1
|
Wei J, Zhu Y, Zhuo L, Liu Y, Fu X, Li F. Efficient Deep Model Ensemble Framework for Drug-Target Interaction Prediction. J Phys Chem Lett 2024; 15:7681-7693. [PMID: 39038219 DOI: 10.1021/acs.jpclett.4c01509] [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: 07/24/2024]
Abstract
Accurate prediction of Drug-Target Interactions (DTI) is crucial for drug development. Current state-of-the-art deep learning methods have significantly advanced the field; however, these methods exhibit limitations in predictive performance and the propensity for false negatives. Therefore, we propose EADTN, a simple and efficient ensemble model. We have designed an innovative feature adaptation technique to automatically extract local weights of drugs and targets, and we utilize clustering-enhanced parameter fine-tuning to overcome the issue of false negatives, thereby enhancing its reliability in drug discovery. Based on EADTN, we also propose a Shapley value-based method for identifying key drug substructures, effectively enhancing the model's interpretability. Additionally, we utilized EADTN to reveal potential interactions between NQO1 targets and the drugs SIRT-IN-1 and LY2183240, which were subsequently validated through wet-lab experiments. Experimental evidence demonstrates that EADTN consistently outperforms existing best-performing models across various data sets, promising significant benefits in fields such as drug repositioning.
Collapse
Affiliation(s)
- Jinhang Wei
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou 325000, China
| | - Yangbin Zhu
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou 325000, China
| | - Linlin Zhuo
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou 325000, China
| | - Yang Liu
- Strait Institute of Flexible Electronics (SIFE, Future Technologies), Fujian Key Laboratory of Flexible Electronics, Fujian Normal University and Strait Laboratory of Flexible Electronics (SLoFE), Fuzhou 350002, China
| | - Xiangzheng Fu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, China
| | - Fushan Li
- Institute of Optoelectronic Technology, Fuzhou University, Fuzhou 350002, China
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou 350116, China
| |
Collapse
|
2
|
A genetically-encoded crosslinker screen identifies SERBP1 as a PKCε substrate influencing translation and cell division. Nat Commun 2021; 12:6934. [PMID: 34836941 PMCID: PMC8626422 DOI: 10.1038/s41467-021-27189-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/08/2021] [Indexed: 01/09/2023] Open
Abstract
The PKCε-regulated genome protective pathway provides transformed cells a failsafe to successfully complete mitosis. Despite the necessary role for Aurora B in this programme, it is unclear whether its requirement is sufficient or if other PKCε cell cycle targets are involved. To address this, we developed a trapping strategy using UV-photocrosslinkable amino acids encoded in the PKCε kinase domain. The validation of the mRNA binding protein SERBP1 as a PKCε substrate revealed a series of mitotic events controlled by the catalytic form of PKCε. PKCε represses protein translation, altering SERBP1 binding to the 40 S ribosomal subunit and promoting the assembly of ribonucleoprotein granules containing SERBP1, termed M-bodies. Independent of Aurora B, SERBP1 is shown to be necessary for chromosome segregation and successful cell division, correlating with M-body formation. This requirement for SERBP1 demonstrates that Aurora B acts in concert with translational regulation in the PKCε-controlled pathway exerting genome protection.
Collapse
|
3
|
Bhaskar BV, Rammohan A, Babu TM, Zheng GY, Chen W, Rajendra W, Zyryanov GV, Gu W. Molecular insight into isoform specific inhibition of PI3K-α and PKC-η with dietary agents through an ensemble pharmacophore and docking studies. Sci Rep 2021; 11:12150. [PMID: 34108504 PMCID: PMC8190100 DOI: 10.1038/s41598-021-90287-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 04/29/2021] [Indexed: 02/05/2023] Open
Abstract
Dietary compounds play an important role in the prevention and treatment of many cancers, although their specific molecular mechanism is not yet known. In the present study, thirty dietary agents were analyzed on nine drug targets through in silico studies. However, nine dietary scaffolds, such as silibinin, flavopiridol, oleandrin, ursolic acid, α-boswellic acid, β-boswellic acid, triterpenoid, guggulsterone, and oleanolic acid potentially bound to the cavity of PI3K-α, PKC-η, H-Ras, and Ras with the highest binding energy. Particularly, the compounds silibinin and flavopiridol have been shown to have broad spectrum anticancer activity. Interestingly, flavopiridol was embedded in the pockets of PI3K-α and PKC-η as bound crystal inhibitors in two different conformations and showed significant interactions with ATP binding pocket residues. However, complex-based pharmacophore modeling achieved two vital pharmacophoric features namely, two H-bond acceptors for PI3K-α, while three are hydrophobic, one cat-donor and one H-bond donor and acceptor for PKC-η, respectively. The database screening with the ChemBridge core library explored potential hits on a valid pharmacophore query. Therefore, to optimize perspective lead compounds from the hits, which were subjected to various constraints such as docking, MM/GBVI, Lipinski rule of five, ADMET and toxicity properties. Henceforth, the top ligands were sorted out and examined for vital interactions with key residues, arguably the top three promising lead compounds for PI3K-α, while seven for PKC-η, exhibiting binding energy from - 11.5 to - 8.5 kcal mol-1. Therefore, these scaffolds could be helpful in the development of novel class of effective anticancer agents.
Collapse
Affiliation(s)
- Baki Vijaya Bhaskar
- Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Xinling Road, Shantou, 515041, Guangdong, China.
| | - Aluru Rammohan
- Department of Organic and Biomolecular Chemistry, Ural Federal University, Ekaterinburg, 620002, Russia
| | | | - Gui Yu Zheng
- Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Xinling Road, Shantou, 515041, Guangdong, China
| | - Weibin Chen
- Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Xinling Road, Shantou, 515041, Guangdong, China
| | - Wudayagiri Rajendra
- Department of Zoology, Sri Venkateswara University, Tirupati, Andhra Pradesh, 517502, India
| | - Grigory V Zyryanov
- Department of Organic and Biomolecular Chemistry, Ural Federal University, Ekaterinburg, 620002, Russia
| | - Wei Gu
- Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Xinling Road, Shantou, 515041, Guangdong, China.
| |
Collapse
|
4
|
Waidha K, Anto NP, Jayaram DR, Golan-Goldhirsh A, Rajendran S, Livneh E, Gopas J. 6,6'-Dihydroxythiobinupharidine (DTBN) Purified from Nuphar lutea Leaves Is an Inhibitor of Protein Kinase C Catalytic Activity. Molecules 2021; 26:molecules26092785. [PMID: 34066895 PMCID: PMC8125885 DOI: 10.3390/molecules26092785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 12/28/2022] Open
Abstract
Water lily (Nuphar) bioactive extracts have been widely used in traditional medicine owing to their multiple applications against human ailments. Phyto-active Nuphar extracts and their purified and synthetic derivatives have attracted the attention of ethnobotanists and biochemists. Here, we report that 6,6'-dihydroxythiobinupharidine (DTBN), purified from extracts of Nuphar lutea (L.) Sm. leaves, is an effective inhibitor of the kinase activity of members of the protein kinase C (PKC) family using in vitro and in silico approaches. We demonstrate that members of the conventional subfamily of PKCs, PKCα and PKCγ, were more sensitive to DTBN inhibition as compared to novel or atypical PKCs. Molecular docking analysis demonstrated the interaction of DTBN, with the kinase domain of PKCs depicting the best affinity towards conventional PKCs, in accordance with our in vitro kinase activity data. The current study reveals novel targets for DTBN activity, functioning as an inhibitor for PKCs kinase activity. Thus, this and other data indicate that DTBN modulates key cellular signal transduction pathways relevant to disease biology, including cancer.
Collapse
Affiliation(s)
- Kamran Waidha
- Defence Institute of High Altitude Research (DIHAR), Defence Research and Development Organisation (DRDO) Leh, Ladakh UT-194101, India;
| | - Nikhil Ponnoor Anto
- The Shraga Segal Department of Microbiology, Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 8400501, Israel; (N.P.A.); (D.R.J.)
| | - Divya Ram Jayaram
- The Shraga Segal Department of Microbiology, Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 8400501, Israel; (N.P.A.); (D.R.J.)
| | - Avi Golan-Goldhirsh
- The Jacob Blaustein Institutes for Desert Research (BIDR), Sede Boqer Campus, French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Beer Sheva 8499000, Israel
- Correspondence: (A.G.-G.); (S.R.); (E.L.); (J.G.)
| | - Saravanakumar Rajendran
- Chemistry Division, Vellore Institute of Technology Chennai Campus, School of Advanced Sciences, Chennai 600127, India
- Correspondence: (A.G.-G.); (S.R.); (E.L.); (J.G.)
| | - Etta Livneh
- The Shraga Segal Department of Microbiology, Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 8400501, Israel; (N.P.A.); (D.R.J.)
- Correspondence: (A.G.-G.); (S.R.); (E.L.); (J.G.)
| | - Jacob Gopas
- The Shraga Segal Department of Microbiology, Immunology and Genetics Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 8400501, Israel; (N.P.A.); (D.R.J.)
- Department of Oncology, Soroka University Medical Center, Beer Sheva 8400501, Israel
- Correspondence: (A.G.-G.); (S.R.); (E.L.); (J.G.)
| |
Collapse
|
5
|
Baffi TR, Lordén G, Wozniak JM, Feichtner A, Yeung W, Kornev AP, King CC, Del Rio JC, Limaye AJ, Bogomolovas J, Gould CM, Chen J, Kennedy EJ, Kannan N, Gonzalez DJ, Stefan E, Taylor SS, Newton AC. mTORC2 controls the activity of PKC and Akt by phosphorylating a conserved TOR interaction motif. Sci Signal 2021; 14:eabe4509. [PMID: 33850054 PMCID: PMC8208635 DOI: 10.1126/scisignal.abe4509] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The complex mTORC2 is accepted to be the kinase that controls the phosphorylation of the hydrophobic motif, a key regulatory switch for AGC kinases, although whether mTOR directly phosphorylates this motif remains controversial. Here, we identified an mTOR-mediated phosphorylation site that we termed the TOR interaction motif (TIM; F-x3-F-pT), which controls the phosphorylation of the hydrophobic motif of PKC and Akt and the activity of these kinases. The TIM is invariant in mTORC2-dependent AGC kinases, is evolutionarily conserved, and coevolved with mTORC2 components. Mutation of this motif in Akt1 and PKCβII abolished cellular kinase activity by impairing activation loop and hydrophobic motif phosphorylation. mTORC2 directly phosphorylated the PKC TIM in vitro, and this phosphorylation event was detected in mouse brain. Overexpression of PDK1 in mTORC2-deficient cells rescued hydrophobic motif phosphorylation of PKC and Akt by a mechanism dependent on their intrinsic catalytic activity, revealing that mTORC2 facilitates the PDK1 phosphorylation step, which, in turn, enables autophosphorylation. Structural analysis revealed that PKC homodimerization is driven by a TIM-containing helix, and biophysical proximity assays showed that newly synthesized, unphosphorylated PKC dimerizes in cells. Furthermore, disruption of the dimer interface by stapled peptides promoted hydrophobic motif phosphorylation. Our data support a model in which mTORC2 relieves nascent PKC dimerization through TIM phosphorylation, recruiting PDK1 to phosphorylate the activation loop and triggering intramolecular hydrophobic motif autophosphorylation. Identification of TIM phosphorylation and its role in the regulation of PKC provides the basis for AGC kinase regulation by mTORC2.
Collapse
Affiliation(s)
- Timothy R Baffi
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gema Lordén
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jacob M Wozniak
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Andreas Feichtner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Alexandr P Kornev
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Charles C King
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jason C Del Rio
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ameya J Limaye
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Julius Bogomolovas
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Christine M Gould
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ju Chen
- Department of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innsbruck A-6020, Austria
| | - Susan S Taylor
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
6
|
Kelly JR, Martini S, Brownlow N, Joshi D, Federico S, Jamshidi S, Kjaer S, Lockwood N, Rahman KM, Fraternali F, Parker PJ, Soliman TN. The Aurora B specificity switch is required to protect from non-disjunction at the metaphase/anaphase transition. Nat Commun 2020; 11:1396. [PMID: 32170202 PMCID: PMC7070073 DOI: 10.1038/s41467-020-15163-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 02/21/2020] [Indexed: 12/22/2022] Open
Abstract
The Aurora B abscission checkpoint delays cytokinesis until resolution of DNA trapped in the cleavage furrow. This process involves PKCε phosphorylation of Aurora B S227. Assessing if this PKCε-Aurora B module provides a more widely exploited genome-protective control for the cell cycle, we show Aurora B phosphorylation at S227 by PKCε also occurs during mitosis. Expression of Aurora B S227A phenocopies inhibition of PKCε in by-passing the delay and resolution at anaphase entry that is associated with non-disjunction and catenation of sister chromatids. Implementation of this anaphase delay is reflected in PKCε activation following cell cycle dependent cleavage by caspase 7; knock-down of caspase 7 phenocopies PKCε loss, in a manner rescued by ectopically expressing/generating a free PKCε catalytic domain. Molecular dynamics indicates that Aurora B S227 phosphorylation induces conformational changes and this manifests in a profound switch in specificity towards S29 TopoIIα phosphorylation, a response necessary for catenation resolution during mitosis.
Collapse
Affiliation(s)
- Joanna R Kelly
- Protein Phosphorylation Laboratory, Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- Cancer Research UK, Manchester Institute, Alderley Park, SK10 4TG, UK
| | - Silvia Martini
- Protein Phosphorylation Laboratory, Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Nicola Brownlow
- Protein Phosphorylation Laboratory, Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- Instituto de Neurociencias, Av. Santiago Ramón y Cajal s/n 03550, San Juan de Alicante, Spain
| | - Dhira Joshi
- Peptide Chemistry Platform, Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Stefania Federico
- Peptide Chemistry Platform, Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Shirin Jamshidi
- School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Svend Kjaer
- Structural Biology Platform, Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Nicola Lockwood
- Protein Phosphorylation Laboratory, Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | | | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Peter J Parker
- Protein Phosphorylation Laboratory, Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK.
- School of Cancer and Pharmaceutical Sciences, King's College London, London, UK.
| | - Tanya N Soliman
- Protein Phosphorylation Laboratory, Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK.
- Barts Cancer Institute, Queen Mary University London, Charterhouse Square, London, EC1M 6BE, UK.
| |
Collapse
|
7
|
Yang Y, Shu C, Li P, Igumenova TI. Structural Basis of Protein Kinase Cα Regulation by the C-Terminal Tail. Biophys J 2019; 114:1590-1603. [PMID: 29642029 DOI: 10.1016/j.bpj.2017.12.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/07/2017] [Accepted: 12/21/2017] [Indexed: 10/17/2022] Open
Abstract
Protein kinase C (PKC) isoenzymes are multi-modular proteins activated at the membrane surface to regulate signal transduction processes. When activated by second messengers, PKC undergoes a drastic conformational and spatial transition from the inactive cytosolic state to the activated membrane-bound state. The complete structure of either state of PKC remains elusive. We demonstrate, using NMR spectroscopy, that the isolated Ca2+-sensing membrane-binding C2 domain of the conventional PKCα interacts with a conserved hydrophobic motif of the kinase C-terminal region, and we report a structural model of the complex. Our data suggest that the C-terminal region plays a dual role in regulating the PKC activity: activating, through sensitization of PKC to intracellular Ca2+ oscillations; and auto-inhibitory, through its interaction with a conserved positively charged region of the C2 domain.
Collapse
Affiliation(s)
- Yuan Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Chang Shu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
| |
Collapse
|
8
|
Research advances in kinase enzymes and inhibitors for cardiovascular disease treatment. Future Sci OA 2017; 3:FSO204. [PMID: 29134113 PMCID: PMC5674217 DOI: 10.4155/fsoa-2017-0010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/29/2017] [Indexed: 12/13/2022] Open
Abstract
The targeting of protein kinases has great future potential for the design of new drugs against cardiovascular diseases (CVDs). Enormous efforts have been made toward achieving this aim. Unfortunately, kinase inhibitors designed to treat CVDs have suffered from numerous limitations such as poor selectivity, bad permeability and toxicity. So, where are we now in terms of discovering effective kinase targeting drugs to treat CVDs? Various drug design techniques have been approached for this purpose since the discovery of the inhibitory activity of Staurosporine against protein kinase C in 1986. This review aims to provide context for the status of several emerging classes of direct kinase modulators to treat CVDs and discuss challenges that are preventing scientists from finding new kinase drugs to treat heart disease.
Collapse
|
9
|
Micheva-Viteva SN, Shou Y, Ganguly K, Wu TH, Hong-Geller E. PKC-η-MARCKS Signaling Promotes Intracellular Survival of Unopsonized Burkholderia thailandensis. Front Cell Infect Microbiol 2017. [PMID: 28638804 PMCID: PMC5461351 DOI: 10.3389/fcimb.2017.00231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pathogenic Burkholderia rely on host factors for efficient intracellular replication and are highly refractory to antibiotic treatment. To identify host genes that are required by Burkholderia spp. during infection, we performed a RNA interference (RNAi) screen of the human kinome and identified 35 host kinases that facilitated Burkholderia thailandensis intracellular survival in human monocytic THP-1 cells. We validated a selection of host kinases using imaging flow cytometry to assess efficiency of B. thailandensis survival in the host upon siRNA-mediated knockdown. We focused on the role of the novel protein kinase C isoform, PKC-η, in Burkholderia infection and characterized PKC-η/MARCKS signaling as a key event that promotes the survival of unopsonized B. thailandensis CDC2721121 within host cells. While infection of lung epithelial cells with unopsonized Gram-negative bacteria stimulated phosphorylation of Ser175/160 in the MARCKS effector domain, siRNA-mediated knockdown of PKC-η expression reduced the levels of phosphorylated MARCKS by >3-fold in response to infection with Bt CDC2721121. We compared the effect of the conventional PKC-α and novel PKC-η isoforms on the growth of B. thailandensis CDC2721121 within monocytic THP-1 cells and found that ≥75% knock-down of PRKCH transcript levels reduced intracellular bacterial load 100% more efficiently when compared to growth in cells siRNA-depleted of the classical PKC-α, suggesting that the PKC-η isoform can specifically mediate Burkholderia intracellular survival. Based on imaging studies of intracellular B. thailandensis, we found that PKC-η function stimulates phagocytic pathways that promote B. thailandensis escape into the cytoplasm leading to activation of autophagosome flux. Identification of host kinases that are targeted by Burkholderia during infection provides valuable molecular insights in understanding Burkholderia pathogenesis, and ultimately, in designing effective host-targeted therapies against infectious disease caused by intracellular pathogens.
Collapse
Affiliation(s)
| | - Yulin Shou
- Bioscience Division, Los Alamos National LaboratoryLos Alamos, NM, United States
| | - Kumkum Ganguly
- Bioscience Division, Los Alamos National LaboratoryLos Alamos, NM, United States
| | - Terry H Wu
- Center for Infectious Disease and Immunity and Department of Internal Medicine, University of New Mexico Health Sciences CenterAlbuquerque, NM, United States
| | | |
Collapse
|
10
|
van Eis MJ, Evenou J, Schuler W, Zenke G, Vangrevelinghe E, Wagner J, von Matt P. Indolyl-naphthyl-maleimides as potent and selective inhibitors of protein kinase C-α/β. Bioorg Med Chem Lett 2017; 27:781-786. [DOI: 10.1016/j.bmcl.2017.01.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/09/2017] [Accepted: 01/12/2017] [Indexed: 12/11/2022]
|
11
|
Arepalli SK, Park B, Jung JK, Lee K, Lee H. A facile one-pot regioselective synthesis of functionalized novel benzo[f]chromeno[4,3-b][1,7]naphthyridines and benzo[f][1,7]naphthyridines via an imino Diels-Alder reaction. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2016.12.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
12
|
Patel AR, Hardianto A, Ranganathan S, Liu F. Divergent response of homologous ATP sites to stereospecific ligand fluorination for selectivity enhancement. Org Biomol Chem 2017; 15:1570-1574. [PMID: 28119986 DOI: 10.1039/c7ob00129k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Acquiring a divergent response from homologous protein domains is essential for selective ligand-protein interactions. Stereospecific fluorination of (-)-balanol, an ATP mimic, uncovers a new source of selectivity from integrated chemical and conformational perturbation that differentiates homologous sites by the level of congruency in their response to local and remote fluorine effects.
Collapse
Affiliation(s)
- Alpesh Ramanlal Patel
- Department of Chemistry & Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | | | | | | |
Collapse
|
13
|
Pike T, Brownlow N, Kjaer S, Carlton J, Parker PJ. PKCɛ switches Aurora B specificity to exit the abscission checkpoint. Nat Commun 2016; 7:13853. [PMID: 28004745 PMCID: PMC5192180 DOI: 10.1038/ncomms13853] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 11/03/2016] [Indexed: 01/21/2023] Open
Abstract
The 'NoCut', or Aurora B abscission checkpoint can be activated if DNA is retained in the cleavage furrow after completion of anaphase. Checkpoint failure leads to incomplete abscission and a binucleate outcome. These phenotypes are also observed after loss of PKCɛ in transformed cell models. Here we show that PKCɛ directly modulates the Aurora B-dependent abscission checkpoint by phosphorylating Aurora B at S227. This phosphorylation invokes a switch in Aurora B specificity, with increased phosphorylation of a subset of target substrates, including the CPC subunit Borealin. This switch is essential for abscission checkpoint exit. Preventing the phosphorylation of Borealin leads to abscission failure, as does expression of a non-phosphorylatable Aurora B S227A mutant. Further, depletion of the ESCRT-III component and Aurora B substrate CHMP4C enables abscission, bypassing the PKCɛ-Aurora B exit pathway. Thus, we demonstrate that PKCɛ signals through Aurora B to exit the abscission checkpoint and complete cell division.
Collapse
Affiliation(s)
- Tanya Pike
- Protein Phosphorylation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicola Brownlow
- Protein Phosphorylation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Svend Kjaer
- Protein Purification Facility, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jeremy Carlton
- Division of Cancer Studies King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| | - Peter J. Parker
- Protein Phosphorylation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Division of Cancer Studies King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
| |
Collapse
|
14
|
Sakram B, Sonyanaik B, Ashok K, Rambabu S, Ravi D, Kurumanna A, Shyam P. Eco-friendly synthesis of 1,8-naphthyridine 5-aryl-1,3,4-oxadiazole derivatives under solvent-free solid-state conditions and their antimicrobial activity. RESEARCH ON CHEMICAL INTERMEDIATES 2016. [DOI: 10.1007/s11164-016-2736-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
15
|
Abstract
Protein kinase C (PKC) is a family of Ser/Thr kinases that regulate a multitude of cellular processes through participation in the phosphoinositide signaling pathway. Significant research efforts have been directed at understanding the structure, function, and regulatory modes of the enzyme since its discovery and identification as the first receptor for tumor-promoting phorbol esters. The activation of PKC involves a transition from the cytosolic autoinhibited latent form to the membrane-associated active form. The membrane recruitment step is accompanied by the conformational rearrangement of the enzyme, which relieves autoinhibitory interactions and thereby allows PKC to phosphorylate its targets. The multidomain structure and intrinsic flexibility of PKC present remarkable challenges and opportunities for the biophysical and structural biology studies of this class of enzymes and their interactions with membranes, the major focus of this Current Topic. I will highlight the recent advances in the field, outline the current challenges, and identify areas where biophysics and structural biology approaches can provide insight into the isoenzyme-specific regulation of PKC activity.
Collapse
|
16
|
Haraburda E, Lledó A, Roglans A, Pla-Quintana A. Dehydrogenative [2 + 2 + 2] Cycloaddition of Cyano-yne-allene Substrates: Convenient Access to 2,6-Naphthyridine Scaffolds. Org Lett 2015; 17:2882-5. [DOI: 10.1021/acs.orglett.5b01554] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ewelina Haraburda
- Institut de Química
Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus de Montilivi, s/n E-17071, Girona, Catalonia, Spain
| | - Agustí Lledó
- Institut de Química
Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus de Montilivi, s/n E-17071, Girona, Catalonia, Spain
| | - Anna Roglans
- Institut de Química
Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus de Montilivi, s/n E-17071, Girona, Catalonia, Spain
| | - Anna Pla-Quintana
- Institut de Química
Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus de Montilivi, s/n E-17071, Girona, Catalonia, Spain
| |
Collapse
|
17
|
Brownlow N, Pike T, Zicha D, Collinson L, Parker PJ. Mitotic catenation is monitored and resolved by a PKCε-regulated pathway. Nat Commun 2014; 5:5685. [PMID: 25483024 PMCID: PMC4272242 DOI: 10.1038/ncomms6685] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 10/27/2014] [Indexed: 12/15/2022] Open
Abstract
Exit from mitosis is controlled by silencing of the spindle assembly checkpoint (SAC). It is important that preceding exit, all sister chromatid pairs are correctly bioriented, and that residual catenation is resolved, permitting complete sister chromatid separation in the ensuing anaphase. Here we determine that the metaphase response to catenation in mammalian cells operates through PKCε. The PKCε-controlled pathway regulates exit from the SAC only when mitotic cells are challenged by retained catenation and this delayed exit is characterized by BubR1-high and Mad2-low kinetochores. In addition, we show that this pathway is necessary to facilitate resolution of retained catenanes in mitosis. When delayed by catenation in mitosis, inhibition of PKCε results in premature entry into anaphase with PICH-positive strands and chromosome bridging. These findings demonstrate the importance of PKCε-mediated regulation in protection from loss of chromosome integrity in cells failing to resolve catenation in G2.
Collapse
Affiliation(s)
- Nicola Brownlow
- Protein Phosphorylation Laboratory, Cancer Research UK London
Research Institute, 44 Lincolns Inn Fields, London
WC2A 3LY, UK
| | - Tanya Pike
- Protein Phosphorylation Laboratory, Cancer Research UK London
Research Institute, 44 Lincolns Inn Fields, London
WC2A 3LY, UK
| | - Daniel Zicha
- Light Microscopy, Cancer Research UK London Research
Institute, London, WC2A 3LY, UK
| | - Lucy Collinson
- Electron Microscopy, Cancer Research UK London Research
Institute, London
WC2A 3LY, UK
| | - Peter J. Parker
- Protein Phosphorylation Laboratory, Cancer Research UK London
Research Institute, 44 Lincolns Inn Fields, London
WC2A 3LY, UK
- Division of Cancer Studies, King’s College London,
New Hunt’s House, Guy’s Campus, London
SE1 1UL, UK
| |
Collapse
|
18
|
Shaw D, Hollingworth G, Soldermann N, Sprague E, Schuler W, Vangrevelinghe E, Duggan N, Thomas M, Kosaka T, Waters N, van Eis MJ. Novel ROCK inhibitors for the treatment of pulmonary arterial hypertension. Bioorg Med Chem Lett 2014; 24:4812-7. [DOI: 10.1016/j.bmcl.2014.09.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/27/2014] [Accepted: 09/01/2014] [Indexed: 10/24/2022]
|
19
|
Ezaki K, Kobayashi K. A Novel Synthesis of Quinazolines by Cyclization of 1-(2-Isocyanophenyl)alkylideneamines Generated by the Treatment of 2-(1-Azidoalkyl)phenyl Isocyanides with NaH. Helv Chim Acta 2014. [DOI: 10.1002/hlca.201300431] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
20
|
Fadel S, Hajbi Y, Khouili M, Lazar S, Suzenet F, Guillaumet G. Synthesis of 3,4-dihydro-1,8-naphthyridin-2(1H)-ones via microwave-activated inverse electron-demand Diels-Alder reactions. Beilstein J Org Chem 2014; 10:282-6. [PMID: 24605148 PMCID: PMC3943289 DOI: 10.3762/bjoc.10.24] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 01/02/2014] [Indexed: 12/13/2022] Open
Abstract
Substituted 3,4-dihydro-1,8-naphthyridin-2(1H)-ones have been synthesized with the inverse electron-demand Diels-Alder reaction from 1,2,4-triazines bearing an acylamino group with a terminal alkyne side chain. Alkynes were first subjected to the Sonogashira cross-coupling reaction with aryl halides, the product of which then underwent an intramolecular inverse electron-demand Diels-Alder reaction to yield 5-aryl-3,4-dihydro-1,8-naphthyridin-2(1H)-ones by an efficient synthetic route.
Collapse
Affiliation(s)
- Salah Fadel
- Laboratoire de Chimie Organique et Analytique, Université Sultan Moulay Slimane, FST Béni-Mellal, BP 523, 23000 Béni-Mellal, Morocco
- Institut de Chimie Organique & Analytique, Université d’Orléans, UMR-CNRS 7311, BP 6759, 45067 Orléans Cedex 2, France
| | - Youssef Hajbi
- Laboratoire de Chimie Organique et Analytique, Université Sultan Moulay Slimane, FST Béni-Mellal, BP 523, 23000 Béni-Mellal, Morocco
- Institut de Chimie Organique & Analytique, Université d’Orléans, UMR-CNRS 7311, BP 6759, 45067 Orléans Cedex 2, France
| | - Mostafa Khouili
- Laboratoire de Chimie Organique et Analytique, Université Sultan Moulay Slimane, FST Béni-Mellal, BP 523, 23000 Béni-Mellal, Morocco
| | - Said Lazar
- Laboratoire de Biochimie, Environnement & Agroalimentaire, URAC 36, Université Hassan II, FST Mohammedia, BP 146, 20800 Mohammedia, Morocco
| | - Franck Suzenet
- Institut de Chimie Organique & Analytique, Université d’Orléans, UMR-CNRS 7311, BP 6759, 45067 Orléans Cedex 2, France
| | - Gérald Guillaumet
- Institut de Chimie Organique & Analytique, Université d’Orléans, UMR-CNRS 7311, BP 6759, 45067 Orléans Cedex 2, France
| |
Collapse
|
21
|
Li C, Mu XY, Li YL, Liu Y, Wang XS. Combinatorial synthesis of fused tetracyclic heterocycles containing [1,6]naphthyridine derivatives under catalyst free conditions. ACS COMBINATORIAL SCIENCE 2013; 15:267-72. [PMID: 23581605 DOI: 10.1021/co400020w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A three-component reaction between an aromatic aldehyde, an amine, and tert-butyl 2,4-dioxopiperidine-1-carboxylate in EtOH at refluxing temperature gave fused tetracyclic heterocycles in high yields. The amines include 1H-indazol-5-amine, 1H-indazol-6-amine, 1H-indol-5-amine, and 1H-benzo[d]imidazol-5-amine, giving 11-aryl-3H-indazolo[5,4-b][1,6] naphthyridine, 11-aryl-1H-indazolo[6,7-b][1,6]naphthyridine, 11-aryl-3H-indolo[5,4-b][1,6]naph-thyridine, and 11-aryl-3H-imidazo[4',5':3,4]benzo[1,2-b][1,6]naphthyridine derivatives, respectively.
Collapse
Affiliation(s)
- Chao Li
- School of Chemistry and Chemical
Engineering, Jiangsu
Key Laboratory of Green Synthetic Chemistry for Functional Materials, Jiangsu Normal University, Xuzhou Jiangsu 221116, P.
R. China
| | - Xing-Ye Mu
- School of Chemistry and Chemical
Engineering, Jiangsu
Key Laboratory of Green Synthetic Chemistry for Functional Materials, Jiangsu Normal University, Xuzhou Jiangsu 221116, P.
R. China
| | - Yu-Ling Li
- School of Chemistry and Chemical
Engineering, Jiangsu
Key Laboratory of Green Synthetic Chemistry for Functional Materials, Jiangsu Normal University, Xuzhou Jiangsu 221116, P.
R. China
| | - Yun Liu
- School of Chemistry and Chemical
Engineering, Jiangsu
Key Laboratory of Green Synthetic Chemistry for Functional Materials, Jiangsu Normal University, Xuzhou Jiangsu 221116, P.
R. China
| | - Xiang-Shan Wang
- School of Chemistry and Chemical
Engineering, Jiangsu
Key Laboratory of Green Synthetic Chemistry for Functional Materials, Jiangsu Normal University, Xuzhou Jiangsu 221116, P.
R. China
| |
Collapse
|
22
|
Cardiovascular effects of a novel selective Rho kinase inhibitor, 2-(1H-indazole-5-yl)amino-4-methoxy-6-piperazino triazine (DW1865). Eur J Pharmacol 2013; 702:218-26. [PMID: 23376156 DOI: 10.1016/j.ejphar.2013.01.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 01/08/2013] [Accepted: 01/16/2013] [Indexed: 11/23/2022]
Abstract
The arising critical implications of Rho kinase signaling in cardiovascular diseases have been attracting attention in the pharmacological potential of Rho kinase inhibitors. We identified a novel inhibitor of Rho kinase (2-(1H-indazole-5-yl)amino-4-methoxy-6-piperazino triazine; DW 1865) and characterized its effects in biochemical, cellular, tissue and animal based assays. DW 1865 potently inhibited the kinase activity of both Rho kinase 1 and Rho kinase 2 in vitro, and behaved as an ATP-competitive inhibitor. Interestingly, DW1865 was 10 times more potent in inhibiting Rho kinase activities than fasudil as a selective Rho kinase inhibitor. The activity of DW1865 was shown to be highly selective for Rho kinase in the panel assay of 13 other kinases. In the isolated vascular tissue study, DW1865 exerted vasorelaxation in phenylephrine- or 5-hydroxytriptamine-induced contraction in a concentration-dependent manner manner. In spontaneously hypertensive rats, administration of DW1865 caused a significant and dose-related reduction in blood pressure. Furthermore, DW1865 blocked angiotensin II-induced stress fiber formation and cellular hypertrophy in rat heart-derived H9c2 cells. Taken together, these results suggest that DW1865 is a highly selective and potent Rho kinase inhibitor that will alleviate the pathophysiological actions of Rho kinase such as stress fiber formation, cellular hypertrophy, and hypertension.
Collapse
|