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Primavera E, Palazzotti D, Barreca ML, Astolfi A. Computer-Aided Identification of Kinase-Targeted Small Molecules for Cancer: A Review on AKT Protein. Pharmaceuticals (Basel) 2023; 16:993. [PMID: 37513905 PMCID: PMC10384952 DOI: 10.3390/ph16070993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
AKT (also known as PKB) is a serine/threonine kinase that plays a pivotal regulatory role in the PI3K/AKT/mTOR signaling pathway. Dysregulation of AKT activity, especially its hyperactivation, is closely associated with the development of various human cancers and resistance to chemotherapy. Over the years, a wide array of AKT inhibitors has been discovered through experimental and computational approaches. In this regard, herein we present a comprehensive overview of AKT inhibitors identified using computer-assisted drug design methodologies (including docking-based and pharmacophore-based virtual screening, machine learning, and quantitative structure-activity relationships) and successfully validated small molecules endowed with anticancer activity. Thus, this review provides valuable insights to support scientists focused on AKT inhibition for cancer treatment and suggests untapped directions for future computer-aided drug discovery efforts.
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Affiliation(s)
- Erika Primavera
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, 06123 Perugia, Italy
| | - Deborah Palazzotti
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, 06123 Perugia, Italy
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, 06123 Perugia, Italy
| | - Andrea Astolfi
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, 06123 Perugia, Italy
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2
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Lorenz R, Wu J, Herberg FW, Taylor SS, Engh RA. Drugging the Undruggable: How Isoquinolines and PKA Initiated the Era of Designed Protein Kinase Inhibitor Therapeutics. Biochemistry 2021; 60:3470-3484. [PMID: 34370450 DOI: 10.1021/acs.biochem.1c00359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In 1984, Japanese researchers led by the biochemist Hiroyoshi Hidaka described the first synthetic protein kinase inhibitors based on an isoquinoline sulfonamide structure (Hidaka et al. Biochemistry, 1984 Oct 9; 23(21): 5036-41. doi: 10.1021/bi00316a032). These led to the first protein kinase inhibitor approved for medical use (fasudil), an inhibitor of the AGC subfamily Rho kinase. With potencies strong enough to compete against endogenous ATP, the isoquinoline compounds established the druggability of the ATP binding site. Crystal structures of their protein kinase complexes, including with cAMP-dependent protein kinase (PKA), showed interactions that, on the one hand, could mimic ATP but, on the other hand, could be optimized for high potency binding, kinase selectivity, and diversification away from adenosine. They also showed the flexibility of the glycine-rich loop, and PKA became a major prototype for crystallographic and nuclear magnetic resonance (NMR) studies of protein kinase mechanism and dynamic activity control. Since fasudil, more than 70 kinase inhibitors have been approved for clinical use, involving efforts that progressively have introduced new paradigms of data-driven drug discovery. Publicly available data alone comprise over 5000 protein kinase crystal structures and hundreds of thousands of binding data. Now, new methods, including artificial intelligence techniques and expansion of protein kinase targeting approaches, together with the expiration of patent protection for optimized inhibitor scaffolds, promise even greater advances in drug discovery. Looking back to the time of the first isoquinoline hinge binders brings the current state-of-the-art into stark contrast. Appropriately for this Perspective article, many of the milestone papers during this time were published in Biochemistry (now ACS Biochemistry).
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Affiliation(s)
- Robin Lorenz
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel 34132, Germany
| | - Jian Wu
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States
| | - Friedrich W Herberg
- Department of Biochemistry, Institute for Biology, University of Kassel, Kassel 34132, Germany
| | - Susan S Taylor
- Department of Pharmacology, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, 9400 Gilman Drive, La Jolla, California 92093-0654, United States
| | - Richard A Engh
- The Norwegian Structural Biology Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromsø 9012, Norway
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3
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Xu X, Chen Y, Fu Q, Ni D, Zhang J, Li X, Lu S. The chemical diversity and structure-based discovery of allosteric modulators for the PIF-pocket of protein kinase PDK1. J Enzyme Inhib Med Chem 2019; 34:361-374. [PMID: 30734603 PMCID: PMC6327997 DOI: 10.1080/14756366.2018.1553167] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 01/06/2023] Open
Abstract
Phosphoinositide-dependent protein kinase-1 (PDK1) is an important protein in mediating the PI3K-AKT pathway and is thus identified as a promising target. The catalytic activity of PDK1 is tightly regulated by allosteric modulators, which bind to the PDK1 Interacting Fragment (PIF) pocket of the kinase domain that is topographically distinct from the orthosteric, ATP binding site. Allosteric modulators by attaching to the less conserved PIF-pocket have remarkable advantages such as higher selectivity, less side effect, and lower toxicity. Targeting allosteric PIF-pocket of PDK1 has become the focus of recent attention. In this review, we summarise the current advances in the structure-based discovery of PDK1 allosteric modulators. We will first present the three-dimensional structure of PDK1 and illustrate the allosteric regulatory mechanism of PDK1 through the modulation of the PIF-pocket. Then, the recent advances of PDK1 allosteric modulators targeting the PIF-pocket will be recapitulated detailly according to the structural similarity of allosteric modulators.
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Affiliation(s)
- Xinyuan Xu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yingyi Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Qiang Fu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Duan Ni
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
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Orabi EA, English AM. Modeling Protein S-Aromatic Motifs Reveals Their Structural and Redox Flexibility. J Phys Chem B 2018. [PMID: 29533644 DOI: 10.1021/acs.jpcb.8b00089] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
S-aromatic motifs are important noncovalent forces for protein stability and function but remain poorly understood. Hence, we performed quantum calculations at the MP2(full)/6-311++G(d,p) level on complexes between Cys (H2S, MeSH) and Met (Me2S) models with models of Phe (benzene, toluene), Trp (indole, 3-methylindole), Tyr (phenol, 4-methylphenol), and His (imidazole, 4-methylimidazole). The most stable gas-phase conformers exhibit binding energies of -2 to -6 kcal/mol, and the S atom lies perpendicular to the ring plane. This reveals preferential interaction with the ring π-system, except in the imidazoles where S binds edge-on to an N atom. Complexation tunes the gas-phase vertical ionization potentials of the ligands over as much as 1 eV, and strong σ- or π-type H-bonding supports charge transfer to the H-bond donor, rendering it more oxidizable. When the S atom acts as an H-bond acceptor (N/O-Har···S), calibration of the CHARMM36 force field (by optimizing pair-specific Lennard-Jones parameters) is required. Implementing the optimized parameters in molecular dynamics simulations in bulk water, we find stable S-aromatic complexes with binding free energies of -0.6 to -1.1 kcal/mol at ligand separations up to 8 Å. The aqueous S-aromatics exhibit flexible binding conformations, but edge-on conformers are less stable in water. Reflecting this, only 0.3 to 10% of the S-indole, S-phenol, and S-imidazole structures are stabilized by N/O-Har···S or S-H···Oar/Nar σ-type H-bonding. The wide range of energies and geometries found for S-aromatic interactions and their tunable redox properties expose the versatility and variability of the S-aromatic motif in proteins and allow us to predict a number of their reported properties.
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Affiliation(s)
- Esam A Orabi
- Centre for Research in Molecular Modeling (CERMM) and PROTEO , Department of Chemistry and Biochemistry , Concordia University , 7141 Sherbrooke Street West , Montréal , Québec H4B 1R6 , Canada
| | - Ann M English
- Centre for Research in Molecular Modeling (CERMM) and PROTEO , Department of Chemistry and Biochemistry , Concordia University , 7141 Sherbrooke Street West , Montréal , Québec H4B 1R6 , Canada
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5
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Orabi EA, English AM. Predicting structural and energetic changes in Met–aromatic motifs on methionine oxidation to the sulfoxide and sulfone. Phys Chem Chem Phys 2018; 20:23132-23141. [DOI: 10.1039/c8cp03277g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Methionine oxidation increases its affinity for aromatics in the gas phase but lowers it for most complexes in water.
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Affiliation(s)
- Esam A. Orabi
- Center for Research in Molecular Modeling (CERMM)
- Quebec Network for Research on Protein Function
- Engineering, and Applications (PROTEO), and Department of Chemistry and Biochemistry
- Concordia University
- Montréal
| | - Ann M. English
- Center for Research in Molecular Modeling (CERMM)
- Quebec Network for Research on Protein Function
- Engineering, and Applications (PROTEO), and Department of Chemistry and Biochemistry
- Concordia University
- Montréal
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6
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Lu Y, Knapp M, Crawford K, Warne R, Elling R, Yan K, Doyle M, Pardee G, Zhang L, Ma S, Mamo M, Ornelas E, Pan Y, Bussiere D, Jansen J, Zaror I, Lai A, Barsanti P, Sim J. Rationally Designed PI3Kα Mutants to Mimic ATR and Their Use to Understand Binding Specificity of ATR Inhibitors. J Mol Biol 2017; 429:1684-1704. [PMID: 28433539 DOI: 10.1016/j.jmb.2017.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/08/2017] [Accepted: 04/11/2017] [Indexed: 12/16/2022]
Abstract
ATR, a protein kinase in the PIKK family, plays a critical role in the cell DNA-damage response and is an attractive anticancer drug target. Several potent and selective inhibitors of ATR have been reported showing significant antitumor efficacy, with most advanced ones entering clinical trials. However, due to the absence of an experimental ATR structure, the determinants contributing to ATR inhibitors' potency and specificity are not well understood. Here we present the mutations in the ATP-binding site of PI3Kα to progressively transform the pocket to mimic that of ATR. The generated PI3Kα mutants exhibit significantly improved affinity for selective ATR inhibitors in multiple chemical classes. Furthermore, we obtained the X-ray structures of the PI3Kα mutants in complex with the ATR inhibitors. The crystal structures together with the analysis on the inhibitor affinity profile elucidate the roles of individual amino acid residues in the binding of ATR inhibitors, offering key insights for the binding mechanism and revealing the structure features important for the specificity of ATR inhibitors. The ability to obtain structural and binding data for these PI3Kα mutants, together with their ATR-like inhibitor binding profiles, makes these chimeric PI3Kα proteins valuable model systems for structure-based inhibitor design.
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Affiliation(s)
- Yipin Lu
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA.
| | - Mark Knapp
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA.
| | - Kenneth Crawford
- Oncology, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Robert Warne
- Oncology, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Robert Elling
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Kelly Yan
- Oncology, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Michael Doyle
- Oncology, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Gwynn Pardee
- Oncology, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Li Zhang
- Oncology, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Sylvia Ma
- Oncology, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Mulugeta Mamo
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Elizabeth Ornelas
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Yue Pan
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Dirksen Bussiere
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Johanna Jansen
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Isabel Zaror
- Oncology, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Albert Lai
- Oncology, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Paul Barsanti
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
| | - Janet Sim
- Oncology, Novartis Institutes for Biomedical Research, Emeryville, CA 94608, USA
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7
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Orabi EA, English AM. Sulfur-Aromatic Interactions: Modeling Cysteine and Methionine Binding to Tyrosinate and Histidinium Ions to Assess Their Influence on Protein Electron Transfer. Isr J Chem 2016. [DOI: 10.1002/ijch.201600047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Esam A. Orabi
- Department of Chemistry and Biochemistry; Concordia University; 7141 Sherbrooke Street West Montréal Québec H4B 1R6 Canada
- Center for Research in Molecular Modeling (CERMM)Quebec; Network for Research on Protein Function, Engineering, and Applications (PROTEO)
- On leave from Department of Chemistry, Faculty of Science; Assiut University; Assiut 71516 Egypt
| | - Ann M. English
- Department of Chemistry and Biochemistry; Concordia University; 7141 Sherbrooke Street West Montréal Québec H4B 1R6 Canada
- Center for Research in Molecular Modeling (CERMM)Quebec; Network for Research on Protein Function, Engineering, and Applications (PROTEO)
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8
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Lauber BS, Hardegger LA, Asraful AK, Lund BA, Dumele O, Harder M, Kuhn B, Engh RA, Diederich F. Addressing the Glycine-Rich Loop of Protein Kinases by a Multi-Facetted Interaction Network: Inhibition of PKA and a PKB Mimic. Chemistry 2015; 22:211-21. [DOI: 10.1002/chem.201503552] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Indexed: 12/25/2022]
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9
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Couty S, Westwood IM, Kalusa A, Cano C, Travers J, Boxall K, Chow CL, Burns S, Schmitt J, Pickard L, Barillari C, McAndrew PC, Clarke PA, Linardopoulos S, Griffin RJ, Aherne GW, Raynaud FI, Workman P, Jones K, van Montfort RLM. The discovery of potent ribosomal S6 kinase inhibitors by high-throughput screening and structure-guided drug design. Oncotarget 2014; 4:1647-61. [PMID: 24072592 PMCID: PMC3858552 DOI: 10.18632/oncotarget.1255] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The ribosomal P70 S6 kinases play a crucial role in PI3K/mTOR regulated signalling pathways and are therefore potential targets for the treatment of a variety of diseases including diabetes and cancer. In this study we describe the identification of three series of chemically distinct S6K1 inhibitors. In addition, we report a novel PKA-S6K1 chimeric protein with five mutations in or near its ATP-binding site, which was used to determine the binding mode of two of the three inhibitor series, and provided a robust system to aid the optimisation of the oxadiazole-substituted benzimidazole inhibitor series. We show that the resulting oxadiazole-substituted aza-benzimidazole is a potent and ligand efficient S6 kinase inhibitor, which blocks the phosphorylation of RPS6 at Ser235/236 in TSC negative HCV29 human bladder cancer cells by inhibiting S6 kinase activity and thus provides a useful tool compound to investigate the function of S6 kinases.
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Affiliation(s)
- Sylvain Couty
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, SM2 5NG, UK
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10
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Pflug A, Johnson KA, Engh RA. Anomalous dispersion analysis of inhibitor flexibility: a case study of the kinase inhibitor H-89. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:873-7. [PMID: 22869112 PMCID: PMC3412763 DOI: 10.1107/s1744309112028655] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/24/2012] [Indexed: 11/10/2022]
Abstract
With its ability to show the interactions between drug-target proteins and small-molecule ligands, X-ray crystallography is an essential tool in drug-discovery programmes. However, its usefulness can be limited by crystallization artifacts or by the data resolution, and in particular when assumptions of unimodal binding (and isotropic motion) do not apply. Discrepancies between the modelled crystal structure and the physiological range of structures generally prevent quantitative estimation of binding energies. Improved crystal structure resolution will often not aid energy estimation because the conditions which provide the highest rigidity and resolution are not likely to reflect physiological conditions. Instead, strategies must be employed to measure and model flexibility and multiple binding modes to supplement crystallographic information. One useful tool is the use of anomalous dispersion for small molecules that contain suitable atoms. Here, an analysis of the binding of the kinase inhibitor H-89 to protein kinase A (PKA) is presented. H-89 contains a bromobenzene moiety that apparently binds with multiple conformations in the kinase ATP pocket. Using anomalous dispersion methods, it was possible to resolve these conformations into two distinct binding geometries.
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Affiliation(s)
- Alexander Pflug
- Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Kenneth A. Johnson
- Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Richard A. Engh
- Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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11
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Abstract
We describe in the present paper mutations of the catalytic subunit α of PKA (protein kinase A) that introduce amino acid side chains into the ATP-binding site and progressively transform the pocket to mimic that of Aurora protein kinases. The resultant PKA variants are enzymatically active and exhibit high affinity for ATP site inhibitors that are specific for Aurora kinases. These features make the Aurora-chimaeric PKA a valuable tool for structure-based drug discovery tasks. Analysis of crystal structures of the chimaera reveal the roles for individual amino acid residues in the binding of a variety of inhibitors, offering key insights into selectivity mechanisms. Furthermore, the high affinity for Aurora kinase-specific inhibitors, combined with the favourable crystallizability properties of PKA, allow rapid determination of inhibitor complex structures at an atomic resolution. We demonstrate the utility of the Aurora-chimaeric PKA by measuring binding kinetics for three Aurora kinase-specific inhibitors, and present the X-ray structures of the chimaeric enzyme in complex with VX-680 (MK-0457) and JNJ-7706621 [Aurora kinase/CDK (cyclin-dependent kinase) inhibitor].
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12
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Yu L, Xu L, Xu M, Wan B, Yu L, Huang Q. Role of Mg2+ions in protein kinase phosphorylation: insights from molecular dynamics simulations of ATP-kinase complexes. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.561430] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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13
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Design and synthesis of novel amide AKT1 inhibitors with selectivity over CDK2. Bioorg Med Chem Lett 2011; 21:5191-6. [DOI: 10.1016/j.bmcl.2011.07.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 07/11/2011] [Accepted: 07/13/2011] [Indexed: 11/19/2022]
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14
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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15
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1172] [Impact Index Per Article: 90.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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16
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Pflug A, Rogozina J, Lavogina D, Enkvist E, Uri A, Engh RA, Bossemeyer D. Diversity of Bisubstrate Binding Modes of Adenosine Analogue–Oligoarginine Conjugates in Protein Kinase A and Implications for Protein Substrate Interactions. J Mol Biol 2010; 403:66-77. [DOI: 10.1016/j.jmb.2010.08.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 08/12/2010] [Accepted: 08/16/2010] [Indexed: 01/11/2023]
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17
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Zeng Q, Bourbeau MP, Wohlhieter GE, Yao G, Monenschein H, Rider JT, Lee MR, Zhang S, Lofgren J, Freeman D, Li C, Tominey E, Huang X, Hoffman D, Yamane H, Tasker AS, Dominguez C, Viswanadhan VN, Hungate R, Zhang X. 2-Aminothiadiazole inhibitors of AKT1 as potential cancer therapeutics. Bioorg Med Chem Lett 2010; 20:1652-6. [DOI: 10.1016/j.bmcl.2010.01.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Revised: 01/08/2010] [Accepted: 01/11/2010] [Indexed: 10/19/2022]
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18
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Lin H, Yamashita DS, Zeng J, Xie R, Wang W, Nidarmarthy S, Luengo JI, Rhodes N, Knick VB, Choudhry AE, Lai Z, Minthorn EA, Strum SL, Wood ER, Elkins PA, Concha NO, Heerding DA. 2,3,5-Trisubstituted pyridines as selective AKT inhibitors-Part I: Substitution at 2-position of the core pyridine for ROCK1 selectivity. Bioorg Med Chem Lett 2009; 20:673-8. [PMID: 20006497 DOI: 10.1016/j.bmcl.2009.11.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 11/11/2009] [Accepted: 11/16/2009] [Indexed: 10/20/2022]
Abstract
2,3,5-Trisubstituted pyridines have been designed as potent AKT inhibitors that are selective against ROCK1 based on the comparison between AKT and ROCK1 structures. Substitution at the 2-position of the core pyridine is the key element to provide selectivity against ROCK1. An X-ray co-crystal structure of 9p in PKA supports the proposed rationale of ROCK1 selectivity.
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Affiliation(s)
- Hong Lin
- Oncology Medicinal Chemistry, GlaxoSmithKline, 1250 S. Collegeville, Rd., Collegeville, PA 19426, United States.
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19
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Structure and functional characterization of the atypical human kinase haspin. Proc Natl Acad Sci U S A 2009; 106:20198-203. [PMID: 19918057 DOI: 10.1073/pnas.0901989106] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The protein kinase haspin/Gsg2 plays an important role in mitosis, where it specifically phosphorylates Thr-3 in histone H3 (H3T3). Its protein sequence is only weakly homologous to other protein kinases and lacks the highly conserved motifs normally required for kinase activity. Here we report structures of human haspin in complex with ATP and the inhibitor iodotubercidin. These structures reveal a constitutively active kinase conformation, stabilized by haspin-specific inserts. Haspin also has a highly atypical activation segment well adapted for specific recognition of the basic histone tail. Despite the lack of a DFG motif, ATP binding to haspin is similar to that in classical kinases; however, the ATP gamma-phosphate forms hydrogen bonds with the conserved catalytic loop residues Asp-649 and His-651, and a His651Ala haspin mutant is inactive, suggesting a direct role for the catalytic loop in ATP recognition. Enzyme kinetic data show that haspin phosphorylates substrate peptides through a rapid equilibrium random mechanism. A detailed analysis of histone modifications in the neighborhood of H3T3 reveals that increasing methylation at Lys-4 (H3K4) strongly decreases substrate recognition, suggesting a key role of H3K4 methylation in the regulation of haspin activity.
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van Montfort RLM, Workman P. Structure-based design of molecular cancer therapeutics. Trends Biotechnol 2009; 27:315-28. [PMID: 19339067 DOI: 10.1016/j.tibtech.2009.02.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 02/16/2009] [Accepted: 02/18/2009] [Indexed: 01/16/2023]
Abstract
Structure-based approaches now impact across the whole continuum of drug discovery, from new target selection through the identification of hits to the optimization of lead compounds. Optimal application of structure-based design involves close integration with other discovery technologies, including fragment-based and virtual screening. Here, we illustrate the use of structural information and of structure-based drug design approaches in the discovery of small-molecule inhibitors for cancer drug targets and provide an outlook on the exploitation of structural information in future cancer drug discovery. Examples include high profile protein kinase targets and structurally related PI3 kinases, histone deacetylases, poly(ADP-ribose)polymerase and the molecular chaperone HSP90. Structure-based design approaches have also been successfully applied to the protein-protein interaction targets p53-MDM2 and the Bcl-2 family.
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Affiliation(s)
- Rob L M van Montfort
- Section of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories, Chelsea, London SW3 6JB, UK.
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21
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Lavogina D, Lust M, Viil I, König N, Raidaru G, Rogozina J, Enkvist E, Uri A, Bossemeyer D. Structural Analysis of ARC-Type Inhibitor (ARC-1034) Binding to Protein Kinase A Catalytic Subunit and Rational Design of Bisubstrate Analogue Inhibitors of Basophilic Protein Kinases. J Med Chem 2008; 52:308-21. [DOI: 10.1021/jm800797n] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Darja Lavogina
- Institute of Chemistry, 2 Jakobi Street, 51014 Tartu, Estonia, Group of Structural Biochemistry, German Cancer Research Centre, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Marje Lust
- Institute of Chemistry, 2 Jakobi Street, 51014 Tartu, Estonia, Group of Structural Biochemistry, German Cancer Research Centre, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Indrek Viil
- Institute of Chemistry, 2 Jakobi Street, 51014 Tartu, Estonia, Group of Structural Biochemistry, German Cancer Research Centre, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Norbert König
- Institute of Chemistry, 2 Jakobi Street, 51014 Tartu, Estonia, Group of Structural Biochemistry, German Cancer Research Centre, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Gerda Raidaru
- Institute of Chemistry, 2 Jakobi Street, 51014 Tartu, Estonia, Group of Structural Biochemistry, German Cancer Research Centre, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jevgenia Rogozina
- Institute of Chemistry, 2 Jakobi Street, 51014 Tartu, Estonia, Group of Structural Biochemistry, German Cancer Research Centre, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Erki Enkvist
- Institute of Chemistry, 2 Jakobi Street, 51014 Tartu, Estonia, Group of Structural Biochemistry, German Cancer Research Centre, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Asko Uri
- Institute of Chemistry, 2 Jakobi Street, 51014 Tartu, Estonia, Group of Structural Biochemistry, German Cancer Research Centre, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Dirk Bossemeyer
- Institute of Chemistry, 2 Jakobi Street, 51014 Tartu, Estonia, Group of Structural Biochemistry, German Cancer Research Centre, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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22
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Muddassar M, Pasha FA, Neaz MM, Saleem Y, Cho SJ. Elucidation of binding mode and three dimensional quantitative structure-activity relationship studies of a novel series of protein kinase B/Akt inhibitors. J Mol Model 2008; 15:183-92. [PMID: 19043747 DOI: 10.1007/s00894-008-0416-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 09/12/2008] [Indexed: 11/27/2022]
Abstract
Protein kinase B (PKB; also known as Akt kinase) is located downstream in the PI-3 kinase pathway. Overexpression and constitutive activation of PKB/Akt leads to human prostate, breast and ovarian carcinomas. A series of 69 PKB/Akt inhibitors were examined to explore their binding modes using FlexX, and three-dimensional quantitative structure-activity relationship (3D-QSAR) studies based on comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed to provide structural insights into these compounds. CoMFA produced statistically significant results, with cross-validated q ( 2 ) and non-cross validated correlation r(2) coefficients of 0.53 and 0.95, respectively. For CoMSIA, steric, hydrophobic and hydrogen bond acceptor fields jointly yielded 'leave one out' q(2) = 0.51 and r(2) = 0.84. The predictive power of CoMFA and CoMSIA was determined using a test set of 13 molecules, which gave correlation coefficients, r(2)(predictive) of 0.58 and 0.62, respectively. Molecular docking revealed that the binding modes of these molecules in the ATP binding sites of the Akt kinase domain were very similar to those of the co-crystallized ligand. The information obtained from 3D contour maps will allow the design of more potent and selective Akt kinase inhibitors.
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Affiliation(s)
- M Muddassar
- Future Fusion Technology Division, Computational Science Center, Korea Institute of Science and Technology, P.O. Box 131, Cheongryang, Seoul 130-650, South Korea.
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23
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Garcia-Echeverria C, Sellers WR. Drug discovery approaches targeting the PI3K/Akt pathway in cancer. Oncogene 2008; 27:5511-26. [PMID: 18794885 DOI: 10.1038/onc.2008.246] [Citation(s) in RCA: 355] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The abnormal activation of the phosphatidylinositol 3-kinase (PI3K)/Akt pathway has been validated by epidemiological and experimental studies as an essential step toward the initiation and maintenance of human tumors. Notable in this regard are the prevalent somatic genetic alterations leading to the inactivation of the tumor suppressor gene PTEN and gain-of-function mutations targeting PIK3CA--the gene encoding the catalytic phosphosinositide-3 kinase subunit p110 alpha. A number of the intracellular components of this pathway have been targeted as anticancer drug discovery activities leading to the current panoply of clinical trials of inhibitors of PI3K, Akt and HSP90 in man. This review summarizes current preclinical knowledge of modulators of the PI3K/Akt pathway in which drug discovery and development activities have been advanced focusing on both the relevant clinical stage inhibitors and other disclosed tool compounds targeting PI3K, PDK1, Akt and HSP90.
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Affiliation(s)
- C Garcia-Echeverria
- Oncology Drug Discovery, Novartis Institutes for Biomedical Research, Basel, Switzerland.
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24
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Caldwell JJ, Davies TG, Donald A, McHardy T, Rowlands MG, Aherne GW, Hunter LK, Taylor K, Ruddle R, Raynaud FI, Verdonk M, Workman P, Garrett MD, Collins I. Identification of 4-(4-Aminopiperidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidines as Selective Inhibitors of Protein Kinase B through Fragment Elaboration. J Med Chem 2008; 51:2147-57. [DOI: 10.1021/jm701437d] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John J. Caldwell
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Thomas G. Davies
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Alastair Donald
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Tatiana McHardy
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Martin G. Rowlands
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - G. Wynne Aherne
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Lisa K. Hunter
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Kevin Taylor
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Ruth Ruddle
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Florence I. Raynaud
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Marcel Verdonk
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Paul Workman
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Michelle D. Garrett
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Ian Collins
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, U.K., and Astex Therapeutics Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
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25
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Engh R. Protein Kinase Inhibitors Highlight the Complexities of Drug-Target Non-Covalent Interactions. BIOTECHNOL BIOTEC EQ 2008. [DOI: 10.1080/13102818.2008.10817551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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26
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27
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Davies TG, Verdonk ML, Graham B, Saalau-Bethell S, Hamlett CCF, McHardy T, Collins I, Garrett MD, Workman P, Woodhead SJ, Jhoti H, Barford D. A structural comparison of inhibitor binding to PKB, PKA and PKA-PKB chimera. J Mol Biol 2007; 367:882-94. [PMID: 17275837 DOI: 10.1016/j.jmb.2007.01.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Revised: 12/20/2006] [Accepted: 01/03/2007] [Indexed: 01/08/2023]
Abstract
Although the crystal structure of the anti-cancer target protein kinase B (PKBbeta/Akt-2) has been useful in guiding inhibitor design, the closely related kinase PKA has generally been used as a structural mimic due to its facile crystallization with a range of ligands. The use of PKB-inhibitor crystallography would bring important benefits, including a more rigorous understanding of factors dictating PKA/PKB selectivity, and the opportunity to validate the utility of PKA-based surrogates. We present a "back-soaking" method for obtaining PKBbeta-ligand crystal structures, and provide a structural comparison of inhibitor binding to PKB, PKA, and PKA-PKB chimera. One inhibitor presented here exhibits no PKB/PKA selectivity, and the compound adopts a similar binding mode in all three systems. By contrast, the PKB-selective inhibitor A-443654 adopts a conformation in PKB and PKA-PKB that differs from that with PKA. We provide a structural explanation for this difference, and highlight the ability of PKA-PKB to mimic the true PKB binding mode in this case.
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Affiliation(s)
- Thomas G Davies
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK.
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28
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Bonn S, Herrero S, Breitenlechner CB, Erlbruch A, Lehmann W, Engh RA, Gassel M, Bossemeyer D. Structural analysis of protein kinase A mutants with Rho-kinase inhibitor specificity. J Biol Chem 2006; 281:24818-30. [PMID: 16699172 DOI: 10.1074/jbc.m512374200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Controlling aberrant kinase-mediated cellular signaling is a major strategy in cancer therapy; successful protein kinase inhibitors such as Tarceva and Gleevec verify this approach. Specificity of inhibitors for the targeted kinase(s), however, is a crucial factor for therapeutic success. Based on homology modeling, we previously identified four amino acids in the active site of Rho-kinase that likely determine inhibitor specificities observed for Rho-kinase relative to protein kinase A (PKA) (in PKA numbering: T183A, L49I, V123M, and E127D), and a fifth (Q181K) that played a surprising role in PKA-PKB hybrid proteins. We have systematically mutated these residues in PKA to their counterparts in Rho-kinase, individually and in combination. Using four Rho-kinase-specific, one PKA-specific, and one pan-kinase-specific inhibitor, we measured the inhibitor-binding properties of the mutated proteins and identify the roles of individual residues as specificity determinants. Two combined mutant proteins, containing the combination of mutations T183A and L49I, closely mimic Rho-kinase. Kinetic results corroborate the hypothesis that side-chain identities form the major determinants of selectivity. An unexpected result of the analysis is the consistent contribution of the individual mutations by simple factors. Crystal structures of the surrogate kinase inhibitor complexes provide a detailed basis for an understanding of these selectivity determinant residues. The ability to obtain kinetic and structural data from these PKA mutants, combined with their Rho-kinase-like selectivity profiles, make them valuable for use as surrogate kinases for structure-based inhibitor design.
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Affiliation(s)
- Stefan Bonn
- Group of Structural Biochemistry, German Cancer Research Center, 69120 Heidelberg
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29
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Breitenlechner CB, Bossemeyer D, Engh RA. Crystallography for protein kinase drug design: PKA and SRC case studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1754:38-49. [PMID: 16269279 DOI: 10.1016/j.bbapap.2005.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2005] [Revised: 09/27/2005] [Accepted: 09/28/2005] [Indexed: 10/25/2022]
Abstract
Protein crystallography can be used throughout the drug discovery process to obtain diverse information critical for structure based drug design. At a minimum, a single target structure may be available. Optimally, and especially for protein kinases, a broad range of crystal structures should be obtained to characterize target flexibility, structure modulation via co-factor binding or posttranslational modification, ligand induced conformational changes, and off-target complex structures for selectivity optimization. The flexibility of the protein kinases is in contrast to the need for "crystallizable" constructs, that is, proteins that crystallize under varying conditions and in varying crystal packing arrangements. Strategies to produce crystallizable protein kinase constructs include truncation to the catalytic domain, co-crystallization with rigidifying ligands, crystallization of known rigid forms, and point mutation to improve homogeneity or mimic less crystallizable proteins. PKA, the prototypical serine/threonine protein kinase, and SRC, a tyrosine kinase and the first identified oncoprotein, provide multiple examples of these various approaches to protein kinase crystallography for drug design.
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30
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Collins I, Caldwell J, Fonseca T, Donald A, Bavetsias V, Hunter LJK, Garrett MD, Rowlands MG, Aherne GW, Davies TG, Berdini V, Woodhead SJ, Davis D, Seavers LCA, Wyatt PG, Workman P, McDonald E. Structure-based design of isoquinoline-5-sulfonamide inhibitors of protein kinase B. Bioorg Med Chem 2005; 14:1255-73. [PMID: 16249095 DOI: 10.1016/j.bmc.2005.09.055] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2005] [Revised: 09/08/2005] [Accepted: 09/23/2005] [Indexed: 11/28/2022]
Abstract
Structure-based drug design of novel isoquinoline-5-sulfonamide inhibitors of PKB as potential antitumour agents was investigated. Constrained pyrrolidine analogues that mimicked the bound conformation of linear prototypes were identified and investigated by co-crystal structure determinations with the related protein PKA. Detailed variation in the binding modes between inhibitors with similar overall conformations was observed. Potent PKB inhibitors from this series inhibited GSK3beta phosphorylation in cellular assays, consistent with inhibition of PKB kinase activity in cells.
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Affiliation(s)
- Ian Collins
- Cancer Research, UK Centre for Cancer Therapeutics, The Institute of Cancer Research, Sutton, Surrey.
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31
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Langer T, Sreeramulu S, Vogtherr M, Elshorst B, Betz M, Schieborr U, Saxena K, Schwalbe H. Folding and activity of cAMP-dependent protein kinase mutants. FEBS Lett 2005; 579:4049-54. [PMID: 16026785 DOI: 10.1016/j.febslet.2005.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Revised: 06/07/2005] [Accepted: 06/10/2005] [Indexed: 11/18/2022]
Abstract
The catalytic subunit of cAMP-dependent protein kinase (PKA) can easily be expressed in Escherichia coli and is catalytically active. Four phosphorylation sites are known in PKA (S10, S139, T197 and S338), and the isolated recombinant protein is a mixture of different phosphorylated forms. Obtaining uniformly phosphorylated protein requires separation of the protein preparation leading to significant loss in protein yield. It is found that the mutant S10A/S139D/S338D has similar properties as the wild-type protein, whereas additional replacement of T197 with either E or D reduces protein expression yield as well as folding propensity of the protein. Due to its high sequence homology to Akt/PKB, which cannot easily be expressed in E. coli, PKA has been used as a surrogate kinase for drug design. Several mutations within the ATP binding site have been described to make PKA even more similar to Akt/PKB. Two proteins with Akt/PKB-like mutations in the ATP binding site were made (PKAB6 and PKAB8), and in addition S10, S139 and S338 phosphorylation sites have been removed. These proteins can be expressed in high yields but have reduced activity compared to the wild-type. Proper folding of all proteins was analyzed by 2D 1H, 15N-TROSY NMR experiments.
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Affiliation(s)
- Thomas Langer
- Johann Wolfgang Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Marie Curie Strasse 11, D-60439 Frankfurt am Main, Germany.
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32
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Langer T, Vogtherr M, Elshorst B, Betz M, Schieborr U, Saxena K, Schwalbe H. NMR backbone assignment of a protein kinase catalytic domain by a combination of several approaches: application to the catalytic subunit of cAMP-dependent protein kinase. Chembiochem 2005; 5:1508-16. [PMID: 15481030 DOI: 10.1002/cbic.200400129] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein phosphorylation is one of the most important mechanisms used for intracellular regulation in eukaryotic cells. Currently, one of the best-characterized protein kinases is the catalytic subunit of cAMP-dependent protein kinase or protein kinase A (PKA). PKA has the typical bilobular structure of kinases, with the active site consisting of a cleft between the two structural lobes. For full kinase activity, the catalytic subunit has to be phosphorylated. The catalytic subunit of PKA has two main phosphorylation sites: Thr197 and Ser338. Binding of ATP or inhibitors to the ATP site induces large structural changes. Here we describe the partial backbone assignment of the PKA catalytic domain by NMR spectroscopy, which represents the first NMR assignment of any protein kinase catalytic domain. Backbone resonance assignment for the 42 kDa protein was accomplished by an approach employing 1) triply ((2)H,(13)C,(15)N) labeled protein and classical NMR assignment experiments, 2) back-calculation of chemical shifts from known X-ray structures, 3) use of paramagnetic adenosine derivatives as spin-labels, and 4) selective amino acid labeling. Interpretation of chemical-shift perturbations allowed mapping of the interaction surface with the protein kinase inhibitor H7. Furthermore, structural conformational changes were observed by comparison of backbone amide shifts obtained by 2D (1)H,(15)N TROSY of an inactive Thr197Ala mutant with the wild-type enzyme.
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Affiliation(s)
- Thomas Langer
- Johann Wolfgang Goethe-Universität Frankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Marie Curie Strasse 11, 60439 Frankfurt am Main, Germany.
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33
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Breitenlechner CB, Friebe WG, Brunet E, Werner G, Graul K, Thomas U, Künkele KP, Schäfer W, Gassel M, Bossemeyer D, Huber R, Engh RA, Masjost B. Design and crystal structures of protein kinase B-selective inhibitors in complex with protein kinase A and mutants. J Med Chem 2005; 48:163-70. [PMID: 15634010 DOI: 10.1021/jm049701n] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein kinase B (PKB)-selective inhibitors were designed, synthesized, and cocrystallized using the AGC kinase family protein kinase A (PKA, often called cAMP-dependent protein kinase); PKA has been used as a surrogate for other members of this family and indeed for protein kinases in general. The high homology between PKA and PKB includes very similar ATP binding sites and hence similar binding pockets for inhibitors, with only few amino acids that differ between the two kinases. A series of these sites were mutated in PKA in order to improve the surrogate model for a design of PKB-selective inhibitors. Namely, the PKA to PKB exchanges F187L and Q84E enable the design of the selective inhibitors described herein which mimic ATP but extend further into a site not occupied by ATP. In this pocket, selectivity over PKA can be achieved by the introduction of bulkier substituents. Analysis of the cocrystal structures and binding studies were performed to rationalize the selectivity and improve the design.
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34
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Abstract
In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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35
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Takami A, Iwakubo M, Okada Y, Kawata T, Odai H, Takahashi N, Shindo K, Kimura K, Tagami Y, Miyake M, Fukushima K, Inagaki M, Amano M, Kaibuchi K, Iijima H. Design and synthesis of Rho kinase inhibitors (I). Bioorg Med Chem 2004; 12:2115-37. [PMID: 15080913 DOI: 10.1016/j.bmc.2004.02.025] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Revised: 02/23/2004] [Accepted: 02/23/2004] [Indexed: 11/20/2022]
Abstract
Several structurally unrelated scaffolds of the Rho kinase inhibitor were designed using pharmacophore information obtained from the results of a high-throughput screening and structural information from a homology model of Rho kinase. A docking simulation using the ligand-binding pocket of the Rho kinase model helped to comprehensively understand and to predict the structure-activity relationship of the inhibitors. This understanding was useful for developing new Rho kinase inhibitors of higher potency and selectivity. We identified several potent platforms for developing the Rho kinase inhibitors, namely, pyridine, 1H-indazole, isoquinoline, and phthalimide.
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Affiliation(s)
- Atsuya Takami
- Pharmaceutical Research Laboratories, Kirin Brewery Co. Ltd, 3 Miyhara-cho, Takasaki-shi, Gunma 370-1295, Japan
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Xu ZB, Chaudhary D, Olland S, Wolfrom S, Czerwinski R, Malakian K, Lin L, Stahl ML, Joseph-McCarthy D, Benander C, Fitz L, Greco R, Somers WS, Mosyak L. Catalytic domain crystal structure of protein kinase C-theta (PKCtheta). J Biol Chem 2004; 279:50401-9. [PMID: 15364937 DOI: 10.1074/jbc.m409216200] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A member of the novel protein kinase C (PKC) subfamily, PKC, is an essential component of the T cell synapse and is required for optimal T cell activation and interleukin-2 production. Selective involvement of PKC in TCR signaling makes this enzyme an attractive therapeutic target in T cell-mediated disease processes. In this report we describe the crystal structure of the catalytic domain of PKC at 2.0-A resolution. Human recombinant PKC kinase domain was expressed in bacteria as catalytically active phosphorylated enzyme and co-crystallized with its subnanomolar, ATP site inhibitor staurosporine. The structure follows the classic bilobal kinase fold and shows the enzyme in its active conformation and phosphorylated state. Inhibitory interactions between conserved features of staurosporine and the ATP-binding cleft are accompanied by closing of the glycine-rich loop, which also maintains an inhibitory arrangement by blocking the phosphate recognition subsite. The two major phosphorylation sites, Thr-538 in the activation loop and Ser-695 in the hydrophobic motif, are both occupied in the structure, playing key roles in stabilizing active conformation of the enzyme and indicative of PKC autocatalytic phosphorylation and activation during bacterial expression. The PKC-staurosporine complex represents the first kinase domain crystal structure of any PKC isotypes to be determined and as such should provide valuable insight into PKC specificity and into rational drug design strategies for PKC selective leads.
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Affiliation(s)
- Zhang-Bao Xu
- Department of Chemical and Screening Sciences, Inflammation Department, Wyeth Research, Cambridge, Massachusetts 02140, USA
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37
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Breitenlechner C, Gassel M, Hidaka H, Kinzel V, Huber R, Engh RA, Bossemeyer D. Protein kinase A in complex with Rho-kinase inhibitors Y-27632, Fasudil, and H-1152P: structural basis of selectivity. Structure 2004; 11:1595-607. [PMID: 14656443 DOI: 10.1016/j.str.2003.11.002] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protein kinases require strict inactivation to prevent spurious cellular signaling; overactivity can cause cancer or other diseases and necessitates selective inhibition for therapy. Rho-kinase is involved in such processes as tumor invasion, cell adhesion, smooth muscle contraction, and formation of focal adhesion fibers, as revealed using inhibitor Y-27632. Another Rho-kinase inhibitor, HA-1077 or Fasudil, is currently used in the treatment of cerebral vasospasm; the related nanomolar inhibitor H-1152P improves on its selectivity and potency. We have determined the crystal structures of HA-1077, H-1152P, and Y-27632 in complexes with protein kinase A (PKA) as a surrogate kinase to analyze Rho-kinase inhibitor binding properties. Features conserved between PKA and Rho-kinase are involved in the key binding interactions, while a combination of residues at the ATP binding pocket that are unique to Rho-kinase may explain the inhibitors' Rho-kinase selectivity. Further, a second H-1152P binding site potentially points toward PKA regulatory domain interaction modulators.
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Breitenlechner C, Engh RA, Huber R, Kinzel V, Bossemeyer D, Gassel M. The typically disordered N-terminus of PKA can fold as a helix and project the myristoylation site into solution. Biochemistry 2004; 43:7743-9. [PMID: 15196017 DOI: 10.1021/bi0362525] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein kinases comprise the major enzyme family critically involved in signal transduction pathways; posttranslational modifications affect their regulation and determine signaling states. The prototype protein kinase A (PKA) possesses an N-terminal alpha-helix (Helix A) that is atypical for kinases and is thus a major distinguishing feature of PKA. Its physiological function may involve myristoylation at the N-terminus and modulation via phosphorylation at serine 10. Here we describe an unusual structure of an unmyristoylated PKA, unphosphorylated at serine 10, with a completely ordered N-terminus. Using standard conditions (e.g., PKI 5-24, ATP site ligand, MEGA-8), a novel 2-fold phosphorylated PKA variant showed the ordered N-terminus in a new crystal packing arrangement. Thus, the critical factor for structuring the N-terminus is apparently the absence of phosphorylation of Ser10. The flexibility of the N-terminus, its myristoylation, and the conformational dependence on the phosphorylation state are consistent with a functional role for myristoylation.
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Gassel M, Breitenlechner CB, König N, Huber R, Engh RA, Bossemeyer D. The Protein Kinase C Inhibitor Bisindolyl Maleimide 2 Binds with Reversed Orientations to Different Conformations of Protein Kinase A. J Biol Chem 2004; 279:23679-90. [PMID: 14996846 DOI: 10.1074/jbc.m314082200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As the key mediators of eukaryotic signal transduction, the protein kinases often cause disease, and in particular cancer, when disregulated. Appropriately selective protein kinase inhibitors are sought after as research tools and as therapeutic drugs; several have already proven valuable in clinical use. The AGC subfamily protein kinase C (PKC) was identified early as a cause of cancer, leading to the discovery of a variety of PKC inhibitors. Despite its importance and early discovery, no crystal structure for PKC has yet been reported. Therefore, we have co-crystallized PKC inhibitor bisindolyl maleimide 2 (BIM2) with PKA variants to study its binding interactions. BIM2 co-crystallized as an asymmetric pair of kinase-inhibitor complexes. In this asymmetric unit, the two kinase domains have different lobe configurations, and two different inhibitor conformers bind in different orientations. One kinase molecule (A) is partially open with respect to the catalytic conformation, the other (B) represents the most open conformation of PKA reported so far. In monomer A, the BIM2 inhibitor binds tightly via an induced fit in the ATP pocket. The indole moieties are rotated out of the plane with respect to the chemically related but planar inhibitor staurosporine. In molecule B a different conformer of BIM2 binds in a reversed orientation relative to the equivalent maleimide atoms in molecule A. Also, a critical active site salt bridge is disrupted, usually indicating the induction of an inactive conformation. Molecular modeling of the clinical phase III PKC inhibitor LY333531 into the electron density of BIM2 reveals the probable binding mechanism and explains selectivity properties of the inhibitor.
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Affiliation(s)
- Michael Gassel
- Department of Pathochemistry, German Cancer Research Center, 69120 Heidelberg, Germany
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Breitenlechner CB, Wegge T, Berillon L, Graul K, Marzenell K, Friebe WG, Thomas U, Schumacher R, Huber R, Engh RA, Masjost B. Structure-Based Optimization of Novel Azepane Derivatives as PKB Inhibitors. J Med Chem 2004; 47:1375-90. [PMID: 14998327 DOI: 10.1021/jm0310479] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novel azepane derivatives were prepared and evaluated for protein kinase B (PKB-alpha) and protein kinase A (PKA) inhibition. The original (-)-balanol-derived lead structure (4R)-4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzoic acid (3R)-3-[(pyridine-4-carbonyl)amino]-azepan-4-yl ester (1) (IC(50) (PKB-alpha) = 5 nM) which contains an ester moiety was found to be plasma unstable and therefore unsuitable as a drug. Based upon molecular modeling studies using the crystal structure of the complex between PKA and 1, the five compounds N-[(3R,4R)-4-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzoylamino]-azepan-3-yl]-isonicotinamide (4), (3R,4R)-N-[4-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzyloxy]-azepan-3-yl]-isonicotinamide (5), N-[(3R,4S)-4-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-phenylamino]-methyl]-azepan-3-yl)-isonicotinamide (6), N-[(3R,4R)-4-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-benzylamino]-azepan-3-yl]-isonicotinamide (7), and N-[(3R,4S)-4-(4-[trans-2-[4-(2-fluoro-6-hydroxy-3-methoxy-benzoyl)-phenyl]-vinyl]-azepan-3-yl)-isonicotinamide (8) with linkers isosteric to the ester were designed, synthesized, and tested for in vitro inhibitory activity against PKA and PKB-alpha and for plasma stability in mouse plasma.(1) Compound 4 was found to be plasma stable and highly active (IC(50) (PKB-alpha) = 4 nM). Cocrystals with PKA were obtained for 4, 5, and 8 and analyzed for binding interactions and conformational changes in the ligands and protein in order to rationalize the different activities of the molecules.
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