1
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Diedrich K, Ehrt C, Graef J, Poppinga M, Ritter N, Rarey M. User-centric design of a 3D search interface for protein-ligand complexes. J Comput Aided Mol Des 2024; 38:23. [PMID: 38814371 PMCID: PMC11139749 DOI: 10.1007/s10822-024-00563-3] [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: 04/03/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024]
Abstract
In this work, we present the frontend of GeoMine and showcase its application, focusing on the new features of its latest version. GeoMine is a search engine for ligand-bound and predicted empty binding sites in the Protein Data Bank. In addition to its basic text-based search functionalities, GeoMine offers a geometric query type for searching binding sites with a specific relative spatial arrangement of chemical features such as heavy atoms and intermolecular interactions. In contrast to a text search that requires simple and easy-to-formulate user input, a 3D input is more complex, and its specification can be challenging for users. GeoMine's new version aims to address this issue from the graphical user interface perspective by introducing an additional visualization concept and a new query template type. In its latest version, GeoMine extends its query-building capabilities primarily through input formulation in 2D. The 2D editor is fully synchronized with GeoMine's 3D editor and provides the same functionality. It enables template-free query generation and template-based query selection directly in 2D pose diagrams. In addition, the query generation with the 3D editor now supports predicted empty binding sites for AlphaFold structures as query templates. GeoMine is freely accessible on the ProteinsPlus web server ( https://proteins.plus ).
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Affiliation(s)
- Konrad Diedrich
- Universität Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany
| | - Christiane Ehrt
- Universität Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany
| | - Joel Graef
- Universität Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany
| | - Martin Poppinga
- Universität Hamburg, Department of Informatics, Vogt-Kölln-Straße 30, 22527, Hamburg, Germany
| | - Norbert Ritter
- Universität Hamburg, Department of Informatics, Vogt-Kölln-Straße 30, 22527, Hamburg, Germany
| | - Matthias Rarey
- Universität Hamburg, ZBH - Center for Bioinformatics, Albert-Einstein-Ring 8-10, 22761, Hamburg, Germany.
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2
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Chen G, Xie H, You M, Liu J, Shao Q, Li M, Su H, Xu Y. Structure-based design of potent FABP4 inhibitors with high selectivity against FABP3. Eur J Med Chem 2024; 264:115984. [PMID: 38043490 DOI: 10.1016/j.ejmech.2023.115984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 12/05/2023]
Abstract
Fatty-acid binding protein 4 (FABP4) presents an attractive target for therapeutic intervention in metabolic and inflammatory diseases in recent years. However, highly similar three-dimensional structures and fatty acid binding ability of multiple FABP family members pose a significant challenge in design of FABP4-selective inhibitors. Particularly, inhibition of FABP3 raises safety concerns such as cardiac dysfunction and exercise intolerance. Here, we reported the discovery of new FABP4 inhibitors with high selectivity over FABP3 by exploiting the little structural difference in the ligand binding pockets of FABP4 and FABP3. On the basis of our previously reported FABP4 inhibitors with nanomolar potency, different substituents were further introduced to perfectly occupy two sub-pockets of FABP4 that are distinct from those of FABP3. Remarkably, a single methyl group introduction leads to the discovery of compound C3 that impressively exhibits a 601-fold selectivity over FABP3 when maintained nanomolar binding affinity for FABP4. Moreover, C3 also shows good metabolic stability and potent cellular anti-inflammatory activity, making it a promising inhibitor for further development. Therefore, the present study highlights the utility of the structure-based rational design strategy for seeking highly selective and potent inhibitors of FABP4 and the importance of identifying the appropriate subsite as well as substituent for gaining the desired selectivity.
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Affiliation(s)
- Guofeng Chen
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang Xie
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Mengyuan You
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jiayuan Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Qiang Shao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minjun Li
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yechun Xu
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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3
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Voitsitskyi T, Bdzhola V, Stratiichuk R, Koleiev I, Ostrovsky Z, Vozniak V, Khropachov I, Henitsoi P, Popryho L, Zhytar R, Yesylevskyy S, Nafiiev A, Starosyla S. Augmenting a training dataset of the generative diffusion model for molecular docking with artificial binding pockets. RSC Adv 2024; 14:1341-1353. [PMID: 38174256 PMCID: PMC10763617 DOI: 10.1039/d3ra08147h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
This study introduces the PocketCFDM generative diffusion model, aimed at improving the prediction of small molecule poses in the protein binding pockets. The model utilizes a novel data augmentation technique, involving the creation of numerous artificial binding pockets that mimic the statistical patterns of non-bond interactions found in actual protein-ligand complexes. An algorithmic method was developed to assess and replicate these interaction patterns in the artificial binding pockets built around small molecule conformers. It is shown that the integration of artificial binding pockets into the training process significantly enhanced the model's performance. Notably, PocketCFDM surpassed DiffDock in terms of non-bond interaction and steric clash numbers, and the inference speed. Future developments and optimizations of the model are discussed. The inference code and final model weights of PocketCFDM are accessible publicly via the GitHub repository: https://github.com/vtarasv/pocket-cfdm.git.
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Affiliation(s)
- Taras Voitsitskyi
- Receptor.AI Inc. 20-22 Wenlock Road London N1 7GU UK
- Department of Physics of Biological Systems, Institute of Physics of The National Academy of Sciences of Ukraine 46 Nauky Ave. Kyiv 03038 Ukraine
| | - Volodymyr Bdzhola
- Institute of Molecular Biology and Genetics of The National Academy of Sciences of Ukraine 150 Zabolotnogo Str. Kyiv 03143 Ukraine
| | - Roman Stratiichuk
- Receptor.AI Inc. 20-22 Wenlock Road London N1 7GU UK
- Department of Biophysics and Medical Informatics, Educational and Scientific Centre "Institute of Biology and Medicine", Taras Shevchenko Kyiv National University 64 Volodymyrska Str. Kyiv 01601 Ukraine
| | - Ihor Koleiev
- Receptor.AI Inc. 20-22 Wenlock Road London N1 7GU UK
- Department of Physics of Biological Systems, Institute of Physics of The National Academy of Sciences of Ukraine 46 Nauky Ave. Kyiv 03038 Ukraine
| | | | | | | | | | | | - Roman Zhytar
- Receptor.AI Inc. 20-22 Wenlock Road London N1 7GU UK
| | - Semen Yesylevskyy
- Receptor.AI Inc. 20-22 Wenlock Road London N1 7GU UK
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Prague 6 CZ-166 10 Czech Republic
- Department of Physics of Biological Systems, Institute of Physics of The National Academy of Sciences of Ukraine 46 Nauky Ave. Kyiv 03038 Ukraine
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc 17 listopadu 12 Olomouc 771 46 Czech Republic
| | - Alan Nafiiev
- Receptor.AI Inc. 20-22 Wenlock Road London N1 7GU UK
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4
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Krummenacher D, He W, Kuhn B, Schnider C, Beurier A, Brom V, Sivasothy T, Marty C, Tosstorff A, Hewings DS, Mesch S, Pinard E, Brändlin M, Hochstrasser R, Westwood P, Rothe J, Kronenberger A, Morandi F, Gutbier S, Schuler A, Heer D, Gloria LE, Joedicke L, Rudolph MG, Müller L, Grüninger F, Baumann K, Kaniyappan S, Manevski N, Bartels B. Discovery of Orally Available and Brain Penetrant AEP Inhibitors. J Med Chem 2023; 66:17026-17043. [PMID: 38090813 DOI: 10.1021/acs.jmedchem.3c01804] [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: 12/29/2023]
Abstract
Alzheimer's Disease (AD) is the most widespread form of dementia, with one of the pathological hallmarks being the formation of neurofibrillary tangles (NFTs). These tangles consist of phosphorylated Tau fragments. Asparagine endopeptidase (AEP) is a key Tau cleaving enzyme that generates aggregation-prone Tau fragments. Inhibition of AEP to reduce the level of toxic Tau fragment formation could represent a promising therapeutic strategy. Here, we report the first orthosteric, selective, orally bioavailable, and brain penetrant inhibitors with an irreversible binding mode. We outline the development of the series starting from reversible molecules and demonstrate the link between inhibition of AEP and reduction of Tau N368 fragment both in vitro and in vivo.
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Affiliation(s)
- Daniela Krummenacher
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Weiping He
- WuXi AppTec (Wuhan) Co. Ltd., Wuhan East Lake High-Tech Development Zone, 666 GaoXin Road, Wuhan, Hubei 430075, China
| | - Bernd Kuhn
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Christian Schnider
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Angélica Beurier
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Virginie Brom
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Thulase Sivasothy
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Christine Marty
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Andreas Tosstorff
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - David S Hewings
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Stefanie Mesch
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Emmanuel Pinard
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Mathis Brändlin
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Remo Hochstrasser
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Paul Westwood
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Judith Rothe
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Alexandra Kronenberger
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Federica Morandi
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Simon Gutbier
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Angelika Schuler
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Dominik Heer
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Ludivine Esteves Gloria
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Lisa Joedicke
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Markus G Rudolph
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Lutz Müller
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Fiona Grüninger
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Karlheinz Baumann
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Senthilvelrajan Kaniyappan
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Nenad Manevski
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
| | - Björn Bartels
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel CH-4070, Switzerland
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5
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West AML, Dominelli‐Whiteley N, Smolyar IV, Nichol GS, Cockroft SL. Experimental Quantification of Halogen⋅⋅⋅Arene van der Waals Contacts. Angew Chem Int Ed Engl 2023; 62:e202309682. [PMID: 37470309 PMCID: PMC10953438 DOI: 10.1002/anie.202309682] [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: 07/07/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Crystallographic and computational studies suggest the occurrence of favourable interactions between polarizable arenes and halogen atoms. However, the systematic experimental quantification of halogen⋅⋅⋅arene interactions in solution has been hindered by the large variance in the steric demands of the halogens. Here we have synthesized molecular balances to quantify halogen⋅⋅⋅arene contacts in 17 solvents and solvent mixtures using 1 H NMR spectroscopy. Calculations indicate that favourable halogen⋅⋅⋅arene interactions arise from London dispersion in the gas phase. In contrast, comparison of our experimental measurements with partitioned SAPT0 energies indicate that dispersion is sufficiently attenuated by the solvent that the halogen⋅⋅⋅arene interaction trend was instead aligned with increasing exchange repulsion as the halogen increased in size (ΔGX ⋅⋅⋅Ph =0 to +1.5 kJ mol-1 ). Halogen⋅⋅⋅arene contacts were slightly less disfavoured in solvents with higher solvophobicities and lower polarizabilities, but strikingly, were always less favoured than CH3 ⋅⋅⋅arene contacts (ΔGMe ⋅⋅⋅Ph =0 to -1.4 kJ mol-1 ).
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Affiliation(s)
- Andrew M. L. West
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Nicholas Dominelli‐Whiteley
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Ivan V. Smolyar
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Gary S. Nichol
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Scott L. Cockroft
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
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6
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Pinel P, Guichaoua G, Najm M, Labouille S, Drizard N, Gaston-Mathé Y, Hoffmann B, Stoven V. Exploring isofunctional molecules: Design of a benchmark and evaluation of prediction performance. Mol Inform 2023; 42:e2200216. [PMID: 36633361 DOI: 10.1002/minf.202200216] [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: 08/30/2022] [Revised: 12/19/2022] [Accepted: 01/11/2023] [Indexed: 01/13/2023]
Abstract
Identification of novel chemotypes with biological activity similar to a known active molecule is an important challenge in drug discovery called 'scaffold hopping'. Small-, medium-, and large-step scaffold hopping efforts may lead to increasing degrees of chemical structure novelty with respect to the parent compound. In the present paper, we focus on the problem of large-step scaffold hopping. We assembled a high quality and well characterized dataset of scaffold hopping examples comprising pairs of active molecules and including a variety of protein targets. This dataset was used to build a benchmark corresponding to the setting of real-life applications: one active molecule is known, and the second active is searched among a set of decoys chosen in a way to avoid statistical bias. This allowed us to evaluate the performance of computational methods for solving large-step scaffold hopping problems. In particular, we assessed how difficult these problems are, particularly for classical 2D and 3D ligand-based methods. We also showed that a machine-learning chemogenomic algorithm outperforms classical methods and we provided some useful hints for future improvements.
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Affiliation(s)
- Philippe Pinel
- Center for Computational Biology, Mines Paris-PSL, PSL Research University, 75006, Paris, France.,Institut Curie, 75248, Paris, France.,INSERM U900, 75428, Paris, France.,Iktos SAS, 75017, Paris, France
| | - Gwenn Guichaoua
- Center for Computational Biology, Mines Paris-PSL, PSL Research University, 75006, Paris, France.,Institut Curie, 75248, Paris, France.,INSERM U900, 75428, Paris, France
| | - Matthieu Najm
- Center for Computational Biology, Mines Paris-PSL, PSL Research University, 75006, Paris, France.,Institut Curie, 75248, Paris, France.,INSERM U900, 75428, Paris, France
| | | | | | | | | | - Véronique Stoven
- Center for Computational Biology, Mines Paris-PSL, PSL Research University, 75006, Paris, France.,Institut Curie, 75248, Paris, France.,INSERM U900, 75428, Paris, France
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7
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Winiewska-Szajewska M, Czapinska H, Kaus-Drobek M, Fricke A, Mieczkowska K, Dadlez M, Bochtler M, Poznański J. Competition between electrostatic interactions and halogen bonding in the protein-ligand system: structural and thermodynamic studies of 5,6-dibromobenzotriazole-hCK2α complexes. Sci Rep 2022; 12:18964. [PMID: 36347916 PMCID: PMC9641685 DOI: 10.1038/s41598-022-23611-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Abstract
CK2 is a member of the CMGC group of eukaryotic protein kinases and a cancer drug target. It can be efficiently inhibited by halogenated benzotriazoles and benzimidazoles. Depending on the scaffold, substitution pattern, and pH, these compounds are either neutral or anionic. Their binding poses are dictated by a hydrophobic effect (desolvation) and a tug of war between a salt bridge/hydrogen bond (to K68) and halogen bonding (to E114 and V116 backbone oxygens). Here, we test the idea that binding poses might be controllable by pH for ligands with near-neutral pKa, using the conditionally anionic 5,6-DBBt and constitutively anionic TBBt as our models. We characterize the binding by low-volume Differential Scanning Fluorimetry (nanoDSF), Isothermal Calorimetry (ITC), Hydrogen/Deuterium eXchange (HDX), and X-ray crystallography (MX). The data indicate that the ligand pose away from the hinge dominates for the entire tested pH range (5.5-8.5). The insensitivity of the binding mode to pH is attributed to the perturbation of ligand pKa upon binding that keeps it anionic in the ligand binding pocket at all tested pH values. However, a minor population of the ligand, detectable only by HDX, shifts towards the hinge in acidic conditions. Our findings demonstrate that electrostatic (ionic) interactions predominate over halogen bonding.
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Affiliation(s)
- Maria Winiewska-Szajewska
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.12847.380000 0004 1937 1290Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-089 Warsaw, Poland
| | - Honorata Czapinska
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.419362.bInternational Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Magdalena Kaus-Drobek
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Anna Fricke
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.419362.bInternational Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Kinga Mieczkowska
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Michał Dadlez
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Matthias Bochtler
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland ,grid.419362.bInternational Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Jarosław Poznański
- grid.418825.20000 0001 2216 0871Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
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8
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Purushotham M, Paul B, Govindachar DM, Singh AK, Periyasamy G, Peter SC. Ortho-halogen effects: n→π* interactions, halogen bonding, and deciphering chiral attributes in N-aryl glycine peptoid foldamers. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Xu G, Liu Z, Wang X, Lu T, DesJarlais RL, Thieu T, Zhang J, Devine ZH, Du F, Li Q, Milligan CM, Shaffer P, Cedervall PE, Spurlino JC, Stratton CF, Pietrak B, Szewczuk LM, Wong V, Steele RA, Bruinzeel W, Chintala M, Silva J, Gaul MD, Macielag MJ, Nargund R. Discovery of Potent and Orally Bioavailable Pyridine N-Oxide-Based Factor XIa Inhibitors through Exploiting Nonclassical Interactions. J Med Chem 2022; 65:10419-10440. [PMID: 35862732 DOI: 10.1021/acs.jmedchem.2c00442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Activated factor XI (FXIa) inhibitors are promising novel anticoagulants with low bleeding risk compared with current anticoagulants. The discovery of potent FXIa inhibitors with good oral bioavailability has been challenging. Herein, we describe our discovery effort, utilizing nonclassical interactions to improve potency, cellular permeability, and oral bioavailability by enhancing the binding while reducing polar atoms. Beginning with literature-inspired pyridine N-oxide-based FXIa inhibitor 1, the imidazole linker was first replaced with a pyrazole moiety to establish a polar C-H···water hydrogen-bonding interaction. Then, structure-based drug design was employed to modify lead molecule 2d in the P1' and P2' regions, with substituents interacting with key residues through various nonclassical interactions. As a result, a potent FXIa inhibitor 3f (Ki = 0.17 nM) was discovered. This compound demonstrated oral bioavailability in preclinical species (rat 36.4%, dog 80.5%, and monkey 43.0%) and displayed a dose-dependent antithrombotic effect in a rabbit arteriovenous shunt model of thrombosis.
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Affiliation(s)
- Guozhang Xu
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Zhijie Liu
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Xinkang Wang
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Tianbao Lu
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Renee L DesJarlais
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Tho Thieu
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Jing Zhang
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Zheng Huang Devine
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Fuyong Du
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Qiu Li
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Cynthia M Milligan
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Paul Shaffer
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Peder E Cedervall
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - John C Spurlino
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Christopher F Stratton
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Beth Pietrak
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Lawrence M Szewczuk
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Victoria Wong
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Ruth A Steele
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Wouter Bruinzeel
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Madhu Chintala
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Jose Silva
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Michael D Gaul
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Mark J Macielag
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
| | - Ravi Nargund
- Janssen Research & Development, L.L.C., 1400 McKean Road, Spring House, Pennsylvania 19477-0776, United States
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10
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Levoin N, Murthy AVR, Narendar V, Kumar NS, Aparna P, Bhavani AKD, Reddy CR, Mosset P, Grée R. Discovery of potent dual ligands for dopamine D4 and σ1 receptors. Bioorg Med Chem 2022; 69:116851. [PMID: 35753263 DOI: 10.1016/j.bmc.2022.116851] [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: 02/25/2022] [Revised: 05/04/2022] [Accepted: 05/20/2022] [Indexed: 11/27/2022]
Abstract
During our work on exploration of molecules with some piperidine-triazole scaffolds, we realized that our compounds display chemical similarity with some σ, as well as dopaminergic receptor ligands. Here we show that this series of molecules has indeed strong affinity both for σ1 and dopamine D4 receptors. Moreover, they appear selective towards σ2, dopamine paralogues D1, D2, D3 and D5 receptors and hERG channel. Extensive molecular dynamics with our lead compound AVRM-13 were carried out on σ1, supporting agonist activity of the ligand. Unexpectedly, several observations suggested the existence of a cation binding domain, a probable regulatory site for calcium.
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Affiliation(s)
- Nicolas Levoin
- Bioprojet-Biotech, 4 rue du Chesnay Beauregard, BP 96205, 35762 Saint Grégoire, France.
| | - Appala Venkata Ramana Murthy
- Chemveda Life Sciences India Pvt. Ltd., #B-11/1, IDA Uppal, Hyderabad 500039, Telangana, India; Jawaharlal Nehru Technological University Hyderabad, Kukatpally, Hyderabad 500 085, Telangana, India
| | - Vennu Narendar
- Chemveda Life Sciences India Pvt. Ltd., #B-11/1, IDA Uppal, Hyderabad 500039, Telangana, India
| | | | - Pasula Aparna
- Jawaharlal Nehru Technological University Hyderabad, Kukatpally, Hyderabad 500 085, Telangana, India
| | | | - Chada Raji Reddy
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - Paul Mosset
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), UMR 6226, F-35000 Rennes, France
| | - René Grée
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), UMR 6226, F-35000 Rennes, France.
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11
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fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions. PLoS Comput Biol 2022; 18:e1009783. [PMID: 35653385 PMCID: PMC9197077 DOI: 10.1371/journal.pcbi.1009783] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/14/2022] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
Computational methods play a pivotal role in drug discovery and are widely applied in virtual screening, structure optimization, and compound activity profiling. Over the last decades, almost all the attention in medicinal chemistry has been directed to protein-ligand binding, and computational tools have been created with this target in mind. With novel discoveries of functional RNAs and their possible applications, RNAs have gained considerable attention as potential drug targets. However, the availability of bioinformatics tools for nucleic acids is limited. Here, we introduce fingeRNAt—a software tool for detecting non-covalent interactions formed in complexes of nucleic acids with ligands. The program detects nine types of interactions: (i) hydrogen and (ii) halogen bonds, (iii) cation-anion, (iv) pi-cation, (v) pi-anion, (vi) pi-stacking, (vii) inorganic ion-mediated, (viii) water-mediated, and (ix) lipophilic interactions. However, the scope of detected interactions can be easily expanded using a simple plugin system. In addition, detected interactions can be visualized using the associated PyMOL plugin, which facilitates the analysis of medium-throughput molecular complexes. Interactions are also encoded and stored as a bioinformatics-friendly Structural Interaction Fingerprint (SIFt)—a binary string where the respective bit in the fingerprint is set to 1 if a particular interaction is present and to 0 otherwise. This output format, in turn, enables high-throughput analysis of interaction data using data analysis techniques. We present applications of fingeRNAt-generated interaction fingerprints for visual and computational analysis of RNA-ligand complexes, including analysis of interactions formed in experimentally determined RNA-small molecule ligand complexes deposited in the Protein Data Bank. We propose interaction fingerprint-based similarity as an alternative measure to RMSD to recapitulate complexes with similar interactions but different folding. We present an application of interaction fingerprints for the clustering of molecular complexes. This approach can be used to group ligands that form similar binding networks and thus have similar biological properties. The fingeRNAt software is freely available at https://github.com/n-szulc/fingeRNAt.
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12
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Narayanan N, Mandal A, Kaushik P, Singh S. Fluorescence turn off azastilbene sensor for detection of pesticides in vegetables: An experimental and computational investigation. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107205] [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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13
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Ding K, Yin S, Li Z, Jiang S, Yang Y, Zhou W, Zhang Y, Huang B. Observing Noncovalent Interactions in Experimental Electron Density for Macromolecular Systems: A Novel Perspective for Protein–Ligand Interaction Research. J Chem Inf Model 2022; 62:1734-1743. [DOI: 10.1021/acs.jcim.1c01406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kang Ding
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Shiqiu Yin
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Zhongwei Li
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Shiju Jiang
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Yang Yang
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Wenbiao Zhou
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Yingsheng Zhang
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
| | - Bo Huang
- Beijing StoneWise Technology Co Ltd., Haidian Street #15, Haidian District, Beijing 100080, China
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14
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Urner LM, Lee GY, Treacy JW, Turlik A, Khan SI, Houk KN, Jung ME. Intramolecular N-H⋅⋅⋅F Hydrogen Bonding Interaction in a Series of 4-Anilino-5-Fluoroquinazolines: Experimental and Theoretical Characterization of Electronic and Conformational Effects. Chemistry 2022; 28:e202103135. [PMID: 34767667 PMCID: PMC9482468 DOI: 10.1002/chem.202103135] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Indexed: 01/12/2023]
Abstract
The 4-anilino-6,7-ethylenedioxy-5-fluoroquinazoline scaffold is presented as a novel model system for the characterization of the weak NH⋅⋅⋅F hydrogen bonding (HB) interaction. In this scaffold, the aniline NH proton is forced into close proximity with the nearby fluorine (dH,F ∼2.0 Å, ∠∼138°), and a through-space interaction is observed by NMR spectroscopy with couplings (1h JNH,F ) of 19±1 Hz. A combination of experimental (NMR spectroscopy and X-ray crystallography) and theoretical methods (DFT calculations) were used for the characterization of this weak interaction. In particular, the effects of conformational rigidity and steric compression on coupling were investigated. This scaffold was used for the direct comparison of fluoride with methoxy as HB acceptors, and the susceptibility of the NH⋅⋅⋅F interaction to changes in electron distribution and resonance was probed by preparing a series of molecules with different electron-donating or -withdrawing groups in the positions para to the NH and F. The results support the idea that fluorine can act as a weak HB acceptor, and the HB strength can be modulated through additive and linear electronic substituent effects.
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Affiliation(s)
- Lorenz M. Urner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Ga Young Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Joseph W. Treacy
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Aneta Turlik
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Saeed I. Khan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Michael E. Jung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
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15
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Montgomery M, Rendine S, Zimmer CT, Elias J, Schaetzer J, Pitterna T, Benfatti F, Skaljac M, Bigot A. Structural Biology-Guided Design, Synthesis, and Biological Evaluation of Novel Insect Nicotinic Acetylcholine Receptor Orthosteric Modulators. J Med Chem 2022; 65:2297-2312. [PMID: 34986308 DOI: 10.1021/acs.jmedchem.1c01767] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The development of novel and safe insecticides remains an important need for a growing world population to protect crops and animal and human health. New chemotypes modulating the insect nicotinic acetylcholine receptors have been recently brought to the agricultural market, yet with limited understanding of their molecular interactions at their target receptor. Herein, we disclose the first crystal structures of these insecticides, namely, sulfoxaflor, flupyradifurone, triflumezopyrim, flupyrimin, and the experimental compound, dicloromezotiaz, in a double-mutated acetylcholine-binding protein which mimics the insect-ion-channel orthosteric site. Enabled by these findings, we discovered novel pharmacophores with a related mode of action, and we describe herein their design, synthesis, and biological evaluation.
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Affiliation(s)
- Mark Montgomery
- Syngenta Crop Protection, Jealott's Hill International Research Centre, RG42 6EY Bracknell, Berkshire, U.K
| | - Stefano Rendine
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Christoph T Zimmer
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Jan Elias
- Syngenta Crop Protection AG, Rosentalstrasse 67, 4002 Basel, Switzerland
| | - Jürgen Schaetzer
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Thomas Pitterna
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Fides Benfatti
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Marisa Skaljac
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Aurélien Bigot
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
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16
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Laxio Arenas J, Retailleau P, Gillet JM, Ghermani NE, Ongeri S, Crousse B. 5-Fluoro-1,2,3-triazole motif in peptides and its electronic properties. Org Biomol Chem 2022; 20:8410-8414. [DOI: 10.1039/d2ob01716d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The 5-fluoro triazole amino acid has been prepared by halogen exchange between the 5-iodo triazole and fluoride salts and incorporated in peptides. X-ray crystallography reveals a cylindrical shape in its deformation electron density.
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Affiliation(s)
- José Laxio Arenas
- UMR 8076, BioCIS, CNRS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Pascal Retailleau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, 91198 Gif-sur-Yvette, France
| | - Jean-Michel Gillet
- UMR CNRS 8580, Ecole Centrale Paris, Grande Voie des Vignes, 92290 Châtenay-Malabry, France
| | - Nour-Eddine Ghermani
- UMR CNRS 8580, Ecole Centrale Paris, Grande Voie des Vignes, 92290 Châtenay-Malabry, France
- UMR CNRS 8612, Université Paris-Saclay, Faculté de Pharmacie, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry, France
| | - Sandrine Ongeri
- UMR 8076, BioCIS, CNRS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Benoît Crousse
- UMR 8076, BioCIS, CNRS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
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17
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Dolbois A, Bedi RK, Bochenkova E, Müller A, Moroz-Omori EV, Huang D, Caflisch A. 1,4,9-Triazaspiro[5.5]undecan-2-one Derivatives as Potent and Selective METTL3 Inhibitors. J Med Chem 2021; 64:12738-12760. [PMID: 34431664 DOI: 10.1021/acs.jmedchem.1c00773] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
N6-methyladenosine (m6A) is the most frequent of the 160 RNA modifications reported so far. Accumulating evidence suggests that the METTL3/METTL14 protein complex, part of the m6A regulation machinery, is a key player in a variety of diseases including several types of cancer, type 2 diabetes, and viral infections. Here we report on a protein crystallography-based medicinal chemistry optimization of a METTL3 hit compound that has resulted in a 1400-fold potency improvement (IC50 of 5 nM for the lead compound 22 (UZH2) in a time-resolved Förster resonance energy transfer (TR-FRET) assay). The series has favorable ADME properties as physicochemical characteristics were taken into account during hit optimization. UZH2 shows target engagement in cells and is able to reduce the m6A/A level of polyadenylated RNA in MOLM-13 (acute myeloid leukemia) and PC-3 (prostate cancer) cell lines.
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Affiliation(s)
- Aymeric Dolbois
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Rajiv K Bedi
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Elena Bochenkova
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Anna Müller
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Elena V Moroz-Omori
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Danzhi Huang
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
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18
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Graef J, Ehrt C, Diedrich K, Poppinga M, Ritter N, Rarey M. Searching Geometric Patterns in Protein Binding Sites and Their Application to Data Mining in Protein Kinase Structures. J Med Chem 2021; 65:1384-1395. [PMID: 34491747 DOI: 10.1021/acs.jmedchem.1c01046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ever-growing number of protein-ligand complex structures can give fundamental insights into protein functions and protein-ligand interactions, especially in the field of protein kinase research. The number of tools to mine this data for individually defined structural motifs is restricted due to the challenging task of developing efficient index structures for 3D data in relational databases. Herein we present GeoMine, a database system with web front-end mining of more than 900 000 binding sites. It enables database searches for geometric (interaction) patterns in protein-ligand interfaces by, for example, textual, numerical, substructure, similarity, and 3D searches. GeoMine processes reasonably selective user-defined queries within minutes. We demonstrate its usability for advancing protein kinase research with a special emphasis on unusual interactions, their use in designing selective kinase inhibitors, and the analysis of reactive cysteine residues that are amenable to covalent kinase inhibitors. GeoMine is freely available as part of our modeling support server at https://proteins.plus.
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Affiliation(s)
- Joel Graef
- ZBH Center for Bioinformatics, Universität Hamburg, Bundesstraße 43, 20146 Hamburg, Germany
| | - Christiane Ehrt
- ZBH Center for Bioinformatics, Universität Hamburg, Bundesstraße 43, 20146 Hamburg, Germany
| | - Konrad Diedrich
- ZBH Center for Bioinformatics, Universität Hamburg, Bundesstraße 43, 20146 Hamburg, Germany
| | - Martin Poppinga
- ZBH Center for Bioinformatics, Universität Hamburg, Bundesstraße 43, 20146 Hamburg, Germany
| | - Norbert Ritter
- ZBH Center for Bioinformatics, Universität Hamburg, Bundesstraße 43, 20146 Hamburg, Germany
| | - Matthias Rarey
- ZBH Center for Bioinformatics, Universität Hamburg, Bundesstraße 43, 20146 Hamburg, Germany
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19
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Frontera A, Bauzá A. Biological halogen bonds in protein-ligand complexes: a combined QTAIM and NCIPlot study in four representative cases. Org Biomol Chem 2021; 19:6858-6864. [PMID: 34319314 DOI: 10.1039/d1ob01212f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this study, the PDB has been manually scrutinized by using a subset of all PDB entries containing organic iodinated ligands. Four structures exhibiting short IA halogen bonding (HaB) contacts (A stands for the σ-hole acceptor) have been selected and further analysed. In most hits, the sigma-hole acceptor corresponds to an O-atom of the amido group belonging to the protein backbone. In a minority of hits, the electron donors are O, S, Se or π-systems of the amino-acid side chains. A judicious selection of four PDB structures presenting all four types of HaB interactions (C-IA, A = O, S, Se, π) has been performed. For these selected structures, a comprehensive RI-MP2/def2-TZVP study has been carried out to evaluate the HaB energetically. Moreover, the interactions have been characterized by combining the quantum theory of "atoms-in-molecules" (QTAIM) and the noncovalent interaction plot (NCIPlot) and rationalized using the molecular electrostatic potential (MEP) surface.
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Affiliation(s)
- Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
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20
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Tosstorff A, Cole JC, Bartelt R, Kuhn B. Augmenting Structure-Based Design with Experimental Protein-Ligand Interaction Data: Molecular Recognition, Interactive Visualization, and Rescoring. ChemMedChem 2021; 16:3428-3438. [PMID: 34342128 DOI: 10.1002/cmdc.202100387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Indexed: 11/10/2022]
Abstract
The previously introduced ratio of frequencies (RF ) framework provides statistically sound information on the relative interaction preferences of atoms in crystal structures. By applying the methodology to protein-ligand complexes, we can investigate the significance of interactions that are employed in structure-based drug design. Here, we revisit three aspects of molecular recognition in the light of the RF framework, namely stacking interactions of heteroaromatic rings with protein amide groups, interactions of acidified C-H groups, and interaction differences between syn and anti lone pairs of carboxylate groups. In addition, we introduce a highly interactive visualization tool that facilitates design idea generation in structure-enabled drug discovery projects. Finally, we show that applying the RF analysis as a simple rescoring tool after docking improves enrichment factors for the DUD-E diverse targets subset supporting the relevance of our approach.
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Affiliation(s)
- Andreas Tosstorff
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Jason C Cole
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, CB2 1EZ, UK
| | - Richard Bartelt
- Chemical Computing Group, Kaiser-Wilhelm-Ring 11, 50672, Cologne, Germany
| | - Bernd Kuhn
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
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21
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Nguyen D, Xie X, Jakobi S, Terwesten F, Metz A, Nguyen TXP, Palchykov VA, Heine A, Reuter K, Klebe G. Targeting a Cryptic Pocket in a Protein-Protein Contact by Disulfide-Induced Rupture of a Homodimeric Interface. ACS Chem Biol 2021; 16:1090-1098. [PMID: 34081441 DOI: 10.1021/acschembio.1c00296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interference with protein-protein interfaces represents an attractive as well as challenging option for therapeutic intervention and drug design. The enzyme tRNA-guanine transglycosylase, a target to fight Shigellosis, is only functional as a homodimer. Although we previously produced monomeric variants by site-directed mutagenesis, we only crystallized the functional dimer, simply because upon crystallization the local protein concentration increases and favors formation of the dimer interface, which represents an optimal and highly stable packing of the protein in the solid state. Unfortunately, this prevents access to structural information about the interface geometry in its monomeric state and complicates the development of modulators that can interfere with and prevent dimer formation. Here, we report on a cysteine-containing protein variant in which, under oxidizing conditions, a disulfide linkage is formed. This reinforces a novel packing geometry of the enzyme. In this captured quasi-monomeric state, the monomer units arrange in a completely different way and, thus, expose a loop-helix motif, originally embedded into the old interface, now to the surface. The motif adopts a geometry incompatible with the original dimer formation. Via the soaking of fragments into the crystals, we identified several hits accommodating a cryptic binding site next to the loop-helix motif and modulated its structural features. Our study demonstrates the druggability of the interface by breaking up the homodimeric protein using an introduced disulfide cross-link. By rational concepts, we increased the potency of these fragments to a level where we confirmed their binding by NMR to a nondisulfide-linked TGT variant. The idea of intermediately introducing a disulfide linkage may serve as a general concept of how to transform a homodimer interface into a quasi-monomeric state and give access to essential structural and design information.
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Affiliation(s)
- Dzung Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Xiulan Xie
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Stephan Jakobi
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Felix Terwesten
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Alexander Metz
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - T. X. Phong Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Vitalii A. Palchykov
- Research Institute of Chemistry and Geology, Oles Honchar Dnipro National University, 72 Gagarina Avenue, Dnipro 49010, Ukraine
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
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22
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Tuerkova A, Ungvári O, Laczkó-Rigó R, Mernyák E, Szakács G, Özvegy-Laczka C, Zdrazil B. Data-Driven Ensemble Docking to Map Molecular Interactions of Steroid Analogs with Hepatic Organic Anion Transporting Polypeptides. J Chem Inf Model 2021; 61:3109-3127. [PMID: 34105971 PMCID: PMC8243326 DOI: 10.1021/acs.jcim.1c00362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Hepatic organic anion transporting polypeptides—OATP1B1,
OATP1B3, and OATP2B1—are expressed at the basolateral membrane
of hepatocytes, being responsible for the uptake of a wide range of
natural substrates and structurally unrelated pharmaceuticals. Impaired
function of hepatic OATPs has been linked to clinically relevant drug–drug
interactions leading to altered pharmacokinetics of administered drugs.
Therefore, understanding the commonalities and differences across
the three transporters represents useful knowledge to guide the drug
discovery process at an early stage. Unfortunately, such efforts remain
challenging because of the lack of experimentally resolved protein
structures for any member of the OATP family. In this study, we established
a rigorous computational protocol to generate and validate structural
models for hepatic OATPs. The multistep procedure is based on the
systematic exploration of available protein structures with shared
protein folding using normal-mode analysis, the calculation of multiple
template backbones from elastic network models, the utilization of
multiple template conformations to generate OATP structural models
with various degrees of conformational flexibility, and the prioritization
of models on the basis of enrichment docking. We employed the resulting
OATP models of OATP1B1, OATP1B3, and OATP2B1 to elucidate binding
modes of steroid analogs in the three transporters. Steroid conjugates
have been recognized as endogenous substrates of these transporters.
Thus, investigating this data set delivers insights into mechanisms
of substrate recognition. In silico predictions were complemented
with in vitro studies measuring the bioactivity of a compound set
on OATP expressing cell lines. Important structural determinants conferring
shared and distinct binding patterns of steroid analogs in the three
transporters have been identified. Overall, this comparative study
provides novel insights into hepatic OATP-ligand interactions and
selectivity. Furthermore, the integrative computational workflow for
structure-based modeling can be leveraged for other pharmaceutical
targets of interest.
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Affiliation(s)
- Alzbeta Tuerkova
- University of Vienna, Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Althanstraße 14, A-1090 Vienna, Austria
| | - Orsolya Ungvári
- Drug Resistance Research Group, Institute of Enzymology, RCNS, Eötvös Loránd Research Network, H-1117, Budapest, Magyar tudósok krt. 2, Hungary
| | - Réka Laczkó-Rigó
- Drug Resistance Research Group, Institute of Enzymology, RCNS, Eötvös Loránd Research Network, H-1117, Budapest, Magyar tudósok krt. 2, Hungary
| | - Erzsébet Mernyák
- Department of Organic Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
| | - Gergely Szakács
- Drug Resistance Research Group, Institute of Enzymology, RCNS, Eötvös Loránd Research Network, H-1117, Budapest, Magyar tudósok krt. 2, Hungary.,Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, A-1090 Vienna, Austria
| | - Csilla Özvegy-Laczka
- Drug Resistance Research Group, Institute of Enzymology, RCNS, Eötvös Loránd Research Network, H-1117, Budapest, Magyar tudósok krt. 2, Hungary
| | - Barbara Zdrazil
- University of Vienna, Department of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, Althanstraße 14, A-1090 Vienna, Austria
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23
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Veale CGL. Into the Fray! A Beginner's Guide to Medicinal Chemistry. ChemMedChem 2021; 16:1199-1225. [PMID: 33591595 DOI: 10.1002/cmdc.202000929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 12/31/2022]
Abstract
Modern medicinal chemistry is a complex, multidimensional discipline that operates at the interface of the chemical and biological sciences. The medicinal chemistry contribution to drug discovery is typically described in the context of the well-recited linear progression of the drug discovery pipeline. However, compound optimization is idiosyncratic to each project, and clear definitions of hit and lead molecules and the subsequent progress along the pipeline becomes easily blurred. In addition, this description lacks insight into the entangled relationship between chemical and pharmacological properties, and thus provides limited guidance on how innovative medicinal chemistry strategies can be applied to solve optimization problems, regardless of the stage in the pipeline. Through discussion and illustrative examples, this article seeks to provide insights into the finesse of medicinal chemistry and the subtlety of balancing chemical properties pharmacology. In so doing, it aims to serve as an accessible and simple-to-digest guide for anyone who wishes to learn about the underlying principles of medicinal chemistry, in a context that has been decoupled from the pipeline description.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg, Scottsville, 3209, South Africa
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24
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Oliveira MP, Andrey M, Rieder SR, Kern L, Hahn DF, Riniker S, Horta BAC, Hünenberger PH. Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes. J Chem Theory Comput 2020; 16:7525-7555. [DOI: 10.1021/acs.jctc.0c00683] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marina P. Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Maurice Andrey
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R. Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Leyla Kern
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - David F. Hahn
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A. C. Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Philippe H. Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Honggerberg, HCI, CH-8093 Zürich, Switzerland
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25
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Erdeljac N, Mück‐Lichtenfeld C, Daniliuc CG, Gilmour R. Conformational Analysis of Acyclic α-Fluoro Sulfur Motifs. Chemistry 2020; 26:13704-13715. [PMID: 32735052 PMCID: PMC7702044 DOI: 10.1002/chem.202003361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 07/29/2020] [Indexed: 12/04/2022]
Abstract
Bioactive small molecules containing α-fluoro sulfur motifs [RS(O)n CH2 F] are appearing with increasing frequency in the pharmaceutical and agrochemical sectors. Prominent examples include the anti-asthma drug Flovent® and the phenylpyrazole insecticide pyrafluprole. Given the popularity of these structural units in bioactive small molecule design, together with the varying oxidation states of sulfur, a conformational analysis of α-fluoro sulfides, sulfoxides, and sulfones, would be instructive in order to delineate the non-covalent interactions that manifest themselves in structure. A combined crystallographic and computational analysis demonstrates the importance of hyperconjugative donor-acceptor interactions in achieving acyclic conformational control. The conformational disparity in the syn- and anti-diastereoisomers of α-fluorosulfoxides is particularly noteworthy.
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Affiliation(s)
- Nathalie Erdeljac
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 3648149MünsterGermany
| | - Christian Mück‐Lichtenfeld
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 3648149MünsterGermany
| | - Constantin G. Daniliuc
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 3648149MünsterGermany
| | - Ryan Gilmour
- Organisch-Chemisches InstitutWestfälische Wilhelms-Universität MünsterCorrensstraße 3648149MünsterGermany
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26
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Tosstorff A, Cole JC, Taylor R, Harris SF, Kuhn B. Identification of Noncompetitive Protein–Ligand Interactions for Structural Optimization. J Chem Inf Model 2020; 60:6595-6611. [DOI: 10.1021/acs.jcim.0c00858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Andreas Tosstorff
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Jason C. Cole
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Robin Taylor
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Seth F. Harris
- Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Bernd Kuhn
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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27
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Douangamath A, Fearon D, Gehrtz P, Krojer T, Lukacik P, Owen CD, Resnick E, Strain-Damerell C, Aimon A, Ábrányi-Balogh P, Brandão-Neto J, Carbery A, Davison G, Dias A, Downes TD, Dunnett L, Fairhead M, Firth JD, Jones SP, Keeley A, Keserü GM, Klein HF, Martin MP, Noble MEM, O'Brien P, Powell A, Reddi RN, Skyner R, Snee M, Waring MJ, Wild C, London N, von Delft F, Walsh MA. Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease. Nat Commun 2020; 11:5047. [PMID: 33028810 PMCID: PMC7542442 DOI: 10.1038/s41467-020-18709-w] [Citation(s) in RCA: 302] [Impact Index Per Article: 75.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.
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Affiliation(s)
- Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Paul Gehrtz
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - C David Owen
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Efrat Resnick
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Anthony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - José Brandão-Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Anna Carbery
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Gemma Davison
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Alexandre Dias
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Thomas D Downes
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Michael Fairhead
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - James D Firth
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - S Paul Jones
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Aaron Keeley
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - György M Keserü
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Hanna F Klein
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Mathew P Martin
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
| | - Martin E M Noble
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
| | - Peter O'Brien
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Ailsa Powell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Rambabu N Reddi
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Rachael Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Matthew Snee
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Michael J Waring
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Conor Wild
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Nir London
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK.
- Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa.
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
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28
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Exploiting binding-site arginines in drug design: Recent examples. Bioorg Med Chem Lett 2020; 30:127442. [DOI: 10.1016/j.bmcl.2020.127442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/19/2020] [Accepted: 07/21/2020] [Indexed: 11/21/2022]
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29
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Lemke C, Cianni L, Feldmann C, Gilberg E, Yin J, Dos Reis Rocho F, de Vita D, Bartz U, Bajorath J, Montanari CA, Gütschow M. N-Sulfonyl dipeptide nitriles as inhibitors of human cathepsin S: In silico design, synthesis and biochemical characterization. Bioorg Med Chem Lett 2020; 30:127420. [PMID: 32763808 DOI: 10.1016/j.bmcl.2020.127420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 11/27/2022]
Abstract
A library of cathepsin S inhibitors of the dipeptide nitrile chemotype, bearing a bioisosteric sulfonamide moiety, was synthesized. Kinetic investigations were performed at four human cysteine proteases, i.e. cathepsins S, B, K and L. Compound 12 with a terminal 3-biphenyl sulfonamide substituent was the most potent (Ki = 4.02 nM; selectivity ratio cathepsin S/K = 5.8; S/L = 67) and 24 with a 4'-fluoro-4-biphenyl sulfonamide substituent the most selective cathepsin S inhibitor (Ki = 35.5 nM; selectivity ratio cathepsin S/K = 57; S/L = 31). In silico design and biochemical evaluation emphasized the impact of the sulfonamide linkage on selectivity and a possible switch of P2 and P3 substituents with respect to the occupation of the corresponding binding sites of cathepsin S.
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Affiliation(s)
- Carina Lemke
- Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Lorenzo Cianni
- Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany; Bonn Aachen International Center for Information Technology BIT, Life Science Informatics, University of Bonn, Endenicher Allee 19c, D-53115 Bonn, Germany; Instituto de Química de Sao Carlos, University of Sao Paulo, Avenida Trabalhador Sancarlense 400, BR-13560-970 Sao Carlos, Brazil
| | - Christian Feldmann
- Bonn Aachen International Center for Information Technology BIT, Life Science Informatics, University of Bonn, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Erik Gilberg
- Bonn Aachen International Center for Information Technology BIT, Life Science Informatics, University of Bonn, Endenicher Allee 19c, D-53115 Bonn, Germany
| | - Jiafei Yin
- Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Fernanda Dos Reis Rocho
- Instituto de Química de Sao Carlos, University of Sao Paulo, Avenida Trabalhador Sancarlense 400, BR-13560-970 Sao Carlos, Brazil
| | - Daniela de Vita
- Instituto de Química de Sao Carlos, University of Sao Paulo, Avenida Trabalhador Sancarlense 400, BR-13560-970 Sao Carlos, Brazil
| | - Ulrike Bartz
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Str. 20, D-53359 Rheinbach, Germany
| | - Jürgen Bajorath
- Bonn Aachen International Center for Information Technology BIT, Life Science Informatics, University of Bonn, Endenicher Allee 19c, D-53115 Bonn, Germany.
| | - Carlos A Montanari
- Instituto de Química de Sao Carlos, University of Sao Paulo, Avenida Trabalhador Sancarlense 400, BR-13560-970 Sao Carlos, Brazil.
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany.
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30
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Zhu Z, Xu Z, Zhu W. Interaction Nature and Computational Methods for Halogen Bonding: A Perspective. J Chem Inf Model 2020; 60:2683-2696. [DOI: 10.1021/acs.jcim.0c00032] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
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31
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Scharf MM, Zimmermann M, Wilhelm F, Stroe R, Waldhoer M, Kolb P. A Focus on Unusual ECL2 Interactions Yields β 2 -Adrenergic Receptor Antagonists with Unprecedented Scaffolds. ChemMedChem 2020; 15:882-890. [PMID: 32301583 PMCID: PMC7318225 DOI: 10.1002/cmdc.201900715] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/11/2020] [Indexed: 11/15/2022]
Abstract
The binding pockets of aminergic G protein-coupled receptors are often targeted by drugs and virtual screening campaigns. In order to find ligands with unprecedented scaffolds for one of the best-investigated receptors of this subfamily, the β2 -adrenergic receptor, we conducted a docking-based screen insisting that molecules would address previously untargeted residues in extracellular loop 2. We here report the discovery of ligands with a previously undescribed coumaran-based scaffold. Furthermore, we provide an analysis of the added value that X-ray structures in different conformations deliver for such docking screens.
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Affiliation(s)
- Magdalena M. Scharf
- Department of Pharmaceutical ChemistryPhilipps-University MarburgMarbacher Weg 635037MarburgGermany
| | | | - Florian Wilhelm
- InterAx BiotechPARK innovAARE5234VilligenSwitzerland
- Department of Biosystems Science and Engineering ETHETH ZürichMattenstrasse 264058BaselSwitzerland
| | - Raimond Stroe
- InterAx BiotechPARK innovAARE5234VilligenSwitzerland
- Department of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | | | - Peter Kolb
- Department of Pharmaceutical ChemistryPhilipps-University MarburgMarbacher Weg 635037MarburgGermany
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32
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Loeffler JR, Fernández-Quintero ML, Schauperl M, Liedl KR. STACKED - Solvation Theory of Aromatic Complexes as Key for Estimating Drug Binding. J Chem Inf Model 2020; 60:2304-2313. [PMID: 32142283 PMCID: PMC7189365 DOI: 10.1021/acs.jcim.9b01165] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
The
use of fragments to biophysically characterize a protein binding
pocket and determine the strengths of certain interactions is a computationally
and experimentally commonly applied approach. Almost all drug like
molecules contain at least one aromatic moiety forming stacking interactions
in the binding pocket. In computational drug design, the strength
of stacking and the resulting optimization of the aromatic core or
moiety is usually calculated using high level quantum mechanical approaches.
However, as these calculations are performed in a vacuum, solvation
properties are neglected. We close this gap by using Grid Inhomogeneous
Solvation Theory (GIST) to describe the properties of individual heteroaromatics
and complexes and thereby estimate the desolvation penalty. In our
study, we investigated the solvation free energies of heteroaromatics
frequently occurring in drug design projects in complex with truncated
side chains of phenylalanine, tyrosine, and tryptophan. Furthermore,
we investigated the properties of drug-fragments crystallized in a
fragment-based lead optimization approach investigating PDE-10-A.
We do not only find good correlation for the estimated desolvation
penalty and the experimental binding free energy, but our calculations
also allow us to predict prominent interaction sites. We highlight
the importance of including the desolvation penalty of the respective
heteroaromatics in stacked complexes to explain the gain or loss in
affinity of potential lead compounds.
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Affiliation(s)
- Johannes R Loeffler
- Institute of General, Inorganic and Theoretical Chemistry, and Center of Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Monica L Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center of Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Michael Schauperl
- Institute of General, Inorganic and Theoretical Chemistry, and Center of Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Tyrol, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center of Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Tyrol, Austria
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33
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Taylor R. Identifying intermolecular atom⋯atom interactions that are not just bonding but also competitive. CrystEngComm 2020. [DOI: 10.1039/d0ce00270d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This highlight criticises the QTAIM method and discusses algorithms for identifying intermolecular interactions that are both bonding and competitive.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre
- Cambridge CB2 1EZ
- UK
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