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McAulay K, Bilsland A, Bon M. Reactivity of Covalent Fragments and Their Role in Fragment Based Drug Discovery. Pharmaceuticals (Basel) 2022; 15:1366. [PMID: 36355538 PMCID: PMC9694498 DOI: 10.3390/ph15111366] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 09/27/2023] Open
Abstract
Fragment based drug discovery has long been used for the identification of new ligands and interest in targeted covalent inhibitors has continued to grow in recent years, with high profile drugs such as osimertinib and sotorasib gaining FDA approval. It is therefore unsurprising that covalent fragment-based approaches have become popular and have recently led to the identification of novel targets and binding sites, as well as ligands for targets previously thought to be 'undruggable'. Understanding the properties of such covalent fragments is important, and characterizing and/or predicting reactivity can be highly useful. This review aims to discuss the requirements for an electrophilic fragment library and the importance of differing warhead reactivity. Successful case studies from the world of drug discovery are then be examined.
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Affiliation(s)
- Kirsten McAulay
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Centre for Targeted Protein Degradation, University of Dundee, Nethergate, Dundee DD1 4HN, UK
| | - Alan Bilsland
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Marta Bon
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
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2
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Bon M, Bilsland A, Bower J, McAulay K. Fragment-based drug discovery-the importance of high-quality molecule libraries. Mol Oncol 2022; 16:3761-3777. [PMID: 35749608 PMCID: PMC9627785 DOI: 10.1002/1878-0261.13277] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/16/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is now established as a complementary approach to high-throughput screening (HTS). Contrary to HTS, where large libraries of drug-like molecules are screened, FBDD screens involve smaller and less complex molecules which, despite a low affinity to protein targets, display more 'atom-efficient' binding interactions than larger molecules. Fragment hits can, therefore, serve as a more efficient start point for subsequent optimisation, particularly for hard-to-drug targets. Since the number of possible molecules increases exponentially with molecular size, small fragment libraries allow for a proportionately greater coverage of their respective 'chemical space' compared with larger HTS libraries comprising larger molecules. However, good library design is essential to ensure optimal chemical and pharmacophore diversity, molecular complexity, and physicochemical characteristics. In this review, we describe our views on fragment library design, and on what constitutes a good fragment from a medicinal and computational chemistry perspective. We highlight emerging chemical and computational technologies in FBDD and discuss strategies for optimising fragment hits. The impact of novel FBDD approaches is already being felt, with the recent approval of the covalent KRASG12C inhibitor sotorasib highlighting the utility of FBDD against targets that were long considered undruggable.
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Affiliation(s)
- Marta Bon
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Alan Bilsland
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Justin Bower
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Kirsten McAulay
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
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3
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Bum-Erdene K, Ghozayel MK, Xu D, Meroueh SO. Covalent Fragment Screening Identifies Rgl2 RalGEF Cysteine for Targeted Covalent Inhibition of Ral GTPase Activation. ChemMedChem 2022; 17:e202100750. [PMID: 35061330 PMCID: PMC9070689 DOI: 10.1002/cmdc.202100750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/17/2022] [Indexed: 11/09/2022]
Abstract
Ral GTPases belong to the RAS superfamily, and they are directly activated by K-RAS. The RalGEF pathway is one of the three major K-RAS signaling pathways. Ral GTPases do not possess a cysteine nucleophile to develop a covalent inhibitor following the strategy that led to a K-RAS G12C therapeutic agent. However, several cysteine amino acids exist on the surface of guanine exchange factors that activate Ral GTPases, such as Rgl2. Here, we screen a library of cysteine electrophile fragments to determine if covalent bond formation at one of the Rgl2 surface cysteines could inhibit Ral GTPase activation. We found several chloroacetamide and acrylamide fragments that inhibited Ral GTPase exchange by Rgl2. Site-directed mutagenesis showed that covalent bond formation at Cys-284, but not other cysteines, leads to inhibition of Ral activation by Rgl2. Follow-up time- and concentration-dependent studies of derivatives identified by substructure search of commercial libraries further confirmed Cys-284 as the reaction site and identified the indoline fragments as the most promising series for further development. Cys-284 is located outside of the Ral ⋅ Rgl2 interface on a loop that has several residues that come in direct contact with Ral GTPases. Our allosteric covalent fragment inhibitors provide a starting point for the development of small-molecule covalent inhibitors to probe Ral GTPases in animal models.
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Affiliation(s)
- Khuchtumur Bum-Erdene
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4021, Indianapolis, IN, 46202, USA
| | - Mona K Ghozayel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4021, Indianapolis, IN, 46202, USA
| | - David Xu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4021, Indianapolis, IN, 46202, USA
| | - Samy O Meroueh
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4021, Indianapolis, IN, 46202, USA
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4
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Rothweiler EM, Brennan PE, Huber KVM. Covalent fragment-based ligand screening approaches for identification of novel ubiquitin proteasome system modulators. Biol Chem 2022; 403:391-402. [PMID: 35191283 DOI: 10.1515/hsz-2021-0396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/07/2022] [Indexed: 12/19/2022]
Abstract
Ubiquitination is a key regulatory mechanism vital for maintenance of cellular homeostasis. Protein degradation is induced by E3 ligases via attachment of ubiquitin chains to substrates. Pharmacological exploitation of this phenomenon via targeted protein degradation (TPD) can be achieved with molecular glues or bifunctional molecules facilitating the formation of ternary complexes between an E3 ligase and a given protein of interest (POI), resulting in ubiquitination of the substrate and subsequent proteolysis by the proteasome. Recently, the development of novel covalent fragment screening approaches has enabled the identification of first-in-class ligands for E3 ligases and deubiquitinases revealing so far unexplored binding sites which highlights the potential of these methods to uncover and expand druggable space for new target classes.
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Affiliation(s)
- Elisabeth M Rothweiler
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK
| | - Paul E Brennan
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, Oxford OX3 7FZ, UK
| | - Kilian V M Huber
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK
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Cordon MB, Jacobsen KM, Nielsen CS, Hjerrild P, Poulsen TB. Forward Chemical Genetic Screen for Oxygen-Dependent Cytotoxins Uncovers New Covalent Fragments that Target GPX4. Chembiochem 2021; 23:e202100253. [PMID: 34252249 DOI: 10.1002/cbic.202100253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/09/2021] [Indexed: 11/09/2022]
Abstract
The identification of growth inhibitory compounds with the ability to selectively target the cellular oxygenation state may be of therapeutic interest. Here, a phenotypic screen of a covalent fragment library revealed diverse compounds containing propiolamide warheads with selective toxicity for liver cancer cells in normoxic conditions. Target identification and validation through CETSA and direct pulldown experiments demonstrated that several compounds target glutathione peroxidase 4 (GPX4) and induce ferroptotic cell death. Although being an oxidative cell death mechanism, ferroptosis can be induced also under hypoxic conditions. Prompted by the selective toxicity discovered in the screen, we mapped the oxygen-dependence of several ferroptosis-inducing compounds across three different cell lines. These studies revealed combinations with notable reductions in sensitivity under hypoxic conditions. These observations are mechanistically interesting and may be relevant for the use of ferroptosis-inducers as anti-cancer agents.
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Affiliation(s)
- Marie B Cordon
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Kristian M Jacobsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Cecilie S Nielsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Per Hjerrild
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Thomas B Poulsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
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Knaup FH, Meyners C, Charalampidou A, Krajczy P, Purder PL, Ross T, Hausch F. Med Chem Remote: The Frontiers in Medicinal Chemistry 2021. ChemMedChem 2021; 16:2411-2416. [PMID: 34101362 DOI: 10.1002/cmdc.202100355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Indexed: 12/21/2022]
Abstract
Digital, but delicious! The Frontiers in Medicinal Chemistry 2021 meeting, originally intended to take place in Darmstadt, carried on as an online event from March 8-10 this year. Even with pandemic restrictions, the event co-presented by the Medicinal Chemistry Division of the German Chemical Society (GDCh), the German Pharmaceutical Society (DPhG), and the Swiss Chemical Society (SCS) proved to be a success, showcasing excellent speakers and facilitating participant interaction in an ingenious virtual setting. Over 350 participants from more than 10 countries gathered to discuss the latest trends and directions in medicinal chemistry, with sessions on molecular glues, covalent fragments, transient binding pockets and more. This report presents a summary of the key lectures and activities at the event.
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Affiliation(s)
- Fabian H Knaup
- Department of Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287, Darmstadt, Germany
| | - Christian Meyners
- Department of Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287, Darmstadt, Germany
| | - Anna Charalampidou
- Department of Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287, Darmstadt, Germany
| | - Patryk Krajczy
- Department of Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287, Darmstadt, Germany
| | - Patrick L Purder
- Department of Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287, Darmstadt, Germany
| | - Tatjana Ross
- Merck Healthcare KGaA, Frankfurter Str. 250, 64293, Darmstadt
| | - Felix Hausch
- Department of Chemistry and Biochemistry, Clemens-Schöpf-Institute, Technical University Darmstadt, Alarich-Weiss Straße 4, 64287, Darmstadt, Germany
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7
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Craven GB, Affron DP, Kösel T, Wong TLM, Jukes ZH, Liu CT, Morgan RML, Armstrong A, Mann DJ. Multiparameter Kinetic Analysis for Covalent Fragment Optimization by Using Quantitative Irreversible Tethering (qIT). Chembiochem 2020; 21:3417-3422. [PMID: 32659037 PMCID: PMC7754465 DOI: 10.1002/cbic.202000457] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Indexed: 12/23/2022]
Abstract
Chemical probes that covalently modify cysteine residues in a protein‐specific manner are valuable tools for biological investigations. Covalent fragments are increasingly implemented as probe starting points, but the complex relationship between fragment structure and binding kinetics makes covalent fragment optimization uniquely challenging. We describe a new technique in covalent probe discovery that enables data‐driven optimization of covalent fragment potency and selectivity. This platform extends beyond the existing repertoire of methods for identifying covalent fragment hits by facilitating rapid multiparameter kinetic analysis of covalent structure–activity relationships through the simultaneous determination of Ki, kinact and intrinsic reactivity. By applying this approach to develop novel probes against electrophile‐sensitive kinases, we showcase the utility of the platform in hit identification and highlight how multiparameter kinetic analysis enabled a successful fragment‐merging strategy.
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Affiliation(s)
- Gregory B Craven
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.,Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Dominic P Affron
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Teresa Kösel
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Tsz Lam M Wong
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Zoë H Jukes
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Chun-Ting Liu
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Rhodri M L Morgan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - David J Mann
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
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8
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Tolmachova KA, Moroz YS, Konovets A, Platonov MO, Vasylchenko OV, Borysko P, Zozulya S, Gryniukova A, Bogolubsky AV, Pipko S, Mykhailiuk PK, Brovarets VS, Grygorenko OO. (Chlorosulfonyl)benzenesulfonyl Fluorides-Versatile Building Blocks for Combinatorial Chemistry: Design, Synthesis and Evaluation of a Covalent Inhibitor Library. ACS Comb Sci 2018; 20:672-680. [PMID: 30354064 DOI: 10.1021/acscombsci.8b00130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multigram synthesis of (chlorosulfonyl)benzenesulfonyl fluorides is described. Selective modification of these building blocks at the sulfonyl chloride function under parallel synthesis conditions is achieved. It is shown that the reaction scope includes the use of (hetero)aromatic and electron-poor aliphatic amines (e.g., amino nitriles). Utility of the method is demonstrated by preparation of the sulfonyl fluoride library for potential use as covalent fragments, which is demonstrated by a combination of in silico and in vitro screening against trypsin as a model enzyme. As a result, several inhibitors were identified with activity on par with that of the known inhibitor.
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Affiliation(s)
- Kateryna A. Tolmachova
- National Taras
Shevchenko University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
- Institute of Bioorganic Chemistry & Petrochemistry, NAS of Ukraine, Murmanska Street 1, Kyiv 02660, Ukraine
| | - Yurii S. Moroz
- National Taras
Shevchenko University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
- Chemspace, Ilukstes iela 38-5, Riga, LV-1082, Latvia
| | - Angelika Konovets
- National Taras
Shevchenko University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
| | | | | | - Petro Borysko
- Bienta/Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
| | - Sergey Zozulya
- Bienta/Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
| | | | | | - Sergey Pipko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
| | - Pavel K. Mykhailiuk
- National Taras
Shevchenko University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
| | - Volodymyr S. Brovarets
- Institute of Bioorganic Chemistry & Petrochemistry, NAS of Ukraine, Murmanska Street 1, Kyiv 02660, Ukraine
| | - Oleksandr O. Grygorenko
- National Taras
Shevchenko University of Kyiv, Volodymyrska Street 60, Kyiv 01601, Ukraine
- Enamine Ltd., Chervonotkatska Street 78, Kyiv 02094, Ukraine
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Erlanson DA, Davis BJ, Jahnke W. Fragment-Based Drug Discovery: Advancing Fragments in the Absence of Crystal Structures. Cell Chem Biol 2018; 26:9-15. [PMID: 30482678 DOI: 10.1016/j.chembiol.2018.10.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/12/2018] [Accepted: 09/28/2018] [Indexed: 01/08/2023]
Abstract
Fragment-based drug discovery typically requires an interplay between screening methods, structural methods, and medicinal chemistry. X-ray crystallography is generally the method of choice to obtain three-dimensional structures of the bound ligand/protein complex, but this can sometimes be difficult, particularly for early, low-affinity fragment hits. In this Perspective, we discuss strategies to advance and evolve fragments in the absence of crystal structures of protein-fragment complexes, although the structure of the unliganded protein may be available. The strategies can involve other structural techniques, such as NMR spectroscopy, molecular modeling, or a variety of chemical approaches. Often, these strategies are aimed at guiding evolution of initial fragment hits to a stage where crystal structures can be obtained for further structure-based optimization.
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Affiliation(s)
- Daniel A Erlanson
- Carmot Therapeutics, Inc., 740 Heinz Avenue, Berkeley, CA 94710, USA.
| | - Ben J Davis
- Vernalis (R&D) Ltd, Granta Park, Cambridge, UK.
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Novartis Campus, Basel, Switzerland.
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10
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Abstract
Covalently binding molecules are frequently regarded as being generally promiscuous. In a recent study, binding selectivities and cellular target proteins of a wide variety of reactive fragments are examined in a proteome-wide context.
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Affiliation(s)
- Oliver Plettenburg
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt GmbH, Institute of Medicinal Chemistry, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.,Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
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