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Cruz-Rodriguez N, Tang H, Bateman B, Tang W, Deininger M. BCR::ABL1 Proteolysis-targeting chimeras (PROTACs): The new frontier in the treatment of Ph + leukemias? Leukemia 2024:10.1038/s41375-024-02365-w. [PMID: 39098922 DOI: 10.1038/s41375-024-02365-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/19/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
BCR::ABL1 tyrosine kinase inhibitors (TKIs) have turned chronic myeloid leukemia (CML) from a lethal condition into a chronic ailment. With optimal management, the survival of CML patients diagnosed in the chronic phase is approaching that of age-matched controls. However, only one-third of patients can discontinue TKIs and enter a state of functional cure termed treatment-free remission (TFR), while the remainder require life-long TKI therapy to avoid the recurrence of active leukemia. Approximately 10% of patients exhibit primary or acquired TKI resistance and eventually progress to the blast phase. It is thought that recurrence after attempted TFR originates from CML stem cells (LSCs) surviving despite continued suppression of BCR::ABL1 kinase. Although kinase activity is indispensable for induction of overt CML, kinase-independent scaffold functions of BCR::ABL1 are known to contribute to leukemogenesis, raising the intriguing but as yet hypothetical possibility, that degradation of BCR::ABL1 protein may accomplish what TKIs fail to achieve - eliminate residual LSCs to turn functional into real cures. The advent of BCR::ABL1 proteolysis targeting chimeras (PROTACs), heterobifunctional molecules linking a TKI-based warhead to an E3 ligase recruiter, has moved clinical protein degradation into the realm of the possible. Here we examine the molecular rationale as well as pros and cons of degrading BCR::ABL1 protein. We review reported BCR::ABL1 PROTACs, point out limitations of available data and compounds and suggest directions for future research. Ultimately, clinical testing of a potent and specific BCR::ABL1 degrader will be required to determine the efficacy and tolerability of this approach.
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Affiliation(s)
| | - Hua Tang
- Lachman Institute of Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Weiping Tang
- Lachman Institute of Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael Deininger
- Versiti Blood Research Institute, Milwaukee, WI, USA.
- Medical College of Wisconsin, Milwaukee, WI, USA.
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2
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Mehra S, Nicholls M, Taylor J. The Evolving Role of Bruton's Tyrosine Kinase Inhibitors in B Cell Lymphomas. Int J Mol Sci 2024; 25:7516. [PMID: 39062757 PMCID: PMC11276629 DOI: 10.3390/ijms25147516] [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: 04/13/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Bruton's tyrosine kinase (BTK), a non-receptor tyrosine kinase crucial for B cell development and function, acts downstream of the B cell receptor (BCR) in the BCR pathway. Other kinases involved downstream of the BCR besides BTK such as Syk, Lyn, PI3K, and Mitogen-activated protein (MAP) kinases also play roles in relaying signals from the BCR to provide pro-survival, activation, and proliferation cues. BTK signaling is implicated in various B-cell lymphomas such as mantle cell lymphoma, Waldenström Macroglobulinemia, follicular lymphoma, and diffuse large B cell lymphoma, leading to the development of transformative treatments like ibrutinib, the first-in-class covalent BTK inhibitor, and pirtobrutinib, the first-in-class noncovalent BTK inhibitor. However, kinase-deficient mutations C481F, C481Y, C481R, and L528W in the BTK gene confer resistance to both covalent and non-covalent BTK inhibitors, facilitating B cell survival and lymphomagenesis despite kinase inactivation. Further studies have revealed BTK's non-catalytic scaffolding function, mediating the assembly and activation of proteins including Toll-like receptor 9 (TLR9), vascular cell adhesion protein 1 (VCAM-1), hematopoietic cell kinase (HCK), and integrin-linked kinase (ILK). This non-enzymatic role promotes cell survival and proliferation independently of kinase activity. Understanding BTK's dual roles unveils opportunities for therapeutics targeting its scaffolding function, promising advancements in disrupting lymphomagenesis and refining B cell lymphoma treatments.
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Affiliation(s)
- Shefali Mehra
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
| | - Miah Nicholls
- College of Arts and Sciences, University of Miami, Coral Gables, FL 33146, USA;
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
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3
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Mao W, Vandecan NM, Bingham CR, Tsang PK, Ulintz P, Sexton R, Bochar DA, Merajver SD, Soellner MB. Selective and Potent PROTAC Degraders of c-Src Kinase. ACS Chem Biol 2024; 19:110-116. [PMID: 38113191 DOI: 10.1021/acschembio.3c00548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Using dasatinib linked to E3 ligase ligands, we identified a potent and selective dual Csk/c-Src PROTAC degrader. We then replaced dasatinib, the c-Src-directed ligand, with a conformation-selective analogue that stabilizes the αC-helix-out conformation of c-Src. Using the αC-helix-out ligand, we identified a PROTAC that is potent and selective for c-Src. We demonstrated a high degree of catalysis with our c-Src PROTACs. Using our c-Src PROTACs, we identified pharmacological advantages of c-Src degradation compared to inhibition with respect to cancer cell proliferation.
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Affiliation(s)
- Wuxiang Mao
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Nathalie M Vandecan
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Christopher R Bingham
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Pui Ki Tsang
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Peter Ulintz
- Department of Internal Medicine, University of Michigan, 1500 E. Medical Avenue, Ann Arbor, Michigan 48109, United States
| | - Rachel Sexton
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Daniel A Bochar
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
| | - Sofia D Merajver
- Department of Internal Medicine, University of Michigan, 1500 E. Medical Avenue, Ann Arbor, Michigan 48109, United States
| | - Matthew B Soellner
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, United States
- Department of Internal Medicine, University of Michigan, 1500 E. Medical Avenue, Ann Arbor, Michigan 48109, United States
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4
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Gormal RS, Martinez-Marmol R, Brooks AJ, Meunier FA. Location, location, location: Protein kinase nanoclustering for optimised signalling output. eLife 2024; 13:e93902. [PMID: 38206309 PMCID: PMC10783869 DOI: 10.7554/elife.93902] [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: 10/24/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Protein kinases (PKs) are proteins at the core of cellular signalling and are thereby responsible for most cellular physiological processes and their regulations. As for all intracellular proteins, PKs are subjected to Brownian thermal energy that tends to homogenise their distribution throughout the volume of the cell. To access their substrates and perform their critical functions, PK localisation is therefore tightly regulated in space and time, relying upon a range of clustering mechanisms. These include post-translational modifications, protein-protein and protein-lipid interactions, as well as liquid-liquid phase separation, allowing spatial restriction and ultimately regulating access to their substrates. In this review, we will focus on key mechanisms mediating PK nanoclustering in physiological and pathophysiological processes. We propose that PK nanoclusters act as a cellular quantal unit of signalling output capable of integration and regulation in space and time. We will specifically outline the various super-resolution microscopy approaches currently used to elucidate the composition and mechanisms driving PK nanoscale clustering and explore the pathological consequences of altered kinase clustering in the context of neurodegenerative disorders, inflammation, and cancer.
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Affiliation(s)
- Rachel S Gormal
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
| | - Ramon Martinez-Marmol
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
| | - Andrew J Brooks
- Frazer Institute, The University of QueenslandWoolloongabbaAustralia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of QueenslandBrisbaneAustralia
- School of Biomedical Sciences, The University of QueenslandSt LuciaAustralia
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5
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Scott KA, Kojima H, Ropek N, Warren CD, Zhang TL, Hogg SJ, Webster C, Zhang X, Rahman J, Melillo B, Cravatt BF, Lyu J, Abdel-Wahab O, Vinogradova EV. Covalent Targeting of Splicing in T Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572199. [PMID: 38187674 PMCID: PMC10769204 DOI: 10.1101/2023.12.18.572199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Despite significant interest in therapeutic targeting of splicing, few chemical probes are available for the proteins involved in splicing. Here, we show that elaborated stereoisomeric acrylamide chemical probe EV96 and its analogues lead to a selective T cell state-dependent loss of interleukin 2-inducible T cell kinase (ITK) by targeting one of the core splicing factors SF3B1. Mechanistic investigations suggest that the state-dependency stems from a combination of differential protein turnover rates and availability of functional mRNA pools that can be depleted due to extensive alternative splicing. We further introduce a comprehensive list of proteins involved in splicing and leverage both cysteine- and protein-directed activity-based protein profiling (ABPP) data with electrophilic scout fragments to demonstrate covalent ligandability for many classes of splicing factors and splicing regulators in primary human T cells. Taken together, our findings show how chemical perturbation of splicing can lead to immune state-dependent changes in protein expression and provide evidence for the broad potential to target splicing factors with covalent chemistry.
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6
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Pegram L, Riccardi D, Ahn N. Activation Loop Plasticity and Active Site Coupling in the MAP Kinase, ERK2. J Mol Biol 2023; 435:168309. [PMID: 37806554 PMCID: PMC10676806 DOI: 10.1016/j.jmb.2023.168309] [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: 04/15/2023] [Revised: 09/03/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
Previous studies of the protein kinase, ERK2, using NMR and hydrogen-exchange measurements have shown changes in dynamics accompanying its activation by phosphorylation. However, knowledge about the conformational motions involved is incomplete. Here, we examined ERK2 using long conventional molecular dynamics (MD) simulations starting from crystal structures of phosphorylated (2P) and unphosphorylated (0P) forms. Individual trajectories were run for (5 to 25) μs, totaling 727 μs. The results show unexpected flexibility of the A-loop, with multiple long-lived (>5 μs) conformational states in both 2P- and 0P-ERK2. Differential contact network and principal component analyses reveal coupling between the A-loop fold and active site dynamics, with evidence for conformational selection in the kinase core of 2P-ERK2 but not 0P-ERK2. Simulations of 2P-ERK2 show A-loop states corresponding to restrained dynamics within the N-lobe, including regions around catalytic residues. One A-loop conformer forms lasting interactions with the L16 segment, leading to reduced RMSF and greater compaction in the active site. By contrast, simulations of 0P-ERK2 reveal excursions of A-loop residues away from the C-lobe, leading to greater active site mobility. Thus, the A-loop in ERK2 switches between distinct conformations that reflect coupling with the active site, possibly via the L16 segment. Crystal packing interactions suggest that lattice contacts with the A-loop may restrain its structural variation in X-ray structures of ERK2. The novel conformational states identified by MD expand our understanding of ERK2 regulation, by linking the activated state of the kinase to reduced dynamics and greater compaction surrounding the catalytic site.
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Affiliation(s)
- Laurel Pegram
- Department of Biochemistry, University of Colorado, Boulder, CO 80305, USA
| | - Demian Riccardi
- Thermodynamics Research Center, Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, CO, USA
| | - Natalie Ahn
- Department of Biochemistry, University of Colorado, Boulder, CO 80305, USA.
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7
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Rivoal M, Dubuquoy L, Millet R, Leleu-Chavain N. Receptor Interacting Ser/Thr-Protein Kinase 2 as a New Therapeutic Target. J Med Chem 2023; 66:14391-14410. [PMID: 37857324 DOI: 10.1021/acs.jmedchem.3c00593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Receptor interacting serine/threonine protein kinase 2 (RIPK2) is a downstream signaling molecule essential for the activation of several innate immune receptors, including the NOD-like receptors (NOD1 and NOD2). Recognition of pathogen-associated molecular pattern proteins by NOD1/2 leads to their interaction with RIPK2, which induces release of pro-inflammatory cytokines through the activation of NF-κB and MAPK pathways, among others. Thus, RIPK2 has emerged as a key mediator of intracellular signal transduction and represents a new potential therapeutic target for the treatment of various conditions, including inflammatory diseases and cancer. In this Perspective, first, an overview of the mechanisms that underlie RIPK2 function will be presented along with its role in several diseases. Then, the existing inhibitors that target RIPK2 and different therapeutic strategies will be reviewed, followed by a discussion on current challenges and outlook.
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Affiliation(s)
- Morgane Rivoal
- Inserm, U1286 - INFINITE - Institute for Translational Research in Inflammation, University of Lille, F-59000 Lille, France
| | - Laurent Dubuquoy
- Inserm, U1286 - INFINITE - Institute for Translational Research in Inflammation, University of Lille, F-59000 Lille, France
| | - Régis Millet
- Inserm, U1286 - INFINITE - Institute for Translational Research in Inflammation, University of Lille, F-59000 Lille, France
| | - Natascha Leleu-Chavain
- Inserm, U1286 - INFINITE - Institute for Translational Research in Inflammation, University of Lille, F-59000 Lille, France
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8
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Tian L, Guo T, Wu F, Bai R, Ai S, Wang H, Song Y, Zhu M, Jiang Y, Ma S, Zhuang X, Guo S. The pseudoenzyme ADPRHL1 affects cardiac function by regulating the ROCK pathway. Stem Cell Res Ther 2023; 14:309. [PMID: 37880701 PMCID: PMC10601310 DOI: 10.1186/s13287-023-03507-0] [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: 08/23/2022] [Accepted: 09/21/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Pseudoenzymes, catalytically deficient variants of active enzymes, have a wide range of regulatory functions. ADP-ribosylhydrolase-like 1 (ADPRHL1), a pseudoenzyme belonging to a small group of ADP-ribosylhydrolase enzymes that lacks the amino acid residues necessary for catalytic activity, may have a significant role in heart development based on accumulating evidence. However, the specific function of ADPRHL1 in this process has not been elucidated. To investigate the role of ADPRHL1 in the heart, we generated the first in vitro human embryonic stem cell model with an ADPRHL1 knockout. METHOD Using the CRISPR/Cas9 system, we generated ADPRHL1 knockout in the human embryonic stem cell (hESC) H9 line. The cells were differentiated into cardiomyocytes using a chemically defined and xeno-free method. We employed confocal laser microscopy to detect calcium transients and microelectrode array (MEA) to assess the electrophysiological activity of ADPRHL1 deficiency cardiomyocytes. Additionally, we investigated the cellular mechanism of ADPRHL1 by Bulk RNA sequencing and western blot. RESULTS The results indicate that the absence of ADPRHL1 in cardiomyocytes led to adhered abnormally, as well as perturbations in calcium transients and electrophysiological activity. We also revealed that disruption of focal adhesion formation in these cardiomyocytes was due to an excessive upregulation of the ROCK-myosin II pathway. Notably, inhibition of ROCK and myosin II effectively restores focal adhesions in ADPRHL1-deficient cardiomyocytes and improved electrical conduction and calcium activity. CONCLUSIONS Our findings demonstrate that ADPRHL1 plays a critical role in maintaining the proper function of cardiomyocytes by regulating the ROCK-myosin II pathway, suggesting that it may serve as a potential drug target for the treatment of ADPRHL1-related diseases.
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Affiliation(s)
- Lei Tian
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
- Department of Nephrology, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, 23 Meishuguanhou Street, Dongcheng District, Beijing, 100010, China
| | - Tianwei Guo
- Beijing Laboratory for Cardiovascular Precision Medicine, The Key Laboratory of Biomedical Engineering for Cardiovascular Disease Research, Ministry of Education, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Fujian Wu
- Translational Medicine Collaborative Innovation Center, The Second Clinical Medical College (Shenzhen People's Hospital), Jinan University, Shenzhen, 518020, China
- Post-Doctoral Scientific Research Station of Basic Medicine, Jinan University, Guangzhou, 510632, China
| | - Rui Bai
- Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, 518057, Guangdong Province, China
| | - Sinan Ai
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Hongyue Wang
- Department of Cardiology, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beilishi Rd 167, Xicheng District, Beijing City, 100037, China
| | - Yuanxiu Song
- Department of Emergency, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 310003, China
| | - Min Zhu
- Department of Cardiology, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beilishi Rd 167, Xicheng District, Beijing City, 100037, China
| | - Youxu Jiang
- Department of Cardiology, The Second Affiliated Hospital of Zhengzhou University, Jingba Road, Zhengzhou, 450053, China
| | - Shuhong Ma
- Department of Cardiology, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beilishi Rd 167, Xicheng District, Beijing City, 100037, China
| | - Xiaofeng Zhuang
- Department of Cardiology, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Fuwai Hospital, Beilishi Rd 167, Xicheng District, Beijing City, 100037, China.
| | - Shuzhen Guo
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China.
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9
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Martin-Vega A, Cobb MH. Navigating the ERK1/2 MAPK Cascade. Biomolecules 2023; 13:1555. [PMID: 37892237 PMCID: PMC10605237 DOI: 10.3390/biom13101555] [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: 09/30/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
The RAS-ERK pathway is a fundamental signaling cascade crucial for many biological processes including proliferation, cell cycle control, growth, and survival; common across all cell types. Notably, ERK1/2 are implicated in specific processes in a context-dependent manner as in stem cells and pancreatic β-cells. Alterations in the different components of this cascade result in dysregulation of the effector kinases ERK1/2 which communicate with hundreds of substrates. Aberrant activation of the pathway contributes to a range of disorders, including cancer. This review provides an overview of the structure, activation, regulation, and mutational frequency of the different tiers of the cascade; with a particular focus on ERK1/2. We highlight the importance of scaffold proteins that contribute to kinase localization and coordinate interaction dynamics of the kinases with substrates, activators, and inhibitors. Additionally, we explore innovative therapeutic approaches emphasizing promising avenues in this field.
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Affiliation(s)
- Ana Martin-Vega
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
| | - Melanie H. Cobb
- Department of Pharmacology, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA;
- Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, 6001 Forest Park Rd., Dallas, TX 75390, USA
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10
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Bradley D, Hogrebe A, Dandage R, Dubé AK, Leutert M, Dionne U, Chang A, Villén J, Landry CR. The fitness cost of spurious phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.08.561337. [PMID: 37873463 PMCID: PMC10592693 DOI: 10.1101/2023.10.08.561337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known, but quantifying this is required to understand the constraints faced by cell systems as they evolve. Here, we use the model organism S. cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, most of the resulting tyrosine phosphorylation is spurious. This provides a suitable system to measure the impact of artificial protein interactions on fitness. We engineered 44 yeast strains each expressing a tyrosine kinase, and quantitatively analysed their phosphoproteomes. This analysis resulted in ~30,000 phosphosites mapping to ~3,500 proteins. Examination of the fitness costs in each strain revealed a strong correlation between the number of spurious pY sites and decreased growth. Moreover, the analysis of pY effects on protein structure and on protein function revealed over 1000 pY events that we predict to be deleterious. However, we also find that a large number of the spurious pY sites have a negligible effect on fitness, possibly because of their low stoichiometry. This result is consistent with our evolutionary analyses demonstrating a lack of phosphotyrosine counter-selection in species with bona fide tyrosine kinases. Taken together, our results suggest that, alongside the risk for toxicity, the cell can tolerate a large degree of non-functional crosstalk as interaction networks evolve.
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Affiliation(s)
- David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexander Hogrebe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rohan Dandage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
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11
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Green JR, Mahalingaiah PKS, Gopalakrishnan SM, Liguori MJ, Mittelstadt SW, Blomme EAG, Van Vleet TR. Off-target pharmacological activity at various kinases: Potential functional and pathological side effects. J Pharmacol Toxicol Methods 2023; 123:107468. [PMID: 37553032 DOI: 10.1016/j.vascn.2023.107468] [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: 03/23/2023] [Revised: 06/16/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
In drug discovery, during the lead optimization and candidate characterization stages, novel small molecules are frequently evaluated in a battery of in vitro pharmacology assays to identify potential unintended, off-target interactions with various receptors, transporters, ion channels, and enzymes, including kinases. Furthermore, these screening panels may also provide utility at later stages of development to provide a mechanistic understanding of unexpected safety findings. Here, we present a compendium of the most likely functional and pathological outcomes associated with interaction(s) to a panel of 95 kinases based on an extensive curation of the scientific literature. This panel of kinases was designed by AbbVie based on safety-related data extracted from the literature, as well as from over 20 years of institutional knowledge generated from discovery efforts. For each kinase, the scientific literature was reviewed using online databases and the most often reported functional and pathological effects were summarized. This work should serve as a practical guide for small molecule drug discovery scientists and clinical investigators to predict and/or interpret adverse effects related to pharmacological interactions with these kinases.
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Affiliation(s)
- Jonathon R Green
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States.
| | | | - Sujatha M Gopalakrishnan
- Drug Discovery Science and Technology, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Michael J Liguori
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Scott W Mittelstadt
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Eric A G Blomme
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
| | - Terry R Van Vleet
- Departments of Preclinical Safety, AbbVie, 1 North Waukegan Road, North Chicago, IL 60064, United States
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12
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Santos M, Hwang JW, Bedford MT. CARM1 arginine methyltransferase as a therapeutic target for cancer. J Biol Chem 2023; 299:105124. [PMID: 37536629 PMCID: PMC10474102 DOI: 10.1016/j.jbc.2023.105124] [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: 05/30/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023] Open
Abstract
Coactivator-associated arginine methyltransferase 1 (CARM1) is an arginine methyltransferase that posttranslationally modifies proteins that regulate multiple levels of RNA production and processing. Its substrates include histones, transcription factors, coregulators of transcription, and splicing factors. CARM1 is overexpressed in many different cancer types, and often promotes transcription factor programs that are co-opted as drivers of the transformed cell state, a process known as transcription factor addiction. Targeting these oncogenic transcription factor pathways is difficult but could be addressed by removing the activity of the key coactivators on which they rely. CARM1 is ubiquitously expressed, and its KO is less detrimental in embryonic development than deletion of the arginine methyltransferases protein arginine methyltransferase 1 and protein arginine methyltransferase 5, suggesting that therapeutic targeting of CARM1 may be well tolerated. Here, we will summarize the normal in vivo functions of CARM1 that have been gleaned from mouse studies, expand on the transcriptional pathways that are regulated by CARM1, and finally highlight recent studies that have identified oncogenic properties of CARM1 in different biological settings. This review is meant to kindle an interest in the development of human drug therapies targeting CARM1, as there are currently no CARM1 inhibitors available for use in clinical trials.
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Affiliation(s)
- Margarida Santos
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| | - Jee Won Hwang
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark T Bedford
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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13
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Sultana S, Abdullah M, Li J, Hochstrasser M, Kachroo AH. Species-specific protein-protein interactions govern the humanization of the 20S proteasome in yeast. Genetics 2023; 225:iyad117. [PMID: 37364278 PMCID: PMC10471208 DOI: 10.1093/genetics/iyad117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Yeast and humans share thousands of genes despite a billion years of evolutionary divergence. While many human genes can functionally replace their yeast counterparts, nearly half of the tested shared genes cannot. For example, most yeast proteasome subunits are "humanizable," except subunits comprising the β-ring core, including β2c (HsPSMB7, a constitutive proteasome subunit). We developed a high-throughput pipeline to humanize yeast proteasomes by generating a large library of Hsβ2c mutants and screening them for complementation of a yeast β2 (ScPup1) knockout. Variants capable of replacing ScPup1 included (1) those impacting local protein-protein interactions (PPIs), with most affecting interactions between the β2c C-terminal tail and the adjacent β3 subunit, and (2) those affecting β2c proteolytic activity. Exchanging the full-length tail of human β2c with that of ScPup1 enabled complementation. Moreover, wild-type human β2c could replace yeast β2 if human β3 was also provided. Unexpectedly, yeast proteasomes bearing a catalytically inactive HsPSMB7-T44A variant that blocked precursor autoprocessing were viable, suggesting an intact propeptide stabilizes late assembly intermediates. In contrast, similar modifications in human β2i (HsPSMB10), an immunoproteasome subunit and the co-ortholog of yeast β2, do not enable complementation in yeast, suggesting distinct interactions are involved in human immunoproteasome core assembly. Broadly, our data reveal roles for specific PPIs governing functional replaceability across vast evolutionary distances.
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Affiliation(s)
- Sarmin Sultana
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC H3G 1M8, Canada
| | - Mudabir Abdullah
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC H3G 1M8, Canada
| | - Jianhui Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Aashiq H Kachroo
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC H3G 1M8, Canada
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14
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Yeh CY, Wang YS, Takahashi Y, Kuusk K, Paul K, Arjus T, Yadlos O, Schroeder JI, Ilves I, Garcia-Sosa AT, Kollist H. MPK12 in stomatal CO 2 signaling: function beyond its kinase activity. THE NEW PHYTOLOGIST 2023; 239:146-158. [PMID: 36978283 PMCID: PMC10247450 DOI: 10.1111/nph.18913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/21/2023] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is a major molecular switch involved in the regulation of stomatal opening and closure. Previous research defined interaction between MAP kinase 12 and Raf-like kinase HT1 as a required step for stomatal movements caused by changes in CO2 concentration. However, whether MPK12 kinase activity is required for regulation of CO2 -induced stomatal responses warrants in-depth investigation. We apply genetic, biochemical, and structural modeling approaches to examining the noncatalytic role of MPK12 in guard cell CO2 signaling that relies on allosteric inhibition of HT1. We show that CO2 /HCO3 - -enhanced MPK12 interaction with HT1 is independent of its kinase activity. By analyzing gas exchange of plant lines expressing various kinase-dead and constitutively active versions of MPK12 in a plant line where MPK12 is deleted, we confirmed that CO2 -dependent stomatal responses rely on MPK12's ability to bind to HT1, but not its kinase activity. We also demonstrate that purified MPK12 and HT1 proteins form a heterodimer in the presence of CO2 /HCO3 - and present structural modeling that explains the MPK12:HT1 interaction interface. These data add to the model that MPK12 kinase-activity-independent interaction with HT1 functions as a molecular switch by which guard cells sense changes in atmospheric CO2 concentration.
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Affiliation(s)
- Chung-Yueh Yeh
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Yuh-Shuh Wang
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Yohei Takahashi
- Institute of Transformative Bio-Molecules, Nagoya University, Furocho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Katarina Kuusk
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Karnelia Paul
- School of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA 92093-0116, USA
| | - Triinu Arjus
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Oleksii Yadlos
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Julian I. Schroeder
- School of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA 92093-0116, USA
| | - Ivar Ilves
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | | | - Hannes Kollist
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
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15
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Torosyan H, Paul MD, Forget A, Lo M, Diwanji D, Pawłowski K, Krogan NJ, Jura N, Verba KA. Structural insights into regulation of the PEAK3 pseudokinase scaffold by 14-3-3. Nat Commun 2023; 14:3543. [PMID: 37336883 PMCID: PMC10279700 DOI: 10.1038/s41467-023-38864-0] [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: 08/24/2022] [Accepted: 05/16/2023] [Indexed: 06/21/2023] Open
Abstract
PEAK pseudokinases are molecular scaffolds which dimerize to regulate cell migration, morphology, and proliferation, as well as cancer progression. The mechanistic role dimerization plays in PEAK scaffolding remains unclear, as there are no structures of PEAKs in complex with their interactors. Here, we report the cryo-EM structure of dimeric PEAK3 in complex with an endogenous 14-3-3 heterodimer. Our structure reveals an asymmetric binding mode between PEAK3 and 14-3-3 stabilized by one pseudokinase domain and the SHED domain of the PEAK3 dimer. The binding interface contains a canonical phosphosite-dependent primary interaction and a unique secondary interaction not observed in previous structures of 14-3-3/client complexes. Additionally, we show that PKD regulates PEAK3/14-3-3 binding, which when prevented leads to PEAK3 nuclear enrichment and distinct protein-protein interactions. Altogether, our data demonstrate that PEAK3 dimerization forms an unusual secondary interface for 14-3-3 binding, facilitating 14-3-3 regulation of PEAK3 localization and interactome diversity.
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Affiliation(s)
- Hayarpi Torosyan
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Michael D Paul
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Antoine Forget
- Quantitative Biosciences Institute (QBI), 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
| | - Megan Lo
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Devan Diwanji
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biochemistry and Microbiology, Warsaw University of Life Sciences, 02-787, Warszawa, Poland
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), 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
- J. David Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA.
- Quantitative Biosciences Institute (QBI), 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.
| | - Kliment A Verba
- Quantitative Biosciences Institute (QBI), 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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16
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Strine MS, Cai WL, Wei J, Alfajaro MM, Filler RB, Biering SB, Sarnik S, Chow RD, Patil A, Cervantes KS, Collings CK, DeWeirdt PC, Hanna RE, Schofield K, Hulme C, Konermann S, Doench JG, Hsu PD, Kadoch C, Yan Q, Wilen CB. DYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent manner. PLoS Biol 2023; 21:e3002097. [PMID: 37310920 PMCID: PMC10263356 DOI: 10.1371/journal.pbio.3002097] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/29/2023] [Indexed: 06/15/2023] Open
Abstract
Identifying host genes essential for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has the potential to reveal novel drug targets and further our understanding of Coronavirus Disease 2019 (COVID-19). We previously performed a genome-wide CRISPR/Cas9 screen to identify proviral host factors for highly pathogenic human coronaviruses. Few host factors were required by diverse coronaviruses across multiple cell types, but DYRK1A was one such exception. Although its role in coronavirus infection was previously undescribed, DYRK1A encodes Dual Specificity Tyrosine Phosphorylation Regulated Kinase 1A and is known to regulate cell proliferation and neuronal development. Here, we demonstrate that DYRK1A regulates ACE2 and DPP4 transcription independent of its catalytic kinase function to support SARS-CoV, SARS-CoV-2, and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) entry. We show that DYRK1A promotes DNA accessibility at the ACE2 promoter and a putative distal enhancer, facilitating transcription and gene expression. Finally, we validate that the proviral activity of DYRK1A is conserved across species using cells of nonhuman primate and human origin. In summary, we report that DYRK1A is a novel regulator of ACE2 and DPP4 expression that may dictate susceptibility to multiple highly pathogenic human coronaviruses.
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Affiliation(s)
- Madison S. Strine
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Wesley L. Cai
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Jin Wei
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Mia Madel Alfajaro
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Renata B. Filler
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Scott B. Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Sylvia Sarnik
- University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Ryan D. Chow
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Ajinkya Patil
- Department of Pediatric Oncology, Dana–Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kasey S. Cervantes
- Department of Pediatric Oncology, Dana–Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Clayton K. Collings
- Department of Pediatric Oncology, Dana–Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Peter C. DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Ruth E. Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kevin Schofield
- Department of Chemistry and Biochemistry, College of Science, The University of Arizona, Tucson, Arizona, United States of America
| | - Christopher Hulme
- Department of Chemistry and Biochemistry, College of Science, The University of Arizona, Tucson, Arizona, United States of America
- Division of Drug Discovery and Development, Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona, United States of America
| | - Silvana Konermann
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Arc Institute, Palo Alto, California, United States of America
| | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Patrick D. Hsu
- Arc Institute, Palo Alto, California, United States of America
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, United States of America
- Center for Computational Biology, University of California, Berkeley, California, United States of America
| | - Cigall Kadoch
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Pediatric Oncology, Dana–Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Craig B. Wilen
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, United States of America
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17
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Pegram L, Riccardi D, Ahn N. Activation loop plasticity and active site coupling in the MAP kinase, ERK2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.537040. [PMID: 37090603 PMCID: PMC10120733 DOI: 10.1101/2023.04.15.537040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Changes in the dynamics of the protein kinase, ERK2, have been shown to accompany its activation by dual phosphorylation. However, our knowledge about the conformational changes represented by these motions is incomplete. Previous NMR relaxation dispersion studies showed that active, dual-phosphorylated ERK2 undergoes global exchange between at least two energetically similar conformations. These findings, combined with measurements by hydrogen exchange mass spectrometry (HX-MS), suggested that the global conformational exchange involves motions of the activation loop (A-loop) that are coupled to regions surrounding the kinase active site. In order to better understand the contribution of dynamics to the activation of ERK2, we applied long conventional molecular dynamics (MD) simulations starting from crystal structures of active, phosphorylated (2P), and inactive, unphosphorylated (0P) ERK2. Individual trajectories were run for (5 to 25) µ s and totaled 727 µ s. The results showed that the A-loop is unexpectedly flexible in both 2P- and 0P-ERK2, and able to adopt multiple long-lived (>5 µ s) conformational states. Simulations starting from the X-ray structure of 2P-ERK2 (2ERK) revealed A-loop states corresponding to restrained dynamics within the N-lobe, including regions surrounding catalytic residues. One A-loop conformer forms lasting interactions with the C-terminal L16 segment and shows reduced RMSF and greater compaction in the active site. By contrast, simulations starting from the most common X-ray conformation of 0P-ERK2 (5UMO) reveal frequent excursions of A-loop residues away from a C-lobe docking site pocket and towards a new state that shows greater dynamics in the N-lobe and disorganization around the active site. Thus, the A-loop in ERK2 appears to switch between distinct conformational states that reflect allosteric coupling with the active site, likely occurring via the L16 segment. Analyses of crystal packing interactions across many structural datasets suggest that the A-loop observed in X-ray structures of ERK2 may be driven by lattice contacts and less representative of the solution structure. The novel conformational states identified by MD expand our understanding of ERK2 regulation, by linking the activated state of the kinase to reduced dynamics and greater compaction surrounding the catalytic site.
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18
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The functions and molecular mechanisms of Tribbles homolog 3 (TRIB3) implicated in the pathophysiology of cancer. Int Immunopharmacol 2023; 114:109581. [PMID: 36527874 DOI: 10.1016/j.intimp.2022.109581] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/21/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Currently, cancer ranks as the second leading cause of death worldwide, and at the same time, the burden of cancer continues to increase. The underlying molecular pathways involved in the initiation and development of cancer are the subject of considerable research worldwide. Further understanding of these pathways may lead to new cancer treatments. Growing data suggest that Tribble's homolog 3 (TRIB3) is essential in oncogenesis in many types of cancer. The mammalian tribbles family's proteins regulate various cellular and physiological functions, such as the cell cycle, stress response, signal transduction, propagation, development, differentiation, immunity, inflammatory processes, and metabolism. To exert their activities, Tribbles proteins must alter key signaling pathways, including the mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3 kinase (PI3K)/AKT pathways. Recent evidence supports that TRIB3 dysregulation has been linked to various diseases, including tumor development and chemoresistance. It has been speculated that TRIB3 may either promote or inhibit the onset and development of cancer. However, it is still unclear how TRIB3 performs this dual function in cancer. In this review, we present and discuss the most recent data on the role of TRIB3 in cancer pathophysiology and chemoresistance. Furthermore, we describe in detail the molecular mechanism TRIB3 regulates in cancer.
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19
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Levillayer L, Cassonnet P, Declercq M, Santos MD, Lebreton L, Danezi K, Demeret C, Sakuntabhai A, Jacob Y, Bureau JF. SKAP2 Modular Organization Differently Recognizes SRC Kinases Depending on Their Activation Status and Localization. Mol Cell Proteomics 2022; 22:100451. [PMID: 36423812 PMCID: PMC9792355 DOI: 10.1016/j.mcpro.2022.100451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/12/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Dimerization of SRC kinase adaptor phosphoprotein 2 (SKAP2) induces an increase of binding for most SRC kinases suggesting a fine-tuning with transphosphorylation for kinase activation. This work addresses the molecular basis of SKAP2-mediated SRC kinase regulation through the lens of their interaction capacities. By combining a luciferase complementation assay and extensive site-directed mutagenesis, we demonstrated that SKAP2 interacts with SRC kinases through a modular organization depending both on their phosphorylation-dependent activation and subcellular localization. SKAP2 contains three interacting modules consisting in the dimerization domain, the SRC homology 3 (SH3) domain, and the second interdomain located between the Pleckstrin homology and the SH3 domains. Functionally, the dimerization domain is necessary and sufficient to bind to most activated and myristyl SRC kinases. In contrast, the three modules are necessary to bind SRC kinases at their steady state. The Pleckstrin homology and SH3 domains of SKAP2 as well as tyrosines located in the interdomains modulate these interactions. Analysis of mutants of the SRC kinase family member hematopoietic cell kinase supports this model and shows the role of two residues, Y390 and K7, on its degradation following activation. In this article, we show that a modular architecture of SKAP2 drives its interaction with SRC kinases, with the binding capacity of each module depending on both their localization and phosphorylation state activation. This work opens new perspectives on the molecular mechanisms of SRC kinases activation, which could have significant therapeutic impact.
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Affiliation(s)
- Laurine Levillayer
- Unité de Génétique Fonctionnelle des Maladies Infectieuses (GFMI), CNRS UMR 2000, Institut Pasteur, Université de Paris, Paris, France
| | - Patricia Cassonnet
- Unité de Génétique Moléculaire des Virus à ARN (GMVR), CNRS UMR3569, Institut Pasteur, Université de Paris, Paris, France
| | - Marion Declercq
- Unité de Génétique Moléculaire des Virus à ARN (GMVR), CNRS UMR3569, Institut Pasteur, Université de Paris, Paris, France
| | - Mélanie Dos Santos
- Unité de Génétique Moléculaire des Virus à ARN (GMVR), CNRS UMR3569, Institut Pasteur, Université de Paris, Paris, France
| | - Louis Lebreton
- Unité de Génétique Fonctionnelle des Maladies Infectieuses (GFMI), CNRS UMR 2000, Institut Pasteur, Université de Paris, Paris, France
| | - Katerina Danezi
- Unité de Génétique Fonctionnelle des Maladies Infectieuses (GFMI), CNRS UMR 2000, Institut Pasteur, Université de Paris, Paris, France
| | - Caroline Demeret
- Unité de Génétique Moléculaire des Virus à ARN (GMVR), CNRS UMR3569, Institut Pasteur, Université de Paris, Paris, France
| | - Anavaj Sakuntabhai
- Unité de Génétique Fonctionnelle des Maladies Infectieuses (GFMI), CNRS UMR 2000, Institut Pasteur, Université de Paris, Paris, France
| | - Yves Jacob
- Unité de Génétique Moléculaire des Virus à ARN (GMVR), CNRS UMR3569, Institut Pasteur, Université de Paris, Paris, France
| | - Jean-François Bureau
- Unité de Génétique Fonctionnelle des Maladies Infectieuses (GFMI), CNRS UMR 2000, Institut Pasteur, Université de Paris, Paris, France,For correspondence: Jean-François Bureau
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20
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Sheetz JB, Lemmon MA. Looking lively: emerging principles of pseudokinase signaling. Trends Biochem Sci 2022; 47:875-891. [PMID: 35585008 PMCID: PMC9464697 DOI: 10.1016/j.tibs.2022.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/06/2022] [Accepted: 04/21/2022] [Indexed: 10/18/2022]
Abstract
Progress towards understanding catalytically 'dead' protein kinases - pseudokinases - in biology and disease has hastened over the past decade. An especially lively area for structural biology, pseudokinases appear to be strikingly similar to their kinase relatives, despite lacking key catalytic residues. Distinct active- and inactive-like conformation states, which are crucial for regulating bona fide protein kinases, are conserved in pseudokinases and appear to be essential for function. We discuss recent structural data on conformational transitions and nucleotide binding by pseudokinases, from which some common principles emerge. In both pseudokinases and bona fide kinases, a conformational toggle appears to control the ability to interact with signaling effectors. We also discuss how biasing this conformational toggle may provide opportunities to target pseudokinases pharmacologically in disease.
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Affiliation(s)
- Joshua B Sheetz
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06505, USA; Yale Cancer Biology Institute, Yale West Campus, West Haven, CT 06516, USA.
| | - Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06505, USA; Yale Cancer Biology Institute, Yale West Campus, West Haven, CT 06516, USA.
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21
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Jamieson SA, Pudjihartono M, Horne CR, Viloria JS, Dunlop JL, McMillan HD, Day RC, Keeshan K, Murphy JM, Mace PD. Nanobodies identify an activated state of the TRIB2 pseudokinase. Structure 2022; 30:1518-1529.e5. [PMID: 36108635 DOI: 10.1016/j.str.2022.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/02/2022] [Accepted: 08/19/2022] [Indexed: 12/23/2022]
Abstract
Tribbles proteins (TRIB1-3) are pseudokinases that recruit substrates to the COP1 ubiquitin ligase. TRIB2 was the first Tribbles ortholog to be implicated as a myeloid leukemia oncogene, because it recruits the C/EBPα transcription factor for ubiquitination by COP1. Here we report identification of nanobodies that bind the TRIB2 pseudokinase domain with low nanomolar affinity. A crystal structure of the TRIB2-Nb4.103 complex identified the nanobody to bind the N-terminal lobe of TRIB2, enabling specific recognition of TRIB2 in an activated conformation that is similar to the C/EBPα-bound state of TRIB1. Characterization in solution revealed that Nb4.103 can stabilize a TRIB2 pseudokinase domain dimer in a face-to-face manner. Conversely, a distinct nanobody (Nb4.101) binds through a similar epitope but does not readily promote dimerization. In combination, this study identifies features of TRIB2 that could be exploited for the development of inhibitors and nanobody tools for future investigation of TRIB2 function.
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Affiliation(s)
- Sam A Jamieson
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Michael Pudjihartono
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Christopher R Horne
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | | | - Jessica L Dunlop
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Hamish D McMillan
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Robert C Day
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Karen Keeshan
- Paul O'Gorman Leukaemia Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, Scotland
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.
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22
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Yuan H, Zhu Y, Cheng Y, Hou J, Jin F, Li M, Jia W, Cheng Z, Xing H, Liu M, Han T. BTK kinase activity is dispensable for the survival of diffuse large B-cell lymphoma. J Biol Chem 2022; 298:102555. [PMID: 36183831 PMCID: PMC9636578 DOI: 10.1016/j.jbc.2022.102555] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/25/2022] Open
Abstract
Inhibitors targeting Bruton's tyrosine kinase (BTK) have revolutionized the treatment for various B-cell malignancies but are limited by acquired resistance after prolonged treatment as a result of mutations in BTK. Here, by a combination of structural modeling, in vitro assays, and deep phospho-tyrosine proteomics, we demonstrated that four clinically observed BTK mutations—C481F, C481Y, C481R, and L528W—inactivated BTK kinase activity both in vitro and in diffused large B-cell lymphoma (DLBCL) cells. Paradoxically, we found that DLBCL cells harboring kinase-inactive BTK exhibited intact B cell receptor (BCR) signaling, unperturbed transcription, and optimal cellular growth. Moreover, we determined that DLBCL cells with kinase-inactive BTK remained addicted to BCR signaling and were thus sensitive to targeted BTK degradation by the proteolysis-targeting chimera. By performing parallel genome-wide CRISPR-Cas9 screening in DLBCL cells with WT or kinase-inactive BTK, we discovered that DLBCL cells with kinase-inactive BTK displayed increased dependence on Toll-like receptor 9 (TLR9) for their growth and/or survival. Our study demonstrates that the kinase activity of BTK is not essential for oncogenic BCR signaling and suggests that BTK’s noncatalytic function is sufficient to sustain the survival of DLBCL.
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Affiliation(s)
- Hongwei Yuan
- College of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences, Beijing, China
| | - Yutong Zhu
- BeiGene (Beijing) Co, Ltd, Beijing, China
| | - Yalong Cheng
- College of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences, Beijing, China
| | | | | | | | - Wei Jia
- Deepkinase Co, Ltd, Beijing, China
| | | | | | - Mike Liu
- BeiGene (Beijing) Co, Ltd, Beijing, China
| | - Ting Han
- College of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences, Beijing, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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23
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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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24
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García-Marín J, Rodríguez-Puyol D, Vaquero JJ. Insight into the mechanism of molecular recognition between human Integrin-Linked Kinase and Cpd22 and its implication at atomic level. J Comput Aided Mol Des 2022; 36:575-589. [PMID: 35869378 PMCID: PMC9512720 DOI: 10.1007/s10822-022-00466-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/11/2022] [Indexed: 10/29/2022]
Abstract
AbsractPseudokinases have received increasing attention over the past decade because of their role in different physiological phenomena. Although pseudokinases lack several active-site residues, thereby hindering their catalytic activity, recent discoveries have shown that these proteins can play a role in intracellular signaling thanks to their non-catalytic functions. Integrin-linked kinase (ILK) was discovered more than two decades ago and was subsequently validated as a promising target for neoplastic diseases. Since then, only a few small-molecule inhibitors have been described, with the V-shaped pyrazole Cpd22 being the most interesting and characterized. However, little is known about its detailed mechanism of action at atomic level. In this study, using a combination of computational chemistry methods including PELE calculations, docking, molecular dynamics and experimental surface plasmon resonance, we were able to prove the direct binding of this molecule to ILK, thus providing the basis of its molecular recognition by the protein and the effect over its architecture. Our breakthroughs show that Cpd22 binding stabilizes the ILK domain by binding to the pseudo-active site in a similar way to the ATP, possibly modulating its scaffolding properties as pseudokinase. Moreover, our results explain the experimental observations obtained during Cpd22 development, thus paving the way to the development of new chemical probes and potential drugs.
Graphical abstract
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25
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Yi X, Wu J, Jiang H, Zhao Y, Mei J. Kinase expression enhances phenolic aldehydes conversion and ethanol fermentability of Zymomonas mobilis. Bioprocess Biosyst Eng 2022; 45:1319-1329. [PMID: 35786774 DOI: 10.1007/s00449-022-02747-3] [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: 03/28/2022] [Accepted: 06/11/2022] [Indexed: 11/26/2022]
Abstract
Kinases modulate the various physiological activities of microbial fermenting strains including the conversion of lignocellulose-derived phenolic aldehydes (4-hydroxyaldehyde, vanillin, and syringaldehyde). Here, we comprehensively investigated the gene transcriptional profiling of the kinases under the stress of phenolic aldehydes for ethanologenic Zymomonas mobilis using DNA microarray. Among 47 kinase genes, three genes of ZMO0003 (adenylylsulfate kinase), ZMO1162 (histidine kinase), and ZMO1391 (diacylglycerol kinase), were differentially expressed against 4-hydroxybenzaldehyde and vanillin, in which the overexpression of ZMO1162 promoted the phenolic aldehydes conversion and ethanol fermentability. The perturbance originated from plasmid-based expression of ZMO1162 gene contributed to a unique expression profiling of genome-encoding genes under all three phenolic aldehydes stress. Differentially expressed ribosome genes were predicted as one of the main contributors to phenolic aldehydes conversion and thus finally enhanced ethanol fermentability for Z. mobilis ZM4. The results provided an insight into the kinases on regulation of phenolic aldehydes conversion and ethanol fermentability for Z. mobilis ZM4, as well as the target object for rational design of robust biorefinery strains.
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Affiliation(s)
- Xia Yi
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, 17 Lufeng Road, Jiujiang, 332000, China.
- National-Local Joint Engineering Research Center for Biomass Refining and High-Quality Utilization, Changzhou University, Changzhou, 213164, China.
| | - Jianfang Wu
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, 17 Lufeng Road, Jiujiang, 332000, China
| | - He Jiang
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, 17 Lufeng Road, Jiujiang, 332000, China
| | - Yan Zhao
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, 17 Lufeng Road, Jiujiang, 332000, China
| | - Jun Mei
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, 17 Lufeng Road, Jiujiang, 332000, China
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26
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Lastun VL, Levet C, Freeman M. The mammalian rhomboid protein RHBDL4 protects against endoplasmic reticulum stress by regulating the morphology and distribution of ER sheets. J Biol Chem 2022; 298:101935. [PMID: 35436469 PMCID: PMC9136127 DOI: 10.1016/j.jbc.2022.101935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
In metazoans, the architecture of the endoplasmic reticulum (ER) differs between cell types and undergoes major changes throughout the cell cycle and according to physiological needs. Although much is known about how the different ER morphologies are generated and maintained, especially ER tubules, how context-dependent changes in ER shape and distribution are regulated and the factors involved are less well characterized, as are the factors that contribute to the positioning of the ER within the cell. By overexpression and KO experiments, we show that the levels of RHBDL4, an ER-resident rhomboid protease, modulate the shape and distribution of the ER, especially during conditions that require rapid changes in the ER sheet distribution, such as ER stress. We demonstrate that RHBDL4 interacts with cytoskeleton-linking membrane protein 63 (CLIMP-63), a protein involved in ER sheet stabilization, as well as with the cytoskeleton. Furthermore, we found that mice lacking RHBDL4 are sensitive to ER stress and develop liver steatosis, a phenotype associated with unresolved ER stress. Taken together, these data suggest a new physiological role for RHBDL4 and also imply that this function does not require its enzymatic activity.
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27
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Rangwala AM, Mingione VR, Georghiou G, Seeliger MA. Kinases on Double Duty: A Review of UniProtKB Annotated Bifunctionality within the Kinome. Biomolecules 2022; 12:biom12050685. [PMID: 35625613 PMCID: PMC9138534 DOI: 10.3390/biom12050685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 01/27/2023] Open
Abstract
Phosphorylation facilitates the regulation of all fundamental biological processes, which has triggered extensive research of protein kinases and their roles in human health and disease. In addition to their phosphotransferase activity, certain kinases have evolved to adopt additional catalytic functions, while others have completely lost all catalytic activity. We searched the Universal Protein Resource Knowledgebase (UniProtKB) database for bifunctional protein kinases and focused on kinases that are critical for bacterial and human cellular homeostasis. These kinases engage in diverse functional roles, ranging from environmental sensing and metabolic regulation to immune-host defense and cell cycle control. Herein, we describe their dual catalytic activities and how they contribute to disease pathogenesis.
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28
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Lal R, Ritchie J, Richmond L, Keeshan K. Detecting endogenous TRIB2 protein expression by flow cytometry and Western blotting. Methods Enzymol 2022; 667:59-77. [PMID: 35525555 DOI: 10.1016/bs.mie.2022.03.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Protein kinases catalyze the transfer of a phosphate group thereby activating proteins and initiating signaling cascades. Their cousins, the pseudokinases, are enzymatically nonactive counterparts of protein kinases that can be considered zombie enzymes. Interestingly, pseudokinases, which constitute about 10% of the human kinome, have been implicated in many cancers, despite their sequences predicting a lack of catalytic activity. Owing to recent research, it has been demonstrated that dysregulation of many pseudokinases triggers changes in cell signaling, proliferation, and drug resistance. This review is aimed at describing methods that can be used for detection of Tribbles family of pseudokinases, specifically TRIB2. We describe intracellular staining by flow cytometry and Western blotting techniques for the detection of endogenous TRIB2 protein.
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Affiliation(s)
- Ridhima Lal
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, SC, United Kingdom
| | - Jake Ritchie
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, SC, United Kingdom
| | - Laura Richmond
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, SC, United Kingdom
| | - Karen Keeshan
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, SC, United Kingdom.
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29
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Sheetz JB, Lemmon MA, Tsutsui Y. Dynamics of protein kinases and pseudokinases by HDX-MS. Methods Enzymol 2022; 667:303-338. [PMID: 35525545 PMCID: PMC9148214 DOI: 10.1016/bs.mie.2022.03.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Dynamics of the protein kinase fold are deeply intertwined with its structure. The past three decades of kinase biophysical studies revealed key dynamic features of the kinase domain and, more recently, how these features may endow catalytically impaired kinases-or pseudokinases-with signaling properties. Hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) is proving to be a valuable approach for studies of kinase and pseudokinase domain dynamics. Here, we briefly discuss the methods that have provided insights into protein kinase dynamics, describe how HDX-MS is being used to answer questions in the kinase/pseudokinase field, and provide a detailed protocol for collecting an HDX-MS dataset to study the impacts of small molecule binding to a pseudokinase domain. As more small molecules are discovered that can disrupt pseudokinase conformations, HDX-MS is likely to be a powerful approach for exploring drug-induced changes in pseudokinase dynamics and structure.
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Affiliation(s)
- Joshua B Sheetz
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, United States
| | - Mark A Lemmon
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, United States.
| | - Yuko Tsutsui
- Department of Pharmacology and Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, CT, United States.
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30
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A suite of in vitro and in vivo assays for monitoring the activity of the pseudokinase Bud32. Methods Enzymol 2022; 667:729-773. [PMID: 35525560 DOI: 10.1016/bs.mie.2022.03.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bud32 is a member of the protein kinase superfamily that is invariably conserved in all eukaryotic and archaeal organisms. In both of these kingdoms, Bud32 forms part of the KEOPS (Kinase, Endopeptidase and Other Proteins of Small size) complex together with the three other core subunits Kae1, Cgi121 and Pcc1. KEOPS functions to generate the universal and essential tRNA post-transcriptional modification N6-theronylcarbamoyl adenosine (t6A), which is present at position A37 in all tRNAs that bind to codons with an A in the first position (ANN decoding tRNAs) and is essential for the fidelity of translation. Mutations in KEOPS genes in humans underlie the severe genetic disease Galloway-Mowat syndrome, which results in childhood death. KEOPS activity depends on two major functions of Bud32. Firstly, Bud32 facilitates efficient tRNA substrate recruitment to KEOPS and helps in positioning the A37 site of the tRNA in the active site of Kae1, which carries out the t6A modification reaction. Secondly, the enzymatic activity of Bud32 is required for the ability of KEOPS to modify tRNA. Unlike conventional protein kinases, which employ their enzymatic activity for phosphorylation of protein substrates, Bud32 employs its enzymatic activity to function as an ATPase. Herein, we present a comprehensive suite of assays to monitor the activity of Bud32 in KEOPS in vitro and in vivo. We present protocols for the purification of the archaeal KEOPS proteins and of a tRNA substrate, as well as protocols for monitoring the ATPase activity of Bud32 and for analyzing its role in tRNA binding. We further present a complementary protocol for monitoring the role Bud32 has in cell growth in yeast.
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31
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Bou-Petit E, Hümmer S, Alarcon H, Slobodnyuk K, Cano-Galietero M, Fuentes P, Guijarro PJ, Muñoz MJ, Suarez-Cabrera L, Santamaria A, Estrada-Tejedor R, Borrell JI, Ramón Y Cajal S. Overcoming Paradoxical Kinase Priming by a Novel MNK1 Inhibitor. J Med Chem 2022; 65:6070-6087. [PMID: 35417652 PMCID: PMC9059116 DOI: 10.1021/acs.jmedchem.1c01941] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Targeting the kinases MNK1 and MNK2 has emerged as a valuable strategy in oncology. However, most of the advanced inhibitors are acting in an adenosine triphosphate (ATP)-competitive mode, precluding the evaluation of different binding modes in preclinical settings. Using rational design, we identified and validated the 4,6-diaryl-pyrazolo[3,4-b]pyridin-3-amine scaffold as the core for MNK inhibitors. Signaling pathway analysis confirmed a direct effect of the hit compound EB1 on MNKs, and in line with the reported function of these kinases, EB1 only affects the growth of tumor but not normal cells. Molecular modeling revealed the binding of EB1 to the inactive conformation of MNK1 and the interaction with the specific DFD motif. This novel mode of action appears to be superior to the ATP-competitive inhibitors, which render the protein in a pseudo-active state. Overcoming this paradoxical activation of MNKs by EB1 represents therefore a promising starting point for the development of a novel generation of MNK inhibitors.
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Affiliation(s)
- Elisabeth Bou-Petit
- Grup de Química Farmacèutica, IQS School of Engineering, Universitat Ramon Llull, Via Augusta, 390, 08017 Barcelona, Spain
| | - Stefan Hümmer
- Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Psg. Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), 28029 Madrid, Spain
| | - Helena Alarcon
- Grup de Química Farmacèutica, IQS School of Engineering, Universitat Ramon Llull, Via Augusta, 390, 08017 Barcelona, Spain
| | - Konstantin Slobodnyuk
- Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Psg. Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), 28029 Madrid, Spain
| | - Marta Cano-Galietero
- Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Psg. Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), 28029 Madrid, Spain
| | - Pedro Fuentes
- Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Psg. Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), 28029 Madrid, Spain
| | - Pedro J Guijarro
- Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Psg. Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - María José Muñoz
- Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Psg. Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), 28029 Madrid, Spain
| | - Leticia Suarez-Cabrera
- Cell Cycle and Cancer Laboratory, Biomedical Research Group in Urology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Psg. Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Anna Santamaria
- Cell Cycle and Cancer Laboratory, Biomedical Research Group in Urology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Psg. Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Roger Estrada-Tejedor
- Grup de Química Farmacèutica, IQS School of Engineering, Universitat Ramon Llull, Via Augusta, 390, 08017 Barcelona, Spain
| | - José I Borrell
- Grup de Química Farmacèutica, IQS School of Engineering, Universitat Ramon Llull, Via Augusta, 390, 08017 Barcelona, Spain
| | - Santiago Ramón Y Cajal
- Translational Molecular Pathology, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Psg. Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), 28029 Madrid, Spain
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32
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ATP allosterically stabilizes integrin-linked kinase for efficient force generation. Proc Natl Acad Sci U S A 2022; 119:e2106098119. [PMID: 35259013 PMCID: PMC8933812 DOI: 10.1073/pnas.2106098119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The pseudokinase integrin-linked kinase (ILK) is a central component of focal adhesions, cytoplasmic multiprotein complexes that integrate and transduce biochemical and mechanical signals from the extracellular environment into the cell and vice versa. However, the precise molecular functions, particularly the mechanosensory properties of ILK and the significance of retained adenosine triphosphate (ATP) binding, are still unclear. Combining molecular-dynamics simulations with cell biology, we establish a role for ATP binding to pseudokinases. We find that ATP promotes the structural stability of ILK, allosterically influences the interaction between ILK and its binding partner parvin at adhesions, and enhances the mechanoresistance of this complex. On the cellular level, ATP binding facilitates efficient traction force buildup, focal adhesion stabilization, and efficient cell migration. Focal adhesions link the actomyosin cytoskeleton to the extracellular matrix regulating cell adhesion, shape, and migration. Adhesions are dynamically assembled and disassembled in response to extrinsic and intrinsic forces, but how the essential adhesion component integrin-linked kinase (ILK) dynamically responds to mechanical force and what role adenosine triphosphate (ATP) bound to this pseudokinase plays remain elusive. Here, we apply force–probe molecular-dynamics simulations of human ILK:α-parvin coupled to traction force microscopy to explore ILK mechanotransducing functions. We identify two key salt-bridge–forming arginines within the allosteric, ATP-dependent force-propagation network of ILK. Disrupting this network by mutation impedes parvin binding, focal adhesion stabilization, force generation, and thus migration. Under tension, ATP shifts the balance from rupture of the complex to protein unfolding, indicating that ATP increases the force threshold required for focal adhesion disassembly. Our study proposes a role of ATP as an obligatory binding partner for structural and mechanical integrity of the pseudokinase ILK, ensuring efficient cellular force generation and migration.
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33
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Agius MP, Ko K, Johnson TK, Phadke S, Soellner MB. Conformation-tunable ATP-competitive kinase inhibitors. Chem Commun (Camb) 2022; 58:3541-3544. [PMID: 35195624 DOI: 10.1039/d1cc06893h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecule kinase inhibitors have shown immense clinical utility for diverse indications. While >60 kinase inhibitors have been approved (and many more in clinical trials), it remains unclear whether the clinical efficacy of a kinase inhibitor is solely dependent on enzymatic inhibition, or whether non-catalytic functions play a role in the efficacy of some kinase inhibitors. Here, we designed and synthesized a series of pyrazolopyrimidine kinase inhibitors that modulate the global kinase conformation of c-Src kinase. Expanding upon our findings from the pyrazolopyrimidine inhibitor series, we designed, synthesized, and evaluated three pair of conformation-selective kinase inhibitors, each with a unique hinge-binding scaffold. We profiled each pair of kinase inhibitors across 468 kinases and identified 38 kinases that could be studied using these pair of conformation-selective inhibitors. We also explore the binding of conformation-selective kinase inhibitors to mutant kinases of EGFR, FLT3, and KIT. Together, these studies yield important insight into the design of conformation-tunable kinase inhibitors and provide a toolset of compounds to study the role of protein conformation on kinase signaling.
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Affiliation(s)
- Michael P Agius
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Kristin Ko
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Taylor K Johnson
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Sameer Phadke
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
| | - Matthew B Soellner
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, USA.
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34
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Targeting Protein Kinases and Epigenetic Control as Combinatorial Therapy Options for Advanced Prostate Cancer Treatment. Pharmaceutics 2022; 14:pharmaceutics14030515. [PMID: 35335890 PMCID: PMC8949110 DOI: 10.3390/pharmaceutics14030515] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 02/02/2023] Open
Abstract
Prostate cancer (PC), the fifth leading cause of cancer-related mortality worldwide, is known as metastatic bone cancer when it spreads to the bone. Although there is still no effective treatment for advanced/metastatic PC, awareness of the molecular events that contribute to PC progression has opened up opportunities and raised hopes for the development of new treatment strategies. Androgen deprivation and androgen-receptor-targeting therapies are two gold standard treatments for metastatic PC. However, acquired resistance to these treatments is a crucial challenge. Due to the role of protein kinases (PKs) in the growth, proliferation, and metastases of prostatic tumors, combinatorial therapy by PK inhibitors may help pave the way for metastatic PC treatment. Additionally, PC is known to have epigenetic involvement. Thus, understanding epigenetic pathways can help adopt another combinatorial treatment strategy. In this study, we reviewed the PKs that promote PC to advanced stages. We also summarized some PK inhibitors that may be used to treat advanced PC and we discussed the importance of epigenetic control in this cancer. We hope the information presented in this article will contribute to finding an effective treatment for the management of advanced PC.
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35
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The Effect and Mechanism of Gene Fam20a on the Development and Function of Salivary Glands in Mice. Arch Oral Biol 2022; 137:105367. [DOI: 10.1016/j.archoralbio.2022.105367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/21/2022]
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36
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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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37
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Aurora A and AKT Kinase Signaling Associated with Primary Cilia. Cells 2021; 10:cells10123602. [PMID: 34944109 PMCID: PMC8699881 DOI: 10.3390/cells10123602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 02/07/2023] Open
Abstract
Dysregulation of kinase signaling is associated with various pathological conditions, including cancer, inflammation, and autoimmunity; consequently, the kinases involved have become major therapeutic targets. While kinase signaling pathways play crucial roles in multiple cellular processes, the precise manner in which their dysregulation contributes to disease is dependent on the context; for example, the cell/tissue type or subcellular localization of the kinase or substrate. Thus, context-selective targeting of dysregulated kinases may serve to increase the therapeutic specificity while reducing off-target adverse effects. Primary cilia are antenna-like structures that extend from the plasma membrane and function by detecting extracellular cues and transducing signals into the cell. Cilia formation and signaling are dynamically regulated through context-dependent mechanisms; as such, dysregulation of primary cilia contributes to disease in a variety of ways. Here, we review the involvement of primary cilia-associated signaling through aurora A and AKT kinases with respect to cancer, obesity, and other ciliopathies.
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38
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Passirani C, Vessières A, La Regina G, Link W, Silvestri R. Modulating undruggable targets to overcome cancer therapy resistance. Drug Resist Updat 2021; 60:100788. [DOI: 10.1016/j.drup.2021.100788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 11/03/2022]
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39
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Atas-Ozcan H, Brault V, Duchon A, Herault Y. Dyrk1a from Gene Function in Development and Physiology to Dosage Correction across Life Span in Down Syndrome. Genes (Basel) 2021; 12:1833. [PMID: 34828439 PMCID: PMC8624927 DOI: 10.3390/genes12111833] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 01/12/2023] Open
Abstract
Down syndrome is the main cause of intellectual disabilities with a large set of comorbidities from developmental origins but also that appeared across life span. Investigation of the genetic overdosage found in Down syndrome, due to the trisomy of human chromosome 21, has pointed to one main driver gene, the Dual-specificity tyrosine-regulated kinase 1A (Dyrk1a). Dyrk1a is a murine homolog of the drosophila minibrain gene. It has been found to be involved in many biological processes during development and in adulthood. Further analysis showed its haploinsufficiency in mental retardation disease 7 and its involvement in Alzheimer's disease. DYRK1A plays a role in major developmental steps of brain development, controlling the proliferation of neural progenitors, the migration of neurons, their dendritogenesis and the function of the synapse. Several strategies targeting the overdosage of DYRK1A in DS with specific kinase inhibitors have showed promising evidence that DS cognitive conditions can be alleviated. Nevertheless, providing conditions for proper temporal treatment and to tackle the neurodevelopmental and the neurodegenerative aspects of DS across life span is still an open question.
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Affiliation(s)
- Helin Atas-Ozcan
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (H.A.-O.); (V.B.); (A.D.)
| | - Véronique Brault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (H.A.-O.); (V.B.); (A.D.)
| | - Arnaud Duchon
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (H.A.-O.); (V.B.); (A.D.)
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France; (H.A.-O.); (V.B.); (A.D.)
- Université de Strasbourg, CNRS, INSERM, Celphedia, Phenomin-Institut Clinique de la Souris (ICS), 1 rue Laurent Fries, 67404 Illkirch Graffenstaden, France
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40
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Montoya S, Soong D, Nguyen N, Affer M, Munamarty SP, Taylor J. Targeted Therapies in Cancer: To Be or Not to Be, Selective. Biomedicines 2021; 9:1591. [PMID: 34829820 PMCID: PMC8615814 DOI: 10.3390/biomedicines9111591] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 12/31/2022] Open
Abstract
Development of targeted therapies in recent years revealed several nonchemotherapeutic options for patients. Chief among targeted therapies is small molecule kinase inhibitors targeting key oncogenic signaling proteins. Through competitive and noncompetitive inhibition of these kinases, and therefore the pathways they activate, cancers can be slowed or completely eradicated, leading to partial or complete remissions for many cancer types. Unfortunately, for many patients, resistance to targeted therapies, such as kinase inhibitors, ultimately develops and can necessitate multiple lines of treatment. Drug resistance can either be de novo or acquired after months or years of drug exposure. Since resistance can be due to several unique mechanisms, there is no one-size-fits-all solution to this problem. However, combinations that target complimentary pathways or potential escape mechanisms appear to be more effective than sequential therapy. Combinations of single kinase inhibitors or alternately multikinase inhibitor drugs could be used to achieve this goal. Understanding how to efficiently target cancer cells and overcome resistance to prior lines of therapy became imperative to the success of cancer treatment. Due to the complexity of cancer, effective treatment options in the future will likely require mixing and matching these approaches in different cancer types and different disease stages.
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Affiliation(s)
| | | | | | | | | | - Justin Taylor
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, 1501 NW 10th Avenue, Miami, FL 33136, USA; (S.M.); (D.S.); (N.N.); (M.A.); (S.P.M.)
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41
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Paul A, Subhadarshini S, Srinivasan N. Pseudokinases repurpose flexibility signatures associated with the protein kinase fold for noncatalytic roles. Proteins 2021; 90:747-764. [PMID: 34708889 DOI: 10.1002/prot.26271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/22/2021] [Accepted: 10/18/2021] [Indexed: 01/27/2023]
Abstract
The bilobal protein kinase-like fold in pseudokinases lack one or more catalytic residues, conserved in canonical protein kinases, and are considered enzymatically deficient. Tertiary structures of pseudokinases reveal that their loops topologically equivalent to activation segments of kinases adopt contracted configurations, which is typically extended in active conformation of kinases. Herein, anisotropic network model based normal mode analysis (NMA) was conducted on 51 active conformation structures of protein kinases and 26 crystal structures of pseudokinases. Our observations indicate that although backbone fluctuation profiles are similar for individual kinase-pseudokinase families, low intensity mean square fluctuations in pseudo-activation segment and other sub-structures impart rigidity to pseudokinases. Analyses of collective motions from functional modes reveal that pseudokinases, compared to active kinases, undergo distinct conformational transitions using the same structural fold. All-atom NMA of protein kinase-pseudokinase pairs from each family, sharing high amino acid sequence identities, yielded distinct community clusters, partitioned by residues exhibiting highly correlated fluctuations. It appears that atomic fluctuations from equivalent activation segments guide community membership and network topologies for respective kinase and pseudokinase. Our findings indicate that such adaptations in backbone and side-chain fluctuations render pseudokinases competent for catalysis-independent roles.
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Affiliation(s)
- Anindita Paul
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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42
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Maciej-Hulme ML. New Insights Into Human Hyaluronidase 4/Chondroitin Sulphate Hydrolase. Front Cell Dev Biol 2021; 9:767924. [PMID: 34746156 PMCID: PMC8564380 DOI: 10.3389/fcell.2021.767924] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
In this review, the current experimental evidence, literature and hypotheses surrounding hyaluronidase 4 [HYAL4, also known as chondroitin sulphate hydrolase (CHSE)] and chondroitin sulphate (CS) are explored. Originally named for its sequence similarity to other members of the hyaluronidase family, HYAL4 is actually a relatively distinct member of the family, particularly for its unique degradation of CS-D (2-O-, 6-O-sulphated CS) motifs and specific expression. Human HYAL4 protein expression and structural features are discussed in relation to different isoforms, activities, potential localisations and protein-protein interaction partners. CS proteoglycan targets of HYAL4 activity include: serglycin, aggrecan, CD44 and sulfatase 2, with other potential proteoglycans yet to be identified. Importantly, changes in HYAL4 expression changes in human disease have been described for testicular, bladder and kidney cancers, with gene mutations reported for several others including: leukaemia, endometrial, ovarian, colorectal, head and neck, stomach, lung and breast cancers. The HYAL4 gene also plays a role in P53 negative human cancer cell proliferation and is linked to stem cell naivety. However, its role in cancer remains relatively unexplored. Finally, current tools and techniques for the detection of specific HYAL4 activity in biological samples are critically assessed. Understanding the role of HYAL4 in human diseases will fortify our understanding of developmental processes and disease manifestation, ultimately providing novel diagnostic opportunities and therapeutic targets for drug discovery.
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43
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Silva GLA, Tosi LRO, McCulloch R, Black JA. Unpicking the Roles of DNA Damage Protein Kinases in Trypanosomatids. Front Cell Dev Biol 2021; 9:636615. [PMID: 34422791 PMCID: PMC8377203 DOI: 10.3389/fcell.2021.636615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 07/13/2021] [Indexed: 12/31/2022] Open
Abstract
To preserve genome integrity when faced with DNA lesions, cells activate and coordinate a multitude of DNA repair pathways to ensure timely error correction or tolerance, collectively called the DNA damage response (DDR). These interconnecting damage response pathways are molecular signal relays, with protein kinases (PKs) at the pinnacle. Focused efforts in model eukaryotes have revealed intricate aspects of DNA repair PK function, including how they direct DDR pathways and how repair reactions connect to wider cellular processes, including DNA replication and transcription. The Kinetoplastidae, including many parasites like Trypanosoma spp. and Leishmania spp. (causative agents of debilitating, neglected tropical infections), exhibit peculiarities in several core biological processes, including the predominance of multigenic transcription and the streamlining or repurposing of DNA repair pathways, such as the loss of non-homologous end joining and novel operation of nucleotide excision repair (NER). Very recent studies have implicated ATR and ATM kinases in the DDR of kinetoplastid parasites, whereas DNA-dependent protein kinase (DNA-PKcs) displays uncertain conservation, questioning what functions it fulfills. The wide range of genetic manipulation approaches in these organisms presents an opportunity to investigate DNA repair kinase roles in kinetoplastids and to ask if further kinases are involved. Furthermore, the availability of kinase inhibitory compounds, targeting numerous eukaryotic PKs, could allow us to test the suitability of DNA repair PKs as novel chemotherapeutic targets. Here, we will review recent advances in the study of trypanosomatid DNA repair kinases.
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Affiliation(s)
- Gabriel L A Silva
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom.,Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz R O Tosi
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Jennifer Ann Black
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom.,Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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44
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Miller S, Blanco MJ. Small molecule therapeutics for neuroinflammation-mediated neurodegenerative disorders. RSC Med Chem 2021; 12:871-886. [PMID: 34223157 PMCID: PMC8221257 DOI: 10.1039/d1md00036e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Chronically activated microglia and the resulting cascade of neuroinflammatory mechanisms have been postulated to play a critical role in neurodegenerative disorders. Microglia are the main component of the brain's innate immune system and become activated by infection, injury, misfolded proteins or a multitude of other stimuli. Activated microglia release pro-inflammatory and cytotoxic factors that can damage neurons and transform astrocytes to become toxic to neurons as well. Therapeutic approaches aiming to modulate microglia activation may be beneficial to mitigate the progression of inflammatory-mediated neurodegenerative diseases. In this literature review, we provide an overview of recent progress on key microglia targets and discovery of small molecule compounds advancing in clinical trials to minimize neuroinflammation.
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Affiliation(s)
- Silke Miller
- Sage Therapeutics, Inc. 215 First Street Cambridge Massachusetts 02142 USA
| | - Maria-Jesus Blanco
- Sage Therapeutics, Inc. 215 First Street Cambridge Massachusetts 02142 USA
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45
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Gaji RY, Sharp AK, Brown AM. Protein kinases in Toxoplasma gondii. Int J Parasitol 2021; 51:415-429. [PMID: 33581139 PMCID: PMC11065138 DOI: 10.1016/j.ijpara.2020.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 02/06/2023]
Abstract
Toxoplasma gondii is an obligatory intracellular pathogen that causes life threatening illness in immunodeficient individuals, miscarriage in pregnant woman, and blindness in newborn children. Similar to any other eukaryotic cell, protein kinases play critical and essential roles in the Toxoplasma life cycle. Accordingly, many studies have focused on identifying and defining the mechanism of function of these signalling proteins with a long-term goal to develop anti-Toxoplasma therapeutics. In this review, we briefly discuss classification and key components of the catalytic domain which are critical for functioning of kinases, with a focus on domains, families, and groups of kinases within Toxoplasma. More importantly, this article provides a comprehensive, current overview of research on kinase groups in Toxoplasma including the established eukaryotic AGC, CAMK, CK1, CMGC, STE, TKL families and the apicomplexan-specific FIKK, ROPK and WNG family of kinases. This work provides an overview and discusses current knowledge on Toxoplasma kinases including their localization, function, signalling network and role in acute and chronic pathogenesis, with a view towards the future in probing kinases as viable drug targets.
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Affiliation(s)
- Rajshekhar Y Gaji
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech University, Blacksburg, VA, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
| | - Amanda K Sharp
- Interdisciplinary Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Anne M Brown
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA; University Libraries, Virginia Tech, Blacksburg, VA, USA
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46
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Loffredo M, Lucero H, Chen DY, O'Connell A, Bergqvist S, Munawar A, Bandara A, De Graef S, Weeks SD, Douam F, Saeed M, Munawar AH. The in-vitro effect of famotidine on sars-cov-2 proteases and virus replication. Sci Rep 2021; 11:5433. [PMID: 33686143 PMCID: PMC7940615 DOI: 10.1038/s41598-021-84782-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/01/2021] [Indexed: 01/07/2023] Open
Abstract
The lack of coronavirus-specific antiviral drugs has instigated multiple drug repurposing studies to redirect previously approved medicines for the treatment of SARS-CoV-2, the coronavirus behind the ongoing COVID-19 pandemic. A recent, large-scale, retrospective clinical study showed that famotidine, when administered at a high dose to hospitalized COVID-19 patients, reduced the rates of intubation and mortality. A separate, patient-reported study associated famotidine use with improvements in mild to moderate symptoms such as cough and shortness of breath. While a prospective, multi-center clinical study is ongoing, two parallel in silico studies have proposed one of the two SARS-CoV-2 proteases, 3CLpro or PLpro, as potential molecular targets of famotidine activity; however, this remains to be experimentally validated. In this report, we systematically analyzed the effect of famotidine on viral proteases and virus replication. Leveraging a series of biophysical and enzymatic assays, we show that famotidine neither binds with nor inhibits the functions of 3CLpro and PLpro. Similarly, no direct antiviral activity of famotidine was observed at concentrations of up to 200 µM, when tested against SARS-CoV-2 in two different cell lines, including a human cell line originating from lungs, a primary target of COVID-19. These results rule out famotidine as a direct-acting inhibitor of SARS-CoV-2 replication and warrant further investigation of its molecular mechanism of action in the context of COVID-19.
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Affiliation(s)
- Madeline Loffredo
- Bisect Therapeutics, Inc., 45 Dan Road, Canton, MA, USA.,Orthogon Therapeutics LLC, 960 Turnpike St, Canton, MA, USA
| | - Hector Lucero
- Bisect Therapeutics, Inc., 45 Dan Road, Canton, MA, USA.,Orthogon Therapeutics LLC, 960 Turnpike St, Canton, MA, USA
| | - Da-Yuan Chen
- National Emerging Infectious Diseases Laboratories (NEIDL), 620 Albany Street, Boston, MA, 02118, USA.,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Aoife O'Connell
- National Emerging Infectious Diseases Laboratories (NEIDL), 620 Albany Street, Boston, MA, 02118, USA.,Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | | | - Ahmad Munawar
- Bisect Therapeutics, Inc., 45 Dan Road, Canton, MA, USA.,Orthogon Therapeutics LLC, 960 Turnpike St, Canton, MA, USA
| | - Asanga Bandara
- Bisect Therapeutics, Inc., 45 Dan Road, Canton, MA, USA.,Orthogon Therapeutics LLC, 960 Turnpike St, Canton, MA, USA
| | - Steff De Graef
- Bisect Therapeutics, Inc., 45 Dan Road, Canton, MA, USA.,Pledge Therapeutics B.V., Gaston Geenslaan 1, Leuven, 3000, Belgium
| | - Stephen D Weeks
- Bisect Therapeutics, Inc., 45 Dan Road, Canton, MA, USA.,Pledge Therapeutics B.V., Gaston Geenslaan 1, Leuven, 3000, Belgium
| | - Florian Douam
- National Emerging Infectious Diseases Laboratories (NEIDL), 620 Albany Street, Boston, MA, 02118, USA.,Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- National Emerging Infectious Diseases Laboratories (NEIDL), 620 Albany Street, Boston, MA, 02118, USA. .,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA.
| | - Ali H Munawar
- Bisect Therapeutics, Inc., 45 Dan Road, Canton, MA, USA. .,Orthogon Therapeutics LLC, 960 Turnpike St, Canton, MA, USA. .,Pledge Therapeutics B.V., Gaston Geenslaan 1, Leuven, 3000, Belgium.
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47
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Sunitinib inhibits RNase L by destabilizing its active dimer conformation. Biochem J 2021; 477:3387-3399. [PMID: 32830849 DOI: 10.1042/bcj20200260] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/27/2020] [Accepted: 08/24/2020] [Indexed: 02/06/2023]
Abstract
The pseudokinase (PK) RNase L is a functional ribonuclease and plays important roles in human innate immunity. The ribonuclease activity of RNase L can be regulated by the kinase inhibitor sunitinib. The combined use of oncolytic virus and sunitinib has been shown to exert synergistic effects in anticancer therapy. In this study, we aimed to uncover the mechanism of action through which sunitinib inhibits RNase L. We solved the crystal structures of RNase L in complex with sunitinib and its analogs toceranib and SU11652. Our results showed that sunitinib bound to the ATP-binding pocket of RNase L. Unexpectedly, the αA helix linking the ankyrin repeat-domain and the PK domain affected the binding mode of sunitinib and resulted in an unusual flipped orientation relative to other structures in PDB. Molecular dynamics simulations and dynamic light scattering results support that the binding of sunitinib in the PK domain destabilized the dimer conformation of RNase L and allosterically inhibited its ribonuclease activity. Our study suggested that dimer destabilization could be an effective strategy for the discovery of RNase L inhibitors and that targeting the ATP-binding pocket in the PK domain of RNase L was an efficient approach for modulating its ribonuclease activity.
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48
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Alabi S, Jaime-Figueroa S, Yao Z, Gao Y, Hines J, Samarasinghe KTG, Vogt L, Rosen N, Crews CM. Mutant-selective degradation by BRAF-targeting PROTACs. Nat Commun 2021; 12:920. [PMID: 33568647 PMCID: PMC7876048 DOI: 10.1038/s41467-021-21159-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/14/2021] [Indexed: 12/26/2022] Open
Abstract
Over 300 BRAF missense mutations have been identified in patients, yet currently approved drugs target V600 mutants alone. Moreover, acquired resistance inevitably emerges, primarily due to RAF lesions that prevent inhibition of BRAF V600 with current treatments. Therefore, there is a need for new therapies that target other mechanisms of activated BRAF. In this study, we use the Proteolysis Targeting Chimera (PROTAC) technology, which promotes ubiquitination and degradation of neo-substrates, to address the limitations of BRAF inhibitor-based therapies. Using vemurafenib-based PROTACs, we achieve low nanomolar degradation of all classes of BRAF mutants, but spare degradation of WT RAF family members. Our lead PROTAC outperforms vemurafenib in inhibiting cancer cell growth and shows in vivo efficacy in a Class 2 BRAF xenograft model. Mechanistic studies reveal that BRAFWT is spared due to weak ternary complex formation in cells owing to its quiescent inactivated conformation, and activation of BRAFWT sensitizes it to degradation. This study highlights the degree of selectivity achievable with degradation-based approaches by targeting mutant BRAF-driven cancers while sparing BRAFWT, providing an anti-tumor drug modality that expands the therapeutic window. Hundreds of BRAF mutations have been identified in patients with cancer but currently approved drugs only target BRAF V600 mutants. Here, the authors develop a vemurafenib-based PROTAC that induces degradation of all classes of BRAF mutants without affecting wild-type RAF proteins.
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Affiliation(s)
| | - Saul Jaime-Figueroa
- Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | - Zhan Yao
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yijun Gao
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Hines
- Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Lea Vogt
- Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | - Neal Rosen
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Craig M Crews
- Department of Pharmacology, New Haven, CT, USA. .,Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA. .,Department of Chemistry, Yale University, New Haven, CT, USA.
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49
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Cheng J, Feng X, Li Z, Zhou F, Yang JM, Zhao Y. Pharmacological inhibition of NF-κB-inducing kinase (NIK) with small molecules for the treatment of human diseases. RSC Med Chem 2021; 12:552-565. [PMID: 34046627 DOI: 10.1039/d0md00361a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/24/2020] [Indexed: 12/14/2022] Open
Abstract
NIK is a key kinase required for the activation of alternative NF-κB signaling pathways. Overactivation of NIK in patients has been observed and is implicated in the pathogenesis of inflammatory diseases, B-cell malignances, and solid tumors. Over the past decade, inhibition of NIK overactivation with small molecules has been pursued as an attractive strategy for drug discovery, where numerous potent and selective NIK inhibitors with novel pharmacophores have been identified. This review summarizes the structural features and key efficacy studies of the NIK inhibitors reported, which justify the mechanism of action of such inhibitors in animal models driven by NIK overactivation. Given the strong pathological associations between overactivation of NIK and human diseases, human clinical trials of NIK inhibitors as drug candidates are eagerly awaited. Information showcased in this review article might be helpful for the discovery and clinical development of the next generation of NIK inhibitors in the near future.
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Affiliation(s)
- Jing Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Rd. Shanghai 201203 China +86 21 50800608.,University of Chinese Academy of Sciences Beijing 100049 China
| | - Xuexin Feng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Rd. Shanghai 201203 China +86 21 50800608.,School of Pharmacy, Yancheng Teachers University Yancheng Jiangsu 224051 China
| | - Zhiqiang Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Rd. Shanghai 201203 China +86 21 50800608.,University of Chinese Academy of Sciences Beijing 100049 China
| | - Feilong Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Rd. Shanghai 201203 China +86 21 50800608
| | - Jin-Ming Yang
- School of Pharmacy, Yancheng Teachers University Yancheng Jiangsu 224051 China
| | - Yujun Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences 555 Zuchongzhi Rd. Shanghai 201203 China +86 21 50800608.,University of Chinese Academy of Sciences Beijing 100049 China.,School of Pharmaceutical Sciences, Zhengzhou University Zhengzhou 450001 China
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Preclinical and Clinical Advances of Targeted Protein Degradation as a Novel Cancer Therapeutic Strategy: An Oncologist Perspective. Target Oncol 2020; 16:1-12. [PMID: 33369705 DOI: 10.1007/s11523-020-00782-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
PROteolysis Targeting Chimeras (PROTACs) are a family of heterobifunctional small molecules that specifically target cellular proteins for degradation. Given that their mode of action is distinct from that of small-molecule inhibitors widely used in clinical practice, PROTACs have the potential to improve current cancer therapies. Multiple studies have suggested that PROTACs exhibit enhanced pharmacodynamics and reduced toxicity both in vitro and in vivo compared to clinically relevant small-molecule kinase inhibitors. In addition, PROTACs have been reported to be less prone to mutation-mediated drug resistance in specific disease settings. Since its development in 2001, the field of targeted protein degradation, in which PROTACs are used, has expanded rapidly. However, earlier studies focused on the advancement of the technology itself, while preclinical and clinical data on the disease-modifying effect of PROTACs have only recently been reported. As preclinical and clinical evidence accumulates, the efficacy of PROTACs as targeted therapeutics-distinct from that of small-molecule kinase inhibitors-suggests potential translational benefit in the clinical setting. In this short review, we aim to describe translational potentials of PROTACs. We offer our perspectives as practicing oncologists on the preclinical and clinical data on PROTACs as novel therapeutics for both solid and hematological malignancies.
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