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Janke JJ, Starr CG, Kingsbury JS, Furtmann N, Roberts CJ, Calero-Rubio C. Computational Screening for mAb Colloidal Stability with Coarse-Grained, Molecular-Scale Simulations. J Phys Chem B 2024; 128:1515-1526. [PMID: 38315822 DOI: 10.1021/acs.jpcb.3c05303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Monoclonal antibodies (mAbs) are an important modality of protein therapeutics with broad applications for numerous diseases. However, colloidal instabilities occurring at high protein concentrations can limit the ability to develop stable, high-concentration liquid dosage forms that are required for patient-centric, device-mediated products. Therefore, it is advantageous to identify colloidally stable mAbs early in the discovery process to ensure that they are selected for development. Experimental screening for colloidal stability can be time- and resource-consuming and is most feasible at the later stages of drug development due to material requirements. Alternatively, computational approaches have emerging potential to provide efficient screening and focus developmental efforts on mAbs with the greatest developability potential, while providing mechanistic relationships for colloidal instability. In this work, coarse-grained, molecular-scale models were fine-tuned to screen for colloidal stability at amino-acid resolution. This model parameterization provides a framework to screen for mAb self-interactions and extrapolate to bulk solution behavior. This approach was applied to a wide array of mAbs under multiple buffer conditions, demonstrating the utility of the presented computational approach to augment early candidate screening and later formulation strategies for protein therapeutics.
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Affiliation(s)
- J Joel Janke
- Biologics Drug Product Development and Manufacturing, Sanofi, Framingham, Massachusetts 01701, United States
| | - Charles G Starr
- Biologics Drug Product Development and Manufacturing, Sanofi, Framingham, Massachusetts 01701, United States
| | - Jonathan S Kingsbury
- Biologics Drug Product Development and Manufacturing, Sanofi, Framingham, Massachusetts 01701, United States
| | - Norbert Furtmann
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Cesar Calero-Rubio
- Biologics Drug Product Development and Manufacturing, Sanofi, Framingham, Massachusetts 01701, United States
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2
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Ziegengeist T, Orth J, Kroll K, Schneider M, Spindler N, Dimova D, Handschuh S, Brandenburg A, Ossola R, Furtmann N, Birkenfeld J, Beil C, Hoffmann D, Schmidt T, Sendak R, Fischer M, Hölper S, Kühn J. High-Throughput and Format-Agnostic Mispairing Assay for Multispecific Antibodies Using Intact Mass Spectrometry. Anal Chem 2023. [PMID: 37369001 DOI: 10.1021/acs.analchem.3c00742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Multispecific antibodies have gained significant importance in a broad indication space due to their ability to engage multiple epitopes simultaneously and to thereby overcome therapeutic barriers. With growing therapeutic potential, however, the molecular complexity increases, thus intensifying the demand for innovative protein engineering and analytical strategies. A major challenge for multispecific antibodies is the correct assembly of light and heavy chains. Engineering strategies exist to stabilize the correct pairing, but typically individual engineering campaigns are required to arrive at the anticipated format. Mass spectrometry has proven to be a versatile tool to identify mispaired species. However, due to manual data analysis procedures, mass spectrometry is limited to lower throughputs. To keep pace with increasing sample numbers, we developed a high-throughput-capable mispairing workflow based on intact mass spectrometry with automated data analysis, peak detection, and relative quantification using Genedata Expressionist. This workflow is capable of detecting mispaired species of ∼1000 multispecific antibodies in three weeks and thus is applicable to complex screening campaigns. As a proof of concept, the assay was applied to engineering a trispecific antibody. Strikingly, the new setup has not only proved successful in mispairing analysis but has also revealed its potential to automatically annotate other product-related impurities. Furthermore, we could confirm the assay to be format-agnostic, as shown by analyzing several different multispecific formats in one run. With these comprehensive capabilities, the new automated intact mass workflow can be applied as a universal tool to detect and annotate peaks in a format-agnostic approach and in high-throughput, thus enabling complex discovery campaigns.
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Affiliation(s)
- Tanja Ziegengeist
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Jennifer Orth
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Katja Kroll
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Marion Schneider
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Nadja Spindler
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Dilyana Dimova
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Severin Handschuh
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | | | | | - Norbert Furtmann
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Joerg Birkenfeld
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
- Perspix Biotech GmbH FiZ Frankfurt Innovation Center Biotechnology, Frankfurt 60438, Germany
| | - Christian Beil
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Dietmar Hoffmann
- Large Molecules Research Platform, Sanofi, Cambridge, Massachusetts 02141, United States
| | - Thorsten Schmidt
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Rebecca Sendak
- Large Molecules Research Platform, Sanofi, Cambridge, Massachusetts 02141, United States
| | - Melanie Fischer
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Soraya Hölper
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
| | - Jennifer Kühn
- Large Molecules Research Platform, Sanofi-Aventis Deutschland GmbH, Frankfurt 65926, Germany
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3
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Promsote W, Xu L, Hataye J, Fabozzi G, March K, Almasri CG, DeMouth ME, Lovelace SE, Talana CA, Doria-Rose NA, McKee K, Hait SH, Casazza JP, Ambrozak D, Beninga J, Rao E, Furtmann N, Birkenfeld J, McCarthy E, Todd JP, Petrovas C, Connors M, Hebert AT, Beck J, Shen J, Zhang B, Levit M, Wei RR, Yang ZY, Pegu A, Mascola JR, Nabel GJ, Koup RA. Trispecific antibody targeting HIV-1 and T cells activates and eliminates latently-infected cells in HIV/SHIV infections. Nat Commun 2023; 14:3719. [PMID: 37349337 PMCID: PMC10287722 DOI: 10.1038/s41467-023-39265-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Agents that can simultaneously activate latent HIV, increase immune activation and enhance the killing of latently-infected cells represent promising approaches for HIV cure. Here, we develop and evaluate a trispecific antibody (Ab), N6/αCD3-αCD28, that targets three independent proteins: (1) the HIV envelope via the broadly reactive CD4-binding site Ab, N6; (2) the T cell antigen CD3; and (3) the co-stimulatory molecule CD28. We find that the trispecific significantly increases antigen-specific T-cell activation and cytokine release in both CD4+ and CD8+ T cells. Co-culturing CD4+ with autologous CD8+ T cells from ART-suppressed HIV+ donors with N6/αCD3-αCD28, results in activation of latently-infected cells and their elimination by activated CD8+ T cells. This trispecific antibody mediates CD4+ and CD8+ T-cell activation in non-human primates and is well tolerated in vivo. This HIV-directed antibody therefore merits further development as a potential intervention for the eradication of latent HIV infection.
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Affiliation(s)
- Wanwisa Promsote
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ling Xu
- Sanofi, 640 Memorial Dr., Cambridge, MA, 02139, USA
- ModeX Therapeutics Inc., 22 Strathmore Road, Natick, MA, 01760, USA
| | - Jason Hataye
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Giulia Fabozzi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kylie March
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cassandra G Almasri
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Megan E DeMouth
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sarah E Lovelace
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Chloe Adrienna Talana
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sabrina Helmold Hait
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joseph P Casazza
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Ercole Rao
- Sanofi, 640 Memorial Dr., Cambridge, MA, 02139, USA
| | | | - Joerg Birkenfeld
- Sanofi, 640 Memorial Dr., Cambridge, MA, 02139, USA
- Perspix Biotech GmbH, FiZ Frankfurt Innovation Center Biotechnology, Altenhoeferallee 3, 60438, Frankfurt, Germany
| | - Elizabeth McCarthy
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John-Paul Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Constantinos Petrovas
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital (chuv) and University of Lausanne, Lausanne, Switzerland
| | | | | | - Jeremy Beck
- Sanofi, 640 Memorial Dr., Cambridge, MA, 02139, USA
| | - Junqing Shen
- Sanofi, 640 Memorial Dr., Cambridge, MA, 02139, USA
| | - Bailin Zhang
- Sanofi, 640 Memorial Dr., Cambridge, MA, 02139, USA
| | | | - Ronnie R Wei
- Sanofi, 640 Memorial Dr., Cambridge, MA, 02139, USA
- ModeX Therapeutics Inc., 22 Strathmore Road, Natick, MA, 01760, USA
| | - Zhi-Yong Yang
- Sanofi, 640 Memorial Dr., Cambridge, MA, 02139, USA
- ModeX Therapeutics Inc., 22 Strathmore Road, Natick, MA, 01760, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- ModeX Therapeutics Inc., 22 Strathmore Road, Natick, MA, 01760, USA
| | - Gary J Nabel
- Sanofi, 640 Memorial Dr., Cambridge, MA, 02139, USA.
- ModeX Therapeutics Inc., 22 Strathmore Road, Natick, MA, 01760, USA.
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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Furtmann N, Schneider M, Spindler N, Steinmann B, Li Z, Focken I, Meyer J, Dimova D, Kroll K, Leuschner WD, Debeaumont A, Mathieu M, Lange C, Dittrich W, Kruip J, Schmidt T, Birkenfeld J. An end-to-end automated platform process for high-throughput engineering of next-generation multi-specific antibody therapeutics. MAbs 2021; 13:1955433. [PMID: 34382900 PMCID: PMC8366542 DOI: 10.1080/19420862.2021.1955433] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Next-generation multi-specific antibody therapeutics (MSATs) are engineered to combine several functional activities into one molecule to provide higher efficacy compared to conventional, mono-specific antibody therapeutics. However, highly engineered MSATs frequently display poor yields and less favorable drug-like properties (DLPs), which can adversely affect their development. Systematic screening of a large panel of MSAT variants in very high throughput (HT) is thus critical to identify potent molecule candidates with good yield and DLPs early in the discovery process. Here we report on the establishment of a novel, format-agnostic platform process for the fast generation and multiparametric screening of tens of thousands of MSAT variants. To this end, we have introduced full automation across the entire value chain for MSAT engineering. Specifically, we have automated the in-silico design of very large MSAT panels such that it reflects precisely the wet-lab processes for MSAT DNA library generation. This includes mass saturation mutagenesis or bulk modular cloning technologies while, concomitantly, enabling library deconvolution approaches using HT Sanger DNA sequencing. These DNA workflows are tightly linked to fully automated downstream processes for compartmentalized mammalian cell transfection expression, and screening of multiple parameters. All sub-processes are seamlessly integrated with tailored workflow supporting bioinformatics. As described here, we used this platform to perform multifactor optimization of a next-generation bispecific, cross-over dual variable domain-Ig (CODV-Ig). Screening of more than 25,000 individual protein variants in mono- and bispecific format led to the identification of CODV-Ig variants with over 1,000-fold increased potency and significantly optimized production titers, demonstrating the power and versatility of the platform.
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Affiliation(s)
- Norbert Furtmann
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Marion Schneider
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Nadja Spindler
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Bjoern Steinmann
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Ziyu Li
- R&D Integrated Drug Discovery Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Ingo Focken
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Joachim Meyer
- Digital R&D, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Dilyana Dimova
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Katja Kroll
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Wulf Dirk Leuschner
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Audrey Debeaumont
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Magali Mathieu
- R&D Integrated Drug Discovery France, Sanofi, Vitry Sur Seine Cedex, France
| | - Christian Lange
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Werner Dittrich
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Jochen Kruip
- IA Specialty Care Digital Innovation Biologics, Sanofi-Aventis Deutschland GmbH, Frankfurt Am Main, Germany
| | - Thorsten Schmidt
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
| | - Joerg Birkenfeld
- R&D Large Molecules Research Platform Germany, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Frankfurt Am Main, Germany
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5
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Iqbal J, Abbasi MS, Zaib S, Afridi S, Furtmann N, Bajorath J, Langer P. Identification of New Chromenone Derivatives as Cholinesterase Inhibitors and Molecular Docking Studies. Med Chem 2018; 14:809-817. [DOI: 10.2174/1573406414666180222091833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 01/27/2018] [Accepted: 01/29/2018] [Indexed: 11/22/2022]
Affiliation(s)
- Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS Institute of Information Technology, Abbottabad, Abbottabad-22060, Pakistan
| | - Muhammad S.A. Abbasi
- Institut für Chemie, Universität Rostock, Albert Einstein Str. 3A, 18059 Rostock, Germany
| | - Sumera Zaib
- Centre for Advanced Drug Research, COMSATS Institute of Information Technology, Abbottabad, Abbottabad-22060, Pakistan
| | - Saifullah Afridi
- Centre for Advanced Drug Research, COMSATS Institute of Information Technology, Abbottabad, Abbottabad-22060, Pakistan
| | - Norbert Furtmann
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich- Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich- Wilhelms-Universität, Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Peter Langer
- Institut für Chemie, Universität Rostock, Albert Einstein Str. 3A, 18059 Rostock, Germany
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Häußler D, Mangold M, Furtmann N, Braune A, Blaut M, Bajorath J, Stirnberg M, Gütschow M. Back Cover: Phosphono Bisbenzguanidines as Irreversible Dipeptidomimetic Inhibitors and Activity-Based Probes of Matriptase-2 (Chem. Eur. J. 25/2016). Chemistry 2016. [DOI: 10.1002/chem.201601295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Daniela Häußler
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Martin Mangold
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Norbert Furtmann
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
- Department of Life Science Informatics, B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; University of Bonn; Dahlmannstrasse 2 53113 Bonn Germany
| | - Annett Braune
- Department of Gastrointestinal Microbiology; German Institute of Human Nutrition Potsdam-Rehbruecke; Arthur-Scheunert-Allee 114-116 14558 Nuthetal Germany
| | - Michael Blaut
- Department of Gastrointestinal Microbiology; German Institute of Human Nutrition Potsdam-Rehbruecke; Arthur-Scheunert-Allee 114-116 14558 Nuthetal Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; University of Bonn; Dahlmannstrasse 2 53113 Bonn Germany
| | - Marit Stirnberg
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Michael Gütschow
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
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7
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Häußler D, Mangold M, Furtmann N, Braune A, Blaut M, Bajorath J, Stirnberg M, Gütschow M. Phosphono Bisbenzguanidines as Irreversible Dipeptidomimetic Inhibitors and Activity-Based Probes of Matriptase-2. Chemistry 2016; 22:8525-35. [DOI: 10.1002/chem.201600206] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Daniela Häußler
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Martin Mangold
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Norbert Furtmann
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
- Department of Life Science Informatics, B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; University of Bonn; Dahlmannstrasse 2 53113 Bonn Germany
| | - Annett Braune
- Department of Gastrointestinal Microbiology; German Institute of Human Nutrition Potsdam-Rehbruecke; Arthur-Scheunert-Allee 114-116 14558 Nuthetal Germany
| | - Michael Blaut
- Department of Gastrointestinal Microbiology; German Institute of Human Nutrition Potsdam-Rehbruecke; Arthur-Scheunert-Allee 114-116 14558 Nuthetal Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; University of Bonn; Dahlmannstrasse 2 53113 Bonn Germany
| | - Marit Stirnberg
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Michael Gütschow
- Pharmaceutical Institute; Pharmaceutical Chemistry I; University of Bonn; An der Immenburg 4 53121 Bonn Germany
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8
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Beckmann AM, Maurer E, Lülsdorff V, Wilms A, Furtmann N, Bajorath J, Gütschow M, Stirnberg M. Cover Picture: En Route to New Therapeutic Options for Iron Overload Diseases: Matriptase-2 as a Target for Kunitz-Type Inhibitors (ChemBioChem 7/2016). Chembiochem 2016. [DOI: 10.1002/cbic.201600126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Eva Maurer
- Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Verena Lülsdorff
- Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Annika Wilms
- Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Norbert Furtmann
- Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
- Department of Life Science Informatics; B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; University of Bonn; Dahlmannstrasse 2 53113 Bonn Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics; B-IT; LIMES Program Unit Chemical Biology and Medicinal Chemistry; University of Bonn; Dahlmannstrasse 2 53113 Bonn Germany
| | - Michael Gütschow
- Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Marit Stirnberg
- Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
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9
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Furtmann N, Bajorath J. Structural and Modeling Studies on ecto-5'-nucleotidase Aiding in Inhibitor Design. Mini Rev Med Chem 2016; 15:34-40. [PMID: 25694084 DOI: 10.2174/1389557515666150219112630] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/24/2014] [Accepted: 10/11/2014] [Indexed: 11/22/2022]
Abstract
Ecto-5'-nucleotidase (e5NT) hydrolyzes extracellular nucleotides and contributes to purinergic signaling. e5NT is implicated in a variety of pathological states including immunological diseases and cancer and represents an emerging drug target. Herein, we review structural and computational studies that have helped to better understand ligand binding characteristics and mechanistic features of the enzyme and led to the identification of new classes of e5NT inhibitors.
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Affiliation(s)
| | - Jurgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universitat, Dahlmannstr. 2, D-53113 Bonn, Germany.
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10
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Beckmann AM, Maurer E, Lülsdorff V, Wilms A, Furtmann N, Bajorath J, Gütschow M, Stirnberg M. En Route to New Therapeutic Options for Iron Overload Diseases: Matriptase-2 as a Target for Kunitz-Type Inhibitors. Chembiochem 2016; 17:595-604. [PMID: 26762582 DOI: 10.1002/cbic.201500651] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Indexed: 02/04/2023]
Abstract
The cell-surface serine protease matriptase-2 is a critical stimulator of iron absorption by negatively regulating hepcidin, the key hormone of iron homeostasis. Thus, it has attracted much attention as a target in primary and secondary iron overload diseases. Here, we have characterised Kunitz-type inhibitors hepatocyte growth factor activator inhibitor 1 (HAI-1) and HAI-2 as powerful, slow-binding matriptase-2 inhibitors. The binding modes of the matriptase-2-HAI complexes were suggested by molecular modelling. Different assays, including cell-free and cell-based measurements of matriptase-2 activity, determination of inhibition constants and evaluation of matriptase-2 inhibition by analysis of downstream effects in human liver cells, demonstrated that matriptase-2 is an excellent target for Kunitz inhibitors. In particular, HAI-2 is considered a promising scaffold for the design of potent and selective matriptase-2 inhibitors.
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Affiliation(s)
| | - Eva Maurer
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Verena Lülsdorff
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Annika Wilms
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Norbert Furtmann
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.,Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Dahlmannstrasse 2, 53113, Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Dahlmannstrasse 2, 53113, Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Marit Stirnberg
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany.
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11
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Furtmann N, Häußler D, Scheidt T, Stirnberg M, Steinmetzer T, Bajorath J, Gütschow M. Limiting the Number of Potential Binding Modes by Introducing Symmetry into Ligands: Structure-Based Design of Inhibitors for Trypsin-Like Serine Proteases. Chemistry 2015; 22:610-25. [DOI: 10.1002/chem.201503534] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Indexed: 12/18/2022]
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12
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Hameed A, Khan KM, Zehra ST, Ahmed R, Shafiq Z, Bakht SM, Yaqub M, Hussain M, de la Vega de León A, Furtmann N, Bajorath J, Shad HA, Tahir MN, Iqbal J. Synthesis, biological evaluation and molecular docking of N-phenyl thiosemicarbazones as urease inhibitors. Bioorg Chem 2015; 61:51-7. [DOI: 10.1016/j.bioorg.2015.06.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/01/2015] [Accepted: 06/20/2015] [Indexed: 11/28/2022]
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13
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Schmitz J, Furtmann N, Ponert M, Frizler M, Löser R, Bartz U, Bajorath J, Gütschow M. Active Site Mapping of Human Cathepsin F with Dipeptide Nitrile Inhibitors. ChemMedChem 2015; 10:1365-77. [PMID: 26119278 DOI: 10.1002/cmdc.201500151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Indexed: 11/09/2022]
Abstract
Cleavage of the invariant chain is the key event in the trafficking pathway of major histocompatibility complex class II. Cathepsin S is the major processing enzyme of the invariant chain, but cathepsin F acts in macrophages as its functional synergist which is as potent as cathepsin S in invariant chain cleavage. Dedicated low-molecular-weight inhibitors for cathepsin F have not yet been developed. An active site mapping with 52 dipeptide nitriles, reacting as covalent-reversible inhibitors, was performed to draw structure-activity relationships for the non-primed binding region of human cathepsin F. In a stepwise process, new compounds with optimized fragment combinations were designed and synthesized. These dipeptide nitriles were evaluated on human cysteine cathepsins F, B, L, K and S. Compounds 10 (N-(4-phenylbenzoyl)-leucylglycine nitrile) and 12 (N-(4-phenylbenzoyl)leucylmethionine nitrile) were found to be potent inhibitors of human cathepsin F, with Ki values <10 nM. With all dipeptide nitriles from our study, a 3D activity landscape was generated to visualize structure-activity relationships for this series of cathepsin F inhibitors.
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Affiliation(s)
- Janina Schmitz
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany).,Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg von-Liebig-Straße 20, 53359 Rheinbach (Germany)
| | - Norbert Furtmann
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany).,Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Dahlmannstraße 2, 53113 Bonn (Germany)
| | - Moritz Ponert
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany)
| | - Maxim Frizler
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany)
| | - Reik Löser
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany).,Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden (Germany)
| | - Ulrike Bartz
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg von-Liebig-Straße 20, 53359 Rheinbach (Germany)
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Dahlmannstraße 2, 53113 Bonn (Germany)
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany).
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14
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Furtmann N, Hu Y, Gütschow M, Bajorath J. Identification of Interaction Hot Spots in Structures of Drug Targets on the Basis of Three-Dimensional Activity Cliff Information. Chem Biol Drug Des 2015; 86:1458-65. [PMID: 26094578 DOI: 10.1111/cbdd.12605] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/04/2015] [Accepted: 06/06/2015] [Indexed: 12/24/2022]
Abstract
Activity cliffs are defined as pairs or groups of structurally similar or analogous compounds that share the same specific activity but have large differences in potency. Although activity cliffs are mostly studied in medicinal chemistry at the level of molecular graphs, they can also be assessed by comparing compound binding modes. If such three-dimensional activity cliffs (3D-cliffs) are studied on the basis of X-ray complex structures, experimental ligand-target interaction details can be taken into account. Rapid growth in the number of 3D-cliffs that can be derived from X-ray complex structures has made it possible to identify targets for which a substantial body of 3D-cliff information is available. Activity cliffs are typically studied to identify structure-activity relationship determinants and aid in compound optimization. However, 3D-cliff information can also be used to search for interaction hot spots and key residues, as reported herein. For six of seven drug targets for which more than 20 3D-cliffs were available, series of 3D-cliffs were identified that were consistently involved in interactions with different hot spots. These 3D-cliffs often encoded chemical modifications resulting in interactions that were characteristic of highly potent compounds but absent in weakly potent ones, thus providing information for structure-based design.
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Affiliation(s)
- Norbert Furtmann
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113, Bonn, Germany.,Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany
| | - Ye Hu
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113, Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr. 2, D-53113, Bonn, Germany
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15
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Hameed A, Zehra ST, Shah SJA, Khan KM, Alharthy RD, Furtmann N, Bajorath J, Tahir MN, Iqbal J. Syntheses, Cholinesterases Inhibition, and Molecular Docking Studies of Pyrido[2,3-b
]pyrazine Derivatives. Chem Biol Drug Des 2015; 86:1115-20. [DOI: 10.1111/cbdd.12579] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 04/17/2015] [Accepted: 04/27/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Abdul Hameed
- H. E. J. Research Institute of Chemistry; International Center for Chemical and Biological Sciences; University of Karachi; Karachi 75270 Pakistan
| | - Syeda T. Zehra
- H. E. J. Research Institute of Chemistry; International Center for Chemical and Biological Sciences; University of Karachi; Karachi 75270 Pakistan
| | - Syed J. A. Shah
- Centre for Advanced Drug Research; COMSATS Institute of Information Technology; Abbottabad 22060 Pakistan
| | - Khalid M. Khan
- H. E. J. Research Institute of Chemistry; International Center for Chemical and Biological Sciences; University of Karachi; Karachi 75270 Pakistan
| | - Rima D. Alharthy
- Department of Chemistry; King Abdulaziz University; Jeddah Saudi Arabia
| | - Norbert Furtmann
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry; Rheinische Friedrich-Wilhelms-Universität; Dahlmann Str. 2 D-53113 Bonn Germany
- Pharmaceutical Institute; University of Bonn; An der Immenburg 4 D-53121 Bonn Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry; Rheinische Friedrich-Wilhelms-Universität; Dahlmann Str. 2 D-53113 Bonn Germany
| | | | - Jamshed Iqbal
- Centre for Advanced Drug Research; COMSATS Institute of Information Technology; Abbottabad 22060 Pakistan
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16
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Abstract
Shown is a superposition of two analogs (green and orange) on crystallographic ligands (magenta and cyan) forming a three-dimensional activity cliff (MMP stands for Matched Molecular Pair).
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Affiliation(s)
- Ye Hu
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Norbert Furtmann
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Jürgen Bajorath
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
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17
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Kohl F, Schmitz J, Furtmann N, Schulz-Fincke AC, Mertens MD, Küppers J, Benkhoff M, Tobiasch E, Bartz U, Bajorath J, Stirnberg M, Gütschow M. Design, characterization and cellular uptake studies of fluorescence-labeled prototypic cathepsin inhibitors. Org Biomol Chem 2015; 13:10310-23. [DOI: 10.1039/c5ob01613d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cysteine cathepsin inhibition and cellular uptake of a coumarin 343-containing dipeptide nitrile was analyzed.
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Affiliation(s)
- Franziska Kohl
- Pharmaceutical Institute
- Pharmaceutical Chemistry I
- University of Bonn
- D-53121 Bonn, Germany
| | - Janina Schmitz
- Pharmaceutical Institute
- Pharmaceutical Chemistry I
- University of Bonn
- D-53121 Bonn, Germany
- Department of Natural Sciences
| | - Norbert Furtmann
- Pharmaceutical Institute
- Pharmaceutical Chemistry I
- University of Bonn
- D-53121 Bonn, Germany
- Department of Life Science Informatics
| | | | - Matthias D. Mertens
- Pharmaceutical Institute
- Pharmaceutical Chemistry I
- University of Bonn
- D-53121 Bonn, Germany
| | - Jim Küppers
- Pharmaceutical Institute
- Pharmaceutical Chemistry I
- University of Bonn
- D-53121 Bonn, Germany
| | - Marcel Benkhoff
- Pharmaceutical Institute
- Pharmaceutical Chemistry I
- University of Bonn
- D-53121 Bonn, Germany
| | - Edda Tobiasch
- Department of Natural Sciences
- Bonn-Rhein-Sieg University of Applied Sciences
- D-53359 Rheinbach, Germany
| | - Ulrike Bartz
- Department of Natural Sciences
- Bonn-Rhein-Sieg University of Applied Sciences
- D-53359 Rheinbach, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- University of Bonn
- D-53113 Bonn, Germany
| | - Marit Stirnberg
- Pharmaceutical Institute
- Pharmaceutical Chemistry I
- University of Bonn
- D-53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical Institute
- Pharmaceutical Chemistry I
- University of Bonn
- D-53121 Bonn, Germany
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18
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Furtmann N, Hu Y, Gütschow M, Bajorath J. Identification and analysis of the currently available high-confidence three-dimensional activity cliffs. RSC Adv 2015. [DOI: 10.1039/c5ra01730k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Shown is an exemplary 3D-cliff formed by two crystallographic ligands with highly similar binding modes and a significant difference in potency. The site of a major interaction difference between these compounds is encircled.
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Affiliation(s)
- Norbert Furtmann
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | - Ye Hu
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
| | | | - Jürgen Bajorath
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn
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19
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Khan I, Ibrar A, Zaib S, Ahmad S, Furtmann N, Hameed S, Simpson J, Bajorath J, Iqbal J. Active compounds from a diverse library of triazolothiadiazole and triazolothiadiazine scaffolds: Synthesis, crystal structure determination, cytotoxicity, cholinesterase inhibitory activity, and binding mode analysis. Bioorg Med Chem 2014; 22:6163-73. [DOI: 10.1016/j.bmc.2014.08.026] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 10/24/2022]
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20
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Furtmann N, Hu Y, Bajorath J. Comprehensive Analysis of Three-Dimensional Activity Cliffs Formed by Kinase Inhibitors with Different Binding Modes and Cliff Mapping of Structural Analogues. J Med Chem 2014; 58:252-64. [DOI: 10.1021/jm5009264] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Norbert Furtmann
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
- Pharmaceutical Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Ye Hu
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
| | - Jürgen Bajorath
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
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21
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Affiliation(s)
- Ye Hu
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
| | - Norbert Furtmann
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
- Pharmaceutical
Institute, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 4, D-53121 Bonn, Germany
| | - Jürgen Bajorath
- Department
of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology
and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
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22
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Aslam S, Zaib S, Ahmad M, Gardiner JM, Ahmad A, Hameed A, Furtmann N, Gütschow M, Bajorath J, Iqbal J. Novel structural hybrids of pyrazolobenzothiazines with benzimidazoles as cholinesterase inhibitors. Eur J Med Chem 2014; 78:106-17. [DOI: 10.1016/j.ejmech.2014.03.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 03/09/2014] [Accepted: 03/12/2014] [Indexed: 12/31/2022]
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23
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Mertens MD, Schmitz J, Horn M, Furtmann N, Bajorath J, Mareš M, Gütschow M. A coumarin-labeled vinyl sulfone as tripeptidomimetic activity-based probe for cysteine cathepsins. Chembiochem 2014; 15:955-9. [PMID: 24648212 DOI: 10.1002/cbic.201300806] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Indexed: 12/15/2022]
Abstract
A coumarin-tetrahydroquinoline hydride 8 was synthesized as a chemical tool for fluorescent labeling. The rigidified tricyclic coumarin structure was chosen for its suitable fluorescence properties. The connection of 8 with a vinyl sulfone building block was accomplished by convergent synthesis thereby leading to the coumarin-based, tripeptidomimetic activity-based probe 10, containing a Gly-Phe-Gly motif. Probe 10 was evaluated as inactivator of the therapeutically relevant human cysteine cathepsins S, L, K, and B: it showed particularly strong inactivation of cathepsin S. The detection of recombinant and native cathepsin S was demonstrated by applying 10 to in-gel fluorescence imaging.
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Affiliation(s)
- Matthias D Mertens
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn (Germany)
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24
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Furtmann N, Bajorath J. Evaluation of molecular model-based discovery of ecto-5’-nucleotidase inhibitors on the basis of X-ray structures. J Cheminform 2014. [PMCID: PMC3980193 DOI: 10.1186/1758-2946-6-s1-p13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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25
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Wysocka M, Gruba N, Miecznikowska A, Popow-Stellmaszyk J, Gütschow M, Stirnberg M, Furtmann N, Bajorath J, Lesner A, Rolka K. Substrate specificity of human matriptase-2. Biochimie 2014; 97:121-7. [DOI: 10.1016/j.biochi.2013.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/01/2013] [Indexed: 01/22/2023]
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26
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Saeed A, Tehseen Y, Rafique H, Furtmann N, Bajorath J, Flörke U, Iqbal J. Benzothiazolyl substituted iminothiazolidinones and benzamido-oxothiazolidines as potent and partly selective aldose reductase inhibitors. Med Chem Commun 2014. [DOI: 10.1039/c4md00206g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two new series of oxothiazolidine benzoate and acetate derivatives were synthesized and evaluated as aldehyde reductase (ALR1) and aldose reductase (ALR2) inhibitors.
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Affiliation(s)
- Aamer Saeed
- Department of Chemistry
- Quaid-i-Azam University
- 1slamabad, Pakistan
| | - Yildiz Tehseen
- Centre for Advanced Drug Research
- COMSATS Institute of Information Technology
- Abbottabad, Pakistan
| | - Hummera Rafique
- Department of Chemistry
- Quaid-i-Azam University
- 1slamabad, Pakistan
| | - Norbert Furtmann
- Department of Life Science Informatics
- B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn, Germany
- Pharmaceutical Institute
| | - Jürgen Bajorath
- Department of Life Science Informatics
- B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- D-53113 Bonn, Germany
| | - Ulrich Flörke
- Department Chemie
- Fakultät für Naturwissenschaften
- Universität Paderborn
- D-33098 Paderborn, Germany
| | - Jamshed Iqbal
- Centre for Advanced Drug Research
- COMSATS Institute of Information Technology
- Abbottabad, Pakistan
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27
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Iqbal J, Saeed A, Raza R, Matin A, Hameed A, Furtmann N, Lecka J, Sévigny J, Bajorath J. Identification of sulfonic acids as efficient ecto-5′-nucleotidase inhibitors. Eur J Med Chem 2013; 70:685-91. [DOI: 10.1016/j.ejmech.2013.10.053] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 10/13/2013] [Accepted: 10/21/2013] [Indexed: 02/01/2023]
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28
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Furtmann N, Bajorath J. Evaluation of molecular model-based discovery of ecto-5′-nucleotidase inhibitors on the basis of X-ray structures. Bioorg Med Chem 2013; 21:6616-22. [DOI: 10.1016/j.bmc.2013.08.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/26/2013] [Accepted: 08/08/2013] [Indexed: 11/25/2022]
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29
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Hu Y, Furtmann N, Gütschow M, Bajorath J. Systematic Identification and Classification of Three-Dimensional Activity Cliffs. J Chem Inf Model 2012; 52:1490-8. [DOI: 10.1021/ci300158v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ye Hu
- Department of Life Science Informatics,
B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr.
2, D-53113 Bonn, Germany
| | - Norbert Furtmann
- Department of Life Science Informatics,
B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr.
2, D-53113 Bonn, Germany
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn,
Germany
| | - Michael Gütschow
- Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn,
Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics,
B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstr.
2, D-53113 Bonn, Germany
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30
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Frizler M, Lohr F, Furtmann N, Kläs J, Gütschow M. Structural Optimization of Azadipeptide Nitriles Strongly Increases Association Rates and Allows the Development of Selective Cathepsin Inhibitors. J Med Chem 2010; 54:396-400. [DOI: 10.1021/jm101272p] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maxim Frizler
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Friederike Lohr
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Norbert Furtmann
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Julia Kläs
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
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