometry. Total elemental Cu in table olives was measured by microwave digestion followed by ICP-MS detection and correlated with the content of Cu-CDP. Pale yellow olives contained <1 mg/kg lipophilic Cu-CDP and <3.5 mg/kg total elemental Cu. Bright green table olives contained 4-22 mg/kg lipophilic Cu-CDP and 14.4-161 mg/kg total elemental Cu in contrast to <6 mg/kg reported for natural abundance, indicating the formation of Cu-CDP was achieved by addition of copper salts. A dark green sample with 2.5 mg/kg of total copper and 0.267 mg/kg lipophilic Cu-CDP may have been processed by addition of sodium copper chlorophyllin (SCC); the higher content of Cu isochlorin e4 compared to Cu 152-Me-chlorin e6 supports this conclusion.
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Affiliation(s)
- Bhakti Petigara Harp
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5001 Campus Drive, College Park, MD, 20740, USA
| | - Peter F Scholl
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5001 Campus Drive, College Park, MD, 20740, USA
| | - Patrick J Gray
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5001 Campus Drive, College Park, MD, 20740, USA
| | - Pierluigi Delmonte
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5001 Campus Drive, College Park, MD, 20740, USA.
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High resolution mass spectral data from the analysis of copper chlorophylls and copper chlorophyll degradation products in bright green table olives. Data Brief 2020; 30:105548. [PMID: 32382596 PMCID: PMC7200247 DOI: 10.1016/j.dib.2020.105548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 11/23/2022] Open
Abstract
This publication reports high resolution mass spectral data for copper chlorophyll and copper chlorophyll degradation products extracted from bright green table olives. These data support analyte identifications made in “Quantitation of copper chlorophylls in green table olives by ultra-high-performance liquid chromatography with inductively coupled plasma isotope dilution mass spectrometry” in the Journal of Chromatography A (Petigara Harp et al., 2020 [1]). Table olive pigments, divided into lipophilic and hydrophilic fractions by liquid-liquid repartition, were separated by ultra-high-performance liquid chromatography and detected by visible wavelength absorbance and high resolution mass spectrometry, using an Orbitrap HF with positive electrospray ionization. Full-scan mass spectra were acquired to assign pigment chemical formulae. Fragment-rich higher-energy collisional dissociation tandem mass spectra were acquired to facilitate structural assignments. Extracted ion chromatograms, full-scan, and tandem mass spectra obtained from representative lipophilic and hydrophilic green table olive extracts are presented in Figures 1-6. Annotated mass spectra comparing experimental and calculated isotope distributions, .raw mass spectral data files, and experimental details linking .raw data files to annotated spectra are provided as Supplementary Material. Spectra extracted from these native data files can be added to mass spectral libraries for use in other studies. Access to native data files uniquely enables rigorous data examination (e.g., molecular ion isotopic distribution, effective mass resolution, presence of overlapping ion series) and use in ways that are not possible when spectra are otherwise reported in simple tables listing mono-isotopic peaks and mass errors. Mass spectra reported here can be used to design multiple-reaction monitoring methods to detect these bright green pigments in agricultural food commodities and finished products.
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Marzullo BP, Morgan TE, Wootton CA, Li M, Perry SJ, Saeed M, Barrow MP, O'Connor PB. Comparison of Fragmentation Techniques for the Structural Characterization of Singly Charged Agrochemicals. Anal Chem 2020; 92:3143-3151. [PMID: 31909982 DOI: 10.1021/acs.analchem.9b04820] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Investigating the structure of active ingredients, such as agrochemicals and their associated metabolites, is a crucial requisite in the discovery and development of these molecules. In this study, structural characterization by electron-induced dissociation (EID) was compared to collisionally activated dissociation (CAD) on a series of agrochemicals. EID fragmentation produced a greater variety of fragment ions and complementary ion pairs leading to more complete functional group characterization compared to CAD. The results obtained displayed many more cross-ring fragmentation of the pyrimidine ring compared to the pyridine ring. Compounds that consisted of one aromatic heterocyclic moiety (azoxystrobin, fluazifop acid, fluazifop-p-butyl, and pirimiphos-methyl) displayed cross-ring fragmentation while compounds with only aromatic hydrocarbon rings (fenpropidin and S-metolachlor) displayed no cross-ring fragmentation. The advantages of high-resolution accurate mass spectrometry (HRAM MS) are shown with the majority of assignments at ppb range error values and the ability to differentiate ions with the same nominal mass but different elemental composition. This highlights the potential for HRAM MS and EID to be used as a tool for structural characterization of small molecules with a wide variety of functional groups and structural motifs.
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Affiliation(s)
- Bryan P Marzullo
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , United Kingdom
| | - Tomos E Morgan
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , United Kingdom
| | | | - Meng Li
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , United Kingdom
| | - Simon J Perry
- Syngenta, Jealott's Hill International Research Centre , Product Metabolism & Analytical Sciences , RG42 6EY Berkshire , United Kingdom
| | - Mansoor Saeed
- Syngenta, Jealott's Hill International Research Centre , Product Metabolism & Analytical Sciences , RG42 6EY Berkshire , United Kingdom
| | - Mark P Barrow
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , United Kingdom
| | - Peter B O'Connor
- Department of Chemistry , University of Warwick , Coventry CV4 7AL , United Kingdom
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Chen P, Zhang D, Li M, Wu Q, Lam YPY, Guo Y, Chen C, Bai N, Malhotra S, Li W, O'Connor PB, Fu H. Discovery of novel, potent, isosteviol-based antithrombotic agents. Eur J Med Chem 2019; 183:111722. [PMID: 31563807 DOI: 10.1016/j.ejmech.2019.111722] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/24/2022]
Abstract
Thrombosis is a pathological coagulation process and can lead to many serious thrombotic diseases. Here, we report a novel potent antithrombotic compound (6k) based on isosteviol with anticoagulant and antiplatelet activities. 6k selectively inhibited FXa (Ki = 0.015 μM) against a panel of serine proteases and showed excellent anticoagulant activity (significant prolongation of ex vivo PT and aPTT over the vehicle, p < 0.01). 6k also significantly inhibited ADP-induced platelet aggregation in rats relative to the vehicle (p < 0.01). Furthermore, 6k exhibited potent ex vivo and in vivo antithrombotic activity in rats relative to the vehicle (p < 0.01 and p < 0.0001, respectively). Novel structure 6k, with potent antithrombotic activity, is expected to lead a promising approach for the development of antithrombotic agents.
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Affiliation(s)
- Peng Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No.38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Dianwen Zhang
- Academy of Chinese Medical Sciences of Jilin Province, No.155 Chuangju Road, Changchun, 130012, China
| | - Meng Li
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Qiong Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No.38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Yuko P Y Lam
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Yan Guo
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No.38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Chen Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No.38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, United States; Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS, 66045, United States
| | - Shipra Malhotra
- Program in Molecular Therapeutics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, United States; Center for Computational Biology, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, United States
| | - Wei Li
- Academy of Chinese Medical Sciences of Jilin Province, No.155 Chuangju Road, Changchun, 130012, China
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Hongzheng Fu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No.38 Xueyuan Road, Haidian District, Beijing, 100191, China.
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