1
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Yu Y, Sternicki LM, Hilko DH, Jarrott RJ, Di Trapani G, Tonissen KF, Poulsen SA. Investigating Active Site Binding of Ligands to High and Low Activity Carbonic Anhydrase Enzymes Using Native Mass Spectrometry. J Med Chem 2024; 67:15862-15872. [PMID: 39161321 DOI: 10.1021/acs.jmedchem.4c01512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Carbonic anhydrases (CAs) are a family of enzymes that play an important pH regulatory role in health and disease. While different CA isozymes have a high degree of structural similarity, they have variable enzymatic activity, with CA III being the least active and having less than 1% of the activity of CA II, the most active. Furthermore, ligand binding studies for CA III are limited, and a resulting lack of chemical probes impedes understanding of this CA isozyme in comparison to other CA family members where studies are abundant. Therefore, we employed native mass spectrometry (nMS), also known as intact mass spectrometry, to assess ligand binding to CA II and CA III and discovered two novel compounds that for the first time display strong binding to CA III. We present a new data visualization and quantification tool developed to display native mass spectra as an intuitive stacked heat map representation for rapidly interpreting the results of ligand-protein binding from nMS screening.
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Affiliation(s)
- Yezhou Yu
- Institute for Biomedicine and Glycomics, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
- School of Environment and Science, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Louise M Sternicki
- Institute for Biomedicine and Glycomics, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - David H Hilko
- Institute for Biomedicine and Glycomics, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Russell J Jarrott
- School of Environment and Science, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Giovanna Di Trapani
- School of Environment and Science, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Kathryn F Tonissen
- Institute for Biomedicine and Glycomics, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
- School of Environment and Science, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Sally-Ann Poulsen
- Institute for Biomedicine and Glycomics, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
- School of Environment and Science, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
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2
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Sternicki LM, Poulsen SA. Fragment-based drug discovery campaigns guided by native mass spectrometry. RSC Med Chem 2024; 15:2270-2285. [PMID: 39026646 PMCID: PMC11253872 DOI: 10.1039/d4md00273c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/19/2024] [Indexed: 07/20/2024] Open
Abstract
Native mass spectrometry (nMS) is well established as a biophysical technique for characterising biomolecules and their interactions with endogenous or investigational small molecule ligands. The high sensitivity mass measurements make nMS particularly well suited for applications in fragment-based drug discovery (FBDD) screening campaigns where the detection of weakly binding ligands to a target biomolecule is crucial. We first reviewed the contributions of nMS to guiding FBDD hit identification in 2013, providing a comprehensive perspective on the early adoption of nMS for fragment screening. Here we update this initial progress with a focus on contributions of nMS that have guided FBDD for the period 2014 until end of 2023. We highlight the development of nMS adoption in FBDD in the context of other biophysical fragment screening techniques. We also discuss the roadmap for increased adoption of nMS for fragment screening beyond soluble proteins, including for guiding the discovery of fragments supporting advances in PROTAC discovery, RNA-binding small molecules and covalent therapeutic drug discovery.
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Affiliation(s)
- Louise M Sternicki
- Griffith Institute for Drug Discovery, Griffith University Nathan Brisbane Queensland 4111 Australia
- ARC Centre for Fragment-Based Design Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University Nathan Brisbane Queensland 4111 Australia
- ARC Centre for Fragment-Based Design Australia
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3
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Phan M, Chandrashekaran IR, Akhtar N, Konstantinidou E, Devine SM, Doak BC, Nebl T, Creek DJ, Scanlon MJ, Norton RS. Multiplexed Native Mass Spectrometry Determination of Ligand Selectivity for Fatty Acid-Binding Proteins. ACS Med Chem Lett 2024; 15:1071-1079. [PMID: 39015264 PMCID: PMC11247632 DOI: 10.1021/acsmedchemlett.4c00154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 07/18/2024] Open
Abstract
Although multiple approaches for characterizing protein-ligand interactions are available in target-based drug discovery, their throughput for determining selectivity is quite limited. Herein, we describe the application of native mass spectrometry for rapid, multiplexed screening of the selectivity of eight small-molecule ligands for five fatty acid-binding protein isoforms. Using high-resolution mass spectrometry, we were able to identify and quantify up to 20 different protein species in a single spectrum. We show that selectivity profiles generated by native mass spectrometry are in good agreement with those of traditional solution-phase techniques such as isothermal titration calorimetry and fluorescence polarization. Furthermore, we propose strategies for effective investigation of selectivity by native mass spectrometry, thus highlighting the potential of this technique to be used as an orthogonal method to traditional biophysical approaches for rapid, multiplexed screening of protein-ligand complexes.
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Affiliation(s)
- Michelle
Q. Phan
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Indu R. Chandrashekaran
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC
Centre for Fragment-Based Design, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Naureen Akhtar
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC
Centre for Fragment-Based Design, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Evgenia Konstantinidou
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC
Centre for Fragment-Based Design, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Shane M. Devine
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Bradley C. Doak
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC
Centre for Fragment-Based Design, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Thomas Nebl
- Biologics
Research and Development Group, Biomedical Manufacturing Program, CSIRO, Clayton, Victoria 3168, Australia
| | - Darren J. Creek
- Drug
Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Martin J. Scanlon
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC
Centre for Fragment-Based Design, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Raymond S. Norton
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- ARC
Centre for Fragment-Based Design, Monash Institute of Pharmaceutical
Sciences, Monash University, Parkville, Victoria 3052, Australia
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4
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Sharma A, Kumar N, Gulati HK, Rana R, Jyoti, Khanna A, Muskan, Singh JV, Bedi PMS. Antidiabetic potential of thiazolidinedione derivatives with efficient design, molecular docking, structural activity relationship, and biological activity: an update review (2021-2023). Mol Divers 2024:10.1007/s11030-023-10793-6. [PMID: 38253844 DOI: 10.1007/s11030-023-10793-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/07/2023] [Indexed: 01/24/2024]
Abstract
Thiazolidinedione has been used successfully by medicinal chemists all over the world in the development of potent antidiabetic derivatives. The few compounds with excellent antidiabetic potency that we have identified in this review could be used as a lead for further research into additional antidiabetic mechanisms. The information provided in this review regarding the design, biological activity, structure-activity relationships, and docking studies may be useful for scientists who wish to further explore this scaffold in order to fully utilize its biological potential and develop antidiabetic agents that would overcome the limitations of currently available medications for the treatment of diabetes. This review outlines the antidiabetic potential of Thiazolidinedione-based derivatives that have been published in the year 2021- till date.
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Affiliation(s)
- Anchal Sharma
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, 143005, India.
| | - Nitish Kumar
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Harmandeep Kaur Gulati
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Rupali Rana
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Jyoti
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Aanchal Khanna
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Muskan
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Jatinder Vir Singh
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
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5
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Sternicki LM, Poulsen SA. Native Mass Spectrometry: Insights and Opportunities for Targeted Protein Degradation. Anal Chem 2023; 95:18655-18666. [PMID: 38090751 DOI: 10.1021/acs.analchem.3c03853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Native mass spectrometry (nMS) is one of the most powerful biophysical methods for the direct observation of noncovalent protein interactions with both small molecules and other proteins. With the advent of targeted protein degradation (TPD), nMS is now emerging as a compelling approach to characterize the multiple fundamental interactions that underpin the TPD mechanism. Specifically, nMS enables the simultaneous observation of the multiple binary and ternary complexes [i.e., all combinations of E3 ligase, target protein of interest, and small molecule proximity-inducing reagents (such as PROteolysis TArgeting Chimeras (PROTACs) and molecular glues)], formed as part of the TPD equilibrium; this is not possible with any other biophysical method. In this paper we overview the proof-of-concept applications of nMS within the field of TPD and demonstrate how it is providing researchers with critical insight into the systems under study. We also provide an outlook on the scope and future opportunities offered by nMS as a core and agnostic biophysical tool for advancing research developments in TPD.
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Affiliation(s)
- Louise M Sternicki
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
- School of Environment and Science, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
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6
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Frühauf A, Behringer M, Meyer-Almes FJ. Significance of Five-Membered Heterocycles in Human Histone Deacetylase Inhibitors. Molecules 2023; 28:5686. [PMID: 37570656 PMCID: PMC10419652 DOI: 10.3390/molecules28155686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/15/2023] [Accepted: 07/15/2023] [Indexed: 08/13/2023] Open
Abstract
Five-membered heteroaromatic rings, in particular, have gained prominence in medicinal chemistry as they offer enhanced metabolic stability, solubility and bioavailability, crucial factors in developing effective drugs. The unique physicochemical properties and biological effects of five-membered heterocycles have positioned them as key structural motifs in numerous clinically effective drugs. Hence, the exploration of five-ring heterocycles remains an important research area in medicinal chemistry, with the aim of discovering new therapeutic agents for various diseases. This review addresses the incorporation of heteroatoms such as nitrogen, oxygen and sulfur into the aromatic ring of these heterocyclic compounds, enhancing their polarity and facilitating both aromatic stacking interactions and the formation of hydrogen bonds. Histone deacetylases are present in numerous multiprotein complexes within the epigenetic machinery and play a central role in various cellular processes. They have emerged as important targets for cancer, neurodegenerative diseases and other therapeutic indications. In histone deacetylase inhibitors (HDACi's), five-ring heterocycles perform various functions as a zinc-binding group, a linker or head group, contributing to binding activity and selective recognition. This review focuses on providing an up-to-date overview of the different five-membered heterocycles utilized in HDACi motifs, highlighting their biological properties. It summarizes relevant publications from the past decade, offering insights into the recent advancements in this field of research.
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Affiliation(s)
- Anton Frühauf
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences, Haardtring 100, 64295 Darmstadt, Germany
| | - Martin Behringer
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences, Haardtring 100, 64295 Darmstadt, Germany
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Sciences, Haardtring 100, 64295 Darmstadt, Germany
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7
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Metwally NH, El-Desoky EA. Novel Thiopyrano[2,3- d]thiazole-pyrazole Hybrids as Potential Nonsulfonamide Human Carbonic Anhydrase IX and XII Inhibitors: Design, Synthesis, and Biochemical Studies. ACS OMEGA 2023; 8:5571-5592. [PMID: 36816682 PMCID: PMC9933482 DOI: 10.1021/acsomega.2c06954] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
In recent years, molecular hybridization strategies have developed into a potent strategy for drug discovery. A series of novel thiopyrano[2,3-d]thiazoles linked to the pyrazole moiety was designed and developed as anticancer agents by a molecular hybridization. Target compounds were synthesized and characterized by spectroscopic tools as well as X-ray crystallography analysis as in the case of thiopyrano[2,3-d]thiazole derivative 5a. The MTT assay was used to demonstrate the in vitro efficacy of compounds 5a-g and 7a-j on MCF-7 and HePG-2. The results showed that some cycloadducts such as bromophenyl-4-thioxo-2-thiazolidinone 3e, 4-methylphenyl derivative of thiopyrano[2,3-d]thiazole 5d, and 6-substituted-thiopyrano[2,3-d]thiazoles 7e-j displayed good to excellent IC50 in the range of 10.08 ± 1.5 to 25.95 ± 2.8 μg/mL against the MCF-7 cell line and from 7.83 ±2.1 to 13.37 ± 1.2 μg/mL against the HePG-2 cell line. To explore the enzymatic tests for isozymes hCAIX and hCAXII, the most promising eight compounds 3e, 5d, and 7e-j with IC50 ranging from 7.83 ± 2.1 to 25.95 ± 2.8 μM were chosen. Compound 7e exhibited an IC50 (0.067 ± 0.003 μM) similar to that of the standard drug AZA against CAIX (0.059 ± 0.003 μM)). For CAXII, the compound 7i had an IC50 equal to 0.123 ± 0.007 μM compared to that of AZA (0.083 ± 0.005 μM). In addition, using flow cytometry, cell cycle analysis and apoptosis studies in HePG-2 were performed for the two potent anticancer and selective carbonic anhydrase agents (7e and 7i). An enzymatic assay of these two compounds against caspase-9 was also examined. Interestingly, the molecular docking studies revealed that compounds 7e and 7i successfully embedded themselves in the active pockets of the CAIX and CAXII enzymes through different interactions. Overall, the novel thiopyrano[2,3-d]thiazole-pyrazole hybrids (7e and 7i) were suggested to be potent and selective inhibitors of CAIX and CAXII.
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8
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Vaaltyn MC, Mateos‐Jimenez M, Müller R, Mackay CL, Edkins AL, Clarke DJ, Veale CGL. Native Mass Spectrometry-Guided Screening Identifies Hit Fragments for HOP-HSP90 PPI Inhibition. Chembiochem 2022; 23:e202200322. [PMID: 36017658 PMCID: PMC9826382 DOI: 10.1002/cbic.202200322] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/25/2022] [Indexed: 01/11/2023]
Abstract
Contemporary medicinal chemistry considers fragment-based drug discovery (FBDD) and inhibition of protein-protein interactions (PPI) as important means of expanding the volume of druggable chemical space. However, the ability to robustly identify valid fragments and PPI inhibitors is an enormous challenge, requiring the application of sensitive biophysical methodology. Accordingly, in this study, we exploited the speed and sensitivity of nanoelectrospray (nano-ESI) native mass spectrometry to identify a small collection of fragments which bind to the TPR2AB domain of HOP. Follow-up biophysical assessment of a small selection of binding fragments confirmed binding to the single TPR2A domain, and that this binding translated into PPI inhibitory activity between TPR2A and the HSP90 C-terminal domain. An in-silico assessment of binding fragments at the PPI interfacial region, provided valuable structural insight for future fragment elaboration strategies, including the identification of losartan as a weak, albeit dose-dependent inhibitor of the target PPI.
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Affiliation(s)
- Michaelone C. Vaaltyn
- The Biomedical Biotechnology Research Unit (BioBRU) Department of Biochemistry and Microbiology DepartmentRhodes UniversityMakhanda6139South Africa
| | - Maria Mateos‐Jimenez
- EaStCHEM School of ChemistryJoseph Black Building, David Brewster RoadEdinburghEH93FJUK
| | - Ronel Müller
- School of Chemistry and PhysicsUniversity of KwaZulu-NatalScottsville3209South Africa
| | - C. Logan Mackay
- EaStCHEM School of ChemistryJoseph Black Building, David Brewster RoadEdinburghEH93FJUK
| | - Adrienne L. Edkins
- The Biomedical Biotechnology Research Unit (BioBRU) Department of Biochemistry and Microbiology DepartmentRhodes UniversityMakhanda6139South Africa
| | - David J. Clarke
- EaStCHEM School of ChemistryJoseph Black Building, David Brewster RoadEdinburghEH93FJUK
| | - Clinton G. L. Veale
- Department of ChemistryUniversity of Cape Town RondeboschCape Town7700South Africa
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A fragment-based drug discovery strategy applied to the identification of NDM-1 β-lactamase inhibitors. Eur J Med Chem 2022; 240:114599. [PMID: 35841882 DOI: 10.1016/j.ejmech.2022.114599] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/26/2022] [Accepted: 07/07/2022] [Indexed: 11/23/2022]
Abstract
Hydrolysis of β-lactam drugs, a major class of antibiotics, by serine or metallo-β-lactamases (SBL or MBL) is one of the main mechanisms for antibiotic resistance. New Delhi Metallo-β-lactamase-1 (NDM-1), an acquired metallo-carbapenemase first reported in 2009, is currently considered one of the most clinically relevant targets for the development of β-lactam-β-lactamase inhibitor combinations active on NDM-producing clinical isolates. Identification of scaffolds that could be further rationally pharmacomodulated to design new and efficient NDM-1 inhibitors is thus urgently needed. Fragment-based drug discovery (FBDD) has become of great interest for the development of new drugs for the past few years and combination of several FBDD strategies, such as virtual and NMR screening, can reduce the drawbacks of each of them independently. Our methodology starting from a high throughput virtual screening on NDM-1 of a large library (more than 700,000 compounds) allowed, after slicing the hit molecules into fragments, to build a targeted library. These hit fragments were included in an in-house untargeted library fragments that was screened by Saturation Transfer Difference (STD) Nuclear Magnetic Resonance (NMR). 37 fragments were finally identified and used to establish a pharmacophore. 10 molecules based on these hit fragments were synthesized to validate our strategy. Indenone 89 that combined two identified fragments shows an inhibitory activity on NDM-1 with a Ki value of 4 μM.
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10
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Cortelazzo-Polisini E, Boisbrun M, Gansmüller AH, Comoy C. Photoisomerization of Arylidene Heterocycles: Toward the Formation of Fused Heterocyclic Quinolines. J Org Chem 2022; 87:9699-9713. [PMID: 35801862 DOI: 10.1021/acs.joc.2c00748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report herein the photoinduced isomerization of a series of arylidene heterocycles 1. The photoreaction mechanism was investigated by a combined UV-vis/photo-NMR spectroscopic study, and we showed that Ar-TZDs exhibit a positive P-type photochromism, which limits their isomerization efficiency. By exploring the solvatochromism in a series of solvents, the conditions favoring the conversion toward one or the other stereoisomer have been studied, in particular by choosing the appropriate wavelengths. Finally, the extension of this photoisomerization study was proposed with a convenient preparation of various fused heterocyclic quinolines in good overall yields.
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Affiliation(s)
| | | | | | - Corinne Comoy
- Université de Lorraine, CNRS, L2CM, F-54000 Nancy, France
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11
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Keenan T, Jean A, Arseniyadis S. Phase-Transfer-Catalyzed Alkylation of Hydantoins. ACS ORGANIC & INORGANIC AU 2022; 2:312-317. [PMID: 36855589 PMCID: PMC9954259 DOI: 10.1021/acsorginorgau.1c00058] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A highly efficient, cost-effective, and environmentally friendly protocol is reported for the C5-selective alkylation of hydantoins under phase-transfer catalysis. The reactions are scalable and only require a catalytic amount of tetrabutylammonium bromide (TBAB) to achieve high yields under mild reaction conditions. Moreover, the method is applicable to a wide range of electrophiles, including alkyl-, allyl-, propargyl-, and benzyl halides, as well as acrylates and dibromoalkanes, but also to virtually any hydantoin precursor. We also highlight the potential for an enantioselective adaptation using a chiral phase-transfer catalyst.
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Affiliation(s)
- Thomas Keenan
- Department
of Chemistry, Queen Mary University of London, Mile End Road, London E1 4NS, U.K.
| | - Alexandre Jean
- Industrial
Research Centre, Oril Industrie, 13 rue Desgenétais, 76210 Bolbec, France,
| | - Stellios Arseniyadis
- Department
of Chemistry, Queen Mary University of London, Mile End Road, London E1 4NS, U.K.,
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12
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Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chem Rev 2021; 122:7327-7385. [PMID: 34449207 DOI: 10.1021/acs.chemrev.1c00293] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Small molecule drug discovery has been propelled by the continual development of novel scientific methodologies to occasion therapeutic advances. Although established biophysical methods can be used to obtain information regarding the molecular mechanisms underlying drug action, these approaches are often inefficient, low throughput, and ineffective in the analysis of heterogeneous systems including dynamic oligomeric assemblies and proteins that have undergone extensive post-translational modification. Native mass spectrometry can be used to probe protein-small molecule interactions with unprecedented speed and sensitivity, providing unique insights into polydisperse biomolecular systems that are commonly encountered during the drug discovery process. In this review, we describe potential and proven applications of native MS in the study of interactions between small, drug-like molecules and proteins, including large multiprotein complexes and membrane proteins. Approaches to quantify the thermodynamic and kinetic properties of ligand binding are discussed, alongside a summary of gas-phase ion activation techniques that have been used to interrogate the structure of protein-small molecule complexes. We additionally highlight some of the key areas in modern drug design for which native mass spectrometry has elicited significant advances. Future developments and applications of native mass spectrometry in drug discovery workflows are identified, including potential pathways toward studying protein-small molecule interactions on a whole-proteome scale.
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Affiliation(s)
- Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Giang T H Nguyen
- School of Chemistry, 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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13
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Mueller SL, Chrysanthopoulos PK, Halili MA, Hepburn C, Nebl T, Supuran CT, Nocentini A, Peat TS, Poulsen SA. The Glitazone Class of Drugs as Carbonic Anhydrase Inhibitors-A Spin-Off Discovery from Fragment Screening. Molecules 2021; 26:3010. [PMID: 34070212 PMCID: PMC8158703 DOI: 10.3390/molecules26103010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 12/22/2022] Open
Abstract
The approved drugs that target carbonic anhydrases (CA, EC 4.2.1.1), a family of zinc metalloenzymes, comprise almost exclusively of primary sulfonamides (R-SO2NH2) as the zinc binding chemotype. New clinical applications for CA inhibitors, particularly for hard-to-treat cancers, has driven a growing interest in the development of novel CA inhibitors. We recently discovered that the thiazolidinedione heterocycle, where the ring nitrogen carries no substituent, is a new zinc binding group and an alternate CA inhibitor chemotype. This heterocycle is curiously also a substructure of the glitazone class of drugs used in the treatment options for type 2 diabetes. Herein, we investigate and characterise three glitazone drugs (troglitazone 11, rosiglitazone 12 and pioglitazone 13) for binding to CA using native mass spectrometry, protein X-ray crystallography and hydrogen-deuterium exchange (HDX) mass spectrometry, followed by CA enzyme inhibition studies. The glitazone drugs all displayed appreciable binding to and inhibition of CA isozymes. Given that thiazolidinediones are not credited as a zinc binding group nor known as CA inhibitors, our findings indicate that CA may be an off-target of these compounds when used clinically. Furthermore, thiazolidinediones may represent a new opportunity for the development of novel CA inhibitors as future drugs.
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Affiliation(s)
- Sarah L. Mueller
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, QLD 4111, Australia; (S.L.M.); (P.K.C.); (M.A.H.)
- ARC Centre for Fragment-Based Design, Griffith University, Nathan, Brisbane, QLD 4111, Australia
- CSIRO, Biomedical Manufacturing Program, Parkville, Melbourne, VIC 3052, Australia; (T.N.); (T.S.P.)
| | - Panagiotis K. Chrysanthopoulos
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, QLD 4111, Australia; (S.L.M.); (P.K.C.); (M.A.H.)
| | - Maria A. Halili
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, QLD 4111, Australia; (S.L.M.); (P.K.C.); (M.A.H.)
- ARC Centre for Fragment-Based Design, Griffith University, Nathan, Brisbane, QLD 4111, Australia
| | - Caryn Hepburn
- Waters Australia Pty Ltd., Rydalmere, NSW 2116, Australia;
| | - Tom Nebl
- CSIRO, Biomedical Manufacturing Program, Parkville, Melbourne, VIC 3052, Australia; (T.N.); (T.S.P.)
| | - Claudiu T. Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche Nutraceutiche, Università Degli Studi di Firenze, Sesto Fiorentino, 50019 Florence, Italy; (C.T.S.); (A.N.)
| | - Alessio Nocentini
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche Nutraceutiche, Università Degli Studi di Firenze, Sesto Fiorentino, 50019 Florence, Italy; (C.T.S.); (A.N.)
| | - Thomas S. Peat
- CSIRO, Biomedical Manufacturing Program, Parkville, Melbourne, VIC 3052, Australia; (T.N.); (T.S.P.)
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, QLD 4111, Australia; (S.L.M.); (P.K.C.); (M.A.H.)
- ARC Centre for Fragment-Based Design, Griffith University, Nathan, Brisbane, QLD 4111, Australia
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14
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Serbian I, Schwarzenberger P, Loesche A, Hoenke S, Al-Harrasi A, Csuk R. Ureidobenzenesulfonamides as efficient inhibitors of carbonic anhydrase II. Bioorg Chem 2019; 91:103123. [PMID: 31336306 DOI: 10.1016/j.bioorg.2019.103123] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 07/04/2019] [Accepted: 07/11/2019] [Indexed: 01/13/2023]
Abstract
Sulfonamides represent an important class of drugs because of their inhibitory effect on carbonic anhydrases (CAs). We therefore synthesized several ureidobenzenesulfonamides and evaluated their bCA II inhibition for their potential use as anti-glaucoma gents. Since these compounds must not show cytotoxic effects, their cytotoxic potential against several human tumor cell lines and non-malignant fibroblasts was investigated. Several fluorophenyl substituted sulfonamides were efficient inhibitors of bCA II. Only one benzylphenyl substituted sulfonamide, however, showed a remarkable selectivity for HT29 colorectal carcinoma cells while being significantly less cytotoxic to non-malignant fibroblasts.
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Affiliation(s)
- Immo Serbian
- Martin-Luther-University Halle-Wittenberg, Organic Chemistry, Kurt-Mothes-Str. 2, D-06120 Halle (Saale), Germany
| | - Philipp Schwarzenberger
- Martin-Luther-University Halle-Wittenberg, Organic Chemistry, Kurt-Mothes-Str. 2, D-06120 Halle (Saale), Germany
| | - Anne Loesche
- Martin-Luther-University Halle-Wittenberg, Organic Chemistry, Kurt-Mothes-Str. 2, D-06120 Halle (Saale), Germany
| | - Sophie Hoenke
- Martin-Luther-University Halle-Wittenberg, Organic Chemistry, Kurt-Mothes-Str. 2, D-06120 Halle (Saale), Germany
| | - Ahmed Al-Harrasi
- University of Nizwa, Chair of Oman's Medicinal Plants and Marine Natural Products, PO Box 33, Birkat Al-Mauz, Nizwa, Oman
| | - René Csuk
- Martin-Luther-University Halle-Wittenberg, Organic Chemistry, Kurt-Mothes-Str. 2, D-06120 Halle (Saale), Germany.
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15
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Mayerthaler F, Finley MF, Pfeifer TA, Antolin AA. Meeting Proceedings from ICBS 2018- Toward Translational Impact. ACS Chem Biol 2019; 14:567-578. [PMID: 30860357 DOI: 10.1021/acschembio.9b00169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Florian Mayerthaler
- Institute of Biochemistry, Department of Chemistry and Pharmacy, University of Münster, Münster, Germany
| | - Michael F. Finley
- Janssen Research & Development, Spring House, Pennsylvania 19477, United States
| | - Tom A. Pfeifer
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada V6T 1Z3
| | - Albert A. Antolin
- The Department of Data Science, The Institute of Cancer Research, London, SM2 5NG, United Kingdom
- The Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, United Kingdom
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16
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Nguyen GH, Tran TN, Podgorski MN, Bell SG, Supuran CT, Donald WA. Nanoscale Ion Emitters in Native Mass Spectrometry for Measuring Ligand-Protein Binding Affinities. ACS CENTRAL SCIENCE 2019; 5:308-318. [PMID: 30834319 PMCID: PMC6396573 DOI: 10.1021/acscentsci.8b00787] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Indexed: 05/20/2023]
Abstract
Electrospray ionization (ESI) mass spectrometry (MS) is a crucial method for rapidly determining the interactions between small molecules and proteins with ultrahigh sensitivity. However, nonvolatile molecules and salts that are often necessary to stabilize the native structures of protein-ligand complexes can readily adduct to protein ions, broaden spectral peaks, and lower signal-to-noise ratios in native MS. ESI emitters with narrow tip diameters (∼250 nm) were used to significantly reduce the extent of adduction of salt and nonvolatile molecules to protein complexes to more accurately measure ligand-protein binding constants than by use of conventional larger-bore emitters under these conditions. As a result of decreased salt adduction, peaks corresponding to protein-ligand complexes that differ in relative molecular weight by as low as 0.06% can be readily resolved. For low-molecular-weight anion ligands formed from sodium salts, anion-bound and unbound protein ions that differ in relative mass by 0.2% were completely baseline resolved using nanoscale emitters, which was not possible under these conditions using conventional emitters. Owing to the improved spectral resolution obtained using narrow-bore emitters and an analytically derived equation, K d values were simultaneously obtained for at least six ligands to a single druggable protein target from one spectrum for the first time. This research suggests that ligand-protein binding constants can be directly and accurately measured from solutions with high concentrations of nonvolatile buffers and salts by native MS.
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Affiliation(s)
- Giang
T. H. Nguyen
- School
of Chemistry, University of New South Wales, Dalton Building, Sydney, New South Wales 2052, Australia
| | - Thinh N. Tran
- School
of Electrical Engineering and Telecommunications, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Matthew N. Podgorski
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen G. Bell
- Department
of Chemistry, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Claudiu T. Supuran
- Department
of Neuroscience, Psychology, Drug Research and Child’s Health,
Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Italy
| | - William A. Donald
- School
of Chemistry, University of New South Wales, Dalton Building, Sydney, New South Wales 2052, Australia
- Phone: +61 (2) 9385 8827. E-mail:
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17
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Kusamoto H, Shiba A, Tsunehiro M, Fujioka H, Kinoshita-Kikuta E, Kinoshita E, Koike T. A simple method for determining the ligand affinity toward a zinc-enzyme model by using a TAMRA/TAMRA interaction. Dalton Trans 2018; 47:1841-1848. [DOI: 10.1039/c7dt04364c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple method for determining the ligand affinity toward a TAMRA-attached zinc-enzyme model under near physiological conditions is developed.
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Affiliation(s)
- Hiroshi Kusamoto
- Department of Functional Molecular Science
- Graduate School of Biomedical & Health Sciences
- Hiroshima University
- Hiroshima 734-8553
- Japan
| | - Akio Shiba
- Department of Functional Molecular Science
- Graduate School of Biomedical & Health Sciences
- Hiroshima University
- Hiroshima 734-8553
- Japan
| | - Masaya Tsunehiro
- Department of Functional Molecular Science
- Graduate School of Biomedical & Health Sciences
- Hiroshima University
- Hiroshima 734-8553
- Japan
| | - Haruto Fujioka
- Laboratory of Organic Medicinal Chemistry
- Faculty of Pharmacy & Pharmaceutical Sciences
- Fukuyama University
- Fukuyama 729-0292
- Japan
| | - Emiko Kinoshita-Kikuta
- Department of Functional Molecular Science
- Graduate School of Biomedical & Health Sciences
- Hiroshima University
- Hiroshima 734-8553
- Japan
| | - Eiji Kinoshita
- Department of Functional Molecular Science
- Graduate School of Biomedical & Health Sciences
- Hiroshima University
- Hiroshima 734-8553
- Japan
| | - Tohru Koike
- Department of Functional Molecular Science
- Graduate School of Biomedical & Health Sciences
- Hiroshima University
- Hiroshima 734-8553
- Japan
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18
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Poulsen SA. Editorial: Excellence in Medicinal Chemistry from Australia. J Med Chem 2017; 60:8253-8256. [PMID: 28991471 DOI: 10.1021/acs.jmedchem.7b01439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
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