1
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Dalwani S, Metz A, Huschmann FU, Weiss MS, Wierenga RK, Venkatesan R. Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them. Acta Crystallogr D Struct Biol 2024; 80:605-619. [PMID: 39012716 DOI: 10.1107/s2059798324006557] [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: 01/12/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024] Open
Abstract
The Mycobacterium tuberculosis trifunctional enzyme (MtTFE) is an α2β2 tetrameric enzyme in which the α-chain harbors the 2E-enoyl-CoA hydratase (ECH) and 3S-hydroxyacyl-CoA dehydrogenase (HAD) active sites, and the β-chain provides the 3-ketoacyl-CoA thiolase (KAT) active site. Linear, medium-chain and long-chain 2E-enoyl-CoA molecules are the preferred substrates of MtTFE. Previous crystallographic binding and modeling studies identified binding sites for the acyl-CoA substrates at the three active sites, as well as the NAD binding pocket at the HAD active site. These studies also identified three additional CoA binding sites on the surface of MtTFE that are different from the active sites. It has been proposed that one of these additional sites could be of functional relevance for the substrate channeling (by surface crawling) of reaction intermediates between the three active sites. Here, 226 fragments were screened in a crystallographic fragment-binding study of MtTFE crystals, resulting in the structures of 16 MtTFE-fragment complexes. Analysis of the 121 fragment-binding events shows that the ECH active site is the `binding hotspot' for the tested fragments, with 41 binding events. The mode of binding of the fragments bound at the active sites provides additional insight into how the long-chain acyl moiety of the substrates can be accommodated at their proposed binding pockets. In addition, the 20 fragment-binding events between the active sites identify potential transient binding sites of reaction intermediates relevant to the possible channeling of substrates between these active sites. These results provide a basis for further studies to understand the functional relevance of the latter binding sites and to identify substrates for which channeling is crucial.
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Affiliation(s)
- Subhadra Dalwani
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Franziska U Huschmann
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin, Germany
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Rajaram Venkatesan
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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2
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Pose, duplicate, then elaborate: Steps towards increased affinity for inhibitors targeting the specificity surface of the Pim-1 kinase. Eur J Med Chem 2022; 245:114914. [DOI: 10.1016/j.ejmech.2022.114914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/03/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022]
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3
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Huang CY, Aumonier S, Engilberge S, Eris D, Smith KML, Leonarski F, Wojdyla JA, Beale JH, Buntschu D, Pauluhn A, Sharpe ME, Metz A, Olieric V, Wang M. Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography. Acta Crystallogr D Struct Biol 2022; 78:964-974. [PMID: 35916221 PMCID: PMC9344481 DOI: 10.1107/s205979832200612x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/09/2022] [Indexed: 12/03/2022] Open
Abstract
A room-temperature X-ray crystallographic method using temperature as a trigger to record movie-like structural snapshots has been developed and applied to study ligand binding and protein plasticity. Continuous developments in cryogenic X-ray crystallography have provided most of our knowledge of 3D protein structures, which has recently been further augmented by revolutionary advances in cryoEM. However, a single structural conformation identified at cryogenic temperatures may introduce a fictitious structure as a result of cryogenic cooling artefacts, limiting the overview of inherent protein physiological dynamics, which play a critical role in the biological functions of proteins. Here, a room-temperature X-ray crystallographic method using temperature as a trigger to record movie-like structural snapshots has been developed. The method has been used to show how TL00150, a 175.15 Da fragment, undergoes binding-mode changes in endothiapepsin. A surprising fragment-binding discrepancy was observed between the cryo-cooled and physiological temperature structures, and multiple binding poses and their interplay with DMSO were captured. The observations here open up new promising prospects for structure determination and interpretation at physiological temperatures with implications for structure-based drug discovery.
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4
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Metz A, Wollenhaupt J, Glöckner S, Messini N, Huber S, Barthel T, Merabet A, Gerber HD, Heine A, Klebe G, Weiss MS. Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking. Acta Crystallogr D Struct Biol 2021; 77:1168-1182. [PMID: 34473087 PMCID: PMC8411975 DOI: 10.1107/s2059798321008196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/09/2021] [Indexed: 11/10/2022] Open
Abstract
In recent years, crystallographic fragment screening has matured into an almost routine experiment at several modern synchrotron sites. The hits of the screening experiment, i.e. small molecules or fragments binding to the target protein, are revealed along with their 3D structural information. Therefore, they can serve as useful starting points for further structure-based hit-to-lead development. However, the progression of fragment hits to tool compounds or even leads is often hampered by a lack of chemical feasibility. As an attractive alternative, compound analogs that embed the fragment hit structurally may be obtained from commercial catalogs. Here, a workflow is reported based on filtering and assessing such potential follow-up compounds by template docking. This means that the crystallographic binding pose was integrated into the docking calculations as a central starting parameter. Subsequently, the candidates are scored on their interactions within the binding pocket. In an initial proof-of-concept study using five starting fragments known to bind to the aspartic protease endothiapepsin, 28 follow-up compounds were selected using the designed workflow and their binding was assessed by crystallography. Ten of these compounds bound to the active site and five of them showed significantly increased affinity in isothermal titration calorimetry of up to single-digit micromolar affinity. Taken together, this strategy is capable of efficiently evolving the initial fragment hits without major synthesis efforts and with full control by X-ray crystallography.
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Affiliation(s)
- Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Steffen Glöckner
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Niki Messini
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Simon Huber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Ahmed Merabet
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Hans-Dieter Gerber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
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5
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Wienen‐Schmidt B, Oebbeke M, Ngo K, Heine A, Klebe G. Two Methods, One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses. ChemMedChem 2021; 16:292-300. [PMID: 33029876 PMCID: PMC7821316 DOI: 10.1002/cmdc.202000565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/02/2020] [Indexed: 11/10/2022]
Abstract
In lead optimization, protein crystallography is an indispensable tool to analyze drug binding. Binding modes and non-covalent interaction inventories are essential to design follow-up synthesis candidates. Two protocols are commonly applied to produce protein-ligand complexes: cocrystallization and soaking. Because of its time and cost effectiveness, soaking is the more popular method. Taking eight ligand hinge binders of protein kinase A, we demonstrate that cocrystallization is superior. Particularly for flexible proteins, such as kinases, and larger ligands cocrystallization captures more reliable the correct binding pose and induced protein adaptations. The geometrical discrepancies between soaking and cocrystallization appear smaller for fragment-sized ligands. For larger flexible ligands that trigger conformational changes of the protein, soaking can be misleading and underestimates the number of possible polar interactions due to inadequate, highly impaired positions of protein amino-acid side and main chain atoms. Thus, if applicable cocrystallization should be the gold standard to study protein-ligand complexes.
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Affiliation(s)
- Barbara Wienen‐Schmidt
- Institut für Pharmazeutische ChemiePhilipps-Universität MarburgMarbacher Weg 635032MarburgGermany
| | - Matthias Oebbeke
- Institut für Pharmazeutische ChemiePhilipps-Universität MarburgMarbacher Weg 635032MarburgGermany
| | - Khang Ngo
- Institut für Pharmazeutische ChemiePhilipps-Universität MarburgMarbacher Weg 635032MarburgGermany
| | - Andreas Heine
- Institut für Pharmazeutische ChemiePhilipps-Universität MarburgMarbacher Weg 635032MarburgGermany
| | - Gerhard Klebe
- Institut für Pharmazeutische ChemiePhilipps-Universität MarburgMarbacher Weg 635032MarburgGermany
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6
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Merchant RR, Lang SB, Yu T, Zhao S, Qi Z, Suzuki T, Bao J. A General One-Pot Protocol for Hindered N-Alkyl Azaheterocycles from Tertiary Carboxylic Acids. Org Lett 2020; 22:4180-4184. [PMID: 32383385 DOI: 10.1021/acs.orglett.0c01254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this letter, we report a general one-pot strategy that utilizes three elementary steps (decarboxylative hydrazination, Boc deprotection, and heterocycle condensation) to regioselectively prepare hindered C(sp3) substituted pyrazoles and triazoles. The operational simplicity of this sequence and ubiquity of tertiary carboxylic acids allow rapid access to hindered N-alkyl azaheterocycles that will be useful to practitioners of medicinal chemistry and agro-chemistry.
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Affiliation(s)
- Rohan R Merchant
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Simon B Lang
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
| | - Tingting Yu
- IDSU, WuXi AppTec Co., Ltd., Shanghai 200131, China
| | | | - Zhiqi Qi
- IDSU, WuXi AppTec Co., Ltd., Shanghai 200131, China
| | - Takao Suzuki
- IDSU, WuXi AppTec Co., Ltd., Shanghai 200131, China
| | - Jianming Bao
- Department of Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States
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7
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Wollenhaupt J, Metz A, Barthel T, Lima GMA, Heine A, Mueller U, Klebe G, Weiss MS. F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening. Structure 2020; 28:694-706.e5. [PMID: 32413289 DOI: 10.1016/j.str.2020.04.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/02/2020] [Accepted: 04/23/2020] [Indexed: 11/15/2022]
Abstract
Crystallographic fragment screening (CFS) provides excellent starting points for projects concerned with drug discovery or biochemical tool compound development. One of the fundamental prerequisites for effective CFS is the availability of a versatile fragment library. Here, we report on the assembly of the 1,103-compound F2X-Universal Library and its 96-compound sub-selection, the F2X-Entry Screen. Both represent the available fragment chemistry and are highly diverse in terms of their 3D-pharmacophore variations. Validation of the F2X-Entry Screen in CFS campaigns using endothiapepsin and the Aar2/RNaseH complex yielded hit rates of 30% and 21%, respectively, and revealed versatile binding sites. Dry presentation of the libraries allows CFS campaigns to be carried out with or without the co-solvent DMSO present. Most of the hits in our validation campaigns could be reproduced also in the absence of DMSO. Consequently, CFS can be carried out more efficiently and for a wider range of conditions and targets.
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Affiliation(s)
- Jan Wollenhaupt
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany; Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Alexander Metz
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany
| | - Tatjana Barthel
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany; Freie Universität Berlin, Institute for Chemistry and Biochemistry, Structural Biochemistry Group, Takustr. 5, 14195 Berlin, Germany
| | - Gustavo M A Lima
- MAX IV Laboratory, Macromolecular Crystallography Group, Lund University, 22100 Lund, Sweden
| | - Andreas Heine
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany
| | - Uwe Mueller
- MAX IV Laboratory, Macromolecular Crystallography Group, Lund University, 22100 Lund, Sweden
| | - Gerhard Klebe
- Philipps-Universität Marburg, Institute of Pharmaceutical Chemistry, Drug Design Group, Marbacher Weg 6, 35032 Marburg, Germany
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography, Albert-Einstein-Str. 15, 12489 Berlin, Germany.
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8
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Konstantinidou M, Magari F, Sutanto F, Haupenthal J, Jumde VR, Ünver MY, Heine A, Camacho CJ, Hirsch AKH, Klebe G, Dömling A. Rapid Discovery of Aspartyl Protease Inhibitors Using an Anchoring Approach. ChemMedChem 2020; 15:680-684. [PMID: 32187447 PMCID: PMC7317454 DOI: 10.1002/cmdc.202000024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/20/2020] [Indexed: 11/11/2022]
Abstract
Pharmacophore searches that include anchors, fragments contributing above average to receptor binding, combined with one‐step syntheses are a powerful approach for the fast discovery of novel bioactive molecules. Here, we are presenting a pipeline for the rapid and efficient discovery of aspartyl protease inhibitors. First, we hypothesized that hydrazine could be a multi‐valent warhead to interact with the active site Asp carboxylic acids. We incorporated the hydrazine anchor in a multicomponent reaction and created a large virtual library of hydrazine derivatives synthetically accessible in one‐step. Next, we performed anchor‐based pharmacophore screening of the libraries and resynthesized top‐ranked compounds. The inhibitory potency of the molecules was finally assessed by an enzyme activity assay and the binding mode confirmed by several soaked crystal structures supporting the validity of the hypothesis and approach. The herein reported pipeline of tools will be of general value for the rapid generation of receptor binders beyond Asp proteases.
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Affiliation(s)
- Markella Konstantinidou
- Department of Pharmacy Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Francesca Magari
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Fandi Sutanto
- Department of Pharmacy Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Jörg Haupenthal
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Varsha R Jumde
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - M Yagiz Ünver
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Carlos Jamie Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Anna K H Hirsch
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Alexander Dömling
- Department of Pharmacy Drug Design Group, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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9
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Glöckner S, Heine A, Klebe G. A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II. Biomolecules 2020; 10:biom10040518. [PMID: 32235320 PMCID: PMC7226012 DOI: 10.3390/biom10040518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 11/16/2022] Open
Abstract
Fragment screening is a powerful tool to identify and characterize binding pockets in proteins. We herein present the results of a proof-of-concept screening campaign of a versatile 96-entry fragment library from our laboratory against the drug target and model protein human carbonic anhydrase II. The screening revealed a novel chemotype for carbonic anhydrase inhibition, as well as less common non-covalent interaction types and unexpected covalent linkages. Lastly, different runs of the PanDDA tool reveal a practical hint for its application.
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10
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Cramer J, Schiebel J, Wulsdorf T, Grohe K, Najbauer EE, Ehrmann FR, Radeva N, Zitzer N, Linne U, Linser R, Heine A, Klebe G. Falsch-positiver Treffer im Fragment-basierten Wirkstoffdesign: Lass Dich nicht auf die falsche Fährte locken! Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jonathan Cramer
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Johannes Schiebel
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Tobias Wulsdorf
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Kristof Grohe
- Abteilung für NMR-basierte Strukturbiologie; Max-Planck-Institut für Biophysikalische Chemie; Am Faßberg 11 37077 Göttingen Deutschland
- Fakultät für Chemie und Pharmazie; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13, Haus F 81377 München Deutschland
| | - Eszter Eva Najbauer
- Abteilung für NMR-basierte Strukturbiologie; Max-Planck-Institut für Biophysikalische Chemie; Am Faßberg 11 37077 Göttingen Deutschland
| | - Frederik R. Ehrmann
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Nedyalka Radeva
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Nina Zitzer
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Uwe Linne
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Straße 4 35043 Marburg Deutschland
| | - Rasmus Linser
- Abteilung für NMR-basierte Strukturbiologie; Max-Planck-Institut für Biophysikalische Chemie; Am Faßberg 11 37077 Göttingen Deutschland
- Fakultät für Chemie und Pharmazie; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13, Haus F 81377 München Deutschland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
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11
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Cramer J, Schiebel J, Wulsdorf T, Grohe K, Najbauer EE, Ehrmann FR, Radeva N, Zitzer N, Linne U, Linser R, Heine A, Klebe G. A False-Positive Screening Hit in Fragment-Based Lead Discovery: Watch out for the Red Herring. Angew Chem Int Ed Engl 2017; 56:1908-1913. [PMID: 28097765 DOI: 10.1002/anie.201609824] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/24/2016] [Indexed: 01/08/2023]
Abstract
With the rising popularity of fragment-based approaches in drug development, more and more attention has to be devoted to the detection of false-positive screening results. In particular, the small size and low affinity of fragments drives screening techniques to their limit. The pursuit of a false-positive hit can cause significant loss of time and resources. Here, we present an instructive and intriguing investigation into the origin of misleading assay results for a fragment that emerged as the most potent binder for the aspartic protease endothiapepsin (EP) across multiple screening assays. This molecule shows its biological effect mainly after conversion into another entity through a reaction cascade that involves major rearrangements of its heterocyclic scaffold. The formed ligand binds EP through an induced-fit mechanism involving remarkable electrostatic interactions. Structural information in the initial screening proved to be crucial for the identification of this false-positive hit.
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Affiliation(s)
- Jonathan Cramer
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Johannes Schiebel
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Tobias Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Kristof Grohe
- Abteilung für NMR-basierte Strukturbiologie, Max Planck Institut für Biophysikalische Chemie, Am Faßberg 11, 37077, Göttingen, Germany.,Fakultät für Chemie und Pharmazie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Haus F, 81377, München, Germany
| | - Eszter Eva Najbauer
- Abteilung für NMR-basierte Strukturbiologie, Max Planck Institut für Biophysikalische Chemie, Am Faßberg 11, 37077, Göttingen, Germany
| | - Frederik R Ehrmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Nedyalka Radeva
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Nina Zitzer
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Uwe Linne
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043, Marburg, Germany
| | - Rasmus Linser
- Abteilung für NMR-basierte Strukturbiologie, Max Planck Institut für Biophysikalische Chemie, Am Faßberg 11, 37077, Göttingen, Germany.,Fakultät für Chemie und Pharmazie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Haus F, 81377, München, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
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