1
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Baker ZD, Rasmussen DM, Levinson NM. Exploring the conformational landscapes of protein kinases: perspectives from FRET and DEER. Biochem Soc Trans 2024; 52:1071-1083. [PMID: 38778760 DOI: 10.1042/bst20230558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Conformational changes of catalytically-important structural elements are a key feature of the regulation mechanisms of protein kinases and are important for dictating inhibitor binding modes and affinities. The lack of widely applicable methods for tracking kinase conformational changes in solution has hindered our understanding of kinase regulation and our ability to design conformationally selective inhibitors. Here we provide an overview of two recently developed methods that detect conformational changes of the regulatory activation loop and αC-helix of kinases and that yield complementary information about allosteric mechanisms. An intramolecular Förster resonance energy transfer-based approach provides a scalable platform for detecting and classifying structural changes in high-throughput, as well as quantifying ligand binding cooperativity, shedding light on the energetics governing allostery. The pulsed electron paramagnetic resonance technique double electron-electron resonance provides lower throughput but higher resolution information on structural changes that allows for unambiguous assignment of conformational states and quantification of population shifts. Together, these methods are shedding new light on kinase regulation and drug interactions and providing new routes for the identification of novel kinase inhibitors and allosteric modulators.
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Affiliation(s)
- Zachary D Baker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, U.S.A
| | - Damien M Rasmussen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, U.S.A
| | - Nicholas M Levinson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, U.S.A
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, U.S.A
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2
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Ribeiro C, Cariello M, Malfait A, Bria M, Fournier D, Lyskawa J, Le Fer G, Potier J, Hoogenboom R, Cooke G, Woisel P. Synergistic topological and supramolecular control of Diels-Alder reactivity based on a tunable self-complexing host-guest molecular switch. Chemistry 2024; 30:e202302300. [PMID: 37991250 DOI: 10.1002/chem.202302300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 11/23/2023]
Abstract
Compartmentalization and binding-triggered conformational change regulate many metabolic processes in living matter. Here, we have synergistically combined these two biorelevant processes to tune the Diels-Alder (DA) reactivity of a synthetic self-complexing host-guest molecular switch CBPQT4+ -Fu, consisting of an electron-rich furan unit covalently attached to the electron-deficient cyclobis(paraquat-p-phenylene) tetrachloride (CBPQT4+ , 4Cl- ) host. This design allows CBPQT4+ -Fu to efficiently compartmentalize the furan ring inside its host cavity in water, thereby protecting it from the DA reaction with maleimide. Remarkably, the self-complexed CBPQT4+ -Fu can undergo a conformational change through intramolecular decomplexation upon the addition of a stronger binding molecular naphthalene derivative as a competitive guest, triggering the DA reaction upon addition of a chemical regulator. Remarkably, connecting the guest to a thermoresponsive lower critical solution temperature (LCST) copolymer regulator controls the DA reaction on command upon heating and cooling the reaction media beyond and below the cloud point temperature of the copolymer, representing a rare example of decreased reactivity upon increasing temperature. Altogether, this work opens up new avenues towards combined topological and supramolecular control over reactivity in synthetic constructs, enabling control over reactivity through molecular regulators or even mild temperature variations.
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Affiliation(s)
- Cédric Ribeiro
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - Michele Cariello
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | - Aurélie Malfait
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - Marc Bria
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - David Fournier
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - Joël Lyskawa
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - Gaëlle Le Fer
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - Jonathan Potier
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
| | - Richard Hoogenboom
- Supramolecular Chemistry Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4-bis, 9000, Ghent, Belgium
| | - Graeme Cooke
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | - Patrice Woisel
- Univ. Lille, CNRS, NRAE, Centrale Lille, UMR 8207 - UMET -, Unité Matériaux et Transformations, F-59000, Lille, France
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3
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Cazier A, Irvin OM, Chávez LS, Dalvi S, Abraham H, Wickramanayake N, Yellayi S, Blazeck J. A Rapid Antibody Enhancement Platform in Saccharomyces cerevisiae Using an Improved, Diversifying CRISPR Base Editor. ACS Synth Biol 2023; 12:3287-3300. [PMID: 37873982 PMCID: PMC10661033 DOI: 10.1021/acssynbio.3c00299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
Abstract
The yeast Saccharomyces cerevisiae is commonly used to interrogate and screen protein variants and to perform directed evolution studies to develop proteins with enhanced features. While several techniques have been described that help enable the use of yeast for directed evolution, there remains a need to increase their speed and ease of use. Here we present yDBE, a yeast diversifying base editor that functions in vivo and employs a CRISPR-dCas9-directed cytidine deaminase base editor to diversify DNA in a targeted, rapid, and high-breadth manner. To develop yDBE, we enhanced the mutation rate of an initial base editor by employing improved deaminase variants and characterizing several scaffolded guide constructs. We then demonstrate the ability of the yDBE platform to improve the affinity of a displayed antibody scFv, rapidly generating diversified libraries and isolating improved binders via cell sorting. By performing high-throughput sequencing analysis of the high-activity yDBE, we show that it enables a mutation rate of 2.13 × 10-4 substitutions/bp/generation over a window of 100 bp. As yDBE functions entirely in vivo and can be easily programmed to diversify nearly any such window of DNA, we posit that it can be a powerful tool for facilitating a variety of directed evolution experiments.
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Affiliation(s)
- Andrew
P. Cazier
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Olivia M. Irvin
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Lizmarie S. Chávez
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Saachi Dalvi
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Hannah Abraham
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Nevinka Wickramanayake
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Sreenivas Yellayi
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - John Blazeck
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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4
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Olivieri C, Li GC, Wang Y, V.S. M, Walker C, Kim J, Camilloni C, De Simone A, Vendruscolo M, Bernlohr DA, Taylor SS, Veglia G. ATP-competitive inhibitors modulate the substrate binding cooperativity of a kinase by altering its conformational entropy. SCIENCE ADVANCES 2022; 8:eabo0696. [PMID: 35905186 PMCID: PMC9337769 DOI: 10.1126/sciadv.abo0696] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
ATP-competitive inhibitors are currently the largest class of clinically approved drugs for protein kinases. By targeting the ATP-binding pocket, these compounds block the catalytic activity, preventing substrate phosphorylation. A problem with these drugs, however, is that inhibited kinases may still recognize and bind downstream substrates, acting as scaffolds or binding hubs for signaling partners. Here, using protein kinase A as a model system, we show that chemically different ATP-competitive inhibitors modulate the substrate binding cooperativity by tuning the conformational entropy of the kinase and shifting the populations of its conformationally excited states. Since we found that binding cooperativity and conformational entropy of the enzyme are correlated, we propose a new paradigm for the discovery of ATP-competitive inhibitors, which is based on their ability to modulate the allosteric coupling between nucleotide and substrate-binding sites.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Geoffrey C. Li
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yingjie Wang
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Manu V.S.
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Caitlin Walker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jonggul Kim
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Alfonso De Simone
- Department of Pharmacy, Università degli Studi di Napoli Federico II, Napoli 80131, Italy
| | | | - David A. Bernlohr
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Susan S. Taylor
- Department of Chemistry and Biochemistry, and Pharmacology, University of California at San Diego, CA 92093, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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5
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Wang Z, Huang W, Zhou K, Ren X, Ding K. Targeting the Non-Catalytic Functions: a New Paradigm for Kinase Drug Discovery? J Med Chem 2022; 65:1735-1748. [PMID: 35000385 DOI: 10.1021/acs.jmedchem.1c01978] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein kinases have been highly fruitful targets for cancer drug discovery in the past two decades, while most of these drugs bind to the "adenosine triphosphate (ATP)-site" and inhibit kinase catalytic activity. Recently, accumulated evidence suggests that kinases possess functions beyond catalysis through their scaffolds, and the scaffolding functions could play critical roles in multiple cellular signaling and cell fate controls. Small molecules modulating the noncatalytic functions of kinases are rarely reported but emerge as new promising therapeutic strategies for various diseases. Herein, we summarize the characterized noncatalytic functions of kinases, and highlight the recent progress on developing small-molecule modulators of the noncatalytic functions of kinases. Mechanisms and characteristics of different kinds of modulators are also discussed. It is also speculated that targeting the noncatalytic functions would represent a new direction for kinase-based drug discovery.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Ling Ling Road, Shanghai 200032, People's Republic of China
| | - Weixue Huang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Ling Ling Road, Shanghai 200032, People's Republic of China
| | - Kaijie Zhou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Ling Ling Road, Shanghai 200032, People's Republic of China
| | - Xiaomei Ren
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People's Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, People's Republic of China
| | - Ke Ding
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, #345 Ling Ling Road, Shanghai 200032, People's Republic of China.,International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MoE) of People's Republic of China, College of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, People's Republic of China.,The First Affiliated Hospital (Huaqiao Hospital), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, People's Republic of China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, People's Republic of China
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6
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Zhang B, Yuan P, Xu G, Chen Z, Li Z, Ye H, Wang J, Shi P, Sun X. DUSP6 expression is associated with osteoporosis through the regulation of osteoclast differentiation via ERK2/Smad2 signaling. Cell Death Dis 2021; 12:825. [PMID: 34475393 PMCID: PMC8413376 DOI: 10.1038/s41419-021-04110-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 01/28/2023]
Abstract
Osteoporosis-related fractures, such as femoral neck and vertebral fractures, are common in aged people, resulting in increased disability rate and health-care costs. Thus, it is of great importance to clarify the mechanism of osteoclast-related osteoporosis and find effective ways to avoid its complication. In this study, gene expression profile analysis and real-time polymerase chain reaction revealed that DUSP6 expression was suppressed in human and mice osteoporosis cases. In vitro experiments confirmed that DUSP6 overexpression prevented osteoclastogenesis, whereas inhibition of DUSP6 by small interference RNA or with a chemical inhibitor, (E/Z)-BCI, had the opposite effect. (E/Z)-BCl significantly accelerated the bone loss process in vivo by enhancing osteoclastogenesis. Bioinformatics analyses and in vitro experiments indicated that miR-181a was an upstream regulator of DUSP6. Moreover, miR-181a positively induced the differentiation and negatively regulated the apoptosis of osteoclasts via DUSP6. Furthermore, downstream signals by ERK2 and SMAD2 were also found to be involved in this process. Evaluation of ERK2-deficiency bone marrow-derived macrophages confirmed the role of ERK2 signaling in the DUSP6-mediated osteoclastogenesis. Additionally, immunoprecipitation assays confirmed that DUSP6 directly modified the phosphorylation status of SMAD2 and the subsequent nuclear transportation of NFATC1 to regulate osteoclast differentiation. Altogether, this study demonstrated for the first time the role of miRNA-181a/DUSP6 in the progression of osteoporosis via the ERK2 and SMAD2 signaling pathway. Hence, DUSP6 may represent a novel target for the treatment of osteoclast-related diseases in the future.
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Affiliation(s)
- Boya Zhang
- Department of Dermatology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Putao Yuan
- Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, China
| | - Guang Xu
- Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, China
| | - Zhijun Chen
- Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, China
| | - Zhifei Li
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China
| | - Huali Ye
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, China
| | - Jiying Wang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, China
| | - Peihua Shi
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, China.
| | - Xuewu Sun
- Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, China.
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7
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Three-Dimensional Interactions Analysis of the Anticancer Target c-Src Kinase with Its Inhibitors. Cancers (Basel) 2020; 12:cancers12082327. [PMID: 32824733 PMCID: PMC7466017 DOI: 10.3390/cancers12082327] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/07/2020] [Accepted: 08/16/2020] [Indexed: 12/13/2022] Open
Abstract
Src family kinases (SFKs) constitute the biggest family of non-receptor tyrosine kinases considered as therapeutic targets for cancer therapy. An aberrant expression and/or activation of the proto-oncogene c-Src kinase, which is the oldest and most studied member of the family, has long been demonstrated to play a major role in the development, growth, progression and metastasis of numerous human cancers, including colon, breast, gastric, pancreatic, lung and brain carcinomas. For these reasons, the pharmacological inhibition of c-Src activity represents an effective anticancer strategy and a few compounds targeting c-Src, together with other kinases, have been approved as drugs for cancer therapy, while others are currently undergoing preclinical studies. Nevertheless, the development of potent and selective inhibitors of c-Src aimed at properly exploiting this biological target for the treatment of cancer still represents a growing field of study. In this review, the co-crystal structures of c-Src kinase in complex with inhibitors discovered in the past two decades have been described, highlighting the key ligand-protein interactions necessary to obtain high potency and the features to be exploited for addressing selectivity and drug resistance issues, thus providing useful information for the design of new and potent c-Src kinase inhibitors.
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8
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Jin ZL, Yao XR, Wen L, Hao G, Kwon JW, Hao J, Kim NH. AIP1 and Cofilin control the actin dynamics to modulate the asymmetric division and cytokinesis in mouse oocytes. FASEB J 2020; 34:11292-11306. [PMID: 32602619 DOI: 10.1096/fj.202000093r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/17/2020] [Accepted: 04/26/2020] [Indexed: 11/11/2022]
Abstract
Actin-interacting protein 1 (AIP1), also known as WD repeat-containing protein 1 (WDR1), is ubiquitous in eukaryotic organisms, and it plays critical roles in the dynamic reorganization of the actin cytoskeleton. However, the biological function and mechanism of AIP1 in mammalian oocyte maturation is still largely unclear. In this study, we demonstrated that AIP1 boosts ADF/Cofilin activity in mouse oocytes. AIP1 is primarily distributed around the spindle region during oocyte maturation, and its depletion impairs meiotic spindle migration and asymmetric division. The knockdown of AIP1 resulted in the gathering of a large number of actin-positive patches around the spindle region. This effect was reduced by human AIP1 (hAIP1) or Cofilin (S3A) expression. AIP1 knockdown also reduced the phosphorylation of Cofilin near the spindle, indicating that AIP1 interacts with ADF/Cofilin-decorated actin filaments and enhances filament disassembly. Moreover, the deletion of AIP1 disrupts Cofilin localization in metaphase I (MI) and induces cytokinesis defects in metaphase II (MII). Taken together, our results provide evidence that AIP1 promotes actin dynamics and cytokinesis via Cofilin in the gametes of female mice.
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Affiliation(s)
- Zhe-Long Jin
- School of Biotechnology and Healthcare, Wuyi University, Jiangmen, China.,Department of Animal Sciences, Chungbuk National University, Cheongju, Korea
| | - Xue-Rui Yao
- School of Biotechnology and Healthcare, Wuyi University, Jiangmen, China.,Department of Animal Sciences, Chungbuk National University, Cheongju, Korea
| | - Liu Wen
- School of Biotechnology and Healthcare, Wuyi University, Jiangmen, China
| | - Guo Hao
- School of Biotechnology and Healthcare, Wuyi University, Jiangmen, China.,Department of Animal Sciences, Chungbuk National University, Cheongju, Korea
| | - Jeong-Woo Kwon
- School of Biotechnology and Healthcare, Wuyi University, Jiangmen, China
| | - Jiang Hao
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, China
| | - Nam-Hyung Kim
- School of Biotechnology and Healthcare, Wuyi University, Jiangmen, China.,Department of Animal Sciences, Chungbuk National University, Cheongju, Korea
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9
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Abstract
Pseudokinases are members of the protein kinase superfamily but signal primarily through noncatalytic mechanisms. Many pseudokinases contribute to the pathologies of human diseases, yet they remain largely unexplored as drug targets owing to challenges associated with modulation of their biological functions. Our understanding of the structure and physiological roles of pseudokinases has improved substantially over the past decade, revealing intriguing similarities between pseudokinases and their catalytically active counterparts. Pseudokinases often adopt conformations that are analogous to those seen in catalytically active kinases and, in some cases, can also bind metal cations and/or nucleotides. Several clinically approved kinase inhibitors have been shown to influence the noncatalytic functions of active kinases, providing hope that similar properties in pseudokinases could be pharmacologically regulated. In this Review, we discuss known roles of pseudokinases in disease, their unique structural features and the progress that has been made towards developing pseudokinase-directed therapeutics.
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10
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Lopez ED, Burastero O, Arcon JP, Defelipe LA, Ahn NG, Marti MA, Turjanski AG. Kinase Activation by Small Conformational Changes. J Chem Inf Model 2019; 60:821-832. [PMID: 31714778 DOI: 10.1021/acs.jcim.9b00782] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein kinases (PKs) are allosteric enzymes that play an essential role in signal transduction by regulating a variety of key cellular processes. Most PKs suffer conformational rearrangements upon phosphorylation that strongly enhance the catalytic activity. Generally, it involves the movement of the phosphorylated loop toward the active site and the rotation of the whole C-terminal lobe. However, not all kinases undergo such a large configurational change: The MAPK extracellular signal-regulated protein kinases ERK1 and ERK2 achieve a 50 000 fold increase in kinase activity with only a small motion of the C-terminal region. In the present work, we used a combination of molecular simulation tools to characterize the conformational landscape of ERK2 in the active (phosphorylated) and inactive (unphosphorylated) states in solution in agreement with NMR experiments. We show that the chemical reaction barrier is strongly dependent on ATP conformation and that the "active" low-barrier configuration is subtly regulated by phosphorylation, which stabilizes a key salt bridge between the conserved Lys52 and Glu69 belonging to helix-C and promotes binding of a second Mg ion. Our study highlights that the on-off switch embedded in the kinase fold can be regulated by small, medium, and large conformational changes.
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Affiliation(s)
- Elias D Lopez
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Ciudad Autónoma de Buenos Aires , Argentina
| | - Osvaldo Burastero
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Ciudad Autónoma de Buenos Aires , Argentina
| | - Juan P Arcon
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Ciudad Autónoma de Buenos Aires , Argentina
| | - Lucas A Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Ciudad Autónoma de Buenos Aires , Argentina
| | - Natalie G Ahn
- Department of Chemistry and Biochemistry , University of Colorado , Boulder , Colorado 80309 , United States
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Ciudad Autónoma de Buenos Aires , Argentina
| | - Adrian G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Ciudad Autónoma de Buenos Aires , Argentina
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11
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Leroux AE, Biondi RM. Renaissance of Allostery to Disrupt Protein Kinase Interactions. Trends Biochem Sci 2019; 45:27-41. [PMID: 31690482 DOI: 10.1016/j.tibs.2019.09.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022]
Abstract
Protein-protein interactions often regulate the activity of protein kinases by allosterically modulating the conformation of the ATP-binding site. Bidirectional allostery implies that reverse modulation (i.e., from the ATP-binding site to the interaction and regulatory sites) must also be possible. Here, we review both the allosteric regulation of protein kinases and recent work describing how compounds binding at the ATP-binding site can promote or inhibit protein kinase interactions at regulatory sites via the reverse mechanism. Notably, the pharmaceutical industry has been developing compounds that bind to the ATP-binding site of protein kinases and potently disrupt protein-protein interactions between target protein kinases and their regulatory interacting partners. Learning to modulate allosteric processes will facilitate the development of protein-protein interaction modulators.
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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
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina; Department of Internal Medicine I, University Hospital, Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; DKTK German Cancer Consortium (DKTK), Frankfurt, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
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12
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Activation loop dynamics are controlled by conformation-selective inhibitors of ERK2. Proc Natl Acad Sci U S A 2019; 116:15463-15468. [PMID: 31311868 DOI: 10.1073/pnas.1906824116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Conformational selection by small molecules expands inhibitory possibilities for protein kinases. Nuclear magnetic resonance (NMR) measurements of the mitogen-activated protein (MAP) kinase ERK2 have shown that activation by dual phosphorylation induces global motions involving exchange between two states, L and R. We show that ERK inhibitors Vertex-11e and SCH772984 exploit the small energetic difference between L and R to shift the equilibrium in opposing directions. An X-ray structure of active 2P-ERK2 complexed with AMP-PNP reveals a shift in the Gly-rich loop along with domain closure to position the nucleotide in a more catalytically productive conformation relative to inactive 0P-ERK2:ATP. X-ray structures of 2P-ERK2 complexed with Vertex-11e or GDC-0994 recapitulate this closure, which is blocked in a complex with a SCH772984 analog. Thus, the L→R shift in 2P-ERK2 is associated with movements needed to form a competent active site. Solution measurements by hydrogen-exchange mass spectrometry (HX-MS) reveal distinct binding interactions for Vertex-11e, GDC-0994, and AMP-PNP with active vs. inactive ERK2, where the extent of HX protection correlates with R state formation. Furthermore, Vertex-11e and SCH772984 show opposite effects on HX near the activation loop. Consequently, these inhibitors differentially affect MAP kinase phosphatase activity toward 2P-ERK2. We conclude that global motions in ERK2 reflect conformational changes at the active site that promote productive nucleotide binding and couple with changes at the activation loop to allow control of dephosphorylation by conformationally selective inhibitors.
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13
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Fang L, Chakraborty S, Dieter EM, Potter ZE, Lombard CK, Maly DJ. Chemoproteomic Method for Profiling Inhibitor-Bound Kinase Complexes. J Am Chem Soc 2019; 141:11912-11922. [PMID: 31274292 DOI: 10.1021/jacs.9b02963] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Small molecule inhibitors often only block a subset of the cellular functions of their protein targets. In many cases, how inhibiting only a portion of a multifunctional protein's functions affects the state of the cell is not well-understood. Therefore, tools that allow the systematic characterization of the cellular interactions that inhibitor-bound proteins make would be of great utility, especially for multifunctional proteins. Here, we describe a chemoproteomic strategy for interrogating the cellular localization and interactomes of inhibitor-bound kinases. By developing a set of orthogonal inhibitors that contain a trans-cyclooctene (TCO) click handle, we are able to enrich and characterize the proteins complexed to a drug-sensitized variant of the multidomain kinase Src. We show that Src's cellular interactions are highly influenced by the intermolecular accessibility of its regulatory domains, which can be allosterically modulated through its ATP-binding site. Furthermore, we find that the signaling status of the cell also has a large effect on Src's interactome. Finally, we demonstrate that our TCO-conjugated probes can be used as a part of a proximity ligation assay to study Src's localization and interactions in situ. Together, our chemoproteomic strategy represents a comprehensive method for studying the localization and interactomes of inhibitor-bound kinases and, potentially, other druggable protein targets.
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14
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Vrijens P, Noppen S, Boogaerts T, Vanstreels E, Ronca R, Chiodelli P, Laporte M, Vanderlinden E, Liekens S, Stevaert A, Naesens L. Influenza virus entry via the GM3 ganglioside-mediated platelet-derived growth factor receptor β signalling pathway. J Gen Virol 2019; 100:583-601. [PMID: 30762518 DOI: 10.1099/jgv.0.001235] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The possible resistance of influenza virus against existing antiviral drugs calls for new therapeutic concepts. One appealing strategy is to inhibit virus entry, in particular at the stage of internalization. This requires a better understanding of virus-host interactions during the entry process, including the role of receptor tyrosine kinases (RTKs). To search for cellular targets, we evaluated a panel of 276 protein kinase inhibitors in a multicycle antiviral assay in Madin-Darby canine kidney cells. The RTK inhibitor Ki8751 displayed robust anti-influenza A and B virus activity and was selected for mechanistic investigations. Ki8751 efficiently disrupted the endocytic process of influenza virus in different cell lines carrying platelet-derived growth factor receptor β (PDGFRβ), an RTK that is known to act at GM3 ganglioside-positive lipid rafts. The more efficient virus entry in CHO-K1 cells compared to the wild-type ancestor (CHO-wt) cells indicated a positive effect of GM3, which is abundant in CHO-K1 but not in CHO-wt cells. Entering virus localized to GM3-positive lipid rafts and the PDGFRβ-containing endosomal compartment. PDGFRβ/GM3-dependent virus internalization involved PDGFRβ phosphorylation, which was potently inhibited by Ki8751, and desialylation of activated PDGFRβ by the viral neuraminidase. Virus uptake coincided with strong activation of the Raf/MEK/Erk cascade, but not of PI3K/Akt or phospholipase C-γ. We conclude that influenza virus efficiently hijacks the GM3-enhanced PDGFRβ signalling pathway for cell penetration, providing an opportunity for host cell-targeting antiviral intervention.
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Affiliation(s)
- Pieter Vrijens
- 1Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Sam Noppen
- 1Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Talitha Boogaerts
- 1Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Els Vanstreels
- 1Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Roberto Ronca
- 2Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Paola Chiodelli
- 2Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Manon Laporte
- 1Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Evelien Vanderlinden
- 1Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Sandra Liekens
- 1Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Annelies Stevaert
- 1Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Lieve Naesens
- 1Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
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15
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Foulkes DM, Byrne DP, Yeung W, Shrestha S, Bailey FP, Ferries S, Eyers CE, Keeshan K, Wells C, Drewry DH, Zuercher WJ, Kannan N, Eyers PA. Covalent inhibitors of EGFR family protein kinases induce degradation of human Tribbles 2 (TRIB2) pseudokinase in cancer cells. Sci Signal 2018; 11:11/549/eaat7951. [PMID: 30254057 DOI: 10.1126/scisignal.aat7951] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A major challenge associated with biochemical and cellular analysis of pseudokinases is a lack of target-validated small-molecule compounds with which to probe function. Tribbles 2 (TRIB2) is a cancer-associated pseudokinase with a diverse interactome, including the canonical AKT signaling module. There is substantial evidence that human TRIB2 promotes survival and drug resistance in solid tumors and blood cancers and therefore is of interest as a therapeutic target. The unusual TRIB2 pseudokinase domain contains a unique cysteine-rich C-helix and interacts with a conserved peptide motif in its own carboxyl-terminal tail, which also supports its interaction with E3 ubiquitin ligases. We found that TRIB2 is a target of previously described small-molecule protein kinase inhibitors, which were originally designed to inhibit the canonical kinase domains of epidermal growth factor receptor tyrosine kinase family members. Using a thermal shift assay, we discovered TRIB2-binding compounds within the Published Kinase Inhibitor Set (PKIS) and used a drug repurposing approach to classify compounds that either stabilized or destabilized TRIB2 in vitro. TRIB2 destabilizing agents, including the covalent drug afatinib, led to rapid TRIB2 degradation in human AML cancer cells, eliciting tractable effects on signaling and survival. Our data reveal new drug leads for the development of TRIB2-degrading compounds, which will also be invaluable for unraveling the cellular mechanisms of TRIB2-based signaling. Our study highlights that small molecule-induced protein down-regulation through drug "off-targets" might be relevant for other inhibitors that serendipitously target pseudokinases.
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Affiliation(s)
- Daniel M Foulkes
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Dominic P Byrne
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Wayland Yeung
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Safal Shrestha
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Fiona P Bailey
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Samantha Ferries
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.,Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.,Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Karen Keeshan
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Scotland, UK
| | - Carrow Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William J Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natarajan Kannan
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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16
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Lombard CK, Davis AL, Inukai T, Maly DJ. Allosteric Modulation of JNK Docking Site Interactions with ATP-Competitive Inhibitors. Biochemistry 2018; 57:5897-5909. [PMID: 30211540 DOI: 10.1021/acs.biochem.8b00776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The c-Jun N-terminal kinases (JNKs) play a wide variety of roles in cellular signaling processes, dictating important, and even divergent, cellular fates. These essential kinases possess docking surfaces distal to their active sites that interact with diverse binding partners, including upstream activators, downstream substrates, and protein scaffolds. Prior studies have suggested that the interactions of certain protein-binding partners with one such JNK docking surface, termed the D-recruitment site (DRS), can allosterically influence the conformational state of the ATP-binding pocket of JNKs. To further explore the allosteric relationship between the ATP-binding pockets and DRSs of JNKs, we investigated how the interactions of the scaffolding protein JIP1, as well as the upstream activators MKK4 and MKK7, are allosterically influenced by the ATP-binding site occupancy of the JNKs. We show that the affinity of the JNKs for JIP1 can be divergently modulated with ATP-competitive inhibitors, with a >50-fold difference in dissociation constant observed between the lowest- and highest-affinity JNK1-inhibitor complexes. Furthermore, we found that we could promote or attenuate phosphorylation of JNK1's activation loop by MKK4 and MKK7, by varying the ATP-binding site occupancy. Given that JIP1, MKK4, and MKK7 all interact with JNK DRSs, these results demonstrate that there is functional allostery between the ATP-binding sites and DRSs of these kinases. Furthermore, our studies suggest that ATP-competitive inhibitors can allosterically influence the intracellular binding partners of the JNKs.
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Affiliation(s)
- Chloe K Lombard
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States
| | - Audrey L Davis
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States
| | - Takayuki Inukai
- Medicinal Chemistry Research Laboratories , Ono Pharmaceutical Company, Ltd. , 3-1-1 Sakurai , Shimamoto, Mishima, Osaka 618-8585 , Japan
| | - Dustin J Maly
- Department of Chemistry , University of Washington , Seattle , Washington 98117 , United States.,Department of Biochemistry , University of Washington , Seattle , Washington 98117 , United States
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17
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Khattab M, Wang F, Clayton AHA. Conformational Plasticity in Tyrosine Kinase Inhibitor-Kinase Interactions Revealed with Fluorescence Spectroscopy and Theoretical Calculations. J Phys Chem B 2018; 122:4667-4679. [PMID: 29629773 DOI: 10.1021/acs.jpcb.8b01530] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
To understand drug-protein dynamics, it is necessary to account for drug molecular flexibility and binding site plasticity. Herein, we exploit fluorescence from a tyrosine kinase inhibitor, AG1478, as a reporter of its conformation and binding site environment when complexed with its cognate kinase. Water-soluble kinases, aminoglycoside phosphotransferase APH(3')-Ia and mitogen-activated protein kinase 14 (MAPK14), were chosen for this study. On the basis of our prior work, the AG1478 conformation (planar or twisted) was inferred from the fluorescence excitation spectrum and the polarity of the AG1478-binding site was deduced from the fluorescence emission spectrum, while red-edge excitation shift (REES) probed the heterogeneity of the binding site (protein conformation and hydration) distributions in the protein conformational ensemble. In the AG1478-APH(3')-Ia complex, both twisted (or partially twisted) and planar AG1478 conformations were evidenced from emission wavelength-dependent excitation spectra. The binding site environment provided by APH(3')-Ia was moderately polar (λmax = 480 nm) with evidence for considerable heterogeneity (REES = 34 nm). In contrast, in the AG1478-MAPK14 complex, AG1478 was in a predominantly planar conformation with a lower degree of conformational heterogeneity. The binding site environment provided by the MAPK14 protein was of relatively low polarity (λmax = 430 nm) with a smaller degree of heterogeneity (REES = 11 nm). The results are compared with the available X-ray data and discussed in the context of our current understanding of tyrosine kinase inhibitor conformation and protein conformational ensembles.
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18
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Survey of solution dynamics in Src kinase reveals allosteric cross talk between the ligand binding and regulatory sites. Nat Commun 2017; 8:2160. [PMID: 29255153 PMCID: PMC5735167 DOI: 10.1038/s41467-017-02240-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/15/2017] [Indexed: 11/09/2022] Open
Abstract
The catalytic domain of protein tyrosine kinases can interconvert between active and inactive conformations in response to regulatory inputs. We recently demonstrated that Src kinase features an allosteric network that couples substrate-binding sites. However, the extent of conformational and dynamic changes that are propagated throughout the kinase domain remains poorly understood. Here, we monitor by NMR the effect of conformationally selective inhibitors on kinase backbone dynamics. We find that inhibitor binding and activation loop autophosphorylation induces dynamic changes across the entire kinase. We identify a highly conserved amino acid, Gly449, that is necessary for Src activation. Finally, we show for the first time how the SH3–SH2 domains perturb the dynamics of the kinase domain in the context of the full length protein. We provide experimental support for long-range communication in Src kinase that leads to the relative stabilization of active or inactive conformations and modulation of substrate affinity. Src is a prototypical signaling non-receptor protein tyrosine kinase that interconverts between distinct conformations. Here the authors use variants of the kinase-inhibitor dasatinib to define three specific conformational states of the Src kinase and shed insight on the effect of conformation-specific inhibitors on Src dynamics.
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19
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Kung JE, Jura N. Structural Basis for the Non-catalytic Functions of Protein Kinases. Structure 2016; 24:7-24. [PMID: 26745528 DOI: 10.1016/j.str.2015.10.020] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/18/2015] [Accepted: 10/04/2015] [Indexed: 01/07/2023]
Abstract
Protein kinases are known primarily for their ability to phosphorylate protein substrates, which constitutes an essential biological process. Recently, compelling evidence has accumulated that the functions of many protein kinases extend beyond phosphorylation and include an impressive spectrum of non-catalytic roles, such as scaffolding, allosteric regulation, or even protein-DNA interactions. How the conserved kinase fold shared by all metazoan protein kinases can accomplish these diverse tasks in a specific and regulated manner is poorly understood. In this review, we analyze the molecular mechanisms supporting phosphorylation-independent signaling by kinases and attempt to identify common and unique structural characteristics that enable kinases to perform non-catalytic functions. We also discuss how post-translational modifications, protein-protein interactions, and small molecules modulate these non-canonical kinase functions. Finally, we highlight current efforts in the targeted design of small-molecule modulators of non-catalytic kinase functions, a new pharmacological challenge for which structural considerations are more important than ever.
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Affiliation(s)
- Jennifer E Kung
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
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20
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Feldman HC, Tong M, Wang L, Meza-Acevedo R, Gobillot TA, Lebedev I, Gliedt MJ, Hari SB, Mitra AK, Backes BJ, Papa FR, Seeliger MA, Maly DJ. Structural and Functional Analysis of the Allosteric Inhibition of IRE1α with ATP-Competitive Ligands. ACS Chem Biol 2016; 11:2195-205. [PMID: 27227314 DOI: 10.1021/acschembio.5b00940] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The accumulation of unfolded proteins under endoplasmic reticulum (ER) stress leads to the activation of the multidomain protein sensor IRE1α as part of the unfolded protein response (UPR). Clustering of IRE1α lumenal domains in the presence of unfolded proteins promotes kinase trans-autophosphorylation in the cytosol and subsequent RNase domain activation. Interestingly, there is an allosteric relationship between the kinase and RNase domains of IRE1α, which allows ATP-competitive inhibitors to modulate the activity of the RNase domain. Here, we use kinase inhibitors to study how ATP-binding site conformation affects the activity of the RNase domain of IRE1α. We find that diverse ATP-competitive inhibitors of IRE1α promote dimerization and activation of RNase activity despite blocking kinase autophosphorylation. In contrast, a subset of ATP-competitive ligands, which we call KIRAs, allosterically inactivate the RNase domain through the kinase domain by stabilizing monomeric IRE1α. Further insight into how ATP-competitive inhibitors are able to divergently modulate the RNase domain through the kinase domain was gained by obtaining the first structure of apo human IRE1α in the RNase active back-to-back dimer conformation. Comparison of this structure with other existing structures of IRE1α and integration of our extensive structure activity relationship (SAR) data has led us to formulate a model to rationalize how ATP-binding site ligands are able to control the IRE1α oligomeric state and subsequent RNase domain activity.
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Affiliation(s)
- Hannah C. Feldman
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
| | - Michael Tong
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York, United States
| | - Likun Wang
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Diabetes
Center, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
- California
Institute for Quantitative Biosciences, University of California−San Francisco, San Francisco, California, United States
| | - Rosa Meza-Acevedo
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Diabetes
Center, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
- California
Institute for Quantitative Biosciences, University of California−San Francisco, San Francisco, California, United States
| | - Theodore A. Gobillot
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
| | - Ivan Lebedev
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York, United States
| | - Micah J. Gliedt
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
| | - Sanjay B. Hari
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
| | - Arinjay K. Mitra
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
| | - Bradley J. Backes
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
| | - Feroz R. Papa
- Department
of Medicine, University of California−San Francisco, San Francisco, California, United States
- Diabetes
Center, University of California−San Francisco, San Francisco, California, United States
- Lung
Biology Center, University of California−San Francisco, San Francisco, California, United States
- California
Institute for Quantitative Biosciences, University of California−San Francisco, San Francisco, California, United States
| | - Markus A. Seeliger
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York, United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Seattle, Washington, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington, United States
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21
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Kwarcinski FE, Brandvold KR, Phadke S, Beleh OM, Johnson TK, Meagher JL, Seeliger MA, Stuckey JA, Soellner MB. Conformation-Selective Analogues of Dasatinib Reveal Insight into Kinase Inhibitor Binding and Selectivity. ACS Chem Biol 2016; 11:1296-304. [PMID: 26895387 PMCID: PMC7306399 DOI: 10.1021/acschembio.5b01018] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the kinase field, there are many widely held tenets about conformation-selective inhibitors that have yet to be validated using controlled experiments. We have designed, synthesized, and characterized a series of kinase inhibitor analogues of dasatinib, an FDA-approved kinase inhibitor that binds the active conformation. This inhibitor series includes two Type II inhibitors that bind the DFG-out inactive conformation and two inhibitors that bind the αC-helix-out inactive conformation. Using this series of compounds, we analyze the impact that conformation-selective inhibitors have on target binding and kinome-wide selectivity.
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Affiliation(s)
- Frank E. Kwarcinski
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | | | - Sameer Phadke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Omar M. Beleh
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Taylor K. Johnson
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | | | - Markus A. Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794
| | - Jeanne A. Stuckey
- Center for Structural Biology, University of Michigan, Ann Arbor, MI 48109
| | - Matthew B. Soellner
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
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22
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Conformational kinetics reveals affinities of protein conformational states. Proc Natl Acad Sci U S A 2015; 112:9352-7. [PMID: 26162682 DOI: 10.1073/pnas.1502084112] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies of reactions that couple binding to conformational change. We monitored the kinetics of ligand-induced conformational changes in a small protein using six different ligands. We analyzed the kinetic data to simultaneously determine both binding affinities for the conformational states and the rate constants of conformational change. The approach we used is sufficiently robust to determine the affinities of three conformational states and detect even modest differences in the protein's affinities for relatively similar ligands. Ligand binding favors higher-affinity conformational states by increasing forward conformational rate constants and/or decreasing reverse conformational rate constants. The amounts by which forward rate constants increase and reverse rate constants decrease are proportional to the ratio of affinities of the conformational states. We also show that both the affinity ratio and another parameter, which quantifies the changes in conformational rate constants upon ligand binding, are strong determinants of the mechanism (conformational selection and/or induced fit) of molecular recognition. Our results highlight the utility of analyzing the kinetics of conformational changes to determine affinities that cannot be determined from equilibrium experiments. Most importantly, they demonstrate an inextricable link between conformational dynamics and the binding affinities of conformational states.
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23
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The Tribbles 2 (TRB2) pseudokinase binds to ATP and autophosphorylates in a metal-independent manner. Biochem J 2015; 467:47-62. [PMID: 25583260 DOI: 10.1042/bj20141441] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The human Tribbles (TRB)-related pseudokinases are CAMK (calcium/calmodulin-dependent protein kinase)-related family members that have evolved a series of highly unusual motifs in the 'pseudocatalytic' domain. In canonical kinases, conserved amino acids bind to divalent metal ions and align ATP prior to efficient phosphoryl-transfer to substrates. However, in pseudokinases, atypical residues give rise to diverse and often unstudied biochemical and structural features that are thought to be central to cellular functions. TRB proteins play a crucial role in multiple signalling networks and overexpression confers cancer phenotypes on human cells, marking TRB pseudokinases out as a novel class of drug target. In the present paper, we report that the human pseudokinase TRB2 retains the ability to both bind and hydrolyse ATP weakly in vitro. Kinase activity is metal-independent and involves a catalytic lysine residue, which is conserved in TRB proteins throughout evolution alongside several unique amino acids in the active site. A similar low level of autophosphorylation is also preserved in the closely related human TRB3. By employing chemical genetics, we establish that the nucleotide-binding site of an 'analogue-sensitive' (AS) TRB2 mutant can be targeted with specific bulky ligands of the pyrazolo-pyrimidine (PP) chemotype. Our analysis confirms that TRB2 retains low levels of ATP binding and/or catalysis that is targetable with small molecules. Given the significant clinical successes associated with targeting of cancer-associated kinases with small molecule inhibitors, it is likely that similar approaches will be useful for further evaluating the TRB pseudokinases, with the translation of this information likely to furnish new leads for drug discovery.
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24
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Abstract
In this issue of Chemistry & Biology, Hari and colleagues show that conformation-selective ATP-competitive kinase inhibitors have distinct noncatalytic effects on Erk2, including the ability to modulate protein-protein interactions outside the ATP-binding site. These findings enhance our knowledge about the diverse array of activities in which kinase inhibitors can target signaling pathways.
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25
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Abstract
The quest for ever more selective kinase inhibitors as potential future drugs has yielded a large repertoire of chemical probes that are selective for specific kinase conformations. These probes have been useful tools to obtain structural snapshots of kinase conformational plasticity. Similarly, kinetic and thermodynamic inhibitor binding experiments provide glimpses at the time scales and energetics of conformational interconversions. These experimental insights are complemented by computational predictions of conformational energy landscapes and simulations of conformational transitions and of the process of inhibitors binding to the protein kinase domain. A picture emerges in which highly selective inhibitors capitalize on the dynamic nature of kinases.
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Affiliation(s)
- Michael Tong
- Department
of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
| | - Markus A. Seeliger
- Department
of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794, United States
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Leonard SE, Register AC, Krishnamurty R, Brighty GJ, Maly DJ. Divergent modulation of Src-family kinase regulatory interactions with ATP-competitive inhibitors. ACS Chem Biol 2014; 9:1894-905. [PMID: 24946274 PMCID: PMC4136698 DOI: 10.1021/cb500371g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Multidomain protein kinases, central
controllers of signal transduction,
use regulatory domains to modulate catalytic activity in a complex
cellular environment. Additionally, these domains regulate noncatalytic
functions, including cellular localization and protein–protein
interactions. Src-family kinases (SFKs) are promising therapeutic
targets for a number of diseases and are an excellent model for studying
the regulation of multidomain kinases. Here, we demonstrate that the
regulatory domains of the SFKs Src and Hck are divergently affected
by ligands that stabilize two distinct inactive ATP-binding site conformations.
Conformation-selective, ATP-competitive inhibitors differentially
modulate the ability of the SH3 and SH2 domains of Src and Hck to
engage in intermolecular interactions and the ability of the kinase–inhibitor
complex to undergo post-translational modification by effector enzymes.
This surprising divergence in regulatory domain behavior by two classes
of inhibitors that each stabilize inactive ATP-binding site conformations
is found to occur through perturbation or stabilization of the αC
helix. These studies provide insight into how conformation-selective,
ATP-competitive inhibitors can be designed to modulate domain interactions
and post-translational modifications distal to the ATP-binding site
of kinases.
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Affiliation(s)
- Stephen E. Leonard
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - A. C. Register
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Ratika Krishnamurty
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gabriel J. Brighty
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
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