1
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Teng M, Luskin MR, Cowan-Jacob SW, Ding Q, Fabbro D, Gray NS. The Dawn of Allosteric BCR-ABL1 Drugs: From a Phenotypic Screening Hit to an Approved Drug. J Med Chem 2022; 65:7581-7594. [PMID: 35609336 DOI: 10.1021/acs.jmedchem.2c00373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chronic myeloid leukemia (CML) is driven by the constitutive activity of the BCR-ABL1 fusion oncoprotein. Despite the great success of drugs that target the BCR-ABL1 ATP-binding site in transforming CML into a manageable disease, emerging resistance point mutations impair inhibitor binding, thereby limiting the effectiveness of these drugs. Recently, allosteric inhibitors that interact with the ABL1 myristate-binding site have been shown to awaken an endogenous regulatory mechanism and reset full-length BCR-ABL1 into an inactive assembled state. The discovery and development of these allosteric inhibitors demonstrates an in-depth understanding of the fundamental regulatory mechanisms of kinases. In this review, we illustrate the structural basis of c-ABL1's dynamic regulation of autoinhibition and activation, discuss the discovery of allosteric inhibitors and the characterization of their mechanism of action, present the therapeutic potential of dual binding to delay the development of mutation-driven acquired resistance, and suggest key lessons learned from this program.
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Affiliation(s)
- Mingxing Teng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Marlise R Luskin
- Division of Hematologic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Sandra W Cowan-Jacob
- Novartis Institutes for BioMedical Research, Novartis Campus, Basel CH-4056, Switzerland
| | - Qiang Ding
- Allorion Therapeutics, Guangzhou, Guangdong 511300, China
| | | | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, California 94305, United States
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2
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Manley PW, Barys L, Cowan-Jacob SW. The specificity of asciminib, a potential treatment for chronic myeloid leukemia, as a myristate-pocket binding ABL inhibitor and analysis of its interactions with mutant forms of BCR-ABL1 kinase. Leuk Res 2020; 98:106458. [DOI: 10.1016/j.leukres.2020.106458] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022]
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3
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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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4
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Hu T, Sprague ER, Fodor M, Stams T, Clark KL, Cowan-Jacob SW. The impact of structural biology in medicine illustrated with four case studies. J Mol Med (Berl) 2017; 96:9-19. [PMID: 28669027 DOI: 10.1007/s00109-017-1565-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 06/12/2017] [Accepted: 06/15/2017] [Indexed: 12/18/2022]
Abstract
The contributions of structural biology to drug discovery have expanded over the last 20 years from structure-based ligand optimization to a broad range of clinically relevant topics including the understanding of disease, target discovery, screening for new types of ligands, discovery of new modes of action, addressing clinical challenges such as side effects or resistance, and providing data to support drug registration. This expansion of scope is due to breakthroughs in the technology, which allow structural information to be obtained rapidly and for more complex molecular systems, but also due to the combination of different technologies such as X-ray, NMR, and other biophysical methods, which allows one to get a more complete molecular understanding of disease and ways to treat it. In this review, we provide examples of the types of impact molecular structure information can have in the clinic for both low molecular weight and biologic drug discovery and describe several case studies from our own work to illustrate some of these contributions.
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Affiliation(s)
- Tiancen Hu
- Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA
| | | | - Michelle Fodor
- Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA
| | - Travis Stams
- Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA
| | - Kirk L Clark
- Novartis Institutes for Biomedical Research, Cambridge, MA, 02139, USA
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5
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Cowan-Jacob SW. The role of structure and biophysics in the discovery of allosteric kinase inhibitors: ABL001, a potent and specific inhibitor of BCR-ABL. Acta Crystallogr A Found Adv 2016. [DOI: 10.1107/s2053273316099927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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6
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Stauffer F, Cowan-Jacob SW, Scheufler C, Furet P. Identification of a 5-[3-phenyl-(2-cyclic-ether)-methylether]-4-aminopyrrolo[2,3-d]pyrimidine series of IGF-1R inhibitors. Bioorg Med Chem Lett 2016; 26:2065-7. [PMID: 26951750 DOI: 10.1016/j.bmcl.2016.02.074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 02/22/2016] [Accepted: 02/24/2016] [Indexed: 11/17/2022]
Abstract
We report structure-guided modifications of the benzyloxy substituent of the Insulin-like Growth Factor-1 Receptor (IGF-1R) inhibitor NVP-AEW541. This chemical group has been shown to confer selectivity against other protein kinases but at the expense of a metabolism liability. X-ray crystallography has revealed that the benzyloxy moiety interacts with a lysine cation of the IGF-1R kinase domain via its ether function and its aromatic π-system and is nicely embedded in an induced hydrophobic pocket. We show that 1,4-diethers displaying an adequate hydrophobic and constrained shape are advantageous benzyloxy replacements. A single digit nanomolar inhibitor (compound 20, IC50=8.9 nM) was identified following this approach.
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Affiliation(s)
- Frédéric Stauffer
- Novartis Institutes for Biomedical Research, Basel, Postfach, 4002 Basel, Switzerland.
| | - Sandra W Cowan-Jacob
- Novartis Institutes for Biomedical Research, Basel, Postfach, 4002 Basel, Switzerland
| | - Clemens Scheufler
- Novartis Institutes for Biomedical Research, Basel, Postfach, 4002 Basel, Switzerland
| | - Pascal Furet
- Novartis Institutes for Biomedical Research, Basel, Postfach, 4002 Basel, Switzerland
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7
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Alexander LT, Möbitz H, Drueckes P, Savitsky P, Fedorov O, Elkins JM, Deane CM, Cowan-Jacob SW, Knapp S. Type II Inhibitors Targeting CDK2. ACS Chem Biol 2015; 10:2116-25. [PMID: 26158339 DOI: 10.1021/acschembio.5b00398] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Kinases can switch between active and inactive conformations of the ATP/Mg(2+) binding motif DFG, which has been explored for the development of type I or type II inhibitors. However, factors modulating DFG conformations remain poorly understood. We chose CDK2 as a model system to study the DFG in-out transition on a target that was thought to have an inaccessible DFG-out conformation. We used site-directed mutagenesis of key residues identified in structural comparisons in conjunction with biochemical and biophysical characterization of the generated mutants. As a result, we identified key residues that facilitate the DFG-out movement, facilitating binding of type II inhibitors. However, surprisingly, we also found that wild type CDK2 is able to bind type II inhibitors. Using protein crystallography structural analysis of the CDK2 complex with an aminopyrimidine-phenyl urea inhibitor (K03861) revealed a canonical type II binding mode and the first available type II inhibitor CDK2 cocrystal structure. We found that the identified type II inhibitors compete with binding of activating cyclins. In addition, analysis of the binding kinetics of the identified inhibitors revealed slow off-rates. The study highlights the importance of residues that may be distant to the ATP binding pocket in modulating the energetics of the DFG-out transition and hence inhibitor binding. The presented data also provide the foundation for a new class of slow off-rate cyclin-competitive CDK2 inhibitors targeting the inactive DFG-out state of this important kinase target.
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Affiliation(s)
- Leila T. Alexander
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom
| | - Henrik Möbitz
- Novartis Institutes of Biomedical Research, Basel, Switzerland, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland
| | - Peter Drueckes
- Novartis Institutes of Biomedical Research, Basel, Switzerland, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland
| | - Pavel Savitsky
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Oleg Fedorov
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford, OX3 7FZ, United Kingdom
| | - Jonathan M. Elkins
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford, OX3 7FZ, United Kingdom
| | - Charlotte M. Deane
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom
| | - Sandra W. Cowan-Jacob
- Novartis Institutes of Biomedical Research, Basel, Switzerland, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland
| | - Stefan Knapp
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford, OX3 7FZ, United Kingdom
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str.
9, D-60438 Frankfurt
am Main, Germany
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8
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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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9
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Fabbro D, Cowan-Jacob SW, Moebitz H. Ten things you should know about protein kinases: IUPHAR Review 14. Br J Pharmacol 2015; 172:2675-700. [PMID: 25630872 DOI: 10.1111/bph.13096] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 12/31/2014] [Accepted: 01/20/2015] [Indexed: 12/12/2022] Open
Abstract
Many human malignancies are associated with aberrant regulation of protein or lipid kinases due to mutations, chromosomal rearrangements and/or gene amplification. Protein and lipid kinases represent an important target class for treating human disorders. This review focus on 'the 10 things you should know about protein kinases and their inhibitors', including a short introduction on the history of protein kinases and their inhibitors and ending with a perspective on kinase drug discovery. Although the '10 things' have been, to a certain extent, chosen arbitrarily, they cover in a comprehensive way the past and present efforts in kinase drug discovery and summarize the status quo of the current kinase inhibitors as well as knowledge about kinase structure and binding modes. Besides describing the potentials of protein kinase inhibitors as drugs, this review also focus on their limitations, particularly on how to circumvent emerging resistance against kinase inhibitors in oncological indications.
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Affiliation(s)
| | | | - Henrik Moebitz
- Novartis Institutes of Biomedical Research, Basel, Switzerland
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10
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D'Arcy A, Bergfors T, Cowan-Jacob SW, Marsh M. Microseed matrix screening for optimization in protein crystallization: what have we learned? Acta Crystallogr F Struct Biol Commun 2014; 70:1117-26. [PMID: 25195878 DOI: 10.1107/s2053230x14015507] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 07/02/2014] [Indexed: 11/10/2022]
Abstract
Protein crystals obtained in initial screens typically require optimization before they are of X-ray diffraction quality. Seeding is one such optimization method. In classical seeding experiments, the seed crystals are put into new, albeit similar, conditions. The past decade has seen the emergence of an alternative seeding strategy: microseed matrix screening (MMS). In this strategy, the seed crystals are transferred into conditions unrelated to the seed source. Examples of MMS applications from in-house projects and the literature include the generation of multiple crystal forms and different space groups, better diffracting crystals and crystallization of previously uncrystallizable targets. MMS can be implemented robotically, making it a viable option for drug-discovery programs. In conclusion, MMS is a simple, time- and cost-efficient optimization method that is applicable to many recalcitrant crystallization problems.
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Affiliation(s)
- Allan D'Arcy
- Actelion Pharmaceuticals Ltd, Basel, Switzerland
| | - Terese Bergfors
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sandra W Cowan-Jacob
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - May Marsh
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
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11
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Wassermann AM, Kutchukian PS, Lounkine E, Luethi T, Hamon J, Bocker MT, Malik HA, Cowan-Jacob SW, Glick M. Efficient search of chemical space: navigating from fragments to structurally diverse chemotypes. J Med Chem 2013; 56:8879-91. [PMID: 24117015 DOI: 10.1021/jm401309q] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We introduce a novel strategy to sample bioactive chemical space, which follows-up on hits from fragment campaigns without the need for a crystal structure. Our results strongly suggest that screening a few hundred or thousand fragments can substantially improve the selection of small-molecule screening subsets. By combining fragment-based screening with virtual fragment linking and HTS fingerprints, we have developed an effective strategy not only to expand from low-affinity hits to potent compounds but also to hop in chemical space to substantially novel chemotypes. In benchmark calculations, our approach accessed subsets of compounds that were substantially enriched in chemically diverse hit compounds for various activity classes. Overall, half of the hits in the screening collection were found by screening only 10% of the library. Furthermore, a prospective application led to the discovery of two structurally novel histone deacetylase 4 inhibitors.
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Affiliation(s)
- Anne Mai Wassermann
- Novartis Institutes for Biomedical Research Inc. , 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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12
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Abstract
Protein and lipid kinases fulfill essential roles in many signaling pathways that regulate normal cell functions. Deregulation of these kinase activities lead to a variety of pathologies ranging from cancer to inflammatory diseases, diabetes, infectious diseases, cardiovascular disorders, cell growth and survival. 518 protein kinases and about 20 lipid-modifying kinases are encoded by the human genome, and a much larger proportion of additional kinases are present in parasite, bacterial, fungal, and viral genomes that are susceptible to exploitation as drug targets. Since many human diseases result from overactivation of protein and lipid kinases due to mutations and/or overexpression, this enzyme class represents an important target for the pharmaceutical industry. Approximately one third of all protein targets under investigation in the pharmaceutical industry are protein or lipid kinases.The kinase inhibitors that have been launched, thus far, are mainly in oncology indications and are directed against a handful of protein and lipid kinases. With one exception, all of these registered kinase inhibitors are directed toward the ATP-site and display different selectivities, potencies, and pharmacokinetic properties. At present, about 150 kinase-targeted drugs are in clinical development and many more in various stages of preclinical development. Kinase inhibitor drugs that are in clinical trials target all stages of signal transduction from the receptor protein tyrosine kinases that initiate intracellular signaling, through second-messenger-dependent lipid and protein kinases, and protein kinases that regulate the cell cycle.This review provides an insight into protein and lipid kinase drug discovery with respect to achievements, binding modes of inhibitors, and novel avenues for the generation of second-generation kinase inhibitors to treat cancers.
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Affiliation(s)
- Doriano Fabbro
- Novartis Institutes for Biomedical Research, Expertise Platform Kinases, Basel, Switzerland.
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13
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van Eis MJ, Evenou JP, Floersheim P, Gaul C, Cowan-Jacob SW, Monovich L, Rummel G, Schuler W, Stark W, Strauss A, von Matt A, Vangrevelinghe E, Wagner J, Soldermann N. 2,6-Naphthyridines as potent and selective inhibitors of the novel protein kinase C isozymes. Bioorg Med Chem Lett 2011; 21:7367-72. [PMID: 22078216 DOI: 10.1016/j.bmcl.2011.10.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 10/05/2011] [Accepted: 10/07/2011] [Indexed: 11/26/2022]
Abstract
The present study describes a novel series of ATP-competitive PKC inhibitors based on the 2,6-naphthyridine template. Example compounds potently inhibit the novel Protein Kinase C (PKC) isotypes δ, ε, η, θ (in particular PKCε/η, and display a 10-100-fold selectivity over the classical PKC isotypes. The prototype compound 11 was found to inhibit PKCθ-dependent pathways in vitro and in vivo. In vitro, a-CD3/a-CD28-induced lymphocyte proliferation could be effectively blocked in 10% rat whole blood. In mice, 11 dose-dependently inhibited Staphylococcus aureus enterotoxin B-triggered IL-2 serum levels after oral dosing.
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Affiliation(s)
- Maurice J van Eis
- Novartis Institutes for BioMedical Research, Forum 1, Novartis Campus, CH-4056 Basel, Switzerland.
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14
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Deng X, Okram B, Ding Q, Zhang J, Choi Y, Adrián FJ, Wojciechowski A, Zhang G, Che J, Bursulaya B, Cowan-Jacob SW, Rummel G, Sim T, Gray NS. Expanding the diversity of allosteric bcr-abl inhibitors. J Med Chem 2010; 53:6934-46. [PMID: 20828158 PMCID: PMC2951064 DOI: 10.1021/jm100555f] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [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: 12/20/2022]
Abstract
Inhibition of Bcr-Abl kinase activity by imatinib for the treatment of chronic myeloid leukemia (CML) currently serves as the paradigm for targeting dominant oncogenes with small molecules. We recently reported the discovery of GNF-2 (1) and GNF-5 (2) as selective non-ATP competitive inhibitors of cellular Bcr-Abl kinase activity that target the myristate binding site. Here, we used cell-based structure-activity relationships to guide the optimization and diversification of ligands that are capable of binding to the myristate binding site and rationalize the findings based upon an Abl-compound 1 cocrystal. We elucidate the structure-activity relationships required to obtain potent antiproliferative activity against Bcr-Abl transformed cells and report the discovery of new compounds (5g, 5h, 6a, 14d, and 21j-I) that display improved potency or pharmacological properties. This work demonstrates that a variety of structures can effectively target the Bcr-Abl myristate binding site and provides new leads for developing drugs that can target this binding site.
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Affiliation(s)
- Xianming Deng
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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15
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Manley PW, Stiefl N, Cowan-Jacob SW, Kaufman S, Mestan J, Wartmann M, Wiesmann M, Woodman R, Gallagher N. Structural resemblances and comparisons of the relative pharmacological properties of imatinib and nilotinib. Bioorg Med Chem 2010; 18:6977-86. [PMID: 20817538 DOI: 10.1016/j.bmc.2010.08.026] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 07/08/2010] [Accepted: 08/11/2010] [Indexed: 02/06/2023]
Abstract
Although orphan drug applications required by the EMEA must include assessments of similarity to pre-existing products, these can be difficult to quantify. Here we illustrate a paradigm in comparing nilotinib to the prototype kinase inhibitor imatinib, and equate the degree of structural similarity to differences in properties. Nilotinib was discovered following re-engineering of imatinib, employing structural biology and medicinal chemistry strategies to optimise cellular potency and selectivity towards BCR-ABL1. Through evolving only to conserve these properties, this resulted in significant structural differences between nilotinib and imatinib, quantified by a Daylight-fingerprint-Tanimoto similarity coefficient of 0.6, with the meaning of this absolute measure being supported by an analysis of similarity distributions of similar drug-like molecules. This dissimilarity is reflected in the drugs having substantially different preclinical pharmacology and a lack of cross-intolerance in CML patients, which translates into nilotinib being an efficacious treatment for CML, with a favourable side-effect profile.
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Affiliation(s)
- Paul W Manley
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
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16
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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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17
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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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18
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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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19
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Wagner J, von Matt P, Sedrani R, Albert R, Cooke N, Ehrhardt C, Geiser M, Rummel G, Stark W, Strauss A, Cowan-Jacob SW, Beerli C, Weckbecker G, Evenou JP, Zenke G, Cottens S. Discovery of 3-(1H-Indol-3-yl)-4-[2-(4-methylpiperazin-1-yl)quinazolin-4-yl]pyrrole-2,5-dione (AEB071), a Potent and Selective Inhibitor of Protein Kinase C Isotypes. J Med Chem 2009; 52:6193-6. [DOI: 10.1021/jm901108b] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jürgen Wagner
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Peter von Matt
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Richard Sedrani
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Rainer Albert
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Nigel Cooke
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Claus Ehrhardt
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Martin Geiser
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Gabriele Rummel
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Wilhelm Stark
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Andre Strauss
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | | | - Christian Beerli
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | | | | | - Gerhard Zenke
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
| | - Sylvain Cottens
- Novartis Institutes for BioMedical Research, Basel CH-4002, Switzerland
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20
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Cowan-Jacob SW, Möbitz H, Fabbro D. Structural biology contributions to tyrosine kinase drug discovery. Curr Opin Cell Biol 2009; 21:280-7. [PMID: 19208462 DOI: 10.1016/j.ceb.2009.01.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 01/14/2009] [Indexed: 11/19/2022]
Abstract
Successful kinase inhibitor drug discovery relies heavily on the structural knowledge of the interaction of inhibitors with the target. Structural biology of kinases and in particular of tyrosine kinases has given detailed insights into the intrinsic flexibility of the catalytic domain and has provided a rational basis for obtaining selective inhibitors. Important progress has been made recently, both in academia and in the pharmaceutical industry, with respect to solving structures of inactive, multidomain or protein-protein complexes of kinases, which helps our understanding of the dynamics of regulation of kinase activity. This leads to a better understanding of how mutations lead to activation of kinases and resistance, in addition to providing opportunities for novel modes of targeting kinases.
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Affiliation(s)
- Sandra W Cowan-Jacob
- Novartis Institutes of Biomedical Research, Novartis Pharma AG, Postfach, Basel, Switzerland.
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21
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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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22
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Vajpai N, Strauss A, Fendrich G, Cowan-Jacob SW, Manley PW, Grzesiek S, Jahnke W. Solution conformations and dynamics of ABL kinase-inhibitor complexes determined by NMR substantiate the different binding modes of imatinib/nilotinib and dasatinib. J Biol Chem 2008; 283:18292-302. [PMID: 18434310 DOI: 10.1074/jbc.m801337200] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Current structural understanding of kinases is largely based on x-ray crystallographic studies, whereas very little data exist on the conformations and dynamics that kinases adopt in the solution state. ABL kinase is an important drug target in the treatment of chronic myelogenous leukemia. Here, we present the first characterization of ABL kinase in complex with three clinical inhibitors (imatinib, nilotinib, and dasatinib) by modern solution NMR techniques. Structural and dynamical results were derived from complete backbone resonance assignments, experimental residual dipolar couplings, and (15)N relaxation data. Residual dipolar coupling data on the imatinib and nilotinib complexes show that the activation loop adopts the inactive conformation, whereas the dasatinib complex preserves the active conformation, which does not support contrary predictions based upon molecular modeling. Nanosecond as well as microsecond dynamics can be detected for certain residues in the activation loop in the inactive and active conformation complexes.
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Affiliation(s)
- Navratna Vajpai
- Novartis Institutes for BioMedical Research, Basel, Switzerland
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23
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Teno N, Miyake T, Ehara T, Irie O, Sakaki J, Ohmori O, Gunji H, Matsuura N, Masuya K, Hitomi Y, Nonomura K, Horiuchi M, Gohda K, Iwasaki A, Umemura I, Tada S, Kometani M, Iwasaki G, Cowan-Jacob SW, Missbach M, Lattmann R, Betschart C. Novel scaffold for cathepsin K inhibitors. Bioorg Med Chem Lett 2007; 17:6096-100. [PMID: 17911019 DOI: 10.1016/j.bmcl.2007.09.047] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Revised: 09/10/2007] [Accepted: 09/12/2007] [Indexed: 11/15/2022]
Abstract
Pyrrolopyrimidine, a novel scaffold, allows to adjust interactions within the S3 subsite of cathepsin K. The core intermediate 10 facilitated the P3 optimization and identified highly potent and selective cathepsin K inhibitors 11-20.
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Affiliation(s)
- Naoki Teno
- Novartis Institutes for BioMedical Research, Ohkubo 8, Tsukuba, Ibaraki, Japan.
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24
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Ray A, Cowan-Jacob SW, Manley PW, Mestan J, Griffin JD. Identification of BCR-ABL point mutations conferring resistance to the Abl kinase inhibitor AMN107 (nilotinib) by a random mutagenesis study. Blood 2007; 109:5011-5. [PMID: 17303698 DOI: 10.1182/blood-2006-01-015347] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Abstract
Patients with advanced stages of chronic myeloid leukemia (CML) often manifest imatinib mesylate resistance associated with point mutations in BCR-ABL. AMN107 is a new higher-potency inhibitor of BCR-ABL. To identify mutations in BCR-ABL that could result in resistance to AMN107, a cDNA library of BCR-ABL mutants was introduced into Ba/F3 cells followed by selection in AMN107 (0.125-0.5 μM). A total of 86 individual, drug-resistant colonies were recovered, and the SH3, SH2, and kinase domains of BCR-ABL were sequenced. A total of 46 colonies had single point mutations in BCR-ABL, with a total of 17 different mutations, all within the kinase domain. The other 40 colonies had multiple point mutations and were not analyzed further. Each of the 17 single point mutants were reconstructed by site-directed mutagenesis of native BCR-ABL and found to be approximately 2.5- to 800-fold more resistant to AMN107 than native BCR-ABL. The mutations included 6 known imatinib mesylate–resistant mutations, including T315I, which showed complete resistance to AMN107. Interestingly, most AMN107-resistant mutants were also resistant to imatinib mesylate. These results may predict some of the resistance mutations that will be detected in clinical trials with this kinase inhibitor.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Cell Line, Tumor
- Drug Resistance, Neoplasm
- Fusion Proteins, bcr-abl/genetics
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Mice
- Models, Molecular
- Mutagenesis
- Mutation
- Point Mutation
- Protein Conformation
- Protein Structure, Tertiary
- Pyrimidines/pharmacology
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Affiliation(s)
- Arghya Ray
- Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
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25
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Weisberg E, Manley PW, Cowan-Jacob SW, Hochhaus A, Griffin JD. Second generation inhibitors of BCR-ABL for the treatment of imatinib-resistant chronic myeloid leukaemia. Nat Rev Cancer 2007; 7:345-56. [PMID: 17457302 DOI: 10.1038/nrc2126] [Citation(s) in RCA: 431] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Imatinib, a small-molecule ABL kinase inhibitor, is a highly effective therapy for early-phase chronic myeloid leukaemia (CML), which has constitutively active ABL kinase activity owing to the expression of the BCR-ABL fusion protein. However, there is a high relapse rate among advanced- and blast-crisis-phase patients owing to the development of mutations in the ABL kinase domain that cause drug resistance. Several second-generation ABL kinase inhibitors have been or are being developed for the treatment of imatinib-resistant CML. Here, we describe the mechanism of action of imatinib in CML, the structural basis of imatinib resistance, and the potential of second-generation BCR-ABL inhibitors to circumvent resistance.
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Affiliation(s)
- Ellen Weisberg
- Dana Farber Cancer Institute, Mayer 540, 44 Binney Street, Boston, MA 02115, USA
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26
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Cowan-Jacob SW, Fendrich G, Floersheimer A, Furet P, Liebetanz J, Rummel G, Rheinberger P, Centeleghe M, Fabbro D, Manley PW. Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia. Acta Crystallogr D Biol Crystallogr 2007; 63:80-93. [PMID: 17164530 PMCID: PMC2483489 DOI: 10.1107/s0907444906047287] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Accepted: 11/08/2006] [Indexed: 11/23/2022]
Abstract
Chronic myelogenous leukaemia (CML) results from the Bcr-Abl oncoprotein, which has a constitutively activated Abl tyrosine kinase domain. Although most chronic phase CML patients treated with imatinib as first-line therapy maintain excellent durable responses, patients who have progressed to advanced-stage CML frequently fail to respond or lose their response to therapy owing to the emergence of drug-resistant mutants of the protein. More than 40 such point mutations have been observed in imatinib-resistant patients. The crystal structures of wild-type and mutant Abl kinase in complex with imatinib and other small-molecule Abl inhibitors were determined, with the aim of understanding the molecular basis of resistance and to aid in the design and optimization of inhibitors active against the resistance mutants. These results are presented in a way which illustrates the approaches used to generate multiple structures, the type of information that can be gained and the way that this information is used to support drug discovery.
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27
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Abstract
Our current understanding of the structure, mechanism of action and modes of regulation of the protein tyrosine kinase family owes a great deal to structural biology. Structures are now available for more than 20 different tyrosine kinase domains, many of these in multiple conformational states. They form the basis for the design of experiments to further investigate the role of different structural elements in the normal function and regulation of the protein and in the pathogenesis of many human diseases. Once thought to be too similar to be specifically inhibited by a small molecule, structural differences between kinases allow the design of compounds which inhibit only an acceptable few. This review gives a general overview of protein tyrosine kinase structural biology, including a discussion of the strengths and limitations of the investigative methods involved.
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Affiliation(s)
- S W Cowan-Jacob
- Novartis Institutes for Biomedical Research, Lichtstrasse 35, WSJ-88.9.08a, Novartis Pharma AG, 4056 Basel, Switzerland.
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28
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Manley PW, Cowan-Jacob SW, Mestan J. Advances in the structural biology, design and clinical development of Bcr-Abl kinase inhibitors for the treatment of chronic myeloid leukaemia. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2005; 1754:3-13. [PMID: 16172030 DOI: 10.1016/j.bbapap.2005.07.040] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Revised: 07/21/2005] [Accepted: 07/21/2005] [Indexed: 11/21/2022]
Abstract
The constitutively activated Abl tyrosine kinase domain of the chimeric Bcr-Abl oncoprotein is responsible for the transformation of haematopoietic stem cells and the symptoms of chronic myeloid leukaemia (CML). Imatinib targets the tyrosine kinase activity of Bcr-Abl and is a first-line therapy for this malignancy. Although highly effective in chronic phase CML, patients who have progressed to the advanced phase of the disease frequently fail to respond to imatinib or develop resistance to therapy and relapse. This is often due to the emergence of clones expressing mutant forms of Bcr-Abl, which exhibit a decreased sensitivity towards inhibition by imatinib. Considerable progress has recently been made in understanding the structural biology of Abl and the molecular basis for resistance, facilitating the discovery and development of second generation drugs designed to combat mutant forms of Bcr-Abl. The first of these compounds to enter clinical development were BMS-354825 (BristolMyersSquibb) and AMN107 (Novartis Pharma) and, from Phase I results, both of these promise a breakthrough in the treatment of imatinib-resistant CML. Recent advances with these and other promising classes of new CML drugs are reviewed.
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Affiliation(s)
- Paul William Manley
- Novartis Institutes for Biomedical Research, WKL-136.4.86, CH-4002 Basel, Switzerland.
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29
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O'Hare T, Walters DK, Stoffregen EP, Jia T, Manley PW, Mestan J, Cowan-Jacob SW, Lee FY, Heinrich MC, Deininger MWN, Druker BJ. In vitro activity of Bcr-Abl inhibitors AMN107 and BMS-354825 against clinically relevant imatinib-resistant Abl kinase domain mutants. Cancer Res 2005; 65:4500-5. [PMID: 15930265 DOI: 10.1158/0008-5472.can-05-0259] [Citation(s) in RCA: 798] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Imatinib, a Bcr-Abl tyrosine kinase inhibitor, is a highly effective therapy for patients with chronic myelogenous leukemia (CML). Despite durable responses in most chronic phase patients, relapses have been observed and are much more prevalent in patients with advanced disease. The most common mechanism of acquired imatinib resistance has been traced to Bcr-Abl kinase domain mutations with decreased imatinib sensitivity. Thus, alternate Bcr-Abl kinase inhibitors that have activity against imatinib-resistant mutants would be useful for patients who relapse on imatinib therapy. Two such Bcr-Abl inhibitors are currently being evaluated in clinical trials: the improved potency, selective Abl inhibitor AMN107 and the highly potent dual Src/Abl inhibitor BMS-354825. In the current article, we compared imatinib, AMN107, and BMS-354825 in cellular and biochemical assays against a panel of 16 kinase domain mutants representing >90% of clinical isolates. We report that AMN107 and BMS-354825 are 20-fold and 325-fold more potent than imatinib against cells expressing wild-type Bcr-Abl and that similar improvements are maintained for all imatinib-resistant mutants tested, with the exception of T315I. Thus, both inhibitors hold promise for treating imatinib-refractory CML.
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Affiliation(s)
- Thomas O'Hare
- Howard Hughes Medical Institute, Oregon Health and Science University Cancer Institute, Portland 97239, USA.
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30
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Cowan-Jacob SW, Fendrich G, Manley PW, Jahnke W, Fabbro D, Liebetanz J, Meyer T. The Crystal Structure of a c-Src Complex in an Active Conformation Suggests Possible Steps in c-Src Activation. Structure 2005; 13:861-71. [PMID: 15939018 DOI: 10.1016/j.str.2005.03.012] [Citation(s) in RCA: 249] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Revised: 03/14/2005] [Accepted: 03/14/2005] [Indexed: 11/28/2022]
Abstract
The regulation of the activity of Abl and Src family tyrosine kinases is mediated by intramolecular interactions between the SH3, SH2, and kinase (SH1) domains. We have determined the crystal structure of an unphosphorylated form of c-Src in which the SH2 domain is not bound to the C-terminal tail. This results in an open structure where the kinase domain adopts an active conformation and the C terminus binds within a hydrophobic pocket in the C-terminal lobe. NMR binding studies support the hypothesis that an N-terminal myristate could bind in this pocket, as observed for Abl, suggesting that c-Src may also be regulated by myristate binding. In addition, the structure contains a des-methyl analog of the antileukemia drug imatinib (STI571; Gleevec). This structure reveals why the drug shows a low affinity for active kinase conformations, contributing to its excellent kinase selectivity profile.
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Affiliation(s)
- Sandra W Cowan-Jacob
- Discovery Technologies, Novartis Institutes for Biomedical Research, CH-4056 Basel, Switzerland.
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31
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Weisberg E, Manley PW, Breitenstein W, Brüggen J, Cowan-Jacob SW, Ray A, Huntly B, Fabbro D, Fendrich G, Hall-Meyers E, Kung AL, Mestan J, Daley GQ, Callahan L, Catley L, Cavazza C, Azam M, Mohammed A, Neuberg D, Wright RD, Gilliland DG, Griffin JD. Characterization of AMN107, a selective inhibitor of native and mutant Bcr-Abl. Cancer Cell 2005; 7:129-41. [PMID: 15710326 DOI: 10.1016/j.ccr.2005.01.007] [Citation(s) in RCA: 1105] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Revised: 10/27/2004] [Accepted: 01/18/2005] [Indexed: 01/17/2023]
Abstract
The Bcr-Abl tyrosine kinase oncogene causes chronic myelogenous leukemia (CML) and Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukemia (ALL). We describe a novel selective inhibitor of Bcr-Abl, AMN107 (IC50 <30 nM), which is significantly more potent than imatinib, and active against a number of imatinib-resistant Bcr-Abl mutants. Crystallographic analysis of Abl-AMN107 complexes provides a structural explanation for the differential activity of AMN107 and imatinib against imatinib-resistant Bcr-Abl. Consistent with its in vitro and pharmacokinetic profile, AMN107 prolonged survival of mice injected with Bcr-Abl-transformed hematopoietic cell lines or primary marrow cells, and prolonged survival in imatinib-resistant CML mouse models. AMN107 is a promising new inhibitor for the therapy of CML and Ph+ ALL.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Benzamides
- Bone Marrow Cells/cytology
- Cell Line
- Cell Line, Tumor
- Cell Survival
- Crystallography, X-Ray
- Dose-Response Relationship, Drug
- Drug Resistance, Neoplasm
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/genetics
- Hematopoietic Stem Cells/cytology
- Imatinib Mesylate
- Inhibitory Concentration 50
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Mice
- Models, Biological
- Models, Chemical
- Mutation
- Mycoplasma/metabolism
- Phosphorylation
- Piperazines/pharmacology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy
- Pyrimidines/chemistry
- Pyrimidines/pharmacology
- Retroviridae/genetics
- Time Factors
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Affiliation(s)
- Ellen Weisberg
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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32
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Manley PW, Breitenstein W, Brüggen J, Cowan-Jacob SW, Furet P, Mestan J, Meyer T. Urea derivatives of STI571 as inhibitors of Bcr-Abl and PDGFR kinases. Bioorg Med Chem Lett 2004; 14:5793-7. [PMID: 15501042 DOI: 10.1016/j.bmcl.2004.09.042] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2004] [Revised: 08/27/2004] [Accepted: 09/17/2004] [Indexed: 11/24/2022]
Abstract
The constitutively active Abl kinase activity of the Bcr-Abl oncoprotein is causative for chronic myelogenous leukemia. Urea derivatives, structurally related to the therapeutic agent STI571, have been identified, which potently inhibit the tyrosine kinase activity of recombinant Abl. In particular a dimethylamino-aniline derivative (18) inhibited c-Abl transphosphorylation with an IC(50) value of 56 nM. Although this activity was not translated into cellular activity against the constitutively activated oncogenic Bcr-Abl, a number of compounds from this series potently inhibited cellular PDGFR autophosphorylation. It was also possible to differentiate between c-Abl and PDGFR kinase inhibition, with compound 22 being selective towards Abl and 23 selective for PDGFR.
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Affiliation(s)
- Paul W Manley
- Disease Area Oncology, Novartis Institutes for Biomedical Research, CH-4002 Basel, Switzerland.
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33
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Abstract
Starting from the high-throughput screening hit 1a, novel cathepsin K inhibitors have been developed based on a purine scaffold. High-resolution X-ray structures of several derivatives have revealed the binding mode of these unique cysteine protease inhibitors.
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Affiliation(s)
- Eva Altmann
- Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland.
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34
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Cowan-Jacob SW, Guez V, Fendrich G, Griffin JD, Fabbro D, Furet P, Liebetanz J, Mestan J, Manley PW. Imatinib (STI571) Resistance in Chronic Myelogenous Leukemia: Molecular Basis of the Underlying Mechanisms and Potential Strategies for Treatment. Mini Rev Med Chem 2004; 4:285-99. [PMID: 15032675 DOI: 10.2174/1389557043487321] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [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: 11/22/2022]
Abstract
Following the paradigm set by STI571, protein tyrosine kinase inhibitors are emerging as a promising class of drugs, capable of modulating intracellular signaling and demonstrating therapeutic potential for the treatment of proliferative diseases. Although the majority of chronic phase CML patients treated with STI571 respond, some patients, especially those with more advanced disease, relapse. This article reviews the reasons for relapse and, in particular, analyses resistance resulting from Bcr-Abl tyrosine kinase domain mutations at the molecular level. Arguments are based upon the structure of the STI571-Abl complex, which is compared to the crystal structures of PD173955-Abl and PD180970-Abl, which bind to the kinase differently. Strategies to potentially circumvent or overcome resistance are discussed.
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MESH Headings
- Animals
- Antineoplastic Agents/therapeutic use
- Benzamides
- Drug Resistance, Neoplasm/genetics
- Enzyme Inhibitors/therapeutic use
- Fusion Proteins, bcr-abl
- Genes, abl/genetics
- Humans
- Imatinib Mesylate
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Mutation
- Piperazines/therapeutic use
- Protein-Tyrosine Kinases/antagonists & inhibitors
- Protein-Tyrosine Kinases/genetics
- Pyrimidines/therapeutic use
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35
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Cowan-Jacob SW, Kaufmann M, Anselmo AN, Stark W, Grütter MG. Structure of rabbit-muscle glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallogr D Biol Crystallogr 2003; 59:2218-27. [PMID: 14646080 DOI: 10.1107/s0907444903020493] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2002] [Accepted: 09/16/2003] [Indexed: 11/10/2022]
Abstract
The crystal structure of the tetrameric form of D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) isolated from rabbit muscle was solved at 2.4 A resolution after careful dynamic light-scattering experiments to find a suitable buffer for crystallization trials. The refined model has a crystallographic R factor of 20.3%. Here, the first detailed model of a mammalian GAPDH is presented. The cofactor NAD(+) (nicotinamide adenine dinucleotide) is bound to two subunits of the tetrameric enzyme, which is consistent with the negative cooperativity of NAD(+) binding to this enzyme. The structure of rabbit-muscle GAPDH is of interest because it shares 91% sequence identity with the human enzyme; human GAPDH is a potential target for the development of anti-apoptotic drugs. In addition, differences in the cofactor-binding pocket compared with the homology-model structure of GAPDH from the malaria parasite Plasmodium falciparum could be exploited in order to develop novel selective and potential antimalaria drugs.
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Affiliation(s)
- Sandra W Cowan-Jacob
- Novartis Pharma AG, Core Technology Area, Analytics and Biomolecular Structure, CH-4002 Basel, Switzerland
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36
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Abstract
The understanding of the pathophysiology of a large number of cancer types provides a strategy to target cancer cells with minimal effect on normal cells. Protein phosphorylation and dephosphorylation play a pivotal role in intracellular signaling; to regulate signal transduction pathways, there are approximately 700 protein kinases and 100 protein phosphatases encoded within the human genome. In cancer, as well as in other proliferative diseases, unregulated cell proliferation, differentiation and survival frequently results from abnormal protein phosphorylation. Although it is often possible to identify a single kinase that plays a pivotal role in a given disease, the development of drugs based upon protein kinase inhibition has been hampered by unacceptable side effects resulting from a lack of target selectivity. With the growing understanding of the molecular biology of protein tyrosine kinases and the use of structural information, the design of potential drugs directed towards the bind adenosine triphosphate (ATP)-binding site of a single target has become possible. These advances have transferred emphasis away from the identification of potent kinase inhibitors and more towards issues of target selectivity, cellular efficacy, therapeutic effectiveness and tolerability. In this paper, the relationship between molecular biology and drug discovery methods, as utilized for the identification of anticancer drugs, will be illustrated.
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Affiliation(s)
- P W Manley
- Novartis Pharma Ltd., Basel, Switzerland.
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37
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Fabbro D, Ruetz S, Buchdunger E, Cowan-Jacob SW, Fendrich G, Liebetanz J, Mestan J, O'Reilly T, Traxler P, Chaudhuri B, Fretz H, Zimmermann J, Meyer T, Caravatti G, Furet P, Manley PW. Protein kinases as targets for anticancer agents: from inhibitors to useful drugs. Pharmacol Ther 2002; 93:79-98. [PMID: 12191602 DOI: 10.1016/s0163-7258(02)00179-1] [Citation(s) in RCA: 252] [Impact Index Per Article: 11.5] [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: 12/31/2022]
Abstract
Many components of mitogenic signaling pathways in normal and neoplastic cells have been identified, including the large family of protein kinases, which function as components of signal transduction pathways, playing a central role in diverse biological processes, such as control of cell growth, metabolism, differentiation, and apoptosis. The development of selective protein kinase inhibitors that can block or modulate diseases caused by abnormalities in these signaling pathways is widely considered a promising approach for drug development. Because of their deregulation in human cancers, protein kinases, such as Bcr-Abl, those in the epidermal growth factor-receptor (HER) family, the cell cycle regulating kinases such as the cyclin-dependent kinases, as well as the vascular endothelial growth factor-receptor kinases involved in the neo-vascularization of tumors, are among the protein kinases considered as prime targets for the development of selective inhibitors. These drug-discovery efforts have generated inhibitors and low-molecular weight therapeutics directed against the ATP-binding site of various protein kinases that are in various stages of development (up to Phase II/III clinical trials). Three examples of inhibitors of protein kinases are reviewed, including low-molecular weight compounds targeting the cell cycle kinases; a potent and selective inhibitor of the HER1/HER2 receptor tyrosine kinase, the pyrollopyrimidine PKI166; and the 2-phenyl-aminopyrimidine STI571 (Glivec(R), Gleevec) a targeted drug therapy directed toward Bcr-Abl, the key player in chronic leukemia (CML). Some members of the HER family of receptor tyrosine kinases, in particular HER1 and HER2, have been found to be overexpressed in a variety of human tumors, suggesting that inhibition of HER signaling would be a viable antiproliferative strategy. The pyrrolo-pyrimidine PKI166 was developed as an HER1/HER2 inhibitor with potent in vitro antiproliferative and in vivo antitumor activity. Based upon its clear association with disease, the Bcr-Abl tyrosine kinase in CML represents the ideal target to validate the clinical utility of protein kinase inhibitors as therapeutic agents. In a preclinical model, STI571 (Glivec(R), Gleevec) showed potent in vitro and in vivo antitumor activity that was selective for Abl, c-Kit, and the platelet-derived growth factor-receptor. Phase I/II studies demonstrated that STI571 is well tolerated, and that it showed promising hematological and cytogenetic responses in CML and clinical responses in the c-Kit-driven gastrointestinal tumors.
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Affiliation(s)
- Doriano Fabbro
- Department of Oncology, Novartis Pharma Inc., WKL-125.4.10, CH-4002, Basel, Switzerland.
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Zhang H, Cowan-Jacob SW, Simonen M, Greenhalf W, Heim J, Meyhack B. Structural basis of BFL-1 for its interaction with BAX and its anti-apoptotic action in mammalian and yeast cells. J Biol Chem 2000; 275:11092-9. [PMID: 10753914 DOI: 10.1074/jbc.275.15.11092] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [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: 11/06/2022] Open
Abstract
BFL-1 is the smallest member of the BCL-2 family and has been shown to retard apoptosis in various cell lines. However, the structural basis for its function remains unclear. Molecular modeling showed that BFL-1 could have a similar core structure as BCL-xL, consisting of seven alpha helices, although both proteins share only the conserved BCL-2 homology domains (BH1 and BH2 domains), but otherwise have very limited sequence homology, particularly in the N-terminal region. We demonstrated in the yeast two-hybrid system that BFL-1 interacts strongly with human BAX but is not able to form homodimers nor to interact with human BCL-2 or BCL-xL. Overexpression experiments in REF52 rat fibroblasts showed that BFL-1 conferred increased resistance to apoptosis induced by serum deprivation. BFL-1 had also the ability to neutralize BAX lethality in yeast. BAX requires the BH3 domain for interaction with BFL-1. However, the minimal region of BFL-1 for the interaction with BAX in coimmunoprecipitation experiments was not sufficient to protect cells from apoptosis. Further examination of BFL-1 and several other anti-apoptotic proteins suggests a more general type of structure based on structural motifs, i.e. a hydrophobic pocket for the binding of proapoptotic proteins, rather than extended sequence homologies.
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Affiliation(s)
- H Zhang
- Novartis Pharma AG, Oncology, Molecular Genetics, CH-4002 Basel, Switzerland
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39
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Prade L, Cowan-Jacob SW, Chemla P, Potter S, Ward E, Fonne-Pfister R. Structures of adenylosuccinate synthetase from Triticum aestivum and Arabidopsis thaliana. J Mol Biol 2000; 296:569-77. [PMID: 10669609 DOI: 10.1006/jmbi.1999.3473] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [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: 11/22/2022]
Abstract
Catalyzing the first step in the de novo synthesis of adenylmonophosphate, adenylosuccinate synthetase (AdSS) is a known target for herbicides and antibiotics. We have purified and crystallized recombinant AdSS from Arabidopsis thaliana and Tritium aestivum, expressed in Escherichia coli. The structures of A. thaliana and T. aestivum AdSS in complex with GDP were solved at 2.9 A and 3.0 A resolution, respectively. Comparison with the known structures from E. coli reveals that the overall fold is very similar to that of the E. coli protein. The longer N terminus in the plant sequences is at the same place as the longer C terminus of the E. coli sequence in the 3D structure. The GDP-binding sites have one additional hydrogen-bonding partner, which is a plausible explanation for the lower K(m) value. Due to its special position, this partner may also enable GTP to initiate a conformational change, which was, in E. coli AdSS, exclusively activated by ligands at the IMP-binding site. The dimer interfaces show up to six hydrogen bonds and six salt-bridges more than in the E. coli structure, although the contact areas have approximately the same size.
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Affiliation(s)
- L Prade
- Novartis Pharma AG, Basel, CH-4056, Switzerland
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40
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Hanessian S, Lu PP, Sancéau JY, Chemla P, Gohda K, Fonne-Pfister R, Prade L, Cowan-Jacob SW. An Enzyme-Bound Bisubstrate Hybrid Inhibitor of Adenylosuccinate Synthetase. Angew Chem Int Ed Engl 1999; 38:3159-3162. [PMID: 10556888 DOI: 10.1002/(sici)1521-3773(19991102)38:21<3159::aid-anie3159>3.0.co;2-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Two relatively weak herbicides, hydantocidin phosphate and hadacidin were linked by a C(3) chain to afford a potent inhibitor (the 2S hybrid is shown) of the enzyme adenylosuccinate synthetase. The crystal structures of the bisubstrate-enzyme complexes were determined.
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Affiliation(s)
- S Hanessian
- Department of Chemistry, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montreal, QC, H3C 3J7 (Canada)
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41
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Landau EM, Rummel G, Cowan-Jacob SW, Rosenbusch JP. Crystallization of a Polar Protein and Small Molecules from the Aqueous Compartment of Lipidic Cubic Phases. J Phys Chem B 1997. [DOI: 10.1021/jp963347q] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ehud M. Landau
- Biozentrum, University of Basel, Klingelbergstr. 70, CH-4056 Basel, Switzerland, and Core Drug Discovery Technologies, K-681.5.47 Ciba Geigy AG, CH-4002 Basel, Switzerland
| | - Gabriele Rummel
- Biozentrum, University of Basel, Klingelbergstr. 70, CH-4056 Basel, Switzerland, and Core Drug Discovery Technologies, K-681.5.47 Ciba Geigy AG, CH-4002 Basel, Switzerland
| | - Sandra W. Cowan-Jacob
- Biozentrum, University of Basel, Klingelbergstr. 70, CH-4056 Basel, Switzerland, and Core Drug Discovery Technologies, K-681.5.47 Ciba Geigy AG, CH-4002 Basel, Switzerland
| | - Jurg P. Rosenbusch
- Biozentrum, University of Basel, Klingelbergstr. 70, CH-4056 Basel, Switzerland, and Core Drug Discovery Technologies, K-681.5.47 Ciba Geigy AG, CH-4002 Basel, Switzerland
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Cowan-Jacob SW, Rahuel J, Nagai A, Iwasaki G, Ohta D. Crystallization and preliminary crystallographic analysis of cabbage histidinol dehydrogenase. Acta Cryst D 1996; 52:1188-90. [PMID: 15299582 DOI: 10.1107/s0907444996008396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Recombinant Brassica oleracea histidinol dehydrogenase (HDH) has been crystallized in various space groups using the method of vapour diffusion. The presence or absence of inhibitors and substrates as well as the use of different precipitants has enabled the growth of five different crystal forms. Extensive searches with the first crystal form (A) failed to produce any useful heavy-atom derivatives, mainly because of the instability of the crystals. This provoked the search for further crystal forms in the hope of finding more suitable crystals. At least two of these crystal forms are of interest for further study.
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Affiliation(s)
- S W Cowan-Jacob
- Core Drug Discovery Technologies, Ciba-Geigy AG, Basel, Switzerland.
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43
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Fonné-Pfister R, Chemla P, Ward E, Girardet M, Kreuz KE, Honzatko RB, Fromm HJ, Schär HP, Grütter MG, Cowan-Jacob SW. The mode of action and the structure of a herbicide in complex with its target: binding of activated hydantocidin to the feedback regulation site of adenylosuccinate synthetase. Proc Natl Acad Sci U S A 1996; 93:9431-6. [PMID: 8790347 PMCID: PMC38445 DOI: 10.1073/pnas.93.18.9431] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.3] [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: 02/02/2023] Open
Abstract
(+)-Hydantocidin, a recently discovered natural spironucleoside with potent herbicidal activity, is shown to be a proherbicide that, after phosphorylation at the 5' position, inhibits adenylosuccinate synthetase, an enzyme involved in de novo purine synthesis. The mode of binding of hydantocidin 5'-monophosphate to the target enzyme was analyzed by determining the crystal structure of the enzyme-inhibitor complex at 2.6-A resolution. It was found that adenylosuccinate synthetase binds the phosphorylated compound in the same fashion as it does adenosine 5'-monophosphate, the natural feedback regulator of this enzyme. This work provides the first crystal structure of a herbicide-target complex reported to date.
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Affiliation(s)
- R Fonné-Pfister
- Pharmaceutical Division, Ciba-Geigy Ltd., Basel, Switzerland
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