Literature DB >> 31274316

Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases.

Christine Yueh, Justin Rettenmaier1, Bing Xia, David R Hall2, Andrey Alekseenko, Kathryn A Porter, Krister Barkovich1, Gyorgy Keseru3, Adrian Whitty, James A Wells1, Sandor Vajda, Dima Kozakov.   

Abstract

The inhibition of kinases has been pursued by the pharmaceutical industry for over 20 years. While the locations of the sites that bind type II and III inhibitors at or near the adenosine 5'-triphosphate binding sites are well defined, the literature describes 10 different regions that were reported as regulatory hot spots in some kinases and thus are potential target sites for type IV inhibitors. Kinase Atlas is a systematic collection of binding hot spots located at the above ten sites in 4910 structures of 376 distinct kinases available in the Protein Data Bank. The hot spots are identified by FTMap, a computational analogue of experimental fragment screening. Users of Kinase Atlas ( https://kinase-atlas.bu.edu ) may view summarized results for all structures of a particular kinase, such as which binding sites are present and how druggable they are, or they may view hot spot information for a particular kinase structure of interest.

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Year:  2019        PMID: 31274316      PMCID: PMC7019049          DOI: 10.1021/acs.jmedchem.9b00089

Source DB:  PubMed          Journal:  J Med Chem        ISSN: 0022-2623            Impact factor:   7.446


  67 in total

1.  Structure and allosteric effects of low-molecular-weight activators on the protein kinase PDK1.

Authors:  Valerie Hindie; Adriana Stroba; Hua Zhang; Laura A Lopez-Garcia; Leila Idrissova; Stefan Zeuzem; Daniel Hirschberg; Francis Schaeffer; Thomas J D Jørgensen; Matthias Engel; Pedro M Alzari; Ricardo M Biondi
Journal:  Nat Chem Biol       Date:  2009-08-30       Impact factor: 15.040

Review 2.  FDA-approved small-molecule kinase inhibitors.

Authors:  Peng Wu; Thomas E Nielsen; Mads H Clausen
Journal:  Trends Pharmacol Sci       Date:  2015-05-12       Impact factor: 14.819

Review 3.  Structure-based Virtual Screening Approaches in Kinase-directed Drug Discovery.

Authors:  David Bajusz; Gyorgy G Ferenczy; Gyorgy M Keseru
Journal:  Curr Top Med Chem       Date:  2017       Impact factor: 3.295

4.  Human breast cancer cells contain elevated levels and activity of the protein kinase, PKR.

Authors:  S H Kim; A P Forman; M B Mathews; S Gunnery
Journal:  Oncogene       Date:  2000-06-22       Impact factor: 9.867

5.  Double-stranded RNA-dependent protein kinase, PKR, binds preferentially to Huntington's disease (HD) transcripts and is activated in HD tissue.

Authors:  A L Peel; R V Rao; B A Cottrell; M R Hayden; L M Ellerby; D E Bredesen
Journal:  Hum Mol Genet       Date:  2001-07-15       Impact factor: 6.150

6.  Activation of the interferon-inducible protein kinase PKR by hepatocellular carcinoma derived-hepatitis C virus core protein.

Authors:  N Delhem; A Sabile; R Gajardo; P Podevin; A Abadie; M A Blaton; D Kremsdorf; L Beretta; C Brechot
Journal:  Oncogene       Date:  2001-09-13       Impact factor: 9.867

7.  A myristoyl/phosphoserine switch controls cAMP-dependent protein kinase association to membranes.

Authors:  Ece C Gaffarogullari; Larry R Masterson; Emily E Metcalfe; Nathaniel J Traaseth; Erica Balatri; Musa M Musa; Daniel Mullen; Mark D Distefano; Gianluigi Veglia
Journal:  J Mol Biol       Date:  2011-06-29       Impact factor: 5.469

8.  Crystal structures of MKK4 kinase domain reveal that substrate peptide binds to an allosteric site and induces an auto-inhibition state.

Authors:  Takashi Matsumoto; Takayoshi Kinoshita; Yasuyuki Kirii; Koichi Yokota; Kensaku Hamada; Toshiji Tada
Journal:  Biochem Biophys Res Commun       Date:  2010-08-21       Impact factor: 3.575

9.  Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening.

Authors:  Michal Brylinski; Jeffrey Skolnick
Journal:  J Chem Inf Model       Date:  2010-10-25       Impact factor: 4.956

Review 10.  Protein kinase C-theta inhibitors: a novel therapy for inflammatory disorders.

Authors:  Sukhvir Chand; Nisha Mehta; Malkeet Singh Bahia; Anshuman Dixit; Om Silakari
Journal:  Curr Pharm Des       Date:  2012       Impact factor: 3.116

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  14 in total

1.  Proline Hydroxylation Primes Protein Kinases for Autophosphorylation and Activation.

Authors:  Sang Bae Lee; Aram Ko; Young Taek Oh; Peiguo Shi; Fulvio D'Angelo; Brulinda Frangaj; Antonius Koller; Emily I Chen; Timothy Cardozo; Antonio Iavarone; Anna Lasorella
Journal:  Mol Cell       Date:  2020-07-07       Impact factor: 17.970

2.  Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer.

Authors:  Vida Ravanmehr; Hannah Blau; Luca Cappelletti; Tommaso Fontana; Leigh Carmody; Ben Coleman; Joshy George; Justin Reese; Marcin Joachimiak; Giovanni Bocci; Peter Hansen; Carol Bult; Jens Rueter; Elena Casiraghi; Giorgio Valentini; Christopher Mungall; Tudor I Oprea; Peter N Robinson
Journal:  NAR Genom Bioinform       Date:  2021-12-08

3.  Positioning of an unprecedented spiro[5.5]undeca ring system into kinase inhibitor space.

Authors:  Arramshetti Venkanna; Lalita Subedi; Mahesh K Teli; Prema Dhorma Lama; Bhargav Gupta Nangunuri; Sang-Yoon Lee; Sun Yeou Kim; Mi-Hyun Kim
Journal:  Sci Rep       Date:  2020-12-04       Impact factor: 4.379

Review 4.  Druggable Transient Pockets in Protein Kinases.

Authors:  Koji Umezawa; Isao Kii
Journal:  Molecules       Date:  2021-01-27       Impact factor: 4.411

5.  Conservation of binding properties in protein models.

Authors:  Megan Egbert; Kathryn A Porter; Usman Ghani; Sergei Kotelnikov; Thu Nguyen; Ryota Ashizawa; Dima Kozakov; Sandor Vajda
Journal:  Comput Struct Biotechnol J       Date:  2021-04-25       Impact factor: 7.271

6.  Inhibitors of BRAF dimers using an allosteric site.

Authors:  Xiomaris M Cotto-Rios; Bogos Agianian; Nadege Gitego; Emmanouil Zacharioudakis; Orsi Giricz; Yang Wu; Yiyu Zou; Amit Verma; Poulikos I Poulikakos; Evripidis Gavathiotis
Journal:  Nat Commun       Date:  2020-09-01       Impact factor: 14.919

7.  In silico Druggability Assessment of the NUDIX Hydrolase Protein Family as a Workflow for Target Prioritization.

Authors:  Maurice Michel; Evert J Homan; Elisée Wiita; Kia Pedersen; Ingrid Almlöf; Anna-Lena Gustavsson; Thomas Lundbäck; Thomas Helleday; Ulrika Warpman Berglund
Journal:  Front Chem       Date:  2020-05-29       Impact factor: 5.221

Review 8.  In silico Methods for Design of Kinase Inhibitors as Anticancer Drugs.

Authors:  Zarko Gagic; Dusan Ruzic; Nemanja Djokovic; Teodora Djikic; Katarina Nikolic
Journal:  Front Chem       Date:  2020-01-08       Impact factor: 5.221

9.  Bcr-Abl Allosteric Inhibitors: Where We Are and Where We Are Going to.

Authors:  Francesca Carofiglio; Daniela Trisciuzzi; Nicola Gambacorta; Francesco Leonetti; Angela Stefanachi; Orazio Nicolotti
Journal:  Molecules       Date:  2020-09-14       Impact factor: 4.411

Review 10.  Inhibitors of Cyclin-Dependent Kinases: Types and Their Mechanism of Action.

Authors:  Paweł Łukasik; Irena Baranowska-Bosiacka; Katarzyna Kulczycka; Izabela Gutowska
Journal:  Int J Mol Sci       Date:  2021-03-10       Impact factor: 5.923

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