Literature DB >> 33079988

The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases.

Matthew E Berginski1, Nienke Moret2, Changchang Liu2, Dennis Goldfarb3,4, Peter K Sorger2, Shawn M Gomez1,5.   

Abstract

Kinases form the backbone of numerous cell signaling pathways, with their dysfunction similarly implicated in multiple pathologies. Further facilitated by their druggability, kinases are a major focus of therapeutic development efforts in diseases such as cancer, infectious disease and autoimmune disorders. While their importance is clear, the role or biological function of nearly one-third of kinases is largely unknown. Here, we describe a data resource, the Dark Kinase Knowledgebase (DKK; https://darkkinome.org), that is specifically focused on providing data and reagents for these understudied kinases to the broader research community. Supported through NIH's Illuminating the Druggable Genome (IDG) Program, the DKK is focused on data and knowledge generation for 162 poorly studied or 'dark' kinases. Types of data provided through the DKK include parallel reaction monitoring (PRM) peptides for quantitative proteomics, protein interactions, NanoBRET reagents, and kinase-specific compounds. Higher-level data is similarly being generated and consolidated such as tissue gene expression profiles and, longer-term, functional relationships derived through perturbation studies. Associated web tools that help investigators interrogate both internal and external data are also provided through the site. As an evolving resource, the DKK seeks to continually support and enhance knowledge on these potentially high-impact druggable targets.
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Year:  2021        PMID: 33079988      PMCID: PMC7778917          DOI: 10.1093/nar/gkaa853

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  30 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

Review 2.  The protein kinase complement of the human genome.

Authors:  G Manning; D B Whyte; R Martinez; T Hunter; S Sudarsanam
Journal:  Science       Date:  2002-12-06       Impact factor: 47.728

3.  Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry.

Authors:  Philipp Mertins; Lauren C Tang; Karsten Krug; David J Clark; Marina A Gritsenko; Lijun Chen; Karl R Clauser; Therese R Clauss; Punit Shah; Michael A Gillette; Vladislav A Petyuk; Stefani N Thomas; D R Mani; Filip Mundt; Ronald J Moore; Yingwei Hu; Rui Zhao; Michael Schnaubelt; Hasmik Keshishian; Matthew E Monroe; Zhen Zhang; Namrata D Udeshi; Deepak Mani; Sherri R Davies; R Reid Townsend; Daniel W Chan; Richard D Smith; Hui Zhang; Tao Liu; Steven A Carr
Journal:  Nat Protoc       Date:  2018-07       Impact factor: 13.491

4.  Tracing the origin and evolution of pseudokinases across the tree of life.

Authors:  Annie Kwon; Steven Scott; Rahil Taujale; Wayland Yeung; Krys J Kochut; Patrick A Eyers; Natarajan Kannan
Journal:  Sci Signal       Date:  2019-04-23       Impact factor: 8.192

5.  The Clinical Kinase Index: A Method to Prioritize Understudied Kinases as Drug Targets for the Treatment of Cancer.

Authors:  Derek Essegian; Rimpi Khurana; Vasileios Stathias; Stephan C Schürer
Journal:  Cell Rep Med       Date:  2020-10-20

6.  Gain-of-function genetic screen of the kinome reveals BRSK2 as an inhibitor of the NRF2 transcription factor.

Authors:  Tigist Y Tamir; Brittany M Bowman; Megan J Agajanian; Dennis Goldfarb; Travis P Schrank; Trent Stohrer; Andrew E Hale; Priscila F Siesser; Seth J Weir; Ryan M Murphy; Kyle M LaPak; Bernard E Weissman; Nathaniel J Moorman; M Ben Major
Journal:  J Cell Sci       Date:  2020-07-15       Impact factor: 5.285

7.  KinView: a visual comparative sequence analysis tool for integrated kinome research.

Authors:  Daniel Ian McSkimming; Shima Dastgheib; Timothy R Baffi; Dominic P Byrne; Samantha Ferries; Steven Thomas Scott; Alexandra C Newton; Claire E Eyers; Krzysztof J Kochut; Patrick A Eyers; Natarajan Kannan
Journal:  Mol Biosyst       Date:  2016-11-15

8.  Pharos: Collating protein information to shed light on the druggable genome.

Authors:  Dac-Trung Nguyen; Stephen Mathias; Cristian Bologa; Soren Brunak; Nicolas Fernandez; Anna Gaulton; Anne Hersey; Jayme Holmes; Lars Juhl Jensen; Anneli Karlsson; Guixia Liu; Avi Ma'ayan; Geetha Mandava; Subramani Mani; Saurabh Mehta; John Overington; Juhee Patel; Andrew D Rouillard; Stephan Schürer; Timothy Sheils; Anton Simeonov; Larry A Sklar; Noel Southall; Oleg Ursu; Dusica Vidovic; Anna Waller; Jeremy Yang; Ajit Jadhav; Tudor I Oprea; Rajarshi Guha
Journal:  Nucleic Acids Res       Date:  2016-11-29       Impact factor: 16.971

9.  The reactome pathway knowledgebase.

Authors:  Bijay Jassal; Lisa Matthews; Guilherme Viteri; Chuqiao Gong; Pascual Lorente; Antonio Fabregat; Konstantinos Sidiropoulos; Justin Cook; Marc Gillespie; Robin Haw; Fred Loney; Bruce May; Marija Milacic; Karen Rothfels; Cristoffer Sevilla; Veronica Shamovsky; Solomon Shorser; Thawfeek Varusai; Joel Weiser; Guanming Wu; Lincoln Stein; Henning Hermjakob; Peter D'Eustachio
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

10.  RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.

Authors:  Stephen K Burley; Helen M Berman; Charmi Bhikadiya; Chunxiao Bi; Li Chen; Luigi Di Costanzo; Cole Christie; Ken Dalenberg; Jose M Duarte; Shuchismita Dutta; Zukang Feng; Sutapa Ghosh; David S Goodsell; Rachel K Green; Vladimir Guranovic; Dmytro Guzenko; Brian P Hudson; Tara Kalro; Yuhe Liang; Robert Lowe; Harry Namkoong; Ezra Peisach; Irina Periskova; Andreas Prlic; Chris Randle; Alexander Rose; Peter Rose; Raul Sala; Monica Sekharan; Chenghua Shao; Lihua Tan; Yi-Ping Tao; Yana Valasatava; Maria Voigt; John Westbrook; Jesse Woo; Huanwang Yang; Jasmine Young; Marina Zhuravleva; Christine Zardecki
Journal:  Nucleic Acids Res       Date:  2019-01-08       Impact factor: 16.971

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  13 in total

1.  Bioinformatic Analysis of the Perilymph Proteome to Generate a Human Protein Atlas.

Authors:  Alina van Dieken; Hinrich Staecker; Heike Schmitt; Jennifer Harre; Andreas Pich; Willi Roßberg; Thomas Lenarz; Martin Durisin; Athanasia Warnecke
Journal:  Front Cell Dev Biol       Date:  2022-04-28

2.  Crowdsourced mapping of unexplored target space of kinase inhibitors.

Authors:  Anna Cichońska; Balaguru Ravikumar; Robert J Allaway; Fangping Wan; Sungjoon Park; Olexandr Isayev; Shuya Li; Michael Mason; Andrew Lamb; Ziaurrehman Tanoli; Minji Jeon; Sunkyu Kim; Mariya Popova; Stephen Capuzzi; Jianyang Zeng; Kristen Dang; Gregory Koytiger; Jaewoo Kang; Carrow I Wells; Timothy M Willson; Tudor I Oprea; Avner Schlessinger; David H Drewry; Gustavo Stolovitzky; Krister Wennerberg; Justin Guinney; Tero Aittokallio
Journal:  Nat Commun       Date:  2021-06-03       Impact factor: 14.919

3.  The 2021 Nucleic Acids Research database issue and the online molecular biology database collection.

Authors:  Daniel J Rigden; Xosé M Fernández
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

4.  Target 2035 - update on the quest for a probe for every protein.

Authors:  Susanne Müller; Suzanne Ackloo; Arij Al Chawaf; Bissan Al-Lazikani; Albert Antolin; Jonathan B Baell; Hartmut Beck; Shaunna Beedie; Ulrich A K Betz; Gustavo Arruda Bezerra; Paul E Brennan; David Brown; Peter J Brown; Alex N Bullock; Adrian J Carter; Apirat Chaikuad; Mathilde Chaineau; Alessio Ciulli; Ian Collins; Jan Dreher; David Drewry; Kristina Edfeldt; Aled M Edwards; Ursula Egner; Stephen V Frye; Stephen M Fuchs; Matthew D Hall; Ingo V Hartung; Alexander Hillisch; Stephen H Hitchcock; Evert Homan; Natarajan Kannan; James R Kiefer; Stefan Knapp; Milka Kostic; Stefan Kubicek; Andrew R Leach; Sven Lindemann; Brian D Marsden; Hisanori Matsui; Jordan L Meier; Daniel Merk; Maurice Michel; Maxwell R Morgan; Anke Mueller-Fahrnow; Dafydd R Owen; Benjamin G Perry; Saul H Rosenberg; Kumar Singh Saikatendu; Matthieu Schapira; Cora Scholten; Sujata Sharma; Anton Simeonov; Michael Sundström; Giulio Superti-Furga; Matthew H Todd; Claudia Tredup; Masoud Vedadi; Frank von Delft; Timothy M Willson; Georg E Winter; Paul Workman; Cheryl H Arrowsmith
Journal:  RSC Med Chem       Date:  2021-12-03

5.  A human kinase yeast array for the identification of kinases modulating phosphorylation-dependent protein-protein interactions.

Authors:  Stefanie Jehle; Natalia Kunowska; Nouhad Benlasfer; Jonathan Woodsmith; Gert Weber; Markus C Wahl; Ulrich Stelzl
Journal:  Mol Syst Biol       Date:  2022-03       Impact factor: 11.429

6.  Regulatory spine RS3 residue of protein kinases: a lipophilic bystander or a decisive element in the small-molecule kinase inhibitor binding?

Authors:  Ekaterina Shevchenko; Tatu Pantsar
Journal:  Biochem Soc Trans       Date:  2022-02-28       Impact factor: 4.919

Review 7.  Recent advances in drug repurposing using machine learning.

Authors:  Fabio Urbina; Ana C Puhl; Sean Ekins
Journal:  Curr Opin Chem Biol       Date:  2021-07-16       Impact factor: 8.822

8.  Pan-Cancer Analysis of Human Kinome Gene Expression and Promoter DNA Methylation Identifies Dark Kinase Biomarkers in Multiple Cancers.

Authors:  Siddesh Southekal; Nitish Kumar Mishra; Chittibabu Guda
Journal:  Cancers (Basel)       Date:  2021-03-10       Impact factor: 6.639

9.  CDKL5 kinase controls transcription-coupled responses to DNA damage.

Authors:  Taran Khanam; Ivan Muñoz; Florian Weiland; Thomas Carroll; Michael Morgan; Barbara N Borsos; Vasiliki Pantazi; Meghan Slean; Miroslav Novak; Rachel Toth; Paul Appleton; Tibor Pankotai; Houjiang Zhou; John Rouse
Journal:  EMBO J       Date:  2021-10-04       Impact factor: 11.598

10.  Identification of Pyrimidine-Based Lead Compounds for Understudied Kinases Implicated in Driving Neurodegeneration.

Authors:  David H Drewry; Joel K Annor-Gyamfi; Carrow I Wells; Julie E Pickett; Verena Dederer; Franziska Preuss; Sebastian Mathea; Alison D Axtman
Journal:  J Med Chem       Date:  2021-08-01       Impact factor: 7.446

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