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Wang X, DeFilippis RA, Yan W, Shah NP, Li HY. Overcoming Secondary Mutations of Type II Kinase Inhibitors. J Med Chem 2024. [PMID: 38837951 DOI: 10.1021/acs.jmedchem.3c01629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Type II kinase inhibitors bind in the "DFG-out" kinase conformation and are generally considered to be more potent and selective than type I inhibitors, which target a DFG-in conformation. Nine type II inhibitors are currently clinically approved, with more undergoing clinical development. Resistance-conferring secondary mutations emerged with the first series of type II inhibitors, most commonly at residues within the kinase activation loop and at the "gatekeeper" position. Recently, new inhibitors have been developed to overcome such mutations; however, mutations activating other pathways (and/or other targets) have subsequently emerged on occasion. Here, we systematically summarize the secondary mutations that confer resistance to type II inhibitors, the structural basis for resistance, newer inhibitors designed to overcome resistance, as well as the challenges and opportunities for the development of new inhibitors to overcome secondary kinase domain mutations.
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Affiliation(s)
- Xiuqi Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
| | - Rosa Anna DeFilippis
- Division of Hematology/Oncology, University of California, San Francisco, California 94143, United States
| | - Wei Yan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Department of Pharmacology, School of Medicine, The University of Texas Health San Antonio, San Antonio, Texas 78229, United States
| | - Neil P Shah
- Division of Hematology/Oncology, University of California, San Francisco, California 94143, United States
| | - Hong-Yu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, United States
- Department of Pharmacology, School of Medicine, The University of Texas Health San Antonio, San Antonio, Texas 78229, United States
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2
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Bremer HJ, Herppich AA, Pflum MKH. Kinase-catalyzed crosslinking: A comparison of ATP-crosslinker analogs. Bioorg Med Chem Lett 2024:129841. [PMID: 38838920 DOI: 10.1016/j.bmcl.2024.129841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/28/2024] [Accepted: 06/02/2024] [Indexed: 06/07/2024]
Abstract
Protein phosphorylation is catalyzed by kinases to regulate cellular events and disease states. Identifying kinase-substrate relationships represents a powerful strategy to understand cell biology and disease yet remains challenging due to the rapid dynamics of phosphorylation. Over the last decade, several γ-phosphoryl modified ATP analogs containing crosslinkers were developed to covalently conjugate kinases, their substrates, and their associated proteins for subsequent characterization. Here, kinetics and crosslinking experiments demonstrated that the UV-activated analogs, ATP-aryl azide and ATP-benzophenone, offered the most robust crosslinking, whereas electrophilic ATP-aryl fluorosulfate promoted the most effective proximity-enabled crosslinking. The data will guide future applications of kinase-catalyzed crosslinking to study normal and disease biology.
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Affiliation(s)
- Hannah J Bremer
- Wayne State University, Department of Chemistry, 5101 Cass Ave., Detroit, MI 48202, United States
| | - Andrew A Herppich
- Wayne State University, Department of Chemistry, 5101 Cass Ave., Detroit, MI 48202, United States
| | - Mary Kay H Pflum
- Wayne State University, Department of Chemistry, 5101 Cass Ave., Detroit, MI 48202, United States.
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3
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Inoue M, Ekimoto T, Yamane T, Ikeguchi M. Computational Analysis of Activation of Dimerized Epidermal Growth Factor Receptor Kinase Using the String Method and Markov State Model. J Chem Inf Model 2024; 64:3884-3895. [PMID: 38670929 DOI: 10.1021/acs.jcim.4c00172] [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: 04/28/2024]
Abstract
Epidermal growth factor receptor (EGFR) activation is accompanied by dimerization. During the activation of the intracellular kinase domain, two EGFR kinases form an asymmetric dimer, and one side of the dimer (receiver) is activated. Using the string method and Markov state model (MSM), we performed a computational analysis of the structural changes in the activation of the EGFR dimer in this study. The string method reveals the minimum free-energy pathway (MFEP) from the inactive to active structure. The MSM was constructed from numerous trajectories of molecular dynamics simulations around the MFEP, which revealed the free-energy map of structural changes. In the activation of the receiver kinase, the unfolding of the activation loop (A-loop) is followed by the rearrangement of the C-helix, as observed in other kinases. However, unlike other kinases, the free-energy map of EGFR at the asymmetric dimer showed that the active state yielded the highest stability and revealed how interactions at the dimer interface induced receiver activation. As the H-helix of the activator approaches the C-helix of the receiver during activation, the A-loop unfolds. Subsequently, L782 of the receiver enters the pocket between the G- and H-helices of the activator, leading to a rearrangement of the hydrophobic residues around L782 of the receiver, which constitutes a structural rearrangement of the C-helix of the receiver from an outward to an inner position. The MSM analysis revealed long-time scale trajectories via kinetic Monte Carlo.
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Affiliation(s)
- Masao Inoue
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tsutomu Yamane
- HPC- and AI-driven Drug Development Platform Division, Center for Computational Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- HPC- and AI-driven Drug Development Platform Division, Center for Computational Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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4
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Verma J, Vashisth H. Molecular basis for differential recognition of an allosteric inhibitor by receptor tyrosine kinases. Proteins 2024. [PMID: 38506327 DOI: 10.1002/prot.26685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/08/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
Understanding kinase-inhibitor selectivity continues to be a major objective in kinase drug discovery. We probe the molecular basis of selectivity of an allosteric inhibitor (MSC1609119A-1) of the insulin-like growth factor-I receptor kinase (IGF1RK), which has been shown to be ineffective for the homologous insulin receptor kinase (IRK). Specifically, we investigated the structural and energetic basis of the allosteric binding of this inhibitor to each kinase by combining molecular modeling, molecular dynamics (MD) simulations, and thermodynamic calculations. We predict the inhibitor conformation in the binding pocket of IRK and highlight that the charged residues in the histidine-arginine-aspartic acid (HRD) and aspartic acid-phenylalanine-glycine (DFG) motifs and the nonpolar residues in the binding pocket govern inhibitor interactions in the allosteric pocket of each kinase. We suggest that the conformational changes in the IGF1RK residues M1054 and M1079, movement of the ⍺C-helix, and the conformational stabilization of the DFG motif favor the selectivity of the inhibitor toward IGF1RK. Our thermodynamic calculations reveal that the observed selectivity can be rationalized through differences observed in the electrostatic interaction energy of the inhibitor in each inhibitor/kinase complex and the hydrogen bonding interactions of the inhibitor with the residue V1063 in IGF1RK that are not attained with the corresponding residue V1060 in IRK. Overall, our study provides a rationale for the molecular basis of recognition of this allosteric inhibitor by IGF1RK and IRK, which is potentially useful in developing novel inhibitors with improved affinity and selectivity.
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Affiliation(s)
- Jyoti Verma
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, New Hampshire, USA
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, New Hampshire, USA
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire, USA
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, New Hampshire, USA
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, New Hampshire, USA
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Fouad MA, Osman AA, Abdelhamid NM, Rashad MW, Nabawy AY, El Kerdawy AM. Discovery of dual kinase inhibitors targeting VEGFR2 and FAK: structure-based pharmacophore modeling, virtual screening, and molecular docking studies. BMC Chem 2024; 18:29. [PMID: 38347617 PMCID: PMC10863211 DOI: 10.1186/s13065-024-01130-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
VEGFR2 and FAK signaling pathways are interconnected and have synergistic effects on tumor angiogenesis, growth, and metastasis. Thus, instead of the conventional targeting of each of these proteins individually with a specific inhibitor, the present work aimed to discover novel dual inhibitors targeting both VEGFR2 and FAK exploiting their association. To this end, receptor-based pharmacophore modeling technique was opted to generate 3D pharmacophore models for VEGFR2 and FAK type II kinase inhibitors. The generated pharmacophore models were validated by assessing their ability to discriminate between active and decoy compounds in a pre-compiled test set of VEGFR2 and FAK active compounds and decoys. ZINCPharmer web tool was then used to screen the ZINC database purchasable subset using the validated pharmacophore models retrieving 42,616 hits for VEGFR2 and 28,475 hits for FAK. Subsequently, they were filtered using various filters leaving 13,023 and 6,832 survived compounds for VEGFR2 and FAK, respectively, with 124 common compounds. Based on molecular docking simulations, thirteen compounds were found to satisfy all necessary interactions with VEGFR2 and FAK kinase domains. Thus, they are predicted to have a possible dual VEGFR2/FAK inhibitory activity. Finally, SwissADME web tool showed that compound ZINC09875266 is not only promising in terms of binding pattern to our target kinases, but also in terms of pharmacokinetic properties.
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Affiliation(s)
- Marwa A Fouad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo, 11562, Egypt.
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt.
| | - Alaa A Osman
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Noha M Abdelhamid
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Mai W Rashad
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Ashrakat Y Nabawy
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Ahmed M El Kerdawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo, 11562, Egypt
- Pharmaceutical Chemistry Department, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
- School of Pharmacy, College of Health and Science, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, Lincolnshire, UK
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6
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Zaky YA, Rashad MW, Zaater MA, El Kerdawy AM. Discovery of dual rho-associated protein kinase 1 (ROCK1)/apoptosis signal-regulating kinase 1 (ASK1) inhibitors as a novel approach for non-alcoholic steatohepatitis (NASH) treatment. BMC Chem 2024; 18:2. [PMID: 38172941 PMCID: PMC10765837 DOI: 10.1186/s13065-023-01081-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024] Open
Abstract
In the current study we suggest a novel approach to curb non-alcoholic steatohepatitis (NASH) progression, and we suggest privileged scaffolds for the design of novel compounds for this aim. NASH is an advanced form of non-alcoholic fatty liver disease that can further progress into fibrosis, cirrhosis, and hepatocellular carcinoma. It is a widely emerging disease affecting 25% of the global population and has no current approved treatments. Protein kinases are key regulators of cellular pathways, of which, Rho-associated protein kinase 1 (ROCK1) and apoptosis signal-regulating kinase 1 (ASK1) play an important role in the progression of NASH and they stand out as promising targets for NASH therapy. Interestingly, their kinase domains are found to be similar in sequence and topology; therefore, dual inhibition of ROCK1 and ASK1 is expected to be amenable and could achieve a more favourable outcome. To reach this goal, a training set of ROCK1 and ASK1 protein structures co-crystalized with type 1 (ATP-competitive) inhibitors was constructed to manually generate receptor-based pharmacophore models representing ROCK1 and ASK1 inhibitors' common pharmacophoric features. The models produced were assessed using a test set of both ROCK1 and ASK1 actives and decoys, and their performance was evaluated using different assessment metrics. The best pharmacophore model obtained, showing a Mathew's correlation coefficient (MCC) of 0.71, was then used to screen the ZINC purchasable database retrieving 6178 hits that were filtered accordingly using several medicinal chemistry and pharmacokinetics filters returning 407 promising compounds. To confirm that these compounds are capable of binding to the target kinases, they were subjected to molecular docking simulations at both protein structures. The results were then assessed individually and filtered, setting the spotlight on various privileged scaffolds that could be exploited as the nucleus for designing novel ROCK1/ASK1 dual inhibitors.
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Affiliation(s)
- Yara A Zaky
- Department of Chemistry, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt.
| | - Mai W Rashad
- Department of Chemistry, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Marwa A Zaater
- Master Postgraduate Program, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ahmed M El Kerdawy
- Department of Chemistry, School of Pharmacy, Newgiza University (NGU), Newgiza, Km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- School of Pharmacy, College of Science, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, Lincolnshire, UK
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Sontag I, Bergmann L, Adamek HE. Severe Hyperglycemia Due to Protein Kinase Inhibitor Therapy in a Patient With Poorly Controlled Diabetes Mellitus. JCEM CASE REPORTS 2024; 2:luad172. [PMID: 38188906 PMCID: PMC10768878 DOI: 10.1210/jcemcr/luad172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Indexed: 01/09/2024]
Abstract
The efficacy and safety of zanubrutinib, a highly selective next-generation Bruton's tyrosine kinase (BTK) inhibitor, in chronic lymphocytic leukemia and lymphoplasmocytoides immunocytoma seems favorable. Adverse events comprise neutropenia, thrombocytopenia, infection, anemia, and atrial fibrillation. This report describes a 75-year-old man suffering from polydipsia, polyuria, and blurred vision for 10 days. He was diagnosed with lymphoplasmocytoides immunocytoma in 2003. After various therapies, he was started on zanubrutinib in October 2022. A diagnosis of diabetes mellitus had never been established before. On arrival in the emergency department, his plasma glucose was 37.2 mmol/L (671 mg/dL) and glycated hemoglobin (HbA1c) was 14.2%. Circulating antibodies showed positivity for glutamic acid decarboxylase (GAD-65), and his C-peptide level was 1.3 nmol/L (normal range, 0.37-1.47 nmol/L), equivalent to 3.9 ng/mL (normal range 1.1-5.0 ng/mL). From the patient's medical history, it became obvious that the metabolic situation had been problematic for many years, and that diabetes could have been taken into account at least in the summer of 2020 when HbA1c was 6.7%. In patients on tyrosine kinase inhibitors, careful assessment of glycemic control (monitoring HbA1c and blood glucose levels periodically even for nondiabetic patients) is recommended to prevent a major diabetic emergency.
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Affiliation(s)
- Isabel Sontag
- Zentrale Notfallambulanz, Klinikum Leverkusen, Academic Hospital of the University of Cologne, Am Gesundheitspark 11, D—51375 Leverkusen, Germany
| | - Laura Bergmann
- Med. Klinik 2, Klinikum Leverkusen, Academic Hospital of the University of Cologne, Am Gesundheitspark 11, D—51375 Leverkusen, Germany
| | - Henning Ernst Adamek
- Med. Klinik 2, Klinikum Leverkusen, Academic Hospital of the University of Cologne, Am Gesundheitspark 11, D—51375 Leverkusen, Germany
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8
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Al-Qadhi MA, Allam HA, Fahim SH, Yahya TAA, Ragab FAF. Design and synthesis of certain 7-Aryl-2-Methyl-3-Substituted Pyrazolo{1,5-a}Pyrimidines as multikinase inhibitors. Eur J Med Chem 2023; 262:115918. [PMID: 37922829 DOI: 10.1016/j.ejmech.2023.115918] [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: 08/11/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Four new series 7a-e, 8a-e, 9a-e, and 10a-e of 7-aryl-3-substituted pyrazolo[1,5-a]pyrimidines were synthesized and tested for their RTK and STK inhibitory activity. Compound 7d demonstrated potent enzymatic inhibitory activity against TrkA and ALK2 with IC50 0.087and 0.105 μM, respectively, and potent antiproliferative activity against KM12 and EKVX cell lines with IC50 0.82 and 4.13 μM, respectively. Compound 10e showed good enzyme inhibitory activity against TrkA, ALK2, c-KIT, EGFR, PIM1, CK2α, CHK1, and CDK2 in submicromolar values. Additionally 10e revealed antiproliferative activity against MCF7, HCT116 and EKVX with IC50 3.36, 1.40 and 3.49 μM, respectively; with good safety profile. Moreover, 10e showed cell cycle arrest at the G1/S phase and G1 phase in MCF7 and HCT116 cells with good apoptotic effect. Molecular docking studies were fulfilled for compound 10e and illustrated good interaction with the hot spots of the active site of the tested enzymes.
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Affiliation(s)
- Mustafa A Al-Qadhi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Sana'a University, P.O. Box, 18084, Sana'a, Yemen
| | - Heba Abdelrasheed Allam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box, 11562, Egypt.
| | - Samar H Fahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box, 11562, Egypt
| | - Tawfeek A A Yahya
- Department of Medicinal Chemistry, Faculty of Pharmacy, Sana'a University, P.O. Box, 18084, Sana'a, Yemen
| | - Fatma A F Ragab
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box, 11562, Egypt
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9
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Kundu S, Nunes L, Adler J, Mathot L, Stoimenov I, Sjöblom T. Recurring EPHB1 mutations in human cancers alter receptor signalling and compartmentalisation of colorectal cancer cells. Cell Commun Signal 2023; 21:354. [PMID: 38102712 PMCID: PMC10722860 DOI: 10.1186/s12964-023-01378-9] [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: 08/25/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Ephrin (EPH) receptors have been implicated in tumorigenesis and metastasis, but the functional understanding of mutations observed in human cancers is limited. We previously demonstrated reduced cell compartmentalisation for somatic EPHB1 mutations found in metastatic colorectal cancer cases. We therefore integrated pan-cancer and pan-EPH mutational data to prioritise recurrent EPHB1 mutations for functional studies to understand their contribution to cancer development and metastasis. METHODS Here, 79,151 somatic mutations in 9,898 samples of 33 different tumour types were analysed with a bioinformatic pipeline to find 3D-mutated cluster pairs and hotspot mutations in EPH receptors. From these, 15 recurring EPHB1 mutations were stably expressed in colorectal cancer followed by confocal microscopy based in vitro compartmentalisation assays and phospho-proteome analysis. RESULTS The 3D-protein structure-based bioinformatics analysis resulted in 63% EPHB1 mutants with compartmentalisation phenotypes vs 43% for hotspot mutations. Whereas the ligand-binding domain mutations C61Y, R90C, and R170W, the fibronectin domain mutation R351L, and the kinase domain mutation D762N displayed reduced to strongly compromised cell compartmentalisation, the kinase domain mutations R743W and G821R enhanced this phenotype. While mutants with reduced compartmentalisation also had reduced ligand induced receptor phosphorylation, the enhanced compartmentalisation was not linked to receptor phosphorylation level. Phosphoproteome mapping pinpointed the PI3K pathway and PIK3C2B phosphorylation in cells harbouring mutants with reduced compartmentalisation. CONCLUSIONS This is the first integrative study of pan-cancer EPH receptor mutations followed by in vitro validation, a robust way to identify cancer-causing mutations, uncovering EPHB1 mutation phenotypes and demonstrating the utility of protein structure-based mutation analysis in characterization of novel cancer genes. Video Abstract.
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Affiliation(s)
- Snehangshu Kundu
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Luís Nunes
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jeremy Adler
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ivaylo Stoimenov
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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10
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Sato JI, Onogi H, Nomura N, Hagiwara M, Inouye S. Bioluminescent immunoassay for serine/threonine protein kinase activity using an aequorin-labeled monoclonal antibody and a synthetic peptide as a substrate. Biochem Biophys Res Commun 2023; 681:180-185. [PMID: 37783115 DOI: 10.1016/j.bbrc.2023.09.062] [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: 08/30/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
A bioluminescent immunoassay system was developed to determine serine/threonine protein kinase activity using an aequorin-labeled monoclonal antibody and a synthetic peptide as the substrate. A monoclonal antibody against the synthetic phosphorylated serine peptide (K9P peptide) of histone H3 (19 amino acid residues), referred to as the H3S10P antibody, was chemically conjugated to maleimide-activated aequorin to prepare aequorin-labeled H3S10P (AQ-S-H3S10P). For the serine/threonine kinase assay, a non-phosphorylated serine peptide (K9C peptide) coated on a microplate was incubated with serine/threonine protein kinase in the presence of ATP and Mg2+. The resulting phosphorylated K9C peptides (K9P peptide) were identified using AQ-S-H3S10P. Thus, after the removal of unbound AQ-S-H3S10P though washing, the serine/threonine kinase activity was determined by the luminescence activity of aequorin from AQ-S-H3S10P bound to the K9P peptide. This assay system, in combination with the K9C peptide and AQ-S-H3S10P, could be used to screen inhibitors of various serine/threonine protein kinases in general.
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Affiliation(s)
- Jun-Ich Sato
- Yokohama Research Center, JNC Co., 5-1 Okawa, Kanazawa-ku, Yokohama, 236-8605, Japan
| | - Hiroshi Onogi
- KinoPharma, Inc. Kyoto-University Katsura Venture Plaza 1-39 Goryoohara, Nishikyo-ku, Kyoto, 615-8245, Japan.
| | - Namiko Nomura
- KinoPharma, Inc. Kyoto-University Katsura Venture Plaza 1-39 Goryoohara, Nishikyo-ku, Kyoto, 615-8245, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Satoshi Inouye
- Yokohama Research Center, JNC Co., 5-1 Okawa, Kanazawa-ku, Yokohama, 236-8605, Japan.
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11
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Welsh CL, Conklin AE, Madan LK. Crystal Structures Reveal Hidden Domain Mechanics in Protein Kinase A (PKA). BIOLOGY 2023; 12:1370. [PMID: 37997969 PMCID: PMC10669547 DOI: 10.3390/biology12111370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 11/25/2023]
Abstract
Cyclic-AMP-dependent protein kinase A (PKA) is a critical enzyme involved in various signaling pathways that plays a crucial role in regulating cellular processes including metabolism, gene transcription, cell proliferation, and differentiation. In this study, the mechanisms of allostery in PKA were investigated by analyzing the vast repertoire of crystal structures available in the RCSB database. From existing structures of murine and human PKA, we elucidated the conformational ensembles and protein dynamics that are altered in a ligand-dependent manner. Distance metrics to analyze conformations of the G-loop were proposed to delineate different states of PKA and were compared to existing structural metrics. Furthermore, ligand-dependent flexibility was investigated through normalized B'-factors to better understand the inherent dynamics in PKA. The presented study provides a contemporary approach to traditional methods in engaging the use of crystal structures for understanding protein dynamics. Importantly, our studies provide a deeper understanding into the conformational ensemble of PKA as the enzyme progresses through its catalytic cycle. These studies provide insights into kinase regulation that can be applied to both PKA individually and protein kinases as a class.
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Affiliation(s)
- Colin L. Welsh
- Department of Cellular and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Abigail E. Conklin
- Department of Cellular and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Lalima K. Madan
- Department of Cellular and Molecular Pharmacology and Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
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12
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Hernandez Garcia A, Nair SK. Structure and Function of a Class III Metal-Independent Lanthipeptide Synthetase. ACS CENTRAL SCIENCE 2023; 9:1944-1956. [PMID: 37901177 PMCID: PMC10604976 DOI: 10.1021/acscentsci.3c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 10/31/2023]
Abstract
In bacteria, Ser/Thr protein kinase-like sequences are found as part of large multidomain polypeptides that biosynthesize lanthipeptides, a class of natural products distinguished by the presence of thioether cross-links. The kinase domain phosphorylates Ser or Thr residues in the peptide substrates. Subsequent β-elimination by a lyase domain yields electrophilic dehydroamino acids, which can undergo cyclase domain-catalyzed cyclization to yield conformationally restricted, bioactive compounds. Here, we reconstitute the biosynthetic pathway for a class III lanthipeptide from Bacillus thuringiensis NRRL B-23139, including characterization of a two-component protease for leader peptide excision. We also describe the first crystal structures of a class III lanthipeptide synthetase, consisting of the lyase, kinase, and cyclase domains, in various states including complexes with its leader peptide and nucleotide. The structure shows interactions between all three domains that result in an active conformation of the kinase domain. Biochemical analysis demonstrates that the three domains undergo movement upon binding of the leader peptide to establish interdomain allosteric interactions that stabilize this active form. These studies inform on the regulatory mechanism of substrate recognition and provide a framework for engineering of variants of biotechnological interest.
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Affiliation(s)
- Andrea Hernandez Garcia
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Roger Adams
Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Roger Adams
Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
- Center
for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Roger Adams Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Drive, Urbana, Illinois 61801, United States
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13
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Polo-Cuadrado E, López-Cuellar L, Acosta-Quiroga K, Rojas-Peña C, Brito I, Cisterna J, Trilleras J, Alderete JB, Duarte Y, Gutiérrez M. Comprehensive analysis of crystal structure, spectroscopic properties, quantum chemical insights, and molecular docking studies of two pyrazolopyridine compounds: potential anticancer agents. RSC Adv 2023; 13:30118-30128. [PMID: 37849708 PMCID: PMC10578360 DOI: 10.1039/d3ra04874h] [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: 07/19/2023] [Accepted: 09/24/2023] [Indexed: 10/19/2023] Open
Abstract
In this study, two pyrazolo[3,4-b]pyridine derivatives (4a and 4b) were grown using a slow evaporation solution growth technique and characterized by FT-IR, HRMS, 1H/13C NMR spectroscopy, and X-ray crystallography. The 4a and 4b structures crystallized in monoclinic and triclinic systems with space groups P21/n and P1̄, respectively. Theoretical calculations were performed at the DFT/B3LYP level for the optimized geometries. The results were in excellent agreement with the experimental data (spectroscopic and XRD). This investigation encompasses molecular modeling studies including Hirshfeld surface analysis, energy framework calculations, and frontier molecular orbital analysis. Intermolecular interactions within the crystal structures of the compounds were explored through Hirshfeld surface analysis, which revealed the notable presence of hydrogen bonding and hydrophobic interactions. This insight provides valuable information on the structural stability and potential solubility characteristics of these compounds. The research was extended to docking analysis with eight distinct kinases (BRAF, HER2, CSF1R, MEK2, PDGFRA, JAK, AKT1, and AKT2). The results of this analysis demonstrate that both 4a and 4b interact effectively with the kinase-binding sites through a combination of hydrophobic interactions and hydrogen bonding. Compound 4a had the best affinity for proteins; this is related to the fact that the compound is not rigid and has a small size, allowing it to sit well at any binding site. This study contributes to the advancement of kinase inhibitor research and offers potential avenues for the development of new therapeutic agents for cancer treatment.
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Affiliation(s)
- Efraín Polo-Cuadrado
- Laboratorio Síntesis Orgánica y Actividad Biológica (LSO-Act-Bio), Instituto de Química de Recursos Naturales, Universidad de Talca Casilla 747 Talca 3460000 Chile
| | - Lorena López-Cuellar
- Laboratorio Síntesis Orgánica y Actividad Biológica (LSO-Act-Bio), Instituto de Química de Recursos Naturales, Universidad de Talca Casilla 747 Talca 3460000 Chile
- Universidad de la Amazonia, Programa de Química Cl. 17 Diagonal 17 con, Cra. 3F Florencia 180001 Colombia
| | - Karen Acosta-Quiroga
- Doctorado en Química, Departamento de Química Inorgánica y Analítica, Universidad de Chile Santiago Chile
| | - Cristian Rojas-Peña
- Doctorado en Química, Departamento de Química Inorgánica y Analítica, Universidad de Chile Santiago Chile
| | - Iván Brito
- Departamento de Química, Facultad de Ciencias Básicas, Universidad de Antofagasta Avenida. Universidad de Antofagasta, Campus Coloso Antofagasta 02800 Chile
| | - Jonathan Cisterna
- Departamento de Química, Facultad de Ciencias, Universidad Católica del Norte Sede Casa Central, Av. Angamos 0610 Antofagasta Chile
| | - Jorge Trilleras
- Grupo de Investigación en Compuestos Heterocíclicos, Universidad del Atlántico Puerto Colombia 081007 Colombia
| | - Joel B Alderete
- Instituto de Química de Recursos Naturales (IQRN), Universidad de Talca Avenida Lircay S/N, Casilla 747 Talca Chile
| | - Yorley Duarte
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad, Andrés Bello Av. Republica 330 Santiago 8370146 Chile
- Interdisciplinary Centre for Neuroscience of Valparaíso, Facultad de Ciencias, Universidad de Valparaíso Valparaíso 2381850 Chile
| | - Margarita Gutiérrez
- Laboratorio Síntesis Orgánica y Actividad Biológica (LSO-Act-Bio), Instituto de Química de Recursos Naturales, Universidad de Talca Casilla 747 Talca 3460000 Chile
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14
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Dedigama-Arachchige PM, Acharige NPN, Zhang X, Bremer HJ, Yi Z, Pflum MKH. Identification of PP1c-PPP1R12A Substrates Using Kinase-Catalyzed Biotinylation to Identify Phosphatase Substrates. ACS OMEGA 2023; 8:35628-35637. [PMID: 37810667 PMCID: PMC10552495 DOI: 10.1021/acsomega.3c01944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/21/2023] [Indexed: 10/10/2023]
Abstract
Protein phosphatase 1 regulatory subunit 12A (PPP1R12A) interacts with the catalytic subunit of protein phosphatase 1 (PP1c) to form the myosin phosphatase complex. In addition to a well-documented role in muscle contraction, the PP1c-PPP1R12A complex is associated with cytoskeleton organization, cell migration and adhesion, and insulin signaling. Despite the variety of biological functions, only a few substrates of the PP1c-PPP1R12A complex are characterized, which limit a full understanding of PP1c-PPP1R12A activities in muscle contraction and cytoskeleton regulation. Here, the chemoproteomics method Kinase-catalyzed Biotinylation to Identify Phosphatase Substrates (K-BIPS) was used to identify substrates of the PP1c-PPP1R12A complex in L6 skeletal muscle cells. K-BIPS enriched 136 candidate substrates with 14 high confidence hits. One high confidence hit, AKT1 kinase, was validated as a novel PP1c-PPP1R12A substrate. Given the previously documented role of AKT1 in PPP1R12A phosphorylation and cytoskeleton organization, the data suggest that PP1c-PPP1R12A regulates its own phosphatase activity through an AKT1-dependent feedback mechanism to influence cytoskeletal arrangement in muscle cells.
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Affiliation(s)
| | - Nuwan P N Acharige
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit 48202-3489, Michigan, United States
| | - Xiangmin Zhang
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Ave, Detroit 48201, Michigan, United States
| | - Hannah J Bremer
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit 48202-3489, Michigan, United States
| | - Zhengping Yi
- Department of Pharmaceutical Sciences, Wayne State University, 259 Mack Ave, Detroit 48201, Michigan, United States
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit 48202-3489, Michigan, United States
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15
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Kim Y, Ahmed S, Miller WT. Colorectal cancer-associated mutations impair EphB1 kinase function. J Biol Chem 2023; 299:105115. [PMID: 37527777 PMCID: PMC10463257 DOI: 10.1016/j.jbc.2023.105115] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
Erythropoietin-producing hepatoma (Eph) receptor tyrosine kinases regulate the migration and adhesion of cells that are required for many developmental processes and adult tissue homeostasis. In the intestinal epithelium, Eph signaling controls the positioning of cell types along the crypt-villus axis. Eph activity can suppress the progression of colorectal cancer (CRC). The most frequently mutated Eph receptor in metastatic CRC is EphB1. However, the functional effects of EphB1 mutations are mostly unknown. We expressed and purified the kinase domains of WT and five cancer-associated mutant EphB1 and developed assays to assess the functional effects of the mutations. Using purified proteins, we determined that CRC-associated mutations reduce the activity and stability of the folded structure of EphB1. By mammalian cell expression, we determined that CRC-associated mutant EphB1 receptors inhibit signal transducer and activator of transcription 3 and extracellular signal-regulated kinases 1 and 2 signaling. In contrast to the WT, the mutant EphB1 receptors are unable to suppress the migration of human CRC cells. The CRC-associated mutations also impair cell compartmentalization in an assay in which EphB1-expressing cells are cocultured with ligand (ephrin B1)-expressing cells. These results suggest that somatic mutations impair the kinase-dependent tumor suppressor function of EphB1 in CRC.
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Affiliation(s)
- Yunyoung Kim
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - Sultan Ahmed
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York, USA; Department of Veterans Affairs Medical Center, Northport, New York, USA.
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16
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Nam K, Tao Y, Ovchinnikov V. Molecular Simulations of Conformational Transitions within the Insulin Receptor Kinase Reveal Consensus Features in a Multistep Activation Pathway. J Phys Chem B 2023. [PMID: 37363953 DOI: 10.1021/acs.jpcb.3c01804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Modulating the transitions between active and inactive conformations of protein kinases is the primary means of regulating their catalytic activity, achieved by phosphorylation of the activation loop (A-loop). To elucidate the mechanism of this conformational activation, we applied the string method to determine the conformational transition path of insulin receptor kinase between the active and inactive conformations and the corresponding free-energy profiles with and without A-loop phosphorylation. The conformational change was found to proceed in three sequential steps: first, the flipping of the DFG motif of the active site; second, rotation of the A-loop; finally, the inward movement of the αC helix. The main energetic bottleneck corresponds to the conformational change in the A-loop, while changes in the DFG motif and αC helix occur before and after A-loop conformational change, respectively. In accordance with this, two intermediate states are identified, the first state just after the DFG flipping and the second state after the A-loop rotation. These intermediates exhibit structural features characteristic of the corresponding inactive and active conformations of other protein kinases. To understand the impact of A-loop phosphorylation on kinase conformation, the free energies of A-loop phosphorylation were determined at several states along the conformational transition path using the free-energy perturbation simulations. The calculated free energies reveal that while the unphosphorylated kinase interconverts between the inactive and active conformations, A-loop phosphorylation restricts access to the inactive conformation, thereby increasing the active conformation population. Overall, this study suggests a consensus mechanism of conformational activation between different protein kinases.
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Affiliation(s)
- Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yunwen Tao
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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17
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Beltman RJ, Herppich AA, Bremer HJ, Pflum MKH. Affinity-Based Kinase-Catalyzed Crosslinking to Study Kinase-Substrate Pairs. Bioconjug Chem 2023; 34:1054-1060. [PMID: 37279085 PMCID: PMC10648467 DOI: 10.1021/acs.bioconjchem.3c00131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Phosphorylation of proteins by kinase enzymes is a post-translational modification involved in a myriad of biological events, including cell signaling and disease development. Identifying the interactions between a kinase and its phosphorylated substrate(s) is necessary to characterize phosphorylation-mediated cellular events and encourage development of kinase-targeting drugs. One method for substrate-kinase identification utilizes photocrosslinking γ-phosphate-modified ATP analogues to covalently link kinases to their substrates for subsequent monitoring. Because photocrosslinking ATP analogues require UV light, which could influence cell biology, we report here two ATP analogues, ATP-aryl fluorosulfate (ATP-AFS) and ATP-hexanoyl bromide (ATP-HexBr), that crosslink kinase-substrate pairs via proximity-mediated reactions without the need for UV irradiation. Both ATP-AFS and ATP-HexBr acted as cosubstrates with a variety of kinases for affinity-based crosslinking, with ATP-AFS showing more robust complexes. Importantly, ATP-AFS promoted crosslinking in lysates, which demonstrates compatibility with complex cellular mixtures for future application to kinase-substrate identification.
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Affiliation(s)
- Rachel J Beltman
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Andrew A Herppich
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Hannah J Bremer
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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18
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Bhattarai S, Marsh L, Knight K, Ali L, Gomez A, Sunderhaus A, Abdel Aziz MH. NH125 Sensitizes Staphylococcus aureus to Cell Wall-Targeting Antibiotics through the Inhibition of the VraS Sensor Histidine Kinase. Microbiol Spectr 2023; 11:e0486122. [PMID: 37227302 PMCID: PMC10269531 DOI: 10.1128/spectrum.04861-22] [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: 11/25/2022] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
Staphylococcus aureus utilizes the two-component regulatory system VraSR to receive and relay environmental stress signals, and it is implicated in the development of bacterial resistance to several antibiotics through the upregulation of cell wall synthesis. VraS inhibition was shown to extend or restore the efficacy of several clinically used antibiotics. In this work, we study the enzymatic activity of the VraS intracellular domain (GST-VraS) to determine the kinetic parameters of the ATPase reaction and characterize the inhibition of NH125 under in vitro and microbiological settings. The rate of the autophosphorylation reaction was determined at different GST-VraS concentrations (0.95 to 9.49 μM) and temperatures (22 to 40°C) as well as in the presence of different divalent cations. The activity and inhibition by NH125, which is a known kinase inhibitor, were assessed in the presence and absence of the binding partner, VraR. The effects of inhibition on the bacterial growth kinetics and gene expression levels were determined. The GST-VraS rate of autophosphorylation increases with temperature and with the addition of VraR, with magnesium being the preferred divalent cation for the metal-ATP substrate complex. The mechanism of inhibition of NH125 was noncompetitive in nature and was attenuated in the presence of VraR. The addition of NH125 in the presence of sublethal doses of the cell wall-targeting antibiotics carbenicillin and vancomycin led to the complete abrogation of Staphylococcus aureus Newman strain growth and significantly decreased the gene expression levels of pbpB, blaZ, and vraSR in the presence of the antibiotics. IMPORTANCE This work characterizes the activity and inhibition of VraS, which is a key histidine kinase in a bacterial two-component system that is involved in Staphylococcus aureus antibiotic resistance. The results show the effect of temperature, divalent ions, and VraR on the activity and the kinetic parameters of ATP binding. The value of the KM of ATP is vital in designing screening assays to discover potent and effective VraS inhibitors with high translational potential. We report the ability of NH125 to inhibit VraS in vitro in a noncompetitive manner and investigate its effect on gene expression and bacterial growth kinetics in the presence and absence of cell wall-targeting antibiotics. NH125 effectively potentiated the effects of the antibiotics on bacterial growth and altered the expression of the genes that are regulated by VraS and are involved in mounting a resistance to antibiotics.
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Affiliation(s)
- Shrijan Bhattarai
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Lane Marsh
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Kelsey Knight
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Liaqat Ali
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Antonio Gomez
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - Allison Sunderhaus
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
| | - May H. Abdel Aziz
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, Texas, USA
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19
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Chang CH, Few LL, Lim BH, Yvonne-Tee GB, Chew AL, See Too WC. Unusual metal ion cofactor requirement of Entamoeba histolytica choline and ethanolamine kinase isoforms. Parasitol Res 2023:10.1007/s00436-023-07869-5. [PMID: 37202563 DOI: 10.1007/s00436-023-07869-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
The de novo biosynthesis of phosphatidylcholine and phosphatidylethanolamine in Entamoeba histolytica is largely dependent on the CDP-choline and CDP-ethanolamine pathways. Although the first enzymes of these pathways, EhCK1 and EhCK2, have been previously characterized, their enzymatic activity was found to be low and undetectable, respectively. This study aimed to identify the unusual characteristics of these enzymes in this deadly parasite. The discovery that EhCKs prefer Mn2+ over the typical Mg2+ as a metal ion cofactor is intriguing for CK/EK family of enzymes. In the presence of Mn2+, the activity of EhCK1 increased by approximately 108-fold compared to that in Mg2+. Specifically, in Mg2+, EhCK1 exhibited a Vmax and K0.5 of 3.5 ± 0.1 U/mg and 13.9 ± 0.2 mM, respectively. However, in Mn2+, it displayed a Vmax of 149.1 ± 2.5 U/mg and a K0.5 of 9.5 ± 0.1 mM. Moreover, when Mg2+ was present at a constant concentration of 12 mM, the K0.5 value for Mn2+ was ~ 2.4-fold lower than that in Mn2+ alone, without affecting its Vmax. Although the enzyme efficiency of EhCK1 was significantly improved by about 25-fold in Mn2+, it is worth noting that its Km for choline and ATP were higher than in equimolar of Mg2+ in a previous study. In contrast, EhCK2 showed specific activity towards ethanolamine in Mn2+, exhibiting Michaelis-Menten kinetic with ethanolamine (Km = 312 ± 27 µM) and cooperativity with ATP (K0.5 = 2.1 ± 0.2 mM). Additionally, we investigated the effect of metal ions on the substrate recognition of human choline and ethanolamine kinase isoforms. Human choline kinase α2 was found to absolutely require Mg2+, while choline kinase β differentially recognized choline and ethanolamine in Mg2+ and Mn2+, respectively. Finally, mutagenesis studies revealed that EhCK1 Tyr129 was critical for Mn2+ binding, while Lys233 was essential for substrate catalysis but not metal ion binding. Overall, these findings provide insight into the unique characteristics of the EhCKs and highlight the potential for new approaches to treating amoebiasis. Amoebiasis is a challenging disease for clinicians to diagnose and treat, as many patients are asymptomatic. However, by studying the enzymes involved in the CDP-choline and CDP-ethanolamine pathways, which are crucial for de novo biosynthesis of phosphatidylcholine and phosphatidylethanolamine in Entamoeba histolytica, there is great potential to discover new therapeutic approaches to combat this disease.
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Affiliation(s)
- Chiat Han Chang
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Ling Ling Few
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Boon Huat Lim
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Get Bee Yvonne-Tee
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Ai Lan Chew
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
| | - Wei Cun See Too
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
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20
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Fatti E, Hirth A, Švorinić A, Günther M, Stier G, Cruciat CM, Acebrón SP, Papageorgiou D, Sinning I, Krijgsveld J, Höfer T, Niehrs C. DEAD box RNA helicases act as nucleotide exchange factors for casein kinase 2. Sci Signal 2023; 16:eabp8923. [PMID: 37098120 DOI: 10.1126/scisignal.abp8923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
DDX RNA helicases promote RNA processing, but DDX3X also activates casein kinase 1 (CK1ε). We show that other DDX proteins also stimulate the protein kinase activity of CK1ε and that this extends to casein kinase 2 (CK2). CK2 enzymatic activity was stimulated by various DDX proteins at high substrate concentrations. DDX1, DDX24, DDX41, and DDX54 were required for full kinase activity in vitro and in Xenopus embryos. Mutational analysis of DDX3X indicated that CK1 and CK2 kinase stimulation engages its RNA binding but not catalytic motifs. Mathematical modeling of enzyme kinetics and stopped-flow spectroscopy showed that DDX proteins function as nucleotide exchange factors toward CK2 and reduce unproductive reaction intermediates and substrate inhibition. Our study reveals protein kinase stimulation by nucleotide exchange as important for kinase regulation and as a generic function of DDX proteins.
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Affiliation(s)
- Edoardo Fatti
- Division of Molecular Embryology, DKFZ-ZMBH-Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls University of Heidelberg, 69120 Heidelberg, Germany
| | - Alexander Hirth
- Division of Molecular Embryology, DKFZ-ZMBH-Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls University of Heidelberg, 69120 Heidelberg, Germany
| | - Andrea Švorinić
- Division of Molecular Embryology, DKFZ-ZMBH-Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
- Faculty of Biosciences, Ruprecht-Karls University of Heidelberg, 69120 Heidelberg, Germany
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
| | - Matthias Günther
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Gunter Stier
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
| | - Cristina-Maria Cruciat
- Division of Molecular Embryology, DKFZ-ZMBH-Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Sergio P Acebrón
- Division of Molecular Embryology, DKFZ-ZMBH-Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Dimitris Papageorgiou
- Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
- Medical Faculty, Heidelberg University, Im Neuenheimer Feld 672, 69120 Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), 69120 Heidelberg, Germany
| | - Jeroen Krijgsveld
- Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
- Medical Faculty, Heidelberg University, Im Neuenheimer Feld 672, 69120 Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christof Niehrs
- Division of Molecular Embryology, DKFZ-ZMBH-Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
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21
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Zhang Y, Chen X, Feng J, Shen Y, Huang Y. The proteome and phosphoproteome uncovers candidate proteins associated with vacuolar phosphate signal multipled by Vacuolar phosphate transporter1 (VPT1) in Arabidopsis. Mol Cell Proteomics 2023; 22:100549. [PMID: 37076046 DOI: 10.1016/j.mcpro.2023.100549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/15/2023] [Accepted: 04/06/2023] [Indexed: 04/21/2023] Open
Abstract
Plant vacuoles serve as the primary intracellular compartments for inorganic phosphate (Pi) storage. Passage of Pi across vacuolar membranes plays a critical role in buffering the cytoplasmic Pi level against fluctuations of external Pi and metabolic activities. To gain new insights into the proteins and processes vacuolar Pi level regulated by Vacuolar phosphate transporter1 (VPT1) in Arabidopsis, we carried out TMT labeling proteome and phosphoproteome profiling of Arabidopsis wild-type (WT) and vpt1 loss-of-function mutant plants. The vpt1 mutant had a marked reduced vacuolar Pi level, and an slight increased cytosol Pi level. The mutant was stunted as reflected in the reduction of the fresh weight compared with WT plants, and bolting earlier under normal growth conditions in soil. Over 5566 proteins and 7965 phosphopeptides were quantified. About 146 and 83 proteins were significantly changed at protein abundance or site-specific phosphorylation levels, but only 6 proteins were shared between them. Functional enrichment analysis revealed that the changes of Pi states in vpt1 is associated with photosynthesis, translation, RNA splicing, and defense response, consistent with similar studies in Arabidopsis. Except for PAP26, EIN2, and KIN10, which were reported to be associated with phosphate starvation signal, we also found many differential proteins involved in abscisic acid (ABA) signaling, such as CARK1, SnRK1, and AREB3, were significantly changed in vpt1. Our study illuminates several new aspects of the phosphate response and identifies important targets for further investigation and potential crop improvement.
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Affiliation(s)
- Yanjun Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Xuexue Chen
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Jinjing Feng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yuanyue Shen
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yun Huang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
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Madan LK, Welsh CL, Kornev AP, Taylor SS. The "violin model": Looking at community networks for dynamic allostery. J Chem Phys 2023; 158:081001. [PMID: 36859094 PMCID: PMC9957607 DOI: 10.1063/5.0138175] [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: 12/09/2022] [Accepted: 02/03/2023] [Indexed: 02/09/2023] Open
Abstract
Allosteric regulation of proteins continues to be an engaging research topic for the scientific community. Models describing allosteric communication have evolved from focusing on conformation-based descriptors of protein structural changes to appreciating the role of internal protein dynamics as a mediator of allostery. Here, we explain a "violin model" for allostery as a contemporary method for approaching the Cooper-Dryden model based on redistribution of protein thermal fluctuations. Based on graph theory, the violin model makes use of community network analysis to functionally cluster correlated protein motions obtained from molecular dynamics simulations. This Review provides the theory and workflow of the methodology and explains the application of violin model to unravel the workings of protein kinase A.
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Affiliation(s)
- Lalima K. Madan
- Author to whom correspondence should be addressed: and . Telephone: 843.792.4525. Fax: 843.792.0481
| | - Colin L. Welsh
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Ave., Charleston, South Carolina 29425, USA
| | - Alexandr P. Kornev
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, San Diego, California, 92093, USA
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23
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Cui X, Du X, Zhao Q, Hu Y, Tian C, Song W. Efficient synthesis of Ala-Tyr by L-amino acid ligase coupled with ATP regeneration system. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04365-5. [PMID: 36689158 DOI: 10.1007/s12010-023-04365-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2023] [Indexed: 01/24/2023]
Abstract
The multi-enzyme coupling reaction system has become a promising biomanufacturing platform for biochemical production. Tyr is an essential amino acid, but the limited solubility restricts its use. Tyrosyl dipeptide has been paid more attention due to its higher solubility. In this study, an efficient enzymatic cascade of Ala-Tyr synthesis was developed by a L-amino acid ligase together with polyphosphate kinase (PPK). Two L-amino acid ligases from Bacillus subtilis and Bacillus pumilus were selected and applied for Ala-Tyr synthesis. The L-amino acid ligase from B. subtilis (Bs) was selected and coupled with the PPK from Sulfurovum lithotrophicum (PPKSL) for regenerating ATP to produce Ala-Tyr in one pot. In the optimization system, 40.1 mM Ala-Tyr was produced within 3 h due to efficient ATP regeneration with hexametaphosphate (PolyP(6)) as the phosphate donor. The molar yield was 0.89 mol/mol based on the substrates added, while the productivity of Ala-Tyr achieved 13.4 mM/h, which were the highest yield and productivity ever reported about Ala-Tyr synthesis with L-amino acid ligase.
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Affiliation(s)
- Xiangwei Cui
- School of Life Science and Bioengineering, Jining University, Jining, 273155, China
| | - Xinxin Du
- School of Life Science and Bioengineering, Jining University, Jining, 273155, China
| | - Qiang Zhao
- School of Life Science and Bioengineering, Jining University, Jining, 273155, China
| | - Yanying Hu
- School of Life Science and Bioengineering, Jining University, Jining, 273155, China
| | - Caihong Tian
- School of Life Science and Bioengineering, Jining University, Jining, 273155, China
| | - Wenlu Song
- School of Engineering, Jining University, Jining, 273155, China.
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24
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Zhang Y, Wang S, Ren A, Guan S, Jingwen E, Luo Z, Yang Z, Zhang X, Du J, Zhang H. Molecular dynamics simulation study on the inhibitory mechanism of RIPK1 by 4,5-dihydropyrazole derivatives. Mol Phys 2023. [DOI: 10.1080/00268976.2023.2166612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yurou Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Aimin Ren
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Shanshan Guan
- College of Biology and Food Engineering, Jilin Engineering Normal University, Changchun, People’s Republic of China
- Key Laboratory of Molecular Nutrition at Universities of Jilin Province, Changchun, People’s Republic of China
| | - E Jingwen
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Zhijian Luo
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Zhijie Yang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Xinyue Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Juan Du
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Hao Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
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25
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Ray Chaudhuri N, Ghosh Dastidar S. Allosteric Boost by TAB1 on the TAK1 Kinase Favorably Sculpts the Thermodynamic Landscape of Activation. J Chem Inf Model 2023; 63:224-239. [PMID: 36374995 DOI: 10.1021/acs.jcim.2c00778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The intricate mechanisms of allosteric regulation in kinases are of general interest to the scientific community for potential therapeutic implications. However, the diversity among kinases and their regulatory routes requires a case-by-case study to widen the repertoire of known mechanisms. The present study achieves this by understanding TAK1 kinase activation by TAB1 as a model phenomenon for the first time. Despite the known capacity of TAK1 to switch between its inactive ("DFG-out") and active-like ("DFG-in") conformations, the questionable role of TAB1 in offering an energetic favor to this has been addressed here using sequential combination of enhanced sampling methods like targeted molecular dynamics (TMD) and Gaussian accelerated molecular dynamics (GaMD). It reveals how a minimal domain of TAB1 sufficiently acts like a "catalytic gear" by favorably sculpting TAK1's thermodynamic landscape (potential of mean force in 2D) that accelerates "in"-"out" conformational switching of the conserved DFG motif. Standard molecular dynamics simulations (∼5 μs) reveal that TAB1 fascinatingly exploits the "lever-like" αF helix of TAK1 kinase domain to remotely propel the DFG motif via subtle helical "unfolding-folding" modifications within the kinase activation loop. The presence of two charged residues on terminal poles of αF helix imparts it, with this unique "lever-like" utility, and this turns out to be one important signature of co-evolution between TAK1 and TAB1. The entire mechanism of TAB1's impact transduction, which is found to be analogous to the moves in the popular "Chinese checker" game, gives a clear proof of the "dynamics-driven allostery" concept in kinases. The findings further benchmark TAK1's known autophosphorylation capacity. A novel insight into kinase allostery is thus provided, which potentiates investigation of similar capacities in other kinases.
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Affiliation(s)
- Nibedita Ray Chaudhuri
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata700054, India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata700054, India
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26
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Systematic Exploration of Privileged Warheads for Covalent Kinase Drug Discovery. Pharmaceuticals (Basel) 2022; 15:ph15111322. [PMID: 36355497 PMCID: PMC9695834 DOI: 10.3390/ph15111322] [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: 08/12/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 12/01/2022] Open
Abstract
Kinase-targeted drug discovery for cancer therapy has advanced significantly in the last three decades. Currently, diverse kinase inhibitors or degraders have been reported, such as allosteric inhibitors, covalent inhibitors, macrocyclic inhibitors, and PROTAC degraders. Out of these, covalent kinase inhibitors (CKIs) have been attracting attention due to their enhanced selectivity and exceptionally strong affinity. Eight covalent kinase drugs have been FDA-approved thus far. Here, we review current developments in CKIs. We explore the characteristics of the CKIs: the features of nucleophilic amino acids and the preferences of electrophilic warheads. We provide systematic insights into privileged warheads for repurposing to other kinase targets. Finally, we discuss trends in CKI development across the whole proteome.
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27
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Sueca-Comes M, Rusu EC, Grabowska AM, Bates DO. Looking Under the Lamppost: The Search for New Cancer Targets in the Human Kinome. Pharmacol Rev 2022; 74:1136-1145. [PMID: 36180110 DOI: 10.1124/pharmrev.121.000410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 02/02/2022] [Accepted: 02/15/2022] [Indexed: 11/22/2022] Open
Abstract
The number of cancer drugs is increasing as new chemical entities are developed to target molecules, often protein kinases, driving cancer progression. In 2009, Fedorov et al. identified that of the protein kinases in the human kinome, most of the focus has been on a small subset. They highlighted that many poorly investigated protein kinases were cancer drivers, but there was no relationship between publications and involvement in cancer development or progression. Since 2009, there has been a doubling in the number of publications, patents, and drugs targeting the kinome. To determine whether this was an expansion in knowledge of well-studied targets-searching in the light under the lamppost-or an explosion of investigations into previously poorly investigated targets, we searched the literature for publications on each kinase, updating Federov et al.'s assessment of the druggable kinome. The proportion of papers focusing on the 50 most-studied kinases had not changed, and the makeup of those 50 had barely changed. The majority of new drugs (80%) were against the same group of 50 kinases identified as targets 10 years ago, and the proportion of studies investigating previously poorly investigated kinases (<1%) was unchanged. With three exceptions [p38 mitogenactivated protein kinase (p38a), AMP-activated protein kinase catalytic α-subunit 1,2, and B-Raf proto-oncogene (BRAF) serine/threonine kinase], >95% of publications addressing kinases still focused on a relatively small proportion (<50%) of the human kinome independently of their involvement as cancer drivers. There is, therefore, still extensive scope for discovery of therapeutics targeting different protein kinases in cancer and still a bias toward well-characterized targets over the innovative searchlight into the unknown. SIGNIFICANCE STATEMENT: This study presents evidence that drug discovery efforts in cancer are still to some extent focused on a narrow group of well-studied kinases 10 years after the identification of multiple novel cancer targets in the human kinome. This suggests that there is still room for researchers in academia, industry, and the not-for-profit sector to develop new and diverse therapies targeting kinases for cancer.
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Affiliation(s)
- Mireia Sueca-Comes
- Division of Cancer and Stem Cells, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom (M.S.-C., A.M.G., D.O.B.); Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Consejo Superior de Investigaciones Científicas, Valencia, Spain (E.C.R.); and SeqPlexing SL, Valencia, Spain (E.C.R.)
| | - Elena Cristina Rusu
- Division of Cancer and Stem Cells, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom (M.S.-C., A.M.G., D.O.B.); Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Consejo Superior de Investigaciones Científicas, Valencia, Spain (E.C.R.); and SeqPlexing SL, Valencia, Spain (E.C.R.)
| | - Anna M Grabowska
- Division of Cancer and Stem Cells, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom (M.S.-C., A.M.G., D.O.B.); Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Consejo Superior de Investigaciones Científicas, Valencia, Spain (E.C.R.); and SeqPlexing SL, Valencia, Spain (E.C.R.)
| | - David O Bates
- Division of Cancer and Stem Cells, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom (M.S.-C., A.M.G., D.O.B.); Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Consejo Superior de Investigaciones Científicas, Valencia, Spain (E.C.R.); and SeqPlexing SL, Valencia, Spain (E.C.R.)
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28
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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: 0] [Impact Index Per Article: 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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29
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Brauer EK, Ahsan N, Popescu GV, Thelen JJ, Popescu SC. Back From the Dead: The Atypical Kinase Activity of a Pseudokinase Regulator of Cation Fluxes During Inducible Immunity. FRONTIERS IN PLANT SCIENCE 2022; 13:931324. [PMID: 36035673 PMCID: PMC9403797 DOI: 10.3389/fpls.2022.931324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Pseudokinases are thought to lack phosphotransfer activity due to altered canonical catalytic residues within their kinase domain. However, a subset of pseudokinases maintain activity through atypical phosphotransfer mechanisms. The Arabidopsis ILK1 is a pseudokinase from the Raf-like MAP3K family and is the only known plant pseudokinase with confirmed protein kinase activity. ILK1 activity promotes disease resistance and molecular pattern-induced root growth inhibition through its stabilization of the HAK5 potassium transporter with the calmodulin-like protein CML9. ILK1 also has a kinase-independent function in salt stress suggesting that it interacts with additional proteins. We determined that members of the ILK subfamily are the sole pseudokinases within the Raf-like MAP3K family and identified 179 novel putative ILK1 protein interactors. We also identified 70 novel peptide targets for ILK1, the majority of which were phosphorylated in the presence of Mn2+ instead of Mg2+ in line with modifications in ILK1's DFG cofactor binding domain. Overall, the ILK1-targeted or interacting proteins included diverse protein types including transporters (HAK5, STP1), protein kinases (MEKK1, MEKK3), and a cytokinin receptor (AHK2). The expression of 31 genes encoding putative ILK1-interacting or phosphorylated proteins, including AHK2, were altered in the root and shoot in response to molecular patterns suggesting a role for these genes in immunity. We describe a potential role for ILK1 interactors in the context of cation-dependent immune signaling, highlighting the importance of K+ in MAMP responses. This work further supports the notion that ILK1 is an atypical kinase with an unusual cofactor dependence that may interact with multiple proteins in the cell.
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Affiliation(s)
- Elizabeth K. Brauer
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, United States
| | - Nagib Ahsan
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - George V. Popescu
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
| | - Jay J. Thelen
- Department of Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Sorina C. Popescu
- Boyce Thompson Institute for Plant Research, Ithaca, NY, United States
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30
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Stein RL, Wilson DM. Kinetic and Mechanistic Studies of the Terminal Uridylyltransferase, Zcchc11 (TUT4). Biochemistry 2022; 61:1614-1624. [PMID: 35797480 DOI: 10.1021/acs.biochem.2c00146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Zcchc11 (TUT4, TENT3A, Z11) is a nucleotidyltransferase that catalyzes the 3'-polyuridylation of RNA. Our interest in this enzyme stems from its role in blocking the biogenesis of let-7, a family of microRNAs whose members act as tumor suppressors. Z11 polyuridylates pre-let-7, the precursor of let-7, when pre-let-7 is complexed with LIN28, an RNA-binding protein. Polyuridylation of pre-let-7 marks it for degradation. In addition to this LIN28-dependent activity, Z11 also has LIN28-independent activities. In this paper, we report the results of experiments that characterize LIN28-independent activities of Z11. Significant observations include the following. (1) Z11 uridylates not only mature let-7 species but also substrates as small as dinucleotides. (2) For both let-7i and the diribonucleotide AG, Z11 follows a steady-state ordered mechanism, with UTP adding before RNA. (3) Uridylation kinetics of let-7i (UGAGGUAGUAGUUUGUGCUGUU) and two truncated derivatives, GCUGUU and UU, indicate that Z11 manifests selectivity in Km,RNA; kcat,RNA values for the three substrates are nearly identical. (4) Z11 preferentially uridylates RNA lacking base-pairing near the 3' terminus. (5) Selectivity of Z11 toward ribonucleoside triphosphates is similar for let-7i and AG, with XTP preference: UTP > CTP > ATP ≫ GTP. Selectivity is manifested in Km,XTP, with kcat,XTP values being similar for UTP, CTP, and ATP. (6) Kinetic parameters for RNA turnover are dependent on the structure of the nucleoside triphosphate, consistent with recent structural data indicating stacking of the nucleoside triphosphate base with the base of the 3'-nucleotide of the substrate RNA (Faehnle et al., Nat. Struct. Mol. Biol. 2017, 24, 658).
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Affiliation(s)
- Ross L Stein
- Twentyeight-Seven Therapeutics, 490 Arsenal Way, Watertown, Massachusetts 02472, United States
| | - David M Wilson
- Twentyeight-Seven Therapeutics, 490 Arsenal Way, Watertown, Massachusetts 02472, United States
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31
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Yang J, Zhao Y, Yang B. Different binding modes of human centrin with peptides of Kar1p, Rad4 and Sfi1. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.113940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Koehler TJ, Tran T, Weingartner KA, Kavran JM. Kinetic Regulation of the Mammalian Sterile 20-like Kinase 2 (MST2). Biochemistry 2022; 61:1683-1693. [PMID: 35895874 PMCID: PMC10167949 DOI: 10.1021/acs.biochem.2c00022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Canonically, MST1/2 functions as a core kinase of the Hippo pathway and noncanonically during both apoptotic signaling and with RASSFs in T-cells. Faithful signal transduction by MST1/2 relies on both appropriate activation and regulated substrate phosphorylation by the activated kinase. Considerable progress has been made in understanding the molecular mechanisms regulating the activation of MST1/2 and identifying downstream signaling events. Here, we investigated the ability of MST2 to phosphorylate a peptide substrate and how that activity is regulated. Using a steady-state kinetic system, we parse the contribution of different factors to substrate phosphorylation, including the domains of MST2, phosphorylation, caspase cleavage, and complex formation. We found that in the unphosphorylated state, the SARAH domain stabilizes interactions with a peptide substrate and promotes turnover. Phosphorylation drives the activity of MST2, and once activated, MST2 is not further regulated by complex formation with other Hippo pathway components (SAV1, MOB1A, and RASSF5). We also show that the phosphorylated, caspase-cleaved MST2 is as active as the full-length one, suggesting that caspase-stimulated activity arises through noncatalytic mechanisms. The kinetic analysis presented here establishes a framework for interpreting how signaling events and post-translational modifications contribute to the signaling of MST2 in vivo.
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Affiliation(s)
- Thomas J Koehler
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Thao Tran
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Kyler A Weingartner
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Jennifer M Kavran
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
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Abstract
The nitrogen mustards are powerful cytotoxic and lymphoablative agents and have been used for more than 60 years. They are employed in the treatment of cancers, sarcomas, and hematologic malignancies. Cyclophosphamide, the most versatile of the nitrogen mustards, also has a place in stem cell transplantation and the therapy of autoimmune diseases. Adverse effects caused by the nitrogen mustards on the central nervous system, kidney, heart, bladder, and gonads remain important issues. Advances in analytical techniques have facilitated the investigation of the pharmacokinetics of the nitrogen mustards, especially the oxazaphosphorines, which are prodrugs requiring metabolic activation. Enzymes involved in the metabolism of cyclophosphamide and ifosfamide are very polymorphic, but a greater understanding of the pharmacogenomic influences on their activity has not yet translated into a personalized medicine approach. In addition to damaging DNA, the nitrogen mustards can act through other mechanisms, such as antiangiogenesis and immunomodulation. The immunomodulatory properties of cyclophosphamide are an area of current exploration. In particular, cyclophosphamide decreases the number and activity of regulatory T cells, and the interaction between cyclophosphamide and the intestinal microbiome is now recognized as an important factor. New derivatives of the nitrogen mustards continue to be assessed. Oxazaphosphorine analogs have been synthesized in attempts to both improve efficacy and reduce toxicity, with varying degrees of success. Combinations of the nitrogen mustards with monoclonal antibodies and small-molecule targeted agents are being evaluated. SIGNIFICANCE STATEMENT: The nitrogen mustards are important, well-established therapeutic agents that are used to treat a variety of diseases. Their role is continuing to evolve.
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Affiliation(s)
- Martin S Highley
- Plymouth Oncology Centre, Derriford Hospital, and Peninsula Medical School, University of Plymouth, Plymouth, United Kingdom (M.S.H.); Department of Animal Physiology and Neurobiology (B.L.) and Laboratory for Experimental Oncology (E.A.D.B.), University of Leuven, Leuven, Belgium; Oncology Department, University Hospital Antwerp, Edegem, Belgium (H.P.); and London Oncology Clinic, London, United Kingdom (P.G.H.)
| | - Bart Landuyt
- Plymouth Oncology Centre, Derriford Hospital, and Peninsula Medical School, University of Plymouth, Plymouth, United Kingdom (M.S.H.); Department of Animal Physiology and Neurobiology (B.L.) and Laboratory for Experimental Oncology (E.A.D.B.), University of Leuven, Leuven, Belgium; Oncology Department, University Hospital Antwerp, Edegem, Belgium (H.P.); and London Oncology Clinic, London, United Kingdom (P.G.H.)
| | - Hans Prenen
- Plymouth Oncology Centre, Derriford Hospital, and Peninsula Medical School, University of Plymouth, Plymouth, United Kingdom (M.S.H.); Department of Animal Physiology and Neurobiology (B.L.) and Laboratory for Experimental Oncology (E.A.D.B.), University of Leuven, Leuven, Belgium; Oncology Department, University Hospital Antwerp, Edegem, Belgium (H.P.); and London Oncology Clinic, London, United Kingdom (P.G.H.)
| | - Peter G Harper
- Plymouth Oncology Centre, Derriford Hospital, and Peninsula Medical School, University of Plymouth, Plymouth, United Kingdom (M.S.H.); Department of Animal Physiology and Neurobiology (B.L.) and Laboratory for Experimental Oncology (E.A.D.B.), University of Leuven, Leuven, Belgium; Oncology Department, University Hospital Antwerp, Edegem, Belgium (H.P.); and London Oncology Clinic, London, United Kingdom (P.G.H.)
| | - Ernst A De Bruijn
- Plymouth Oncology Centre, Derriford Hospital, and Peninsula Medical School, University of Plymouth, Plymouth, United Kingdom (M.S.H.); Department of Animal Physiology and Neurobiology (B.L.) and Laboratory for Experimental Oncology (E.A.D.B.), University of Leuven, Leuven, Belgium; Oncology Department, University Hospital Antwerp, Edegem, Belgium (H.P.); and London Oncology Clinic, London, United Kingdom (P.G.H.)
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34
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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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35
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Mao J, Zhu K, Long Z, Zhang H, Xiao B, Xi W, Wang Y, Huang J, Liu J, Shi X, Jiang H, Lu T, Wen Y, Zhang N, Meng Q, Zhou H, Ruan Z, Wang J, Luo C, Xi X. Targeting the RT loop of Src SH3 in Platelets Prevents Thrombosis without Compromising Hemostasis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103228. [PMID: 35023301 PMCID: PMC8895158 DOI: 10.1002/advs.202103228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/30/2021] [Indexed: 05/05/2023]
Abstract
Conventional antiplatelet agents indiscriminately inhibit both thrombosis and hemostasis, and the increased bleeding risk thus hampers their use at more aggressive dosages to achieve adequate effect. Blocking integrin αIIbβ3 outside-in signaling by separating the β3/Src interaction, yet to be proven in vivo, may nonetheless resolve this dilemma. Identification of a specific druggable target for this strategy remains a fundamental challenge as Src SH3 is known to be responsible for binding to not only integrin β3 but also the proteins containing the PXXP motif. In vitro and in vivo mutational analyses show that the residues, especially E97, in the RT loop of Src SH3 are critical for interacting with β3. DCDBS84, a small molecule resulting from structure-based virtual screening, is structurally validated to be directed toward the projected target. It specifically disrupts β3/Src interaction without affecting canonical PXXP binding and thus inhibits the outside-in signaling-regulated platelet functions. Treatment of mice with DCDBS84 causes a profound inhibition of thrombosis, equivalent to that induced by extremely high doses of αIIbβ3 antagonist, but does not compromise primary hemostasis. Specific targets are revealed for a preferential inhibition of thrombosis that may lead to new classes of potent antithrombotics without hemorrhagic side effects.
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Affiliation(s)
- Jianhua Mao
- State Key Laboratory of Medical GenomicsShanghai Institute of HematologyCollaborative Innovation Center of HematologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Kongkai Zhu
- Drug Discovery and Design Centerthe Center for Chemical BiologyState Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai201203China
| | - Zhangbiao Long
- State Key Laboratory of Medical GenomicsShanghai Institute of HematologyCollaborative Innovation Center of HematologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Huimin Zhang
- Drug Discovery and Design Centerthe Center for Chemical BiologyState Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai201203China
- School of Life Science and TechnologyShanghai Tech UniversityShanghai201210China
| | - Bing Xiao
- State Key Laboratory of Medical GenomicsShanghai Institute of HematologyCollaborative Innovation Center of HematologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Wenda Xi
- Shanghai Institute of HypertensionRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Yun Wang
- State Key Laboratory of Medical GenomicsShanghai Institute of HematologyCollaborative Innovation Center of HematologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Jiansong Huang
- State Key Laboratory of Medical GenomicsShanghai Institute of HematologyCollaborative Innovation Center of HematologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Jingqiu Liu
- Drug Discovery and Design Centerthe Center for Chemical BiologyState Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai201203China
| | - Xiaofeng Shi
- State Key Laboratory of Medical GenomicsShanghai Institute of HematologyCollaborative Innovation Center of HematologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Hao Jiang
- Drug Discovery and Design Centerthe Center for Chemical BiologyState Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai201203China
| | - Tian Lu
- Drug Discovery and Design Centerthe Center for Chemical BiologyState Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai201203China
| | - Yi Wen
- Drug Discovery and Design Centerthe Center for Chemical BiologyState Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai201203China
| | - Naixia Zhang
- Drug Discovery and Design Centerthe Center for Chemical BiologyState Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai201203China
| | - Qian Meng
- Drug Discovery and Design Centerthe Center for Chemical BiologyState Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai201203China
| | - Hu Zhou
- Drug Discovery and Design Centerthe Center for Chemical BiologyState Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai201203China
| | - Zheng Ruan
- State Key Laboratory of Medical GenomicsShanghai Institute of HematologyCollaborative Innovation Center of HematologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Jin Wang
- State Key Laboratory of Medical GenomicsShanghai Institute of HematologyCollaborative Innovation Center of HematologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
| | - Cheng Luo
- Drug Discovery and Design Centerthe Center for Chemical BiologyState Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai201203China
- School of Life Science and TechnologyShanghai Tech UniversityShanghai201210China
- School of Pharmaceutical Science and TechnologyHangzhou Institute for Advanced StudyUCASHangzhou310024China
| | - Xiaodong Xi
- State Key Laboratory of Medical GenomicsShanghai Institute of HematologyCollaborative Innovation Center of HematologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025China
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36
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Phosphoproteomic Analysis of Breast Cancer-Derived Small Extracellular Vesicles Reveals Disease-Specific Phosphorylated Enzymes. Biomedicines 2022; 10:biomedicines10020408. [PMID: 35203617 PMCID: PMC8962341 DOI: 10.3390/biomedicines10020408] [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] [Received: 12/27/2021] [Revised: 01/28/2022] [Accepted: 02/05/2022] [Indexed: 12/16/2022] Open
Abstract
Small membrane-derived extracellular vesicles have been proposed as participating in several cancer diseases, including breast cancer (BC). We performed a phosphoproteomic analysis of breast cancer-derived small extracellular vesicles (sEVs) to provide insight into the molecular and cellular regulatory mechanisms important for breast cancer tumor progression and metastasis. We examined three cell line models for breast cancer: MCF10A (non-malignant), MCF7 (estrogen and progesterone receptor-positive, metastatic), and MDA-MB-231 (triple-negative, highly metastatic). To obtain a comprehensive overview of the sEV phosphoproteome derived from each cell line, effective phosphopeptide enrichment techniques IMAC and TiO2, followed by LC-MS/MS, were performed. The phosphoproteome was profiled to a depth of 2003 phosphopeptides, of which 207, 854, and 1335 were identified in MCF10A, MCF7, and MDA-MB-231 cell lines, respectively. Furthermore, 2450 phosphorylation sites were mapped to 855 distinct proteins, covering a wide range of functions. The identified proteins are associated with several diseases, mostly related to cancer. Among the phosphoproteins, we validated four enzymes associated with cancer and present only in sEVs isolated from MCF7 and MDA-MB-231 cell lines: ATP citrate lyase (ACLY), phosphofructokinase-M (PFKM), sirtuin-1 (SIRT1), and sirtuin-6 (SIRT6). With the exception of PFKM, the specific activity of these enzymes was significantly higher in MDA-MB-231 when compared with MCF10A-derived sEVs. This study demonstrates that sEVs contain functional metabolic enzymes that could be further explored for their potential use in early BC diagnostic and therapeutic applications.
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37
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Analysis of protein kinases by Phos-tag SDS-PAGE. J Proteomics 2022; 255:104485. [DOI: 10.1016/j.jprot.2022.104485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/18/2022]
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38
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Nakae S, Kitamura M, Fujiwara D, Sawa M, Shirai T, Fujii I, Tada T. Structure of mitogen-activated protein kinase kinase 1 in the DFG-out conformation. Acta Crystallogr F Struct Biol Commun 2021; 77:459-464. [PMID: 34866601 DOI: 10.1107/s2053230x21011687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/04/2021] [Indexed: 01/04/2023] Open
Abstract
Eukaryotic protein kinases contain an Asp-Phe-Gly (DFG) motif, the conformation of which is involved in controlling the catalytic activity, at the N-terminus of the activation segment. The motif can be switched between active-state (DFG-in) and inactive-state (DFG-out) conformations: however, the mechanism of conformational change is poorly understood, partly because there are few reports of the DFG-out conformation. Here, a novel crystal structure of nonphosphorylated human mitogen-activated protein kinase kinase 1 (MEK1; amino acids 38-381) complexed with ATP-γS is reported in which MEK1 adopts the DFG-out conformation. The crystal structure revealed that the structural elements (the αC helix and HRD motif) surrounding the active site are involved in the formation/stabilization of the DFG-out conformation. The ATP-γS molecule was bound to the canonical ATP-binding site in a different binding mode that has never been found in previously determined crystal structures of MEK1. This novel ATP-γS binding mode provides a starting point for the design of high-affinity inhibitors of nonphosphorylated inactive MEK1 that adopts the DFG-out conformation.
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Affiliation(s)
- Setsu Nakae
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Maho Kitamura
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Daisuke Fujiwara
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Masaaki Sawa
- Carna Biosciences Inc., BMA 3F 1-5-5 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama 526-0829, Japan
| | - Ikuo Fujii
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Toshiji Tada
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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39
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Sun C, Li Z, Ning X, Xu W, Li Z. In vitro biosynthesis of ATP from adenosine and polyphosphate. BIORESOUR BIOPROCESS 2021; 8:117. [PMID: 38650279 PMCID: PMC10992290 DOI: 10.1186/s40643-021-00469-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/21/2021] [Indexed: 11/10/2022] Open
Abstract
Adenosine triphosphate (ATP) acts as a crucial energy currency in vivo, and it is a widely used energy and/or phosphate donor for enzyme-catalyzed reactions in vitro. In this study, we established an in vitro multi-enzyme cascade system for ATP production. Using adenosine and inorganic polyphosphate (polyP) as key substrates, we combined adenosine kinase and two functionally distinct polyphosphate kinases (PPKs) in a one-pot reaction to achieve chain-like ATP regeneration and production. Several sources of PPK were screened and characterized, and two suitable PPKs were selected to achieve high rates of ATP production. Among these, Sulfurovum lithotrophicum PPK (SlPPK) exhibited excellent activity over a wide pH range (pH 4.0-9.0) and synthesized ATP from ADP using short-chain polyP. Furthermore, it had a half-life > 155.6 h at 45 °C. After optimizing the reaction conditions, we finally carried out the coupling-catalyzed reaction with different initial adenosine concentrations of 10, 20, and 30 mM. The highest yields of ATP were 76.0, 70.5, and 61.3%, respectively.
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Affiliation(s)
- Chuanqi Sun
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Zonglin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
| | - Xiao Ning
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Wentian Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, China.
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40
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Stoppelman JP, Ng TT, Nerenberg PS, Wang LP. Development and Validation of AMBER-FB15-Compatible Force Field Parameters for Phosphorylated Amino Acids. J Phys Chem B 2021; 125:11927-11942. [PMID: 34668708 DOI: 10.1021/acs.jpcb.1c07547] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Phosphorylation of select amino acid residues is one of the most common biological mechanisms for regulating protein structures and functions. While computational modeling can be used to explore the detailed structural changes associated with phosphorylation, most molecular mechanics force fields developed for the simulation of phosphoproteins have been noted to be inconsistent with experimental data. In this work, we parameterize force fields for the phosphorylated forms of the amino acids serine, threonine, and tyrosine using the ForceBalance software package with the goal of improving agreement with experiments for these residues. Our optimized force field, denoted as FB18, is parameterized using high-quality ab initio potential energy scans and is designed to be fully compatible with the AMBER-FB15 protein force field. When utilized in MD simulations together with the TIP3P-FB water model, we find that FB18 consistently enhances the prediction of experimental quantities such as 3J NMR couplings and intramolecular hydrogen-bonding propensities in comparison to previously published models. As was reported with AMBER-FB15, we also see improved agreement with the reference QM calculations in regions at and away from local minima. We thus believe that the FB18 parameter set provides a promising route for the further investigation of the varied effects of protein phosphorylation.
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Affiliation(s)
- John P Stoppelman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Tracey T Ng
- Department of Physics & Astronomy, California State University, Los Angeles, California 90032, United States
| | - Paul S Nerenberg
- Department of Physics & Astronomy, California State University, Los Angeles, California 90032, United States.,Department of Biological Sciences, California State University, Los Angeles, California 90032, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, California 95616, United States
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41
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Chen S, Wang X, Jia H, Li F, Ma Y, Liesche J, Liao M, Ding X, Liu C, Chen Y, Li N, Li J. Persulfidation-induced structural change in SnRK2.6 establishes intramolecular interaction between phosphorylation and persulfidation. MOLECULAR PLANT 2021; 14:1814-1830. [PMID: 34242849 DOI: 10.1016/j.molp.2021.07.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/11/2021] [Accepted: 07/04/2021] [Indexed: 05/22/2023]
Abstract
Post-translational modifications (PTMs), including phosphorylation and persulfidation, regulate the activity of SNF1-RELATED PROTEIN KINASE2.6 (SnRK2.6). Here, we report how persulfidations and phosphorylations of SnRK2.6 influence each other. The persulfidation of cysteine C131/C137 alters SnRK2.6 structure and brings the serine S175 residue closer to the aspartic acid D140 that acts as ATP-γ-phosphate proton acceptor, thereby improving the transfer efficiency of phosphate groups to S175 to enhance the phosphorylation level of S175. Interestingly, we predicted that S267 and C137 were predicted to lie in close proximity on the protein surface and found that the phosphorylation status of S267 positively regulates the persulfidation level at C137. Analyses of the responses of dephosphorylated and depersulfidated mutants to abscisic acid and the H2S-donor NaHS during stomatal closure, water loss, gas exchange, Ca2+ influx, and drought stress revealed that S175/S267-associated phosphorylation and C131/137-associated persulfidation are essential for SnRK2.6 function in vivo. In light of these findings, we propose a mechanistic model in which certain phosphorylations facilitate persulfidation, thereby changing the structure of SnRK2.6 and increasing its activity.
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Affiliation(s)
- Sisi Chen
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaofeng Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Viva Biotech (Shanghai) Ltd., Shanghai 201203, China
| | - Honglei Jia
- School of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, Shaanxi 710021, China
| | - Fali Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Ma
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Johannes Liesche
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingzhi Liao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xueting Ding
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cuixia Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Chen
- Viva Biotech (Shanghai) Ltd., Shanghai 201203, China
| | - Na Li
- Viva Biotech (Shanghai) Ltd., Shanghai 201203, China
| | - Jisheng Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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42
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Biswal J, Jayaprakash P, Rayala SK, Venkatraman G, Rangaswamy R, Jeyaraman J. WaterMap and Molecular Dynamic Simulation-Guided Discovery of Potential PAK1 Inhibitors Using Repurposing Approaches. ACS OMEGA 2021; 6:26829-26845. [PMID: 34693105 PMCID: PMC8529594 DOI: 10.1021/acsomega.1c02032] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Indexed: 06/13/2023]
Abstract
p21-Activated kinase 1 (PAK1) is positioned at the nexus of several oncogenic signaling pathways. Currently, there are no approved inhibitors for disabling the transfer of phosphate in the active site directly, as they are limited by lower affinity, and poor kinase selectivity. In this work, a repurposing study utilizing FDA-approved drugs from the DrugBank database was pursued with an initial selection of 27 molecules out of ∼2162 drug molecules, based on their docking energies and molecular interaction patterns. From the molecules that were considered for WaterMap analysis, seven molecules, namely, Mitoxantrone, Labetalol, Acalabrutinib, Sacubitril, Flubendazole, Trazodone, and Niraparib, ascertained the ability to overlap with high-energy hydration sites. Considering many other displaced unfavorable water molecules, only Acalabrutinib, Flubendazole, and Trazodone molecules highlighted their prominence in terms of binding affinity gains through ΔΔG that ranges between 6.44 and 2.59 kcal/mol. Even if Mitoxantrone exhibited the highest docking score and greater interaction strength, it did not comply with the WaterMap and molecular dynamics simulation results. Moreover, detailed MD simulation trajectory analyses suggested that the drug molecules Flubendazole, Niraparib, and Acalabrutinib were highly stable, observed from their RMSD values and consistent interaction pattern with Glu315, Glu345, Leu347, and Asp407 including the hydrophobic interactions maintained in the three replicates. However, the drug molecule Trazodone displayed a loss of crucial interaction with Leu347, which was essential to inhibit the kinase activity of PAK1. The molecular orbital and electrostatic potential analyses elucidated the reactivity and strong complementarity potentials of the drug molecules in the binding pocket of PAK1. Therefore, the CADD-based reposition efforts, reported in this work, helped in the successful identification of new PAK1 inhibitors that requires further investigation by in vitro analysis.
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Affiliation(s)
- Jayashree Biswal
- Structural
Biology and Bio-Computing Laboratory, Department of Bioinformatics,
Science Block, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
| | - Prajisha Jayaprakash
- Structural
Biology and Bio-Computing Laboratory, Department of Bioinformatics,
Science Block, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
| | - Suresh Kumar Rayala
- Department
of Biotechnology, Indian Institute of Technology
Madras, Room No. BT 306, Chennai 600 036, Tamil Nadu, India
| | - Ganesh Venkatraman
- Department
of Human Genetics, College of Biomedical Sciences, Sri Ramachandra University, Porur, Chennai 600 116, Tamil Nadu, India
| | - Raghu Rangaswamy
- Structural
Biology and Bio-Computing Laboratory, Department of Bioinformatics,
Science Block, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
| | - Jeyakanthan Jeyaraman
- Structural
Biology and Bio-Computing Laboratory, Department of Bioinformatics,
Science Block, Alagappa University, Karaikudi 630 004, Tamil Nadu, India
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43
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Kinase Inhibition in Relapsed/Refractory Leukemia and Lymphoma Settings: Recent Prospects into Clinical Investigations. Pharmaceutics 2021; 13:pharmaceutics13101604. [PMID: 34683897 PMCID: PMC8540545 DOI: 10.3390/pharmaceutics13101604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/21/2021] [Accepted: 09/25/2021] [Indexed: 01/19/2023] Open
Abstract
Cancer is still a major barrier to life expectancy increase worldwide, and hematologic neoplasms represent a relevant percentage of cancer incidence rates. Tumor dependence of continuous proliferative signals mediated through protein kinases overexpression instigated increased strategies of kinase inhibition in the oncologic practice over the last couple decades, and in this review, we focused our discussion on relevant clinical trials of the past five years that investigated kinase inhibitor (KI) usage in patients afflicted with relapsed/refractory (R/R) hematologic malignancies as well as in the pharmacological characteristics of available KIs and the dissertation about traditional chemotherapy treatment approaches and its hindrances. A trend towards investigations on KI usage for the treatment of chronic lymphoid leukemia and acute myeloid leukemia in R/R settings was observed, and it likely reflects the existence of already established treatment protocols for chronic myeloid leukemia and acute lymphoid leukemia patient cohorts. Overall, regimens of KI treatment are clinically manageable, and results are especially effective when allied with tumor genetic profiles, giving rise to encouraging future prospects of an era where chemotherapy-free treatment regimens are a reality for many oncologic patients.
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44
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Ramanayake-Mudiyanselage V, Embogama DM, Pflum MKH. Kinase-Catalyzed Biotinylation to Map Cell Signaling Pathways: Application to Epidermal Growth Factor Signaling. J Proteome Res 2021; 20:4852-4861. [PMID: 34491762 DOI: 10.1021/acs.jproteome.1c00562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cell signaling involves a network of protein-protein interactions and post-translational modifications that govern cellular responses to environmental cues. To understand and ultimately modulate these signaling pathways to confront disease, the complex web of proteins that becomes phosphorylated after extracellular stimulation has been studied using mass spectrometry-based proteomics methods. To complement prior work and fully characterize all phosphorylated proteins after the stimulation of cell signaling, we developed K-BMAPS (kinase-catalyzed biotinylation to map signaling), which utilizes ATP-biotin as a kinase cosubstrate to biotin label substrates. As a first application of the K-BMAPS method, the well-characterized epidermal growth factor receptor (EGFR) kinase signaling pathway was monitored by treating epidermal growth factor (EGF)-stimulated HeLa lysates with ATP-biotin, followed by streptavidin enrichment and quantitative mass spectrometry analysis. On the basis of the dynamic phosphoproteins identified, a pathway map was developed considering functional categories and known interactors of EGFR. Remarkably, 94% of the K-BMAPS hit proteins were included in the EGFR pathway map. With many proteins involved in transcription, translation, cell adhesion, and GTPase signaling, K-BMAPS identified phosphoproteins were associated with late and continuous signaling events. In summary, the K-BMAPS method is a powerful tool to map the dynamic phosphorylation governing cell signaling pathways.
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Affiliation(s)
| | - D Maheeka Embogama
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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45
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Lin SN, Mao R, Qian C, Bettenworth D, Wang J, Li J, Bruining D, Jairath V, Feagan B, Chen M, Rieder F. Development of Anti-fibrotic Therapy in Stricturing Crohn's Disease: Lessons from Randomized Trials in Other Fibrotic Diseases. Physiol Rev 2021; 102:605-652. [PMID: 34569264 DOI: 10.1152/physrev.00005.2021] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Intestinal fibrosis is considered an inevitable complication of Crohn's disease (CD) that results in symptoms of obstruction and stricture formation. Endoscopic or surgical treatment is required to treat the majority of patients. Progress in the management of stricturing CD is hampered by the lack of effective anti-fibrotic therapy; however, this situation is likely to change because of recent advances in other fibrotic diseases of the lung, liver and skin. In this review, we summarized data from randomized controlled trials (RCT) of anti-fibrotic therapies in these conditions. Multiple compounds have been tested for the anti-fibrotic effects in other organs. According to their mechanisms, they were categorized into growth factor modulators, inflammation modulators, 5-hydroxy-3-methylgultaryl-coenzyme A (HMG-CoA) reductase inhibitors, intracellular enzymes and kinases, renin-angiotensin system (RAS) modulators and others. From our review of the results from the clinical trials and discussion of their implications in the gastrointestinal tract, we have identified several molecular candidates that could serve as potential therapies for intestinal fibrosis in CD.
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Affiliation(s)
- Si-Nan Lin
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio, United States
| | - Ren Mao
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio, United States
| | - Chenchen Qian
- Department of Internal Medicine, UPMC Pinnacle, Harrisburg, Pennsylvania, United States
| | - Dominik Bettenworth
- Department of Medicine B, Gastroenterology and Hepatology, University Hospital Münster, Münster, Germany
| | - Jie Wang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio, United States.,Henan Key Laboratory of Immunology and Targeted Drug, Xinxiang Medical University, Xinxiang, Henan Province, China
| | - Jiannan Li
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio, United States
| | - David Bruining
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States
| | - Vipul Jairath
- Alimentiv Inc., London, ON, Canada.,Department of Medicine, Western University, London, ON, Canada.,Department of Biostatistics and Epidemiology, Western University, London, ON, Canada
| | - Brian Feagan
- Alimentiv Inc., London, ON, Canada.,Department of Medicine, Western University, London, ON, Canada.,Department of Biostatistics and Epidemiology, Western University, London, ON, Canada
| | - Minhu Chen
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | | | - Florian Rieder
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, United States.,Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio, United States
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46
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Huang YMM. Multiscale computational study of ligand binding pathways: Case of p38 MAP kinase and its inhibitors. Biophys J 2021; 120:3881-3892. [PMID: 34453922 PMCID: PMC8511166 DOI: 10.1016/j.bpj.2021.08.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/07/2021] [Accepted: 08/20/2021] [Indexed: 01/09/2023] Open
Abstract
Protein kinases are one of the most important drug targets in the past 10 years. Understanding the inhibitor association processes will profoundly impact new binder designs with preferred binding kinetics. However, after more than a decade of effort, a complete atomistic-level study of kinase inhibitor binding pathways is still lacking. As all kinases share a similar scaffold, we used p38 kinase as a model system to investigate the conformational dynamics and free energy transition of inhibitor binding toward kinases. Two major kinase conformations, Asp-Phe-Gly (DFG)-in and DFG-out, and three types of inhibitors, type I, II, and III, were thoroughly investigated in this work. We performed Brownian dynamics simulations and up to 340 μs Gaussian-accelerated molecular dynamics simulations to capture the inhibitor binding paths and a series of conformational transitions of the p38 kinase from its apo to inhibitor-bound form. Eighteen successful binding trajectories, including all types of inhibitors, are reported herein. Our simulations suggest a mechanism of inhibitor recruitment, a faster ligand association step to a pre-existing DFG-in/DFG-out p38 protein, followed by a slower molecular rearrangement step to adjust the protein-ligand conformation followed by a shift in the energy landscape to reach the final bound state. The ligand association processes also reflect the energetic favor of type I and type II/III inhibitor binding through ATP and allosteric channels, respectively. These different binding routes are directly responsible for the fast (type I binders) and slow (type II/III binders) kinetics of different types of p38 inhibitors. Our findings also echo the recent study of p38 inhibitor dissociation, implying that ligand unbinding could undergo a reverse path of binding, and both processes share similar metastates. This study deepens the understanding of molecular and energetic features of kinase inhibitor-binding processes and will inspire future drug development from a kinetic point of view.
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Affiliation(s)
- Yu-Ming M Huang
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan.
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47
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Zheng F, Meng T, Jiang D, Sun J, Yao H, Zhu J, Min Q. Nanomediator–Effector Cascade Systems for Amplified Protein Kinase Activity Imaging and Phosphorylation‐Induced Drug Release In Vivo. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fenfen Zheng
- State Key Laboratory of Analytical Chemistry for life Science Chemistry and Biomedicine Innovation Center School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
- School of Environmental & Chemical Engineering Jiangsu University of Science and Technology Zhenjiang Jiangsu 212003 China
| | - Tiantian Meng
- State Key Laboratory of Analytical Chemistry for life Science Chemistry and Biomedicine Innovation Center School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
| | - Difei Jiang
- School of Environmental & Chemical Engineering Jiangsu University of Science and Technology Zhenjiang Jiangsu 212003 China
| | - Jiamin Sun
- School of Environmental & Chemical Engineering Jiangsu University of Science and Technology Zhenjiang Jiangsu 212003 China
| | - Haiyang Yao
- School of Environmental & Chemical Engineering Jiangsu University of Science and Technology Zhenjiang Jiangsu 212003 China
| | - Jun‐Jie Zhu
- State Key Laboratory of Analytical Chemistry for life Science Chemistry and Biomedicine Innovation Center School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for life Science Chemistry and Biomedicine Innovation Center School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China
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48
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Yan Z, He M, Zhang Y, Hu G, Li H. Methylene blue-enhanced electrochemical oxidation of tyrosine residues in native/denatured bovine serum albumin and HIV-1 Tat peptide. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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49
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Nilkanth VV, Mande SC. Structure-sequence features based prediction of phosphosites of serine/threonine protein kinases of Mycobacterium tuberculosis. Proteins 2021; 90:131-141. [PMID: 34329517 DOI: 10.1002/prot.26195] [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: 03/03/2021] [Revised: 07/11/2021] [Accepted: 07/12/2021] [Indexed: 11/07/2022]
Abstract
Elucidation of signaling events in a pathogen is potentially important to tackle the infection caused by it. Such events mediated by protein phosphorylation play important roles in infection, and therefore, to predict the phosphosites and substrates of the serine/threonine protein kinases, we have developed a Machine learning-based approach for Mycobacterium tuberculosis serine/threonine protein kinases using kinase-peptide structure-sequence data. This approach utilizes features derived from kinase three-dimensional-structure environment and known phosphosite sequences to generate support vector machine (SVM)-based kinase-specific predictions of phosphosites of serine/threonine protein kinases (STPKs) with no or scarce data of their substrates. SVM outperformed the four machine learning algorithms we tried (random forest, logistic regression, SVM, and k-nearest neighbors) with an area under the curve receiver-operating characteristic value of 0.88 on the independent testing dataset and a 10-fold cross-validation accuracy of ~81.6% for the final model. Our predicted phosphosites of M. tuberculosis STPKs form a useful resource for experimental biologists enabling elucidation of STPK mediated posttranslational regulation of important cellular processes.
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Affiliation(s)
- Vipul V Nilkanth
- National Centre for Cell Science, S.P. Pune University Campus, Pune, India
| | - Shekhar C Mande
- Council of Scientific and Industrial Research, New Delhi, India
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50
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Zheng F, Meng T, Jiang D, Sun J, Yao H, Zhu JJ, Min Q. Nanomediator-Effector Cascade Systems for Amplified Protein Kinase Activity Imaging and Phosphorylation-Induced Drug Release In Vivo. Angew Chem Int Ed Engl 2021; 60:21565-21574. [PMID: 34322988 DOI: 10.1002/anie.202109108] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 11/06/2022]
Abstract
Protein kinases constitute a rich pool of biomarkers and therapeutic targets of tremendous diseases including cancer. However, sensing kinase activity in vivo while implementing treatments according to kinase hyperactivation remains challenging. Herein, we present a nanomediator-effector cascade system that can in situ magnify the subtle events of kinase-catalyzed phosphorylation via DNA amplification machinery to achieve kinase activity imaging and kinase-responsive drug release in vivo. In this cascade, the phosphorylation-mediated disassembly of DNA/peptide complex on the nanomediators initiated the detachment of fluorescent hairpin DNAs from the nanoeffectors via hybridization chain reaction (HCR), leading to fluorescence recovery and therapeutic cargo release. We demonstrated that this nanosystem simultaneously enabled trace protein kinase A (PKA) activity imaging and on-demand drug delivery for inhibition of tumor cell growth both in vitro and in vivo, affording a kinase-specific sense-and-treat paradigm for cancer theranostics.
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Affiliation(s)
- Fenfen Zheng
- State Key Laboratory of Analytical Chemistry for life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.,School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212003, China
| | - Tiantian Meng
- State Key Laboratory of Analytical Chemistry for life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Difei Jiang
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212003, China
| | - Jiamin Sun
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212003, China
| | - Haiyang Yao
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212003, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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