1
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Turberville A, Semple H, Davies G, Ivanov D, Holdgate GA. A perspective on the discovery of enzyme activators. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:419-427. [PMID: 36089246 DOI: 10.1016/j.slasd.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/26/2022] [Accepted: 09/06/2022] [Indexed: 12/15/2022]
Abstract
Enzyme activation remains a largely under-represented and poorly exploited area of drug discovery despite some key literature examples of the successful application of enzyme activators by various mechanisms and their importance in a wide range of therapeutic interventions. Here we describe the background nomenclature, present the current position of this field of drug discovery and discuss the challenges of hit identification for enzyme activation, as well as our perspectives on the approaches needed to overcome these challenges in early drug discovery.
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Affiliation(s)
- Antonia Turberville
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Hannah Semple
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Gareth Davies
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Delyan Ivanov
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Geoffrey A Holdgate
- High-throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom.
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2
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Smolobochkin AV, Gazizov AS, Burilov AR, Pudovik MA, Sinyashin OG. Advances in the synthesis of heterocycles bearing an endocyclic urea moiety. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4988] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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3
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Danyliuk IY, Vaskevych AI, Vaskevych RI, Rusanov EB, Vovk MV. Cyclosulfenylation of N-(1(2)-naphthyl) styrylacetamides as a synthetic route to 4(2)-arylthio naphtho[1,2-b]([2,1-b])azepin-2(4)-ones. J Sulphur Chem 2020. [DOI: 10.1080/17415993.2020.1855431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Ivanna Yu. Danyliuk
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alla I. Vaskevych
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- “Enamine Ltd” Scientific Production Association, Kyiv, Ukraine
| | - Ruslan I. Vaskevych
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Eduard B. Rusanov
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Mykhailo V. Vovk
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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4
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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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5
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Leroux AE, Schulze JO, Biondi RM. AGC kinases, mechanisms of regulation and innovative drug development. Semin Cancer Biol 2017; 48:1-17. [PMID: 28591657 DOI: 10.1016/j.semcancer.2017.05.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/16/2017] [Accepted: 05/31/2017] [Indexed: 12/22/2022]
Abstract
The group of AGC kinases consists of 63 evolutionarily related serine/threonine protein kinases comprising PDK1, PKB/Akt, SGK, PKC, PRK/PKN, MSK, RSK, S6K, PKA, PKG, DMPK, MRCK, ROCK, NDR, LATS, CRIK, MAST, GRK, Sgk494, and YANK, while two other families, Aurora and PLK, are the most closely related to the group. Eight of these families are physiologically activated downstream of growth factor signalling, while other AGC kinases are downstream effectors of a wide range of signals. The different AGC kinase families share aspects of their mechanisms of inhibition and activation. In the present review, we update the knowledge of the mechanisms of regulation of different AGC kinases. The conformation of the catalytic domain of many AGC kinases is regulated allosterically through the modulation of the conformation of a regulatory site on the small lobe of the kinase domain, the PIF-pocket. The PIF-pocket acts like an ON-OFF switch in AGC kinases with different modes of regulation, i.e. PDK1, PKB/Akt, LATS and Aurora kinases. In this review, we make emphasis on how the knowledge of the molecular mechanisms of regulation can guide the discovery and development of small allosteric modulators. Molecular probes stabilizing the PIF-pocket in the active conformation are activators, while compounds stabilizing the disrupted site are allosteric inhibitors. One challenge for the rational development of allosteric modulators is the lack of complete structural information of the inhibited forms of full-length AGC kinases. On the other hand, we suggest that the available information derived from molecular biology and biochemical studies can already guide screening strategies for the identification of innovative mode of action molecular probes and the development of selective allosteric drugs for the treatment of human diseases.
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Affiliation(s)
- Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina.
| | - Jörg O Schulze
- Research Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina; Research Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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6
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Arencibia JM, Fröhner W, Krupa M, Pastor-Flores D, Merker P, Oellerich T, Neimanis S, Schmithals C, Köberle V, Süß E, Zeuzem S, Stark H, Piiper A, Odadzic D, Schulze JO, Biondi RM. An Allosteric Inhibitor Scaffold Targeting the PIF-Pocket of Atypical Protein Kinase C Isoforms. ACS Chem Biol 2017; 12:564-573. [PMID: 28045490 DOI: 10.1021/acschembio.6b00827] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
There is a current and pressing need for improved cancer therapies. The use of small molecule kinase inhibitors and their application in combinatorial regimens represent an approach to personalized targeted cancer therapy. A number of AGC kinases, including atypical Protein Kinase C enzymes (PKCs), are validated drug targets for cancer treatment. Most drug development programs for protein kinases focus on the development of drugs that bind at the ATP-binding site. Alternatively, allosteric drugs have great potential for the development of future innovative drugs. However, the rational development of allosteric drugs poses important challenges because the compounds not only must bind to a given site but also must stabilize forms of the protein with a desired effect at a distant site. Here we describe the development of a new class of compounds targeting a regulatory site (PIF-pocket) present in the kinase domain and provide biochemical and crystallographic data showing that these compounds allosterically inhibit the activity of atypical PKCs. PS432, a representative compound, decreased the rate of proliferation of non-small cell lung cancer cells more potently than aurothiomalate, an atypical PKCι inhibitor currently under evaluation in clinical trials, and significantly reduced tumor growth without side effects in a mouse xenograft model. The druglike chemical class provides ample possibilities for the synthesis of derivative compounds, with the potential to allosterically modulate the activity of atypical PKCs and other kinases.
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Affiliation(s)
- Jose M. Arencibia
- Research
Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, 60590 Frankfurt am Main, Germany
| | - Wolfgang Fröhner
- Pharmaceutical
and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Magdalena Krupa
- Research
Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, 60590 Frankfurt am Main, Germany
| | - Daniel Pastor-Flores
- Research
Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, 60590 Frankfurt am Main, Germany
| | - Piotr Merker
- Research
Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, 60590 Frankfurt am Main, Germany
| | - Thomas Oellerich
- Department
of Hematology/Oncology, Johann Wolfgang Goethe University, Frankfurt am
Main, Germany
| | - Sonja Neimanis
- Research
Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, 60590 Frankfurt am Main, Germany
| | - Christian Schmithals
- Research
Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, 60590 Frankfurt am Main, Germany
| | - Verena Köberle
- Research
Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, 60590 Frankfurt am Main, Germany
| | - Evelyn Süß
- Research
Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, 60590 Frankfurt am Main, Germany
| | - Stefan Zeuzem
- Research
Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, 60590 Frankfurt am Main, Germany
| | - Holger Stark
- Institut
für Pharmazeutische Chemie, Johann Wolfgang Goethe Universität, Frankfurt am Main, Germany
| | - Albrecht Piiper
- Research
Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, 60590 Frankfurt am Main, Germany
| | - Dalibor Odadzic
- Institut
für Pharmazeutische Chemie, Johann Wolfgang Goethe Universität, Frankfurt am Main, Germany
| | - Jörg O. Schulze
- Research
Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, 60590 Frankfurt am Main, Germany
| | - Ricardo M. Biondi
- Research
Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, 60590 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
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7
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Schulze JO, Saladino G, Busschots K, Neimanis S, Süß E, Odadzic D, Zeuzem S, Hindie V, Herbrand AK, Lisa MN, Alzari PM, Gervasio FL, Biondi RM. Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase. Cell Chem Biol 2016; 23:1193-1205. [PMID: 27693059 DOI: 10.1016/j.chembiol.2016.06.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/06/2016] [Accepted: 06/30/2016] [Indexed: 01/10/2023]
Abstract
Allostery is a phenomenon observed in many proteins where binding of a macromolecular partner or a small-molecule ligand at one location leads to specific perturbations at a site not in direct contact with the region where the binding occurs. The list of proteins under allosteric regulation includes AGC protein kinases. AGC kinases have a conserved allosteric site, the phosphoinositide-dependent protein kinase 1 (PDK1)-interacting fragment (PIF) pocket, which regulates protein ATP-binding, activity, and interaction with substrates. In this study, we identify small molecules that bind to the ATP-binding site and affect the PIF pocket of AGC kinase family members, PDK1 and Aurora kinase. We describe the mechanistic details and show that although PDK1 and Aurora kinase inhibitors bind to the conserved ATP-binding site, they differentially modulate physiological interactions at the PIF-pocket site. Our work outlines a strategy for developing bidirectional small-molecule allosteric modulators of protein kinases and other signaling proteins.
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Affiliation(s)
- Jörg O Schulze
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Giorgio Saladino
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Katrien Busschots
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Sonja Neimanis
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Evelyn Süß
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Dalibor Odadzic
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Stefan Zeuzem
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Valerie Hindie
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Amanda K Herbrand
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - María-Natalia Lisa
- Structural Biochemistry Unit, Pasteur Institute, Rue du Docteur Roux 25, 75724 Paris, France
| | - Pedro M Alzari
- Structural Biochemistry Unit, Pasteur Institute, Rue du Docteur Roux 25, 75724 Paris, France
| | - Francesco L Gervasio
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK; Research Department of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.
| | - Ricardo M Biondi
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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8
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Rodrik-Outmezguine VS, Okaniwa M, Yao Z, Novotny CJ, McWhirter C, Banaji A, Won H, Wong W, Berger M, de Stanchina E, Barratt DG, Cosulich S, Klinowska T, Rosen N, Shokat KM. Overcoming mTOR resistance mutations with a new-generation mTOR inhibitor. Nature 2016; 534:272-6. [PMID: 27279227 PMCID: PMC4902179 DOI: 10.1038/nature17963] [Citation(s) in RCA: 322] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/31/2016] [Indexed: 01/17/2023]
Abstract
Precision medicines exert selective pressure on tumour cells that leads to the preferential growth of resistant subpopulations, necessitating the development of next-generation therapies to treat the evolving cancer. The PIK3CA-AKT-mTOR pathway is one of the most commonly activated pathways in human cancers, which has led to the development of small-molecule inhibitors that target various nodes in the pathway. Among these agents, first-generation mTOR inhibitors (rapalogs) have caused responses in 'N-of-1' cases, and second-generation mTOR kinase inhibitors (TORKi) are currently in clinical trials. Here we sought to delineate the likely resistance mechanisms to existing mTOR inhibitors in human cell lines, as a guide for next-generation therapies. The mechanism of resistance to the TORKi was unusual in that intrinsic kinase activity of mTOR was increased, rather than a direct active-site mutation interfering with drug binding. Indeed, identical drug-resistant mutations have been also identified in drug-naive patients, suggesting that tumours with activating MTOR mutations will be intrinsically resistant to second-generation mTOR inhibitors. We report the development of a new class of mTOR inhibitors that overcomes resistance to existing first- and second-generation inhibitors. The third-generation mTOR inhibitor exploits the unique juxtaposition of two drug-binding pockets to create a bivalent interaction that allows inhibition of these resistant mutants.
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Affiliation(s)
| | - Masanori Okaniwa
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, USA
| | - Zhan Yao
- Program in Molecular Pharmacology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Chris J Novotny
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, USA
| | | | - Arpitha Banaji
- Program in Molecular Pharmacology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Helen Won
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Wai Wong
- Anti-Tumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Mike Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Elisa de Stanchina
- Anti-Tumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Derek G Barratt
- AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Sabina Cosulich
- AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | | | - Neal Rosen
- Program in Molecular Pharmacology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Kevan M Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, USA.,Department of Chemistry, University of California Berkeley, Berkeley, California 94720, USA
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9
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Kroon E, Schulze JO, Süß E, Camacho CJ, Biondi RM, Dömling A. Discovery of a Potent Allosteric Kinase Modulator by Combining Computational and Synthetic Methods. Angew Chem Int Ed Engl 2015; 54:13933-6. [PMID: 26385475 PMCID: PMC4721676 DOI: 10.1002/anie.201506310] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/12/2015] [Indexed: 12/14/2022]
Abstract
The rational design of allosteric kinase modulators is challenging but rewarding. The protein kinase PDK1, which lies at the center of the growth-factor signaling pathway, possesses an allosteric regulatory site previously validated both in vitro and in cells. ANCHOR.QUERY software was used to discover a potent allosteric PDK1 kinase modulator. Using a recently published PDK1 compound as a template, several new scaffolds that bind to the allosteric target site were generated and one example was validated. The inhibitor can be synthesized in one step by multicomponent reaction (MCR) chemistry when using the ANCHOR.QUERY approach. Our results are significant because the outlined approach allows rapid and efficient scaffold hopping from known molecules into new easily accessible and biologically active ones. Based on increasing interest in allosteric-site drug discovery, we foresee many potential applications for this approach.
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Affiliation(s)
- Edwin Kroon
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen (The Netherlands) http://www.drugdesign.nl
| | - Jörg O Schulze
- Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt (Germany)
| | - Evelyn Süß
- Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt (Germany)
| | - Carlos J Camacho
- University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15261 (USA)
| | - Ricardo M Biondi
- Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt (Germany)
| | - Alexander Dömling
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen (The Netherlands) http://www.drugdesign.nl.
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10
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Rettenmaier TJ, Fan H, Karpiak J, Doak A, Sali A, Shoichet BK, Wells JA. Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking. J Med Chem 2015; 58:8285-8291. [PMID: 26443011 DOI: 10.1021/acs.jmedchem.5b01216] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Finding small molecules that target allosteric sites remains a grand challenge for ligand discovery. In the protein kinase field, only a handful of highly selective allosteric modulators have been found. Thus, more general methods are needed to discover allosteric modulators for additional kinases. Here, we use virtual screening against an ensemble of both crystal structures and comparative models to identify ligands for an allosteric peptide-binding site on the protein kinase PDK1 (the PIF pocket). We optimized these ligands through an analog-by-catalog search that yielded compound 4, which binds to PDK1 with 8 μM affinity. We confirmed the docking poses by determining a crystal structure of PDK1 in complex with 4. Because the PIF pocket appears to be a recurring structural feature of the kinase fold, known generally as the helix αC patch, this approach may enable the discovery of allosteric modulators for other kinases.
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Affiliation(s)
- T Justin Rettenmaier
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California 94158, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Hao Fan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, Matrix No. 07-01, 138671, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Joel Karpiak
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California 94158, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Allison Doak
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
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11
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Kroon E, Schulze JO, Süß E, Camacho CJ, Biondi RM, Dömling A. Discovery of a Potent Allosteric Kinase Modulator by Combining Computational and Synthetic Methods. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506310] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Edwin Kroon
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen (The Netherlands) http://www.drugdesign.nl
| | - Jörg O. Schulze
- Universitätsklinikum Frankfurt, Theodor‐Stern‐Kai 7, 60590 Frankfurt (Germany)
| | - Evelyn Süß
- Universitätsklinikum Frankfurt, Theodor‐Stern‐Kai 7, 60590 Frankfurt (Germany)
| | - Carlos J. Camacho
- University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15261 (USA)
| | - Ricardo M. Biondi
- Universitätsklinikum Frankfurt, Theodor‐Stern‐Kai 7, 60590 Frankfurt (Germany)
| | - Alexander Dömling
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV Groningen (The Netherlands) http://www.drugdesign.nl
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12
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Guo G, Yang C, Li GF, Li H, Ma QL, Guo Q, Yang XM. Computational insights into allosteric interaction between benzoazepin-2-ones and lung cancer-associated PDK1: Implications for activator design. CHEMICAL PAPERS 2015. [DOI: 10.1515/chempap-2015-0131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract3-Phosphoinositide-dependent kinase-1 (PDK1) plays a key role in the regulation of physiological processes and its catalytic activity is tightly regulated by allosteric modulators which bind to the PDK1 Interacting Fragment (PIF) pocket. However, details on the allosteric modulators regulation of the PDK1 catalytic activity remain elusive. Here, molecular docking and molecular dynamics (MD) simulations were performed to investigate the allosteric regulation of PDK1 induced by one of the benzoazepin-2-ones, the most potent compound 17 (BAZ2O). Molecular docking and MD simulation revealed that BAZ2O was located in the PIF pocket formed by residues from β4 and β5 sheets and helices αB and αC. BAZ2O formed a hydrogen bond with Arg131 and participated in hydrophobic interactions with Ile119, Thr148, Gln150, Leu155 and Phe157. Further comparative analyses of PDK1 in its apo and BAZ2O-bound states unveiled that BAZ2O promoted the structural coupling between the important catalytic domains of PDK1, including the activation loop and the helices αB and αC, thereby stabilizing the PDK1 conformation for catalysis. Understanding the allosteric interaction of PDK1 with small molecules provides a potentially valuable possibility of designing more potent allosteric modulators with therapeutic implications for lung cancer.
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13
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A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1. Proc Natl Acad Sci U S A 2014; 111:18590-5. [PMID: 25518860 DOI: 10.1073/pnas.1415365112] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
There is great interest in developing selective protein kinase inhibitors by targeting allosteric sites, but these sites often involve protein-protein or protein-peptide interfaces that are very challenging to target with small molecules. Here we present a systematic approach to targeting a functionally conserved allosteric site on the protein kinase PDK1 called the PDK1-interacting fragment (PIF)tide-binding site, or PIF pocket. More than two dozen prosurvival and progrowth kinases dock a conserved peptide tail into this binding site, which recruits them to PDK1 to become activated. Using a site-directed chemical screen, we identified and chemically optimized ligand-efficient, selective, and cell-penetrant small molecules (molecular weight ∼ 380 Da) that compete with the peptide docking motif for binding to PDK1. We solved the first high-resolution structure of a peptide docking motif (PIFtide) bound to PDK1 and mapped binding energy hot spots using mutational analysis. We then solved structures of PDK1 bound to the allosteric small molecules, which revealed a binding mode that remarkably mimics three of five hot-spot residues in PIFtide. These allosteric small molecules are substrate-selective PDK1 inhibitors when used as single agents, but when combined with an ATP-competitive inhibitor, they completely suppress the activation of the downstream kinases. This work provides a promising new scaffold for the development of high-affinity PIF pocket ligands, which may be used to enhance the anticancer activity of existing PDK1 inhibitors. Moreover, our results provide further impetus for exploring the helix αC patches of other protein kinases as potential therapeutic targets even though they involve protein-protein interfaces.
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14
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Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases. Future Med Chem 2014; 6:541-61. [PMID: 24649957 DOI: 10.4155/fmc.13.216] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Protein kinases are involved in many essential cellular processes and their deregulation can lead to a variety of diseases, including cancer. The pharmaceutical industry has invested heavily in the identification of kinase inhibitors to modulate these disease-promoting pathways, resulting in several successful drugs. However, the field is challenging as it is difficult to identify novel selective inhibitors with good pharmacokinetic/pharmacodynamic properties. In addition, resistance to kinase inhibitor treatment frequently arises. The identification of non-ATP site targeting ('allosteric') inhibitors, the identification of kinase activators and the expansion of kinase target space to include the less studied members of the family, including atypical- and pseudo-kinases, are potential avenues to overcome these challenges. In this perspective, the opportunities and challenges of following these approaches and others will be discussed.
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15
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Busschots K, Lopez-Garcia LA, Lammi C, Stroba A, Zeuzem S, Piiper A, Alzari PM, Neimanis S, Arencibia JM, Engel M, Schulze JO, Biondi RM. Substrate-selective inhibition of protein kinase PDK1 by small compounds that bind to the PIF-pocket allosteric docking site. ACTA ACUST UNITED AC 2014; 19:1152-63. [PMID: 22999883 DOI: 10.1016/j.chembiol.2012.07.017] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 06/04/2012] [Accepted: 07/24/2012] [Indexed: 12/28/2022]
Abstract
The PIF-pocket of AGC protein kinases participates in the physiologic mechanism of regulation by acting as a docking site for substrates and as a switch for the transduction of the conformational changes needed for activation or inhibition. We describe the effects of compounds that bind to the PIF-pocket of PDK1. In vitro, PS210 is a potent activator of PDK1, and the crystal structure of the PDK1-ATP-PS210 complex shows that PS210 stimulates the closure of the kinase domain. However, in cells, the prodrug of PS210 (PS423) acts as a substrate-selective inhibitor of PDK1, inhibiting the phosphorylation and activation of S6K, which requires docking to the PIF-pocket, but not affecting PKB/Akt. This work describes a tool to study the dynamics of PDK1 activity and a potential approach for drug discovery.
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Affiliation(s)
- Katrien Busschots
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
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16
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Zhang H, Neimanis S, Lopez-Garcia LA, Arencibia JM, Amon S, Stroba A, Zeuzem S, Proschak E, Stark H, Bauer AF, Busschots K, Jørgensen TJD, Engel M, Schulze JO, Biondi RM. Molecular mechanism of regulation of the atypical protein kinase C by N-terminal domains and an allosteric small compound. ACTA ACUST UNITED AC 2014; 21:754-65. [PMID: 24836908 DOI: 10.1016/j.chembiol.2014.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Revised: 03/15/2014] [Accepted: 04/04/2014] [Indexed: 11/30/2022]
Abstract
Protein kinases play important regulatory roles in cells and organisms. Therefore, they are subject to specific and tight mechanisms of regulation that ultimately converge on the catalytic domain and allow the kinases to be activated or inhibited only upon the appropriate stimuli. AGC protein kinases have a pocket in the catalytic domain, the PDK1-interacting fragment (PIF)-pocket, which is a key mediator of the activation. We show here that helix αC within the PIF-pocket of atypical protein kinase C (aPKC) is the target of the interaction with its inhibitory N-terminal domains. We also provide structural evidence that the small compound PS315 is an allosteric inhibitor that binds to the PIF-pocket of aPKC. PS315 exploits the physiological dynamics of helix αC for its binding and allosteric inhibition. The results will support research on allosteric mechanisms and selective drug development efforts against PKC isoforms.
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Affiliation(s)
- Hua Zhang
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Sonja Neimanis
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Laura A Lopez-Garcia
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - José M Arencibia
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Sabine Amon
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Adriana Stroba
- Department of Pharmaceutical and Medicinal Chemistry, University of Saarland, 66041 Saarbrücken, Germany
| | - Stefan Zeuzem
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Ewgen Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Holger Stark
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Angelika F Bauer
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Katrien Busschots
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Matthias Engel
- Department of Pharmaceutical and Medicinal Chemistry, University of Saarland, 66041 Saarbrücken, Germany
| | - Jörg O Schulze
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Ricardo M Biondi
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
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17
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Hertz NT, Berthet A, Sos ML, Thorn KS, Burlingame AL, Nakamura K, Shokat KM. A neo-substrate that amplifies catalytic activity of parkinson's-disease-related kinase PINK1. Cell 2013; 154:737-47. [PMID: 23953109 PMCID: PMC3950538 DOI: 10.1016/j.cell.2013.07.030] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/30/2013] [Accepted: 07/22/2013] [Indexed: 12/22/2022]
Abstract
Mitochondria have long been implicated in the pathogenesis of Parkinson's disease (PD). Mutations in the mitochondrial kinase PINK1 that reduce kinase activity are associated with mitochondrial defects and result in an autosomal-recessive form of early-onset PD. Therapeutic approaches for enhancing the activity of PINK1 have not been considered because no allosteric regulatory sites for PINK1 are known. Here, we show that an alternative strategy, a neo-substrate approach involving the ATP analog kinetin triphosphate (KTP), can be used to increase the activity of both PD-related mutant PINK1(G309D) and PINK1(WT). Moreover, we show that application of the KTP precursor kinetin to cells results in biologically significant increases in PINK1 activity, manifest as higher levels of Parkin recruitment to depolarized mitochondria, reduced mitochondrial motility in axons, and lower levels of apoptosis. Discovery of neo-substrates for kinases could provide a heretofore-unappreciated modality for regulating kinase activity.
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Affiliation(s)
- Nicholas T. Hertz
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
- Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Amandine Berthet
- Gladstone Institute of Neurological Disease, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Martin L. Sos
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kurt S. Thorn
- Department of Biochemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Al L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology and Graduate Programs in Neuroscience and Biomedical Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan M. Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
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18
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Arencibia JM, Pastor-Flores D, Bauer AF, Schulze JO, Biondi RM. AGC protein kinases: from structural mechanism of regulation to allosteric drug development for the treatment of human diseases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1302-21. [PMID: 23524293 DOI: 10.1016/j.bbapap.2013.03.010] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/07/2013] [Indexed: 01/15/2023]
Abstract
The group of AGC protein kinases includes more than 60 protein kinases in the human genome, classified into 14 families: PDK1, AKT/PKB, SGK, PKA, PKG, PKC, PKN/PRK, RSK, NDR, MAST, YANK, DMPK, GRK and SGK494. This group is also widely represented in other eukaryotes, including causative organisms of human infectious diseases. AGC kinases are involved in diverse cellular functions and are potential targets for the treatment of human diseases such as cancer, diabetes, obesity, neurological disorders, inflammation and viral infections. Small molecule inhibitors of AGC kinases may also have potential as novel therapeutic approaches against infectious organisms. Fundamental in the regulation of many AGC kinases is a regulatory site termed the "PIF-pocket" that serves as a docking site for substrates of PDK1. This site is also essential to the mechanism of activation of AGC kinases by phosphorylation and is involved in the allosteric regulation of N-terminal domains of several AGC kinases, such as PKN/PRKs and atypical PKCs. In addition, the C-terminal tail and its interaction with the PIF-pocket are involved in the dimerization of the DMPK family of kinases and may explain the molecular mechanism of allosteric activation of GRKs by GPCR substrates. In this review, we briefly introduce the AGC kinases and their known roles in physiology and disease and the discovery of the PIF-pocket as a regulatory site in AGC kinases. Finally, we summarize the current status and future therapeutic potential of small molecules directed to the PIF-pocket; these molecules can allosterically activate or inhibit the kinase as well as act as substrate-selective inhibitors. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).
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Affiliation(s)
- José M Arencibia
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
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19
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Medina JR. Selective 3-Phosphoinositide-Dependent Kinase 1 (PDK1) Inhibitors: Dissecting the Function and Pharmacology of PDK1. J Med Chem 2013; 56:2726-37. [DOI: 10.1021/jm4000227] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jesús R. Medina
- Oncology Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
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20
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Fang Z, Grütter C, Rauh D. Strategies for the selective regulation of kinases with allosteric modulators: exploiting exclusive structural features. ACS Chem Biol 2013; 8:58-70. [PMID: 23249378 DOI: 10.1021/cb300663j] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The modulation of kinase function has become an important goal in modern drug discovery and chemical biology research. In cancer-targeted therapies, kinase inhibitors have been experiencing an upsurge, which can be measured by the increasing number of kinase inhibitors approved by the FDA in recent years. However, lack of efficacy, limited selectivity, and the emergence of acquired drug resistance still represent major bottlenecks in the clinic and challenge inhibitor development. Most known kinase inhibitors target the active kinase and are ATP competitive. A second class of small organic molecules, which address remote sites of the kinase and stabilize enzymatically inactive conformations, is rapidly moving to the forefront of kinase inhibitor research. Such allosteric modulators bind to sites that are less conserved across the kinome and only accessible upon conformational changes. These molecules are therefore thought to provide various advantages such as higher selectivity and extended drug target residence times. This review highlights various strategies that have been developed to utilizing exclusive structural features of kinases and thereby modulating their activity allosterically.
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Affiliation(s)
- Zhizhou Fang
- Technische Universität Dortmund, Fakultät
Chemie − Chemische Biologie, Otto-Hahn-Strasse
6, D-44227 Dortmund, Germany
| | - Christian Grütter
- Technische Universität Dortmund, Fakultät
Chemie − Chemische Biologie, Otto-Hahn-Strasse
6, D-44227 Dortmund, Germany
| | - Daniel Rauh
- Technische Universität Dortmund, Fakultät
Chemie − Chemische Biologie, Otto-Hahn-Strasse
6, D-44227 Dortmund, Germany
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21
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Wilhelm A, Lopez-Garcia LA, Busschots K, Fröhner W, Maurer F, Boettcher S, Zhang H, Schulze JO, Biondi RM, Engel M. 2-(3-Oxo-1,3-diphenylpropyl)malonic Acids as Potent Allosteric Ligands of the PIF Pocket of Phosphoinositide-Dependent Kinase-1: Development and Prodrug Concept. J Med Chem 2012; 55:9817-30. [DOI: 10.1021/jm3010477] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Adriana Wilhelm
- Pharmaceutical and Medicinal
Chemistry, Saarland University, Campus
C2.3, D-66123 Saarbrücken, Germany
| | - Laura A. Lopez-Garcia
- Department of Internal Medicine
I, University of Frankfurt, Theodor-Stern-Kai
7, D-60590 Frankfurt a.M., Germany
| | - Katrien Busschots
- Department of Internal Medicine
I, University of Frankfurt, Theodor-Stern-Kai
7, D-60590 Frankfurt a.M., Germany
| | - Wolfgang Fröhner
- Pharmaceutical and Medicinal
Chemistry, Saarland University, Campus
C2.3, D-66123 Saarbrücken, Germany
| | - Frauke Maurer
- Organic Chemistry, Saarland University, Campus C2.3, D-66123 Saarbrücken,
Germany
| | - Stefan Boettcher
- Pharmaceutical and Medicinal
Chemistry, Saarland University, Campus
C2.3, D-66123 Saarbrücken, Germany
| | - Hua Zhang
- Department of Internal Medicine
I, University of Frankfurt, Theodor-Stern-Kai
7, D-60590 Frankfurt a.M., Germany
| | - Jörg O. Schulze
- Department of Internal Medicine
I, University of Frankfurt, Theodor-Stern-Kai
7, D-60590 Frankfurt a.M., Germany
| | - Ricardo M. Biondi
- Department of Internal Medicine
I, University of Frankfurt, Theodor-Stern-Kai
7, D-60590 Frankfurt a.M., Germany
| | - Matthias Engel
- Pharmaceutical and Medicinal
Chemistry, Saarland University, Campus
C2.3, D-66123 Saarbrücken, Germany
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22
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Lopez-Garcia LA, Schulze JO, Fröhner W, Zhang H, Süss E, Weber N, Navratil J, Amon S, Hindie V, Zeuzem S, Jørgensen TJD, Alzari PM, Neimanis S, Engel M, Biondi RM. Allosteric regulation of protein kinase PKCζ by the N-terminal C1 domain and small compounds to the PIF-pocket. ACTA ACUST UNITED AC 2012; 18:1463-73. [PMID: 22118680 DOI: 10.1016/j.chembiol.2011.08.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 07/28/2011] [Accepted: 08/05/2011] [Indexed: 02/08/2023]
Abstract
Protein kinases are key mediators of cellular signaling, and therefore, their activities are tightly controlled. AGC kinases are regulated by phosphorylation and by N- and C-terminal regions. Here, we studied the molecular mechanism of inhibition of atypical PKCζ and found that the inhibition by the N-terminal region cannot be explained by a simple pseudosubstrate inhibitory mechanism. Notably, we found that the C1 domain allosterically inhibits PKCζ activity and verified an allosteric communication between the PIF-pocket of atypical PKCs and the binding site of the C1 domain. Finally, we developed low-molecular-weight compounds that bind to the PIF-pocket and allosterically inhibit PKCζ activity. This work establishes a central role for the PIF-pocket on the regulation of PKCζ and allows us to envisage development of drugs targeting the PIF-pocket that can either activate or inhibit AGC kinases.
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Affiliation(s)
- Laura A Lopez-Garcia
- Research Group PhosphoSites, Department of Internal Medicine I, Universitätsklinikum Frankfurt, 60590 Frankfurt, Germany
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23
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Hall J, Aulabaugh A, Rajamohan F, Liu S, Kaila N, Wan ZK, Ryan M, Magyar R, Qiu X. Biophysical and mechanistic insights into novel allosteric inhibitor of spleen tyrosine kinase. J Biol Chem 2012; 287:7717-27. [PMID: 22219190 DOI: 10.1074/jbc.m111.311993] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Extracellular stimulation of the B cell receptor or mast cell FcεRI receptor activates a cascade of protein kinases, ultimately leading to antigenic or inflammation immune responses, respectively. Syk is a soluble kinase responsible for transmission of the receptor activation signal from the membrane to cytosolic targets. Control of Syk function is, therefore, critical to the human antigenic and inflammation immune response, and an inhibitor of Syk could provide therapy for autoimmune or inflammation diseases. We report here a novel allosteric Syk inhibitor, X1, that is noncompetitive against ATP (K(i) 4 ± 1 μM) and substrate peptide (K(i) 5 ± 1 μM), and competitive against activation of Syk by its upstream regulatory kinase LynB (K(i) 4 ± 1 μM). The inhibition mechanism was interrogated using a combination of structural, biophysical, and kinetic methods, which suggest the compound inhibits Syk by reinforcing the natural regulatory interactions between the SH2 and kinase domains. This novel mode of inhibition provides a new opportunity to improve the selectivity profile of Syk inhibitors for the development of safer drug candidates.
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Affiliation(s)
- Justin Hall
- Structural Biology and Biophysics Group, Pfizer, Groton, Connecticut 06340, USA.
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24
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Dar AC, Shokat KM. The evolution of protein kinase inhibitors from antagonists to agonists of cellular signaling. Annu Rev Biochem 2011; 80:769-95. [PMID: 21548788 DOI: 10.1146/annurev-biochem-090308-173656] [Citation(s) in RCA: 284] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Kinases are highly regulated enzymes with diverse mechanisms controlling their catalytic output. Over time, chemical discovery efforts for kinases have produced ATP-competitive compounds, allosteric regulators, irreversible binders, and highly specific inhibitors. These distinct classes of small molecules have revealed many novel aspects about kinase-mediated signaling, and some have progressed from simple tool compounds into clinically validated therapeutics. This review explores several small-molecule inhibitors for kinases highlighting elaborate mechanisms by which kinase function is modulated. A complete surprise of targeted kinase drug discovery has been the finding of ATP-competitive inhibitors that behave as agonists, rather than antagonists, of their direct kinase target. These studies hint at a connection between ATP-binding site occupancy and networks of communication that are independent of kinase catalysis. Indeed, kinase inhibitors that induce changes in protein localization, protein-protein interactions, and even enhancement of catalytic activity of the target kinase have been found. The relevance of these findings to the therapeutic efficacy of kinase inhibitors and to the future identification of new classes of drug targets is discussed.
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Affiliation(s)
- Arvin C Dar
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA.
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25
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Fröhner W, Lopez-Garcia LA, Neimanis S, Weber N, Navratil J, Maurer F, Stroba A, Zhang H, Biondi RM, Engel M. 4-benzimidazolyl-3-phenylbutanoic acids as novel PIF-pocket-targeting allosteric inhibitors of protein kinase PKCζ. J Med Chem 2011; 54:6714-23. [PMID: 21863889 DOI: 10.1021/jm2005892] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Protein kinase inhibitors with an allosteric mode of action are expected to reach, in many cases, higher selectivity for the target enzyme than ATP-competitive compounds. Therefore, basic research is aiming at identifying and establishing novel sites on the catalytic domain of protein kinases which might be targeted by allosteric inhibitors. We previously published the first structure-activity relationships (SARs) for allosteric activators of protein kinase PDK1. Here, we present the design, synthesis, and SAR data on a series of novel compounds, 4-benzimidazolyl-3-phenylbutanoic acids, that inhibit the atypical protein kinace C (PKC) ζ via binding to the PIF-pocket. Key positions were identified in the compounds that can be modified to increase potency and selectivity. Some congeners showed a high selectivity toward PKCζ, lacking inhibition of the most closely related isoform, PKCι, and of further AGC kinases. Furthermore, evidence is provided that these compounds are also active toward cellular PKCζ without loss of potency compared to the cell-free assay.
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Affiliation(s)
- Wolfgang Fröhner
- Pharmaceutical and Medicinal Chemistry, Saarland University, P.O. Box 151150, D-66041 Saarbrücken, Germany
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