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Woodhead AJ, Erlanson DA, de Esch IJP, Holvey RS, Jahnke W, Pathuri P. Fragment-to-Lead Medicinal Chemistry Publications in 2022. J Med Chem 2024; 67:2287-2304. [PMID: 38289623 DOI: 10.1021/acs.jmedchem.3c02070] [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: 02/02/2024]
Abstract
This Perspective is the eighth in an annual series that summarizes successful fragment-to-lead (F2L) case studies published each year. A tabulated summary of relevant articles published in 2022 is provided, and features such as target class, screening methods, and ligand efficiency are discussed both for the 2022 examples and for the combined examples over the years 2015-2022. In addition, trends and new developments in the field are summarized. In 2022, 18 publications described successful fragment-to-lead studies, including the development of three clinical compounds (MTRX1719, MK-8189, and BI-823911).
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Affiliation(s)
- Andrew J Woodhead
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Blvd., South San Francisco, California 94080, United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Rhian S Holvey
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Wolfgang Jahnke
- Novartis Biomedical Research, Discovery Sciences, 4002 Basel, Switzerland
| | - Puja Pathuri
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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2
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Schütz S, Bergsdorf C, Hänni-Holzinger S, Lingel A, Renatus M, Gossert AD, Jahnke W. Intrinsically Disordered Regions in the Transcription Factor MYC:MAX Modulate DNA Binding via Intramolecular Interactions. Biochemistry 2024. [PMID: 38264995 DOI: 10.1021/acs.biochem.3c00608] [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: 01/25/2024]
Abstract
The basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factor (TF) MYC is in large part an intrinsically disordered oncoprotein. In complex with its obligate heterodimerization partner MAX, MYC preferentially binds E-Box DNA sequences (CANNTG). At promoters containing these sequence motifs, MYC controls fundamental cellular processes such as cell cycle progression, metabolism, and apoptosis. A vast network of proteins in turn regulates MYC function via intermolecular interactions. In this work, we establish another layer of MYC regulation by intramolecular interactions. We used nuclear magnetic resonance (NMR) spectroscopy to identify and map multiple binding sites for the C-terminal MYC:MAX DNA-binding domain (DBD) on the intrinsically disordered regions (IDRs) in the MYC N-terminus. We find that these binding events in trans are driven by electrostatic attraction, that they have distinct affinities, and that they are competitive with DNA binding. Thereby, we observe the strongest effects for the N-terminal MYC box 0 (Mb0), a conserved motif involved in MYC transactivation and target gene induction. We prepared recombinant full-length MYC:MAX complex and demonstrate that the interactions identified in this work are also relevant in cis, i.e., as intramolecular interactions. These findings are supported by surface plasmon resonance (SPR) experiments, which revealed that intramolecular IDR:DBD interactions in MYC decelerate the association of MYC:MAX complexes to DNA. Our work offers new insights into how bHLH-LZ TFs are regulated by intramolecular interactions, which open up new possibilities for drug discovery.
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Affiliation(s)
- Stefan Schütz
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christian Bergsdorf
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sandra Hänni-Holzinger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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3
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Abstract
This Perspective is the seventh in an annual series that summarizes successful Fragment-to-Lead (F2L) case studies published in a given year. A tabulated summary of relevant articles published in 2021 is provided, and features such as target class, screening methods, and ligand efficiency are discussed, both for the 2021 examples and for the combined examples over the years 2015-2021. In addition, trends and new developments in the field are summarized. In particular, the use of structural information in fragment-based drug discovery is discussed.
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Affiliation(s)
- Louise Walsh
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Blvd., South San Francisco, California 94080, United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Andrew Woodhead
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Ella Wren
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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4
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Jahnke W, Paladini J, Habazettl JM, Wiget A, Loo A, Cowan Jacob SW, Grzesiek S, Manley PW. Correspondence on “Synergy and Antagonism between Allosteric and Active‐Site Inhibitors of Abl Tyrosine Kinase”**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117276] [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: 11/10/2022]
Affiliation(s)
- Wolfgang Jahnke
- Novartis Institutes for Biomedical Research 4002 Basel Switzerland
| | | | | | - Andrea Wiget
- Research Institute of Organic Agriculture (FiBL) 5070 Frick Switzerland
| | - Alice Loo
- Novartis Institutes for BioMedical Research Cambridge MA 02139 USA
| | | | | | - Paul W. Manley
- Novartis Institutes for Biomedical Research 4002 Basel Switzerland
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5
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Jahnke W, Paladini J, Habazettl JM, Wiget A, Loo A, Cowan Jacob SW, Grzesiek S, Manley PW. Correspondence on “Synergy and Antagonism between Allosteric and Active‐Site Inhibitors of Abl Tyrosine Kinase”**. Angew Chem Int Ed Engl 2022; 61:e202117276. [DOI: 10.1002/anie.202117276] [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] [Received: 12/20/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Wolfgang Jahnke
- Novartis Institutes for Biomedical Research 4002 Basel Switzerland
| | | | | | - Andrea Wiget
- Research Institute of Organic Agriculture (FiBL) 5070 Frick Switzerland
| | - Alice Loo
- Novartis Institutes for BioMedical Research Cambridge MA 02139 USA
| | | | | | - Paul W. Manley
- Novartis Institutes for Biomedical Research 4002 Basel Switzerland
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6
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Schütz S, Bergsdorf C, Goretzki B, Lingel A, Renatus M, Gossert AD, Jahnke W. The disordered MAX N-terminus modulates DNA binding of the transcription factor MYC:MAX. J Mol Biol 2022; 434:167833. [PMID: 36174765 DOI: 10.1016/j.jmb.2022.167833] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 07/22/2022] [Revised: 09/05/2022] [Accepted: 09/17/2022] [Indexed: 11/15/2022]
Abstract
The intrinsically disordered protein MYC belongs to the family of basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factors (TFs). In complex with its cognate binding partner MAX, MYC preferentially binds to E-Box promotor sequences where it controls fundamental cellular processes such as cell cycle progression, metabolism, and apoptosis. Intramolecular regulation of MYC:MAX has not yet been investigated in detail. In this work, we use Nuclear Magnetic Resonance (NMR) spectroscopy to identify and map interactions between the disordered MAX N-terminus and the MYC:MAX DNA binding domain (DBD). We find that this binding event is mainly driven by electrostatic interactions and that it is competitive with DNA binding. Using Nuclear Magnetic resonance (NMR) spectroscopy and Surface Plasmon Resonance (SPR), we demonstrate that the MAX N-terminus serves to accelerate DNA binding kinetics of MYC:MAX and MAX:MAX dimers, while it simultaneously provides specificity for E-Box DNA. We also establish that these effects are further enhanced by Casein Kinase 2-mediated phosphorylation of two serine residues in the MAX N-terminus. Our work provides new insights how bHLH-LZ TFs are regulated by intramolecular interactions between disordered regions and the folded DNA binding domain.
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Affiliation(s)
- Stefan Schütz
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christian Bergsdorf
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Benedikt Goretzki
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Alvar D Gossert
- Department of Biology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland.
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7
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Abstract
Fragment-based drug discovery (FBDD) continues to evolve and make an impact in the pharmaceutical sciences. We summarize successful fragment-to-lead studies that were published in 2020. Having systematically analyzed annual scientific outputs since 2015, we discuss trends and best practices in terms of fragment libraries, target proteins, screening technologies, hit-optimization strategies, and the properties of hit fragments and the leads resulting from them. As well as the tabulated Fragment-to-Lead (F2L) programs, our 2020 literature review identifies several trends and innovations that promise to further increase the success of FBDD. These include developing structurally novel screening fragments, improving fragment-screening technologies, using new computer-aided design and virtual screening approaches, and combining FBDD with other innovative drug-discovery technologies.
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Affiliation(s)
- Iwan J. P. de Esch
- Division
of Medicinal Chemistry, Amsterdam Institute of Molecular and Life
Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Daniel A. Erlanson
- Frontier
Medicines, 151 Oyster
Point Blvd., South San Francisco, California 94080, United States
| | - Wolfgang Jahnke
- Novartis
Institutes for Biomedical Research, Chemical
Biology and Therapeutics, 4002 Basel, Switzerland
| | - Christopher N. Johnson
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Louise Walsh
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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8
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Romasanta AKS, van der Sijde PC, Smit MJ, de Esch IJP, Jahnke W, van Muijlwijk-Koezen JE. Career development in fragment-based drug discovery. Drug Discov Today Technol 2021; 37:107-116. [PMID: 34895649 DOI: 10.1016/j.ddtec.2020.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/16/2020] [Indexed: 11/20/2022]
Abstract
The pharmaceutical industry is highly reliant on researchers who not only possess the technical knowledge but also the professional skills to collaborate in drug development. To prepare future practitioners to thrive in this interdisciplinary environment, Innovative Training Networks (ITNs) have become increasingly important in doctoral training. In this piece, we explore the benefits of these ITNs in training future practitioners in drug discovery. Through a bibliometric review, we find that the top researchers in fragment-based drug discovery have a high degree of collaboration and mobility across institutes. We then investigate which aspects of the ITN training program enable PhD students to gain these skills. We find that secondments, the short-term stays that students have in partner research institutes, are useful in preparing students to have both broad knowledge of drug discovery and specialization in their field of interest. Aside from imparting technical skills, we find that the collaborative environment in ITNs enables students to communicate better and to work effectively in teams. Doctoral students benefit by being exposed to relevant experiences that they can later apply as they navigate through the complex web of relationships and competencies in the industry. We conclude by recommending best practices to further improve ITNs in the training of future practitioners.
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Affiliation(s)
- A K S Romasanta
- Division of Science, Business & Innovation, Faculty of Science, VU University Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands; Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
| | - P C van der Sijde
- Division of Science, Business & Innovation, Faculty of Science, VU University Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - M J Smit
- Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - I J P de Esch
- Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - W Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - J E van Muijlwijk-Koezen
- Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands; Division of Innovation in Human Health & Life Sciences, Faculty of Science, VU University Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
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9
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Ciulli A, Hamann L, Jahnke W, Kalgutkar AS, Magauer T, Ritter T, Steadman V, Williams SD, Winter G, Hoegenauer K, Krawinkler KH, Stepan AF. The 2 nd Alpine Winter Conference on Medicinal and Synthetic Chemistry. ChemMedChem 2021; 16:2417-2423. [PMID: 34114371 DOI: 10.1002/cmdc.202100372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 11/07/2022]
Abstract
The second biannual Alpine Winter Conference on Medicinal and Synthetic Chemistry (short: Alpine Winter Conference) took place January 19-23, 2020, in St. Anton in western Austria. There were roughly 180 attendees from around the globe, making this mid-sized conference particularly conducive to networking and exchanging ideas over the course of four and a half days. This report summarizes the key events and presentations given by researchers working in both industry and academia.
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Affiliation(s)
- Alessio Ciulli
- Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Lawrence Hamann
- Drug Discovery Sciences, Takeda Pharmaceuticals, 30 Landsdowne Street, Cambridge, MA 02139, USA
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, 4002, Basel, Switzerland
| | - Amit S Kalgutkar
- Medicine Design, Pfizer, Inc., 1 Portland Street, Cambridge, MA 02139, USA
| | - Thomas Magauer
- Department of Chemistry and Pharmacy, Institute of Organic Chemistry, Leopold-Franzens-University Innsbruck, Innrain 80-82, L02.012, 6020, Innsbruck, Austria
| | - Tobias Ritter
- Max-Planck Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Muelheim an der Ruhr, Germany
| | | | | | - Georg Winter
- Research Center for Molecular Medicine (CeMM), Austrian Academy of Sciences, 1090, Vienna, Austria
| | | | | | - Antonia F Stepan
- F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland
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Jahnke W, Erlanson DA, de Esch IJP, Johnson CN, Mortenson PN, Ochi Y, Urushima T. Fragment-to-Lead Medicinal Chemistry Publications in 2019. J Med Chem 2020; 63:15494-15507. [PMID: 33226222 DOI: 10.1021/acs.jmedchem.0c01608] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fragment-based drug discovery (FBDD) has grown and matured to a point where it is valuable to keep track of its extent and details of application. This Perspective summarizes successful fragment-to-lead stories published in 2019. It is the fifth in a series that started with literature published in 2015. The analysis of screening methods, optimization strategies, and molecular properties of hits and leads are presented in the hope of informing best practices for FBDD. Moreover, FBDD is constantly evolving, and the latest technologies and emerging trends are summarized. These include covalent FBDD, FBDD for the stabilization of proteins or protein-protein interactions, FBDD for enzyme activators, new screening technologies, and advances in library design and chemical synthesis.
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Affiliation(s)
- Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Boulevard, South San Francisco, California 94080, United States of America
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Yuji Ochi
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Tatsuya Urushima
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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11
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Münzker L, Petrick JK, Schleberger C, Clavel D, Cornaciu I, Wilcken R, Márquez JA, Klebe G, Marzinzik A, Jahnke W. Fragment-Based Discovery of Non-bisphosphonate Binders of Trypanosoma brucei Farnesyl Pyrophosphate Synthase. Chembiochem 2020; 21:3096-3111. [PMID: 32537808 DOI: 10.1002/cbic.202000246] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/29/2020] [Indexed: 12/26/2022]
Abstract
Trypanosoma brucei is the causative agent of human African trypanosomiasis (HAT). Nitrogen-containing bisphosphonates, a current treatment for bone diseases, have been shown to block the growth of the T. brucei parasites by inhibiting farnesyl pyrophosphate synthase (FPPS); however, due to their poor pharmacokinetic properties, they are not well suited for antiparasitic therapy. Recently, an allosteric binding pocket was discovered on human FPPS, but its existence on trypanosomal FPPS was unclear. We applied NMR and X-ray fragment screening to T. brucei FPPS and report herein on four fragments bound to this previously unknown allosteric site. Surprisingly, non-bisphosphonate active-site binders were also identified. Moreover, fragment screening revealed a number of additional binding sites. In an early structure-activity relationship (SAR) study, an analogue of an active-site binder was unexpectedly shown to bind to the allosteric site. Overlaying identified fragment binders of a parallel T. cruzi FPPS fragment screen with the T. brucei FPPS structure, and medicinal chemistry optimisation based on two binders revealed another example of fragment "pocket hopping". The discovery of binders with new chemotypes sets the framework for developing advanced compounds with pharmacokinetic properties suitable for the treatment of parasitic infections by inhibition of FPPS in T. brucei parasites.
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Affiliation(s)
- Lena Münzker
- Novartis Institutes for Biomedical Research Novartis Campus, 4002, Basel, Switzerland
| | - Joy Kristin Petrick
- Novartis Institutes for Biomedical Research Novartis Campus, 4002, Basel, Switzerland
| | - Christian Schleberger
- Novartis Institutes for Biomedical Research Novartis Campus, 4002, Basel, Switzerland
| | - Damien Clavel
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, CEDEX 9, France
| | - Irina Cornaciu
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, CEDEX 9, France.,ALPX, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, CEDEX 9, France
| | - Rainer Wilcken
- Novartis Institutes for Biomedical Research Novartis Campus, 4002, Basel, Switzerland
| | - José A Márquez
- EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, CEDEX 9, France.,ALPX, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, CEDEX 9, France
| | - Gerhard Klebe
- Institut für Pharmazie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Andreas Marzinzik
- Novartis Institutes for Biomedical Research Novartis Campus, 4002, Basel, Switzerland
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research Novartis Campus, 4002, Basel, Switzerland
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12
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Norton RS, Jahnke W. Correction to: NMR in pharmaceutical discovery and development. J Biomol NMR 2020; 74:477. [PMID: 33185771 DOI: 10.1007/s10858-020-00351-9] [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] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The article "Boeszoermenyi A, Ogórek B, Jain A, Arthanari H, Wagner G (2020) The precious fluorine on the ring: fluorine NMR for biological systems. J Biomol NMR. https ://doi.org/10.1007/s10858-020-00331-z" was written for the "Special Issue: NMR in Pharmaceutical Discovery and Development". However, unfortunately, it was published in an earlier issue of this journal owing to a publisher error. Further, the ORCID ID of author Wolfgang Jahnke is updated in the article. The original article has been corrected.
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Affiliation(s)
- Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
- ARC Centre for Fragment-Based Design, Monash University, Parkville, VIC, 3052, Australia.
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Virchow-16.3.249, 4002, Basel, Switzerland.
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13
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Affiliation(s)
- Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
- ARC Centre for Fragment-Based Design, Monash University, Parkville, VIC, 3052, Australia.
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Virchow-16.3.249, 4002, Basel, Switzerland.
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14
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Fairhurst RA, Knoepfel T, Buschmann N, Leblanc C, Mah R, Todorov M, Nimsgern P, Ripoche S, Niklaus M, Warin N, Luu VH, Madoerin M, Wirth J, Graus-Porta D, Weiss A, Kiffe M, Wartmann M, Kinyamu-Akunda J, Sterker D, Stamm C, Adler F, Buhles A, Schadt H, Couttet P, Blank J, Galuba I, Trappe J, Voshol J, Ostermann N, Zou C, Berghausen J, Del Rio Espinola A, Jahnke W, Furet P. Discovery of Roblitinib (FGF401) as a Reversible-Covalent Inhibitor of the Kinase Activity of Fibroblast Growth Factor Receptor 4. J Med Chem 2020; 63:12542-12573. [PMID: 32930584 DOI: 10.1021/acs.jmedchem.0c01019] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
FGF19 signaling through the FGFR4/β-klotho receptor complex has been shown to be a key driver of growth and survival in a subset of hepatocellular carcinomas, making selective FGFR4 inhibition an attractive treatment opportunity. A kinome-wide sequence alignment highlighted a poorly conserved cysteine residue within the FGFR4 ATP-binding site at position 552, two positions beyond the gate-keeper residue. Several strategies for targeting this cysteine to identify FGFR4 selective inhibitor starting points are summarized which made use of both rational and unbiased screening approaches. The optimization of a 2-formylquinoline amide hit series is described in which the aldehyde makes a hemithioacetal reversible-covalent interaction with cysteine 552. Key challenges addressed during the optimization are improving the FGFR4 potency, metabolic stability, and solubility leading ultimately to the highly selective first-in-class clinical candidate roblitinib.
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Affiliation(s)
- Robin A Fairhurst
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Thomas Knoepfel
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Nicole Buschmann
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Catherine Leblanc
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Robert Mah
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Milen Todorov
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Pierre Nimsgern
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Sebastien Ripoche
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Michel Niklaus
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Nicolas Warin
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Van Huy Luu
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Mario Madoerin
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Jasmin Wirth
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Diana Graus-Porta
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Andreas Weiss
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Michael Kiffe
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Markus Wartmann
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | | | - Dario Sterker
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Christelle Stamm
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Flavia Adler
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Alexandra Buhles
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Heiko Schadt
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Philippe Couttet
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Jutta Blank
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Inga Galuba
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Jörg Trappe
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Johannes Voshol
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Nils Ostermann
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Chao Zou
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Jörg Berghausen
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | | | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
| | - Pascal Furet
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland
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15
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Abstract
This Perspective, the fourth in an annual series, summarizes fragment-to-lead (F2L) success stories published during 2018. Topics such as target class, screening methods, physicochemical properties, and ligand efficiency are discussed for the 2018 examples as well as for the combined 111 F2L examples covering 2015-2018. While the overall properties of fragments and leads have remained constant, a number of new trends are noted, for example, broadening of target class coverage and application of FBDD to covalent inhibitors. Moreover, several studies make use of fragment hits that were previously described in the literature, illustrating that fragments are versatile starting points that can be optimized to structurally diverse leads. By focusing on success stories, the hope is that this Perspective will identify and inform best practices in fragment-based drug discovery.
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Affiliation(s)
- Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Boulevard, South San Francisco, California 94080, United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, 4002 Basel, Switzerland
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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16
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Sijbesma E, Hallenbeck KK, Leysen S, de Vink PJ, Skóra L, Jahnke W, Brunsveld L, Arkin MR, Ottmann C. Site-Directed Fragment-Based Screening for the Discovery of Protein–Protein Interaction Stabilizers. J Am Chem Soc 2019; 141:3524-3531. [DOI: 10.1021/jacs.8b11658] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Kenneth K. Hallenbeck
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California, San Francisco 94143, United States
| | - Seppe Leysen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Pim J. de Vink
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Lukasz Skóra
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, CH-4056 Basel, Switzerland
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, CH-4056 Basel, Switzerland
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Michelle R. Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California, San Francisco 94143, United States
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Department of Chemistry, University of Duisburg-Essen, 47057 Essen, Germany
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17
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Abstract
This Miniperspective is the third in a series reviewing fragment-to-lead publications from a given year. Following our reviews for 2015 and 2016, this Miniperspective provides tabulated summaries of relevant articles published in 2017 along with some general observations. In addition, we discuss insights obtained from analysis of the combined data set of 85 examples from all three years of publications.
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Affiliation(s)
- Paul N Mortenson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - Daniel A Erlanson
- Carmot Therapeutics Inc. , 740 Heinz Avenue , Berkeley , California 94710 , United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ , Amsterdam , The Netherlands
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics , Novartis Institutes for Biomedical Research , 4002 Basel , Switzerland
| | - Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
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18
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Fang Z, Marshall CB, Nishikawa T, Gossert AD, Jansen JM, Jahnke W, Ikura M. Inhibition of K-RAS4B by a Unique Mechanism of Action: Stabilizing Membrane-Dependent Occlusion of the Effector-Binding Site. Cell Chem Biol 2018; 25:1327-1336.e4. [DOI: 10.1016/j.chembiol.2018.07.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 02/21/2018] [Accepted: 07/24/2018] [Indexed: 12/19/2022]
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19
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Erlanson DA, Davis BJ, Jahnke W. Fragment-Based Drug Discovery: Advancing Fragments in the Absence of Crystal Structures. Cell Chem Biol 2018; 26:9-15. [PMID: 30482678 DOI: 10.1016/j.chembiol.2018.10.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/12/2018] [Accepted: 09/28/2018] [Indexed: 01/08/2023]
Abstract
Fragment-based drug discovery typically requires an interplay between screening methods, structural methods, and medicinal chemistry. X-ray crystallography is generally the method of choice to obtain three-dimensional structures of the bound ligand/protein complex, but this can sometimes be difficult, particularly for early, low-affinity fragment hits. In this Perspective, we discuss strategies to advance and evolve fragments in the absence of crystal structures of protein-fragment complexes, although the structure of the unliganded protein may be available. The strategies can involve other structural techniques, such as NMR spectroscopy, molecular modeling, or a variety of chemical approaches. Often, these strategies are aimed at guiding evolution of initial fragment hits to a stage where crystal structures can be obtained for further structure-based optimization.
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Affiliation(s)
- Daniel A Erlanson
- Carmot Therapeutics, Inc., 740 Heinz Avenue, Berkeley, CA 94710, USA.
| | - Ben J Davis
- Vernalis (R&D) Ltd, Granta Park, Cambridge, UK.
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Novartis Campus, Basel, Switzerland.
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20
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Schoepfer J, Jahnke W, Berellini G, Buonamici S, Cotesta S, Cowan-Jacob SW, Dodd S, Drueckes P, Fabbro D, Gabriel T, Groell JM, Grotzfeld RM, Hassan AQ, Henry C, Iyer V, Jones D, Lombardo F, Loo A, Manley PW, Pellé X, Rummel G, Salem B, Warmuth M, Wylie AA, Zoller T, Marzinzik AL, Furet P. Discovery of Asciminib (ABL001), an Allosteric Inhibitor of the Tyrosine Kinase Activity of BCR-ABL1. J Med Chem 2018; 61:8120-8135. [DOI: 10.1021/acs.jmedchem.8b01040] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Joseph Schoepfer
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | | | - Simona Cotesta
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sandra W. Cowan-Jacob
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Stephanie Dodd
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Peter Drueckes
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Tobias Gabriel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Jean-Marc Groell
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Robert M. Grotzfeld
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Chrystèle Henry
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Darryl Jones
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Alice Loo
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Paul W. Manley
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Xavier Pellé
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Gabriele Rummel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Bahaa Salem
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | | | - Thomas Zoller
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas L. Marzinzik
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Pascal Furet
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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21
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Abstract
The popularity of fragment-based drug discovery (FBDD) is demonstrated by the number of recent successful fragment-to-lead (F2L) publications. This Miniperspective provides a tabulated summary of the F2L literature published in the year 2016, along with discussion of general trends. It uses the same format as our summary of the 2015 literature and is intended to be a resource for both FBDD practitioners and medicinal chemists in general.
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Affiliation(s)
- Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - Daniel A Erlanson
- Carmot Therapeutics Inc. , 740 Heinz Avenue , Berkeley , California 94710 , United States
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics , 4002 Basel , Switzerland
| | - Paul N Mortenson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - David C Rees
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
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22
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Sijbesma E, Skora L, Leysen S, Brunsveld L, Koch U, Nussbaumer P, Jahnke W, Ottmann C. Identification of Two Secondary Ligand Binding Sites in 14-3-3 Proteins Using Fragment Screening. Biochemistry 2017; 56:3972-3982. [PMID: 28681606 PMCID: PMC5543393 DOI: 10.1021/acs.biochem.7b00153] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Proteins
typically interact with multiple binding partners, and
often different parts of their surfaces are employed to establish
these protein–protein interactions (PPIs). Members of the class
of 14-3-3 adapter proteins bind to several hundred other proteins
in the cell. Multiple small molecules for the modulation of 14-3-3
PPIs have been disclosed; however, they all target the conserved phosphopeptide
binding channel, so that selectivity is difficult to achieve. Here
we report on the discovery of two individual secondary binding sites
that have been identified by combining nuclear magnetic resonance-based
fragment screening and X-ray crystallography. The two pockets that
these fragments occupy are part of at least three physiologically
relevant and structurally characterized 14-3-3 PPI interfaces, including
those with serotonin N-acetyltransferase and plant
transcription factor FT. In addition, the high degree of conservation
of the two sites implies their relevance for 14-3-3 PPIs. This first
identification of secondary sites on 14-3-3 proteins bound by small
molecule ligands might facilitate the development of new chemical
tool compounds for more selective PPI modulation.
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Affiliation(s)
- Eline Sijbesma
- Department of Biomedical Engineering, Laboratory of Chemical Biology, and Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lukasz Skora
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research , 4002 Basel, Switzerland
| | - Seppe Leysen
- Department of Biomedical Engineering, Laboratory of Chemical Biology, and Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Department of Biomedical Engineering, Laboratory of Chemical Biology, and Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Uwe Koch
- Lead Discovery Center GmbH , Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Peter Nussbaumer
- Lead Discovery Center GmbH , Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research , 4002 Basel, Switzerland
| | - Christian Ottmann
- Department of Biomedical Engineering, Laboratory of Chemical Biology, and Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen , Essen, Germany
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23
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Abstract
In modern kinase drug discovery, allosteric inhibitors have become a focus of attention due to their potential selectivity, but such compounds are difficult to identify. Here we describe an NMR-based competition assay using 19F-containing reporter molecules, which allows for rapid identification and discrimination between ATP-competitive and allosteric kinase inhibitors. We illustrate the principle of such a dual-site competition assay with the example of catalytic and allosteric ABL1 kinase inhibitors. The assay can also be used to identify and characterize mixed binding modes of well-known drugs, as shown for crizotinib and fingolimod.
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Affiliation(s)
- Lukasz Skora
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
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24
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Jansen JM, Wartchow C, Jahnke W, Fong S, Tsang T, Pfister K, Zavorotinskaya T, Bussiere D, Cheng JM, Crawford K, Dai Y, Dove J, Fang E, Feng Y, Florent JM, Fuller J, Gossert AD, Hekmat-Nejad M, Henry C, Klopp J, Lenahan WP, Lingel A, Ma S, Meyer A, Mishina Y, Narberes J, Pardee G, Ramurthy S, Rieffel S, Stuart D, Subramanian S, Tandeske L, Widger S, Widmer A, Winterhalter A, Zaror I, Hardy S. Inhibition of prenylated KRAS in a lipid environment. PLoS One 2017; 12:e0174706. [PMID: 28384226 PMCID: PMC5383040 DOI: 10.1371/journal.pone.0174706] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/14/2017] [Indexed: 12/30/2022] Open
Abstract
RAS mutations lead to a constitutively active oncogenic protein that signals through multiple effector pathways. In this chemical biology study, we describe a novel coupled biochemical assay that measures activation of the effector BRAF by prenylated KRASG12V in a lipid-dependent manner. Using this assay, we discovered compounds that block biochemical and cellular functions of KRASG12V with low single-digit micromolar potency. We characterized the structural basis for inhibition using NMR methods and showed that the compounds stabilized the inactive conformation of KRASG12V. Determination of the biophysical affinity of binding using biolayer interferometry demonstrated that the potency of inhibition matches the affinity of binding only when KRAS is in its native state, namely post-translationally modified and in a lipid environment. The assays we describe here provide a first-time alignment across biochemical, biophysical, and cellular KRAS assays through incorporation of key physiological factors regulating RAS biology, namely a negatively charged lipid environment and prenylation, into the in vitro assays. These assays and the ligands we discovered are valuable tools for further study of KRAS inhibition and drug discovery.
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Affiliation(s)
- Johanna M. Jansen
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
- * E-mail:
| | - Charles Wartchow
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Wolfgang Jahnke
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Susan Fong
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Tiffany Tsang
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Keith Pfister
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Tatiana Zavorotinskaya
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Dirksen Bussiere
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Jan Marie Cheng
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Kenneth Crawford
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Yumin Dai
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Jeffrey Dove
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Eric Fang
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Yun Feng
- Department of Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Jean-Michel Florent
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - John Fuller
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Alvar D. Gossert
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Mohammad Hekmat-Nejad
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Chrystèle Henry
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Julia Klopp
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - William P. Lenahan
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Andreas Lingel
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Sylvia Ma
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Arndt Meyer
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Yuji Mishina
- Department of Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Jamie Narberes
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Gwynn Pardee
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Savithri Ramurthy
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Sebastien Rieffel
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Darrin Stuart
- Department of Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Sharadha Subramanian
- Department of Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Laura Tandeske
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Stephania Widger
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Armin Widmer
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Aurelie Winterhalter
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Isabel Zaror
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Stephen Hardy
- Department of Oncology, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
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25
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Mobitz H, Jahnke W, Cowan-Jacob S. Expanding the Opportunities for Modulating Kinase Targets with Allosteric Approaches. Curr Top Med Chem 2016; 17:59-70. [DOI: 10.2174/1568026616666160719165314] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 12/17/2015] [Accepted: 01/15/2016] [Indexed: 11/22/2022]
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26
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Gossert AD, Jahnke W. NMR in drug discovery: A practical guide to identification and validation of ligands interacting with biological macromolecules. Prog Nucl Magn Reson Spectrosc 2016; 97:82-125. [PMID: 27888841 DOI: 10.1016/j.pnmrs.2016.09.001] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 05/12/2023]
Abstract
Protein-ligand interactions are at the heart of drug discovery research. NMR spectroscopy is an excellent technology to identify and validate protein-ligand interactions. A plethora of NMR methods are available which are powerful, robust and information-rich, but also have pitfalls and limitations. In this review, we will focus on how to choose between different experiments, and assess their strengths and liabilities. We introduce the concept of the validation cross, which helps to categorize experiments according to their information content and to simplify the choice of the right experiment in order to address a specific question. Additionally, we will provide the framework for drawing correct conclusions from experimental results in order to accurately evaluate such interactions. Out of scope for this review are methods for subsequent characterization of the interaction such as quantitative KD determination, binding mode analysis, or structure determination.
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Affiliation(s)
- Alvar D Gossert
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002 Basel, Switzerland.
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002 Basel, Switzerland
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27
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Abstract
Drug discovery is a complex process, and a variety of technologies contribute to its success. Biophysical methods have gained widespread attention within the last decade, and in particular NMR spectroscopy as the most versatile biophysical method has seen numerous applications and significant impact to drug discovery. Here we summarize the potential of NMR to support drug discovery, and highlight a number of recent applications.
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Affiliation(s)
- Lukasz Skora
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4002 Basel, Switzerland
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Novartis Campus, CH-4002 Basel, Switzerland.
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28
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Jahnke W, Bold G, Marzinzik AL, Ofner S, Pellé X, Cotesta S, Bourgier E, Lehmann S, Henry C, Hemmig R, Stauffer F, Hartwieg JCD, Green JR, Rondeau JM. A General Strategy for Targeting Drugs to Bone. Angew Chem Int Ed Engl 2015; 54:14575-9. [PMID: 26457482 DOI: 10.1002/anie.201507064] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 07/30/2015] [Indexed: 11/08/2022]
Abstract
Targeting drugs to their desired site of action can increase their safety and efficacy. Bisphosphonates are prototypical examples of drugs targeted to bone. However, bisphosphonate bone affinity is often considered too strong and cannot be significantly modulated without losing activity on the enzymatic target, farnesyl pyrophosphate synthase (FPPS). Furthermore, bisphosphonate bone affinity comes at the expense of very low and variable oral bioavailability. FPPS inhibitors were developed with a monophosphonate as a bone-affinity tag that confers moderate affinity to bone, which can furthermore be tuned to the desired level, and the relationship between structure and bone affinity was evaluated by using an NMR-based bone-binding assay. The concept of targeting drugs to bone with moderate affinity, while retaining oral bioavailability, has broad application to a variety of other bone-targeted drugs.
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Affiliation(s)
- Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland).
| | - Guido Bold
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland)
| | - Andreas L Marzinzik
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland)
| | - Silvio Ofner
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland)
| | - Xavier Pellé
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland)
| | - Simona Cotesta
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland)
| | - Emmanuelle Bourgier
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland)
| | - Sylvie Lehmann
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland)
| | - Chrystelle Henry
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland)
| | - René Hemmig
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland)
| | - Frédéric Stauffer
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland)
| | - J Constanze D Hartwieg
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland)
| | - Jonathan R Green
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland)
| | - Jean-Michel Rondeau
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry and Oncology Research, 4002 Basel (Switzerland)
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29
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Jahnke W, Bold G, Marzinzik AL, Ofner S, Pellé X, Cotesta S, Bourgier E, Lehmann S, Henry C, Hemmig R, Stauffer F, Hartwieg JCD, Green JR, Rondeau JM. Gezielte Anreicherung von Wirkstoffen am Knochen am Beispiel von allosterischen FPPS-Inhibitoren. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Marzinzik AL, Amstutz R, Bold G, Bourgier E, Cotesta S, Glickman JF, Götte M, Henry C, Lehmann S, Hartwieg JCD, Ofner S, Pellé X, Roddy TP, Rondeau JM, Stauffer F, Stout SJ, Widmer A, Zimmermann J, Zoller T, Jahnke W. Discovery of Novel Allosteric Non-Bisphosphonate Inhibitors of Farnesyl Pyrophosphate Synthase by Integrated Lead Finding. ChemMedChem 2015; 10:1884-91. [PMID: 26381451 DOI: 10.1002/cmdc.201500338] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 07/30/2015] [Indexed: 12/27/2022]
Abstract
Farnesyl pyrophosphate synthase (FPPS) is an established target for the treatment of bone diseases, but also shows promise as an anticancer and anti-infective drug target. Currently available anti-FPPS drugs are active-site-directed bisphosphonate inhibitors, the peculiar pharmacological profile of which is inadequate for therapeutic indications beyond bone diseases. The recent discovery of an allosteric binding site has paved the way toward the development of novel non-bisphosphonate FPPS inhibitors with broader therapeutic potential, notably as immunomodulators in oncology. Herein we report the discovery, by an integrated lead finding approach, of two new chemical classes of allosteric FPPS inhibitors that belong to the salicylic acid and quinoline chemotypes. We present their synthesis, biochemical and cellular activities, structure-activity relationships, and provide X-ray structures of several representative FPPS complexes. These novel allosteric FPPS inhibitors are devoid of any affinity for bone mineral and could serve as leads to evaluate their potential in none-bone diseases.
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Affiliation(s)
| | - René Amstutz
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,Conim AG, Oberwiler Kirchweg 4c, 6300, Zug, Switzerland
| | - Guido Bold
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | | | - Simona Cotesta
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - J Fraser Glickman
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,High Throughput and Spectroscopy Resource Center, Rockefeller University, New York, NY, 10065, USA
| | - Marjo Götte
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Christelle Henry
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Sylvie Lehmann
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | | | - Silvio Ofner
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Xavier Pellé
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Thomas P Roddy
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,Agios, Cambridge, MA, 02139-4169, USA
| | | | - Frédéric Stauffer
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Steven J Stout
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,Merck Research Laboratories, 126 E. Lincoln Avenue, Rahway, NJ, 07065, USA
| | - Armin Widmer
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Johann Zimmermann
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.,Polyphor, Hegenheimermattweg 125, 4123, Allschwil, Switzerland
| | - Thomas Zoller
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Basel, 4002, Switzerland.
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31
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Skora L, Kempf D, Mestan J, D'Orazio D, Jahnke W. Phosphorylation of Tyr245 in the open-inhibited state of Abelson kinase does not induce downstream signaling. Eur J Haematol 2015; 96:502-6. [DOI: 10.1111/ejh.12627] [Citation(s) in RCA: 2] [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] [Accepted: 07/02/2015] [Indexed: 01/30/2023]
Affiliation(s)
- Lukasz Skora
- Center for Proteomic Chemistry; Novartis Institutes for Biomedical Research; Basel Switzerland
| | - Dominique Kempf
- Autoimmunity, Transplantation and Inflammatory Disease; Novartis Institutes for Biomedical Research; Basel Switzerland
| | - Jürgen Mestan
- Center for Proteomic Chemistry; Novartis Institutes for Biomedical Research; Basel Switzerland
| | - Daniel D'Orazio
- Autoimmunity, Transplantation and Inflammatory Disease; Novartis Institutes for Biomedical Research; Basel Switzerland
| | - Wolfgang Jahnke
- Center for Proteomic Chemistry; Novartis Institutes for Biomedical Research; Basel Switzerland
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32
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Karpov AS, Amiri P, Bellamacina C, Bellance MH, Breitenstein W, Daniel D, Denay R, Fabbro D, Fernandez C, Galuba I, Guerro-Lagasse S, Gutmann S, Hinh L, Jahnke W, Klopp J, Lai A, Lindvall MK, Ma S, Möbitz H, Pecchi S, Rummel G, Shoemaker K, Trappe J, Voliva C, Cowan-Jacob SW, Marzinzik AL. Optimization of a Dibenzodiazepine Hit to a Potent and Selective Allosteric PAK1 Inhibitor. ACS Med Chem Lett 2015; 6:776-81. [PMID: 26191365 DOI: 10.1021/acsmedchemlett.5b00102] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [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: 03/10/2015] [Accepted: 05/22/2015] [Indexed: 01/07/2023] Open
Abstract
The discovery of inhibitors targeting novel allosteric kinase sites is very challenging. Such compounds, however, once identified could offer exquisite levels of selectivity across the kinome. Herein we report our structure-based optimization strategy of a dibenzodiazepine hit 1, discovered in a fragment-based screen, yielding highly potent and selective inhibitors of PAK1 such as 2 and 3. Compound 2 was cocrystallized with PAK1 to confirm binding to an allosteric site and to reveal novel key interactions. Compound 3 modulated PAK1 at the cellular level and due to its selectivity enabled valuable research to interrogate biological functions of the PAK1 kinase.
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Affiliation(s)
- Alexei S. Karpov
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Payman Amiri
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Cornelia Bellamacina
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Marie-Helene Bellance
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Werner Breitenstein
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Dylan Daniel
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Regis Denay
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Doriano Fabbro
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Cesar Fernandez
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Inga Galuba
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Sascha Gutmann
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Linda Hinh
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Julia Klopp
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Albert Lai
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mika K. Lindvall
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Sylvia Ma
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Henrik Möbitz
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sabina Pecchi
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Gabriele Rummel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Kevin Shoemaker
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Joerg Trappe
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Charles Voliva
- Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Sandra W. Cowan-Jacob
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas L. Marzinzik
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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33
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Jansen J, Jahnke W, Fong S, Tandeske L, Wartchow C, Pfister K, Zavorotinskaya T, Blechschmidt A, Bussiere D, Dai Y, Dove J, Fang E, Farley D, Florent JM, Fuller J, Gokhin S, Gossert A, Hekmat-Nejad M, Henry C, Klopp J, Lenahan B, Lingel A, Meyer A, Narberes J, Pardee G, Paris CG, Ramurthy S, Renhowe P, Rieffel S, Shoemaker K, Subramanian S, Tsang T, Widger S, Widmer A, Zaror I, Hardy S. Abstract B38: Inhibiting mutated KRAS, a broken switch of effector pathways. Mol Cancer Res 2015. [DOI: 10.1158/1557-3125.rasonc14-b38] [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: 11/16/2022]
Abstract
Abstract
Mutated forms of KRAS are no longer able to switch effectors between “on” and “off” states. It is known that the function of KRAS is controlled by key parts in the C-terminus, including six consecutive lysines, a terminal prenyl moiety and a terminal carboxymethyl functional group. We set out to discover compounds which would inhibit the function of mutated KRAS as an activator for effectors. This campaign yielded several compounds that blocked biochemical and cellular functions of KRAS with low micromolar activity while not affecting markers outside of KRAS pathways in cells. In order to understand the mode of binding of these compounds to KRAS, we generated different forms of the protein, including unprenylated truncated and fully processed full-length protein. NMR studies with truncated protein (amino acids 1-169) identified a site at which compound binding stabilized the inactive conformation of KRAS. This site is located adjacent to switch-II and is similar to sites described by others. The Kd determined for this binding event is almost 3 orders of magnitude higher than the IC50 and EC50 values measured in biochemical and cellular assays. In order to understand this difference, we developed a biophysical assay using the Fortebio system which enabled binding studies in a system with full-length prenylated protein in the presence of lipids, to match the context of the biochemical and cellular assays. Micromolar binding to the full-length prenylated KRAS protein was observed in the Fortebio assay and binding was not observed in the absence of prenylation, consistent with the near millimolar Kd observed by NMR for truncated KRAS. Curiously, similar micromolar binding was seen to a peptide derived from the C-terminus of KRAS (amino acids 168-185) with and without prenyl modification while related compounds that do not bind to the full-length prenylated KRAS also do not bind to these peptides. It is still unclear whether binding to the terminal peptide in lipid context is related to the binding site adjacent to switch-II. From a drug discovery perspective, it remains to be confirmed whether current inhibitors can be optimized.
Citation Format: Johanna Jansen, Wolfgang Jahnke, Susan Fong, Laura Tandeske, Charles Wartchow, Keith Pfister, Tatiana Zavorotinskaya, Anke Blechschmidt, Dirksen Bussiere, Yumin Dai, Jeff Dove, Eric Fang, David Farley, Jean-Michel Florent, John Fuller, Simona Gokhin, Alvar Gossert, Mohammad Hekmat-Nejad, Chrystèle Henry, Julia Klopp, Bill Lenahan, Andreas Lingel, Arndt Meyer, Jamie Narberes, Gwynn Pardee, C Gregory Paris, Savithri Ramurthy, Paul Renhowe, Sebastien Rieffel, Kevin Shoemaker, Sharadha Subramanian, Tiffany Tsang, Stephania Widger, Armin Widmer, Isabel Zaror, Stephen Hardy. Inhibiting mutated KRAS, a broken switch of effector pathways. [abstract]. In: Proceedings of the AACR Special Conference on RAS Oncogenes: From Biology to Therapy; Feb 24-27, 2014; Lake Buena Vista, FL. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(12 Suppl):Abstract nr B38. doi: 10.1158/1557-3125.RASONC14-B38
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Affiliation(s)
- Johanna Jansen
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Wolfgang Jahnke
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland,
| | - Susan Fong
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Laura Tandeske
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | | | - Keith Pfister
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | | | | | | | - Yumin Dai
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Jeff Dove
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Eric Fang
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - David Farley
- 3Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - John Fuller
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Simona Gokhin
- 3Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Alvar Gossert
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland,
| | | | - Chrystèle Henry
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland,
| | - Julia Klopp
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland,
| | - Bill Lenahan
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Andreas Lingel
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Arndt Meyer
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland,
| | - Jamie Narberes
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Gwynn Pardee
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | | | | | - Paul Renhowe
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | | | - Kevin Shoemaker
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | | | - Tiffany Tsang
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | | | - Armin Widmer
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland,
| | - Isabel Zaror
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
| | - Stephen Hardy
- 1Novartis Institutes for BioMedical Research, Emeryville, CA,
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34
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Salcius M, Bauer AJ, Hao Q, Li S, Tutter A, Raphael J, Jahnke W, Rondeau JM, Bourgier E, Tallarico J, Michaud GA. SEC-TID: A Label-Free Method for Small-Molecule Target Identification. ACTA ACUST UNITED AC 2014; 19:917-27. [PMID: 24554445 DOI: 10.1177/1087057114522691] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 01/08/2014] [Indexed: 11/16/2022]
Abstract
Bioactive small molecules are an invaluable source of therapeutics and chemical probes for exploring biological pathways. Yet, significant hurdles in drug discovery often come from lacking a comprehensive view of the target(s) for both early tool molecules and even late-stage drugs. To address this challenge, a method is provided that allows for assessing the interactions of small molecules with thousands of targets without any need to modify the small molecule of interest or attach any component to a surface. We describe size-exclusion chromatography for target identification (SEC-TID), a method for accurately and reproducibly detecting ligand-macromolecular interactions for small molecules targeting nucleic acid and several protein classes. We report the use of SEC-TID, with a library consisting of approximately 1000 purified proteins derived from the protein databank (PDB), to identify the efficacy targets tankyrase 1 and 2 for the Wnt inhibitor XAV939. In addition, we report novel interactions for the tumor-vascular disrupting agent vadimezan/ASA404 (interacting with farnesyl pyrophosphate synthase) and the diuretic mefruside (interacting with carbonic anhydrase XIII). We believe this method can dramatically enhance our understanding of the mechanism of action and potential liabilities for small molecules in drug discovery pipelines through comprehensive profiling of candidate druggable targets.
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Affiliation(s)
- Michael Salcius
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Andras J Bauer
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Qin Hao
- Analytical Sciences, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Shu Li
- Analytical Sciences, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Antonin Tutter
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jacob Raphael
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Wolfgang Jahnke
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jean-Michel Rondeau
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Emmanuelle Bourgier
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - John Tallarico
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Gregory A Michaud
- Developmental and Molecular Pathways Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
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35
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Widler L, Jahnke W, R. Green J. The Chemistry of Bisphosphonates: From Antiscaling Agents to Clinical Therapeutics. Anticancer Agents Med Chem 2012; 12:95-101. [DOI: 10.2174/187152012799014959] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 08/04/2011] [Accepted: 08/05/2011] [Indexed: 11/22/2022]
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37
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Gossert AD, Hinniger A, Gutmann S, Jahnke W, Strauss A, Fernández C. A simple protocol for amino acid type selective isotope labeling in insect cells with improved yields and high reproducibility. J Biomol NMR 2011; 51:449-456. [PMID: 21964698 DOI: 10.1007/s10858-011-9570-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 09/12/2011] [Indexed: 05/31/2023]
Abstract
An easy to use and robust approach for amino acid type selective isotope labeling in insect cells is presented. It relies on inexpensive commercial media and can be implemented in laboratories without sophisticated infrastructure. In contrast to previous protocols, where either high protein amounts or high incorporation ratios were obtained, here we achieve both at the same time. By supplementing media with a well considered amount of yeast extract, similar protein amounts as with full media are obtained, without compromising on isotope incorporation. In single and dual amino acid labeling experiments incorporation ratios are consistently ≥90% for all amino acids tested. This enables NMR studies of eukaryotic proteins and their interactions even for proteins with low expression levels. We show applications with human kinases, where protein-ligand interactions are characterized by 2D [(15)N, (1)H]- and [(13)C, (1)H]-HSQC spectra.
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Affiliation(s)
- Alvar D Gossert
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
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38
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Kieffer B, Homans S, Jahnke W. Chapter 2. Nuclear Magnetic Resonance of Ligand Binding to Proteins. Biophysical Approaches Determining Ligand Binding to Biomolecular Targets 2011. [DOI: 10.1039/9781849732666-00015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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39
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Jahnke W, Rondeau JM, Cotesta S, Marzinzik A, Pellé X, Geiser M, Strauss A, Götte M, Bitsch F, Hemmig R, Henry C, Lehmann S, Glickman JF, Roddy TP, Stout SJ, Green JR. Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery. Nat Chem Biol 2010; 6:660-6. [DOI: 10.1038/nchembio.421] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 07/12/2010] [Indexed: 12/31/2022]
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40
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Jahnke W, Grotzfeld RM, Pellé X, Strauss A, Fendrich G, Cowan-Jacob SW, Cotesta S, Fabbro D, Furet P, Mestan J, Marzinzik AL. Binding or Bending: Distinction of Allosteric Abl Kinase Agonists from Antagonists by an NMR-Based Conformational Assay. J Am Chem Soc 2010; 132:7043-8. [DOI: 10.1021/ja101837n] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | | | - Xavier Pellé
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - André Strauss
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Gabriele Fendrich
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | | | - Simona Cotesta
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Doriano Fabbro
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Pascal Furet
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Jürgen Mestan
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
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Revesz L, Schlapbach A, Aichholz R, Feifel R, Hawtin S, Heng R, Hiestand P, Jahnke W, Koch G, Kroemer M, Möbitz H, Scheufler C, Velcicky J, Huppertz C. In vivo and in vitro SAR of tetracyclic MAPKAP-K2 (MK2) inhibitors. Part I. Bioorg Med Chem Lett 2010; 20:4715-8. [PMID: 20594847 DOI: 10.1016/j.bmcl.2010.04.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 04/07/2010] [Accepted: 04/07/2010] [Indexed: 11/29/2022]
Abstract
Pyrrolo[2,3-f]isoquinoline based amino acids, tetracyclic lactams and cyclic ketone analogues are described as novel MK2 inhibitors with IC(50) as low as 5nM and good selectivity profiles against a number of related kinases including ERK, p38alpha and JNKs. TNFalpha release was suppressed from human peripheral blood mononuclear cells (hPBMCs), and a representative compound inhibited LPS induced TNFalpha release in mice illustrating the potential of this series to provide orally active MK2 inhibitors.
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Affiliation(s)
- Laszlo Revesz
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland.
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42
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Fabbro D, Manley PW, Jahnke W, Liebetanz J, Szyttenholm A, Fendrich G, Strauss A, Zhang J, Gray NS, Adrian F, Warmuth M, Pelle X, Grotzfeld R, Berst F, Marzinzik A, Cowan-Jacob SW, Furet P, Mestan J. Inhibitors of the Abl kinase directed at either the ATP- or myristate-binding site. Biochim Biophys Acta 2010; 1804:454-62. [PMID: 20152788 DOI: 10.1016/j.bbapap.2009.12.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Revised: 12/11/2009] [Accepted: 12/14/2009] [Indexed: 11/20/2022]
Abstract
The ATP-competitive inhibitors dasatinib and nilotinib, which bind to catalytically different conformations of the Abl kinase domain, have recently been approved for the treatment of imatinib-resistant CML. These two new drugs, albeit very efficient against most of the imatinib-resistant mutants of Bcr-Abl, fail to effectively suppress the Bcr-Abl activity of the T315I (or gatekeeper) mutation. Generating new ATP site-binding drugs that target the T315I in Abl has been hampered, amongst others, by target selectivity, which is frequently an issue when developing ATP-competitive inhibitors. Recently, using an unbiased cellular screening approach, GNF-2, a non-ATP-competitive inhibitor, has been identified that demonstrates cellular activity against Bcr-Abl transformed cells. The exquisite selectivity of GNF-2 is due to the finding that it targets the myristate binding site located near the C-terminus of the Abl kinase domain, as demonstrated by genetic approaches, solution NMR and X-ray crystallography. GNF-2, like myristate, is able to induce and/or stabilize the clamped inactive conformation of Abl analogous to the SH2-Y527 interaction of Src. The molecular mechanism for allosteric inhibition by the GNF-2 inhibitor class, and the combined effects with ATP-competitive inhibitors such as nilotinib and imatinib on wild-type Abl and imatinib-resistant mutants, in particular the T315I gatekeeper mutant, are reviewed.
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Affiliation(s)
- Doriano Fabbro
- Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland.
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Zhang J, Adrián FJ, Jahnke W, Cowan-Jacob SW, Li AG, Iacob RE, Sim T, Powers J, Dierks C, Sun F, Guo GR, Ding Q, Okram B, Choi Y, Wojciechowski A, Deng X, Liu G, Fendrich G, Strauss A, Vajpai N, Grzesiek S, Tuntland T, Liu Y, Bursulaya B, Azam M, Manley PW, Engen JR, Daley GQ, Warmuth M, Gray NS. Targeting Bcr-Abl by combining allosteric with ATP-binding-site inhibitors. Nature 2010; 463:501-6. [PMID: 20072125 DOI: 10.1038/nature08675] [Citation(s) in RCA: 448] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 11/11/2009] [Indexed: 11/09/2022]
Abstract
In an effort to find new pharmacological modalities to overcome resistance to ATP-binding-site inhibitors of Bcr-Abl, we recently reported the discovery of GNF-2, a selective allosteric Bcr-Abl inhibitor. Here, using solution NMR, X-ray crystallography, mutagenesis and hydrogen exchange mass spectrometry, we show that GNF-2 binds to the myristate-binding site of Abl, leading to changes in the structural dynamics of the ATP-binding site. GNF-5, an analogue of GNF-2 with improved pharmacokinetic properties, when used in combination with the ATP-competitive inhibitors imatinib or nilotinib, suppressed the emergence of resistance mutations in vitro, displayed additive inhibitory activity in biochemical and cellular assays against T315I mutant human Bcr-Abl and displayed in vivo efficacy against this recalcitrant mutant in a murine bone-marrow transplantation model. These results show that therapeutically relevant inhibition of Bcr-Abl activity can be achieved with inhibitors that bind to the myristate-binding site and that combining allosteric and ATP-competitive inhibitors can overcome resistance to either agent alone.
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Affiliation(s)
- Jianming Zhang
- Dana-Farber Cancer Institute, Harvard Medical School, Department of Cancer Biology, Seeley G. Mudd Building 628, Boston, Massachusetts 02115, USA
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Zhang J, Gray NS, Sim T, Choi Y, Deng X, Adrián F, Li A, Sun F, Liu Y, Okram B, Warmuth M, Iacob R, Engen J, Powers J, Azam M, Daley G, Jahnke W, Cowan-Jacob S, Manley P. Abstract B165: Abl kinase myristate-site inhibitor, mechanism and application. Mol Cancer Ther 2009. [DOI: 10.1158/1535-7163.targ-09-b165] [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: 11/16/2022]
Abstract
Abstract
We recently reported a new class of allosteric inhibitors, exemplified by GNF-2, that selectively inhibit the proliferation of Bcr-Abl dependent cells. Here we demonstrate, using selection for resistant Bcr-Abl clones, site-directed mutagenesis, affinity chromatography, and steady-state kinetics, that GNF-2 inhibits Bcr-Abl kinase activity by binding to the Abl myristate binding pocket and stabilizes the auto-inhibited conformation. We demonstrate that the 2-hydroxyethyl amide analog of GNF-2, GNF-5, in combination with ATP-competitive inhibitors such as nilotinib and dasatinib can overcome the T315I “gatekeeper” mutant of Bcr-Abl which is resistant to all clinically approved Bcr-Abl inhibitors. These studies demonstrate that targeting of the Abl myristate binding site can provide an important pharmacological means to overcome mutations that cause resistance to ATP-competitive inhibitors.
Citation Information: Mol Cancer Ther 2009;8(12 Suppl):B165.
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Affiliation(s)
| | | | - Taebo Sim
- 1 Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Francisco Adrián
- 2 Genomics Institute of the Novartis Research Foundation, San Deigo, CA
| | - Allen Li
- 2 Genomics Institute of the Novartis Research Foundation, San Deigo, CA
| | - Frank Sun
- 2 Genomics Institute of the Novartis Research Foundation, San Deigo, CA
| | - Yi Liu
- 2 Genomics Institute of the Novartis Research Foundation, San Deigo, CA
| | - Barun Okram
- 2 Genomics Institute of the Novartis Research Foundation, San Deigo, CA
| | - Markus Warmuth
- 2 Genomics Institute of the Novartis Research Foundation, San Deigo, CA
| | | | | | | | | | | | - Wolfgang Jahnke
- 5 Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Paul Manley
- 5 Novartis Institutes for Biomedical Research, Basel, Switzerland
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Affiliation(s)
- Patrick Chene
- Novartis Pharma AG, Lichtstrasse, 4002 Basel, Switzerland
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Gossert AD, Henry C, Blommers MJJ, Jahnke W, Fernández C. Time efficient detection of protein-ligand interactions with the polarization optimized PO-WaterLOGSY NMR experiment. J Biomol NMR 2009; 43:211-217. [PMID: 19205897 DOI: 10.1007/s10858-009-9303-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Accepted: 01/16/2009] [Indexed: 05/27/2023]
Abstract
The identification of compounds that bind to a protein of interest is of central importance in contemporary drug research. For screening of compound libraries, NMR techniques are widely used, in particular the Water-Ligand Observed via Gradient SpectroscopY (WaterLOGSY) experiment. Here we present an optimized experiment, the polarization optimized WaterLOGSY (PO-WaterLOGSY). Based on a water flip-back strategy in conjunction with model calculations and numerical simulations, the PO-WaterLOGSY is optimized for water polarization recovery. Compared to a standard setup with the conventional WaterLOGSY, time consuming relaxation delays have been considerably shortened and can even be omitted through this approach. Furthermore, the robustness of the pulse sequence in an industrial setup was increased by the use of hard pulse trains for selective water excitation and water suppression. The PO-WaterLOGSY thus yields increased time efficiency by factor of 3-5 when compared with previously published schemes. These time savings have a substantial impact in drug discovery, since significantly larger compound libraries can be tested in screening campaigns.
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Affiliation(s)
- Alvar D Gossert
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, 4002, Basel, Switzerland
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Vajpai N, Strauss A, Fendrich G, Cowan-Jacob SW, Manley PW, Jahnke W, Grzesiek S. Backbone NMR resonance assignment of the Abelson kinase domain in complex with imatinib. Biomol NMR Assign 2008; 2:41-42. [PMID: 19636920 DOI: 10.1007/s12104-008-9079-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Accepted: 01/09/2008] [Indexed: 05/28/2023]
Abstract
Imatinib (Glivec or Gleevec) potently inhibits the tyrosine kinase activity of BCR-ABL, a constitutively activated kinase, which causes chronic myelogenous leukemia (CML). Here we report the first almost complete backbone assignment of c-ABL kinase domain in complex with imatinib.
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Affiliation(s)
- Navratna Vajpai
- Biozentrum, University of Basel, Klingelbergstrasse 70, Basel, Switzerland
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