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Semi-quantitatively Predicting the Residence Time of Three Natural Products on Endothelin Receptor A by Peak Profiling Using the Receptor Functionalized Macroporous Silica Gel as Stationary Phase. JOURNAL OF ANALYSIS AND TESTING 2022. [DOI: 10.1007/s41664-022-00240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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2
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Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
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Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
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3
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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4
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Rapid analysis of S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) isotopologues in stable isotope-resolved metabolomics (SIRM) using direct infusion nanoelectrospray ultra-high-resolution Fourier transform mass spectrometry (DI-nESI-UHR-FTMS). Anal Chim Acta 2021; 1181:338873. [PMID: 34556237 DOI: 10.1016/j.aca.2021.338873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/15/2021] [Accepted: 07/22/2021] [Indexed: 01/02/2023]
Abstract
S-Adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) are important metabolites in the one-carbon cycle that modulates cellular methylation required for proliferation and epigenetic regulation. Their concentrations, synthesis, and turnover are difficult to determine conveniently and reliably. We have developed such a method by coupling a simple and rapid purification scheme that efficiently captures both compounds, with high sensitivity, sample throughput direct infusion nanoelectrospray ultra-high-resolution Fourier transform mass spectrometry (DI-nESI-UHR-FTMS). This method is compatible with Stable Isotope-Resolved Metabolomic (SIRM) analysis of numerous other metabolites. The limits of detection for both SAM and SAH were <1 nM, and the linearity range was up to 1000 nM. The method was first illustrated for SAM/SAH analysis of mouse livers, and lung adenocarcinoma A549 cells. We then applied the method to track 13C1-CH3-Met incorporation into SAM and 13C6-glucose transformation into SAM and SAH via de novo synthesis. We further used the method to show the distinct effects on A549 and H1299 cells with treatment of anti-cancer methylseleninic acid (MSA), selenite, and selenomethionine, notably SAM depletion and increased SAM to SAH ratio by MSA, which implicates altered epigenetic regulation.
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Eddershaw AR, Stubbs CJ, Edwardes LV, Underwood E, Hamm GR, Davey PRJ, Clarkson PN, Syson K. Characterization of the Kinetic Mechanism of Human Protein Arginine Methyltransferase 5. Biochemistry 2020; 59:4775-4786. [PMID: 33274632 DOI: 10.1021/acs.biochem.0c00554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein arginine methyltransferases (PRMTs) are of great interest for the development of therapeutics due to their involvement in a number of malignancies, such as lung and colon cancer. PRMT5 catalyzes the formation of symmetrical dimethylarginine of a wide variety of substrates and is responsible for the majority of this mark within cells. To gain insight into the mechanism of PRMT5 inhibition, we co-expressed the human PRMT5:MEP50 complex (hPRMT5:MEP50) in insect cells for a detailed mechanistic study. In this report, we carry out steady state, product, and dead-end inhibitor studies that show hPRMT5:MEP50 uses a rapid equilibrium random order mechanism with EAP and EBQ dead-end complexes. We also provide evidence of ternary complex formation in solution using hydrogen/deuterium exchange mass spectrometry. Isotope exchange and intact protein mass spectrometry further rule out ping-pong as a potential enzyme mechanism, and finally, we show that PRMT5 exhibits a pre-steady state burst that corresponds to an initial slow turnover with all four active sites of the hetero-octamer being catalytically active.
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Affiliation(s)
- Alice R Eddershaw
- Discovery Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Christopher J Stubbs
- Discovery Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Lucy V Edwardes
- Discovery Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Elizabeth Underwood
- Discovery Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Gregory R Hamm
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals, R&D AstraZeneca, Cambridge CB4 0WG, U.K
| | - Paul R J Davey
- Chemistry, Oncology, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Paul N Clarkson
- Discovery Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Karl Syson
- Discovery Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
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Development of a high-performance, enterprise-level, multimode LC–MS/MS autosampler for drug discovery. Bioanalysis 2017; 9:1643-1654. [DOI: 10.4155/bio-2017-0149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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7
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Beeman K, Baumgärtner J, Laubenheimer M, Hergesell K, Hoffmann M, Pehl U, Fischer F, Pieck JC. Integration of an In Situ MALDI-Based High-Throughput Screening Process: A Case Study with Receptor Tyrosine Kinase c-MET. SLAS DISCOVERY 2017; 22:1203-1210. [DOI: 10.1177/2472555217727701] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Mass spectrometry (MS) is known for its label-free detection of substrates and products from a variety of enzyme reactions. Recent hardware improvements have increased interest in the use of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS for high-throughput drug discovery. Despite interest in this technology, several challenges remain and must be overcome before MALDI-MS can be integrated as an automated “in-line reader” for high-throughput drug discovery. Two such hurdles include in situ sample processing and deposition, as well as integration of MALDI-MS for enzymatic screening assays that usually contain high levels of MS-incompatible components. Here we adapt our c-MET kinase assay to optimize for MALDI-MS compatibility and test its feasibility for compound screening. The pros and cons of the Echo (Labcyte) as a transfer system for in situ MALDI-MS sample preparation are discussed. We demonstrate that this method generates robust data in a 1536-grid format. We use the MALDI-MS to directly measure the ratio of c-MET substrate and phosphorylated product to acquire IC50 curves and demonstrate that the pharmacology is unaffected. The resulting IC50 values correlate well between the common label-based capillary electrophoresis and the label-free MALDI-MS detection method. We predict that label-free MALDI-MS-based high-throughput screening will become increasingly important and more widely used for drug discovery.
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Affiliation(s)
- Katrin Beeman
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Jens Baumgärtner
- Analytics Healthcare, Biomolecule Analytics, Merck KGaA, Darmstadt, Germany
| | - Manuel Laubenheimer
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Karlheinz Hergesell
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Martin Hoffmann
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Ulrich Pehl
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
| | - Frank Fischer
- Analytics Healthcare, Biomolecule Analytics, Merck KGaA, Darmstadt, Germany
| | - Jan-Carsten Pieck
- Global Research & Development, Discovery Technologies, Discovery Pharmacology, Merck KGaA, Darmstadt, Germany
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8
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Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A. Nat Chem Biol 2017; 13:785-792. [PMID: 28553945 DOI: 10.1038/nchembio.2384] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 03/07/2017] [Indexed: 12/15/2022]
Abstract
S-Adenosyl-L-methionine (SAM) is an enzyme cofactor used in methyl transfer reactions and polyamine biosynthesis. The biosynthesis of SAM from ATP and L-methionine is performed by the methionine adenosyltransferase enzyme family (Mat; EC 2.5.1.6). Human methionine adenosyltransferase 2A (Mat2A), the extrahepatic isoform, is often deregulated in cancer. We identified a Mat2A inhibitor, PF-9366, that binds an allosteric site on Mat2A that overlaps with the binding site for the Mat2A regulator, Mat2B. Studies exploiting PF-9366 suggested a general mode of Mat2A allosteric regulation. Allosteric binding of PF-9366 or Mat2B altered the Mat2A active site, resulting in increased substrate affinity and decreased enzyme turnover. These data support a model whereby Mat2B functions as an inhibitor of Mat2A activity when methionine or SAM levels are high, yet functions as an activator of Mat2A when methionine or SAM levels are low. The ramification of Mat2A activity modulation in cancer cells is also described.
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Hsiao K, Zegzouti H, Goueli SA. Methyltransferase-Glo: a universal, bioluminescent and homogenous assay for monitoring all classes of methyltransferases. Epigenomics 2016; 8:321-39. [DOI: 10.2217/epi.15.113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aim: To develop a homogenous, nonradioactive, antibody-free and universal assay for diverse families of methyltransferases and monitor the activity of these enzymes in a high-throughput format. Materials & methods: The assay conditions are optimized for monitoring the enzymatic activity of a broad range of methyltransferases regardless of the chemical structure or nature of the enzyme substrate in a low- and high-throughput-formatted protocols. The assay detects S-adenosyl-l-homocysteine, the universal reaction products of all methyltransferases. Results: We demonstrate the utility of using this protocol to determine the activity of DNA, protein methyltransferases and also to determine kinetic parameters of several inhibitors using purified enzymes. The assay is sensitive (20–30 nM of S-adenosyl-l-homocysteine) and robust. Conclusion: The methyltransferase Glo is nonradioactive, antibody-free and homogenous, universal assay to determine enzyme activity of diverse families of methyltransferases. The assay is formatted to meet the requirements of high-throughput screening in drug discovery programs searching for modulators of methyltransferases.
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Affiliation(s)
- Kevin Hsiao
- Promega Corporation, R&D Department, 2800 Woods Hollow Road, Madison, WI 53711, USA
| | - Hicham Zegzouti
- Promega Corporation, R&D Department, 2800 Woods Hollow Road, Madison, WI 53711, USA
| | - Said A Goueli
- Promega Corporation, R&D Department, 2800 Woods Hollow Road, Madison, WI 53711, USA
- Department of Pathology & Laboratory Medicine, University of Wisconsin School of Medicine & Public Health, Madison, WI 53726, USA
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10
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Doyle SK, Pop MS, Evans HL, Koehler AN. Advances in discovering small molecules to probe protein function in a systems context. Curr Opin Chem Biol 2015; 30:28-36. [PMID: 26615565 DOI: 10.1016/j.cbpa.2015.10.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/30/2015] [Accepted: 10/30/2015] [Indexed: 12/15/2022]
Abstract
High throughput screening (HTS) has historically been used for drug discovery almost exclusively by the pharmaceutical industry. Due to a significant decrease in costs associated with establishing a high throughput facility and an exponential interest in discovering probes of development and disease associated biomolecules, HTS core facilities have become an integral part of most academic and non-profit research institutions over the past decade. This major shift has led to the development of new HTS methodologies extending beyond the capabilities and target classes used in classical drug discovery approaches such as traditional enzymatic activity-based screens. In this brief review we describe some of the most interesting developments in HTS technologies and methods for chemical probe discovery.
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Affiliation(s)
- Shelby K Doyle
- David H. Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marius S Pop
- David H. Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helen L Evans
- David H. Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Angela N Koehler
- David H. Koch Institute for Integrative Cancer Research, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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