TY - JOUR
T1 - Development of novel molecular probes of the Rio1 atypical protein kinase
AU - Mielecki, Marcin
AU - Krawiec, Krzysztof
AU - Kiburu, Irene
AU - Grzelak, Krystyna
AU - Zagórski, Włodzimierz
AU - Kierdaszuk, Borys
AU - Kowa, Kamila
AU - Fokt, Izabela
AU - Szymanski, Slawomir
AU - Świerk, Piotr
AU - Szeja, Wiesław
AU - Priebe, Waldemar
AU - Lesyng, Bogdan
AU - Laronde-Leblanc, Nicole
N1 - Funding Information:
We acknowledge the financial support by the Biocentrum-Ochota project ( POIG 02.03.00-00-003/09 ) of the Medical Research Centre Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Polish Academy of Sciences and the University of Warsaw (BST/BF funds), and the National Institutes of Health National Cancer Institute grant ( K22CA123152 ) to N.L.-L. Data collection was conducted at the Advanced Photon Source on the Northeastern Collaborative Access Team beamlines, supported by grants from the National Center for Research Resources ( 5P41RR015301-10 ) and the National Institute of General Medical Sciences ( 8 P41 GM103403-10 ) from the National Institutes of Health. Use of the Advanced Photon Source, an Office of Science User Facility operated for the U.S. Department of Energy (DOE) Office of Science by Argonne National Laboratory, was supported by the U.S. DOE under Contract No. DE-AC02-06CH11357 . Atomic coordinates and structure factors for the AfRio1-WP1086 crystal structure have been deposited in the Protein Data Bank under accession number PDB ID: 4JIN .
PY - 2013
Y1 - 2013
N2 - The RIO kinases are essential protein factors required for the synthesis of new ribosomes in eukaryotes. Conserved in archaeal organisms as well, RIO kinases are among the most ancient of protein kinases. Their exact molecular mechanisms are under investigation and progress of this research would be significantly improved with the availability of suitable molecular probes that selectively block RIO kinases. RIO kinases contain a canonical eukaryotic protein kinase fold, but also display several unusual structural features that potentially create opportunity for the design of selective inhibitors. In an attempt to identify structural leads to target the RIO kinases, a series of pyridine caffeic acid benzyl amides (CABA) were tested for their ability to inhibit the autophosphorylation activity of Archeaoglobus fulgidus Rio1 (AfRio1). Screening of a small library of CABA molecules resulted in the identification of four compounds that measurably inhibited AfRio1 activity. Additional biochemical characterization of binding and inhibition activity of these compounds demonstrated an ATP competitive inhibition mode, and allowed identification of the functional groups that result in the highest binding affinity. In addition, docking of the compound to the structure of Rio1 and determination of the X-ray crystal structure of a model compound (WP1086) containing the desired functional groups allowed detailed analysis of the interactions between these compounds and the enzyme. Furthermore, the X-ray crystal structure demonstrated that these compounds stabilize an inactive form of the enzyme. Taken together, these results provide an important step in identification of a scaffold for the design of selective molecular probes to study molecular mechanisms of Rio1 kinases in vitro and in vivo. In addition, it provides a rationale for the future design of potent inhibitors with drug-like properties targeting an inactive form of the enzyme. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).
AB - The RIO kinases are essential protein factors required for the synthesis of new ribosomes in eukaryotes. Conserved in archaeal organisms as well, RIO kinases are among the most ancient of protein kinases. Their exact molecular mechanisms are under investigation and progress of this research would be significantly improved with the availability of suitable molecular probes that selectively block RIO kinases. RIO kinases contain a canonical eukaryotic protein kinase fold, but also display several unusual structural features that potentially create opportunity for the design of selective inhibitors. In an attempt to identify structural leads to target the RIO kinases, a series of pyridine caffeic acid benzyl amides (CABA) were tested for their ability to inhibit the autophosphorylation activity of Archeaoglobus fulgidus Rio1 (AfRio1). Screening of a small library of CABA molecules resulted in the identification of four compounds that measurably inhibited AfRio1 activity. Additional biochemical characterization of binding and inhibition activity of these compounds demonstrated an ATP competitive inhibition mode, and allowed identification of the functional groups that result in the highest binding affinity. In addition, docking of the compound to the structure of Rio1 and determination of the X-ray crystal structure of a model compound (WP1086) containing the desired functional groups allowed detailed analysis of the interactions between these compounds and the enzyme. Furthermore, the X-ray crystal structure demonstrated that these compounds stabilize an inactive form of the enzyme. Taken together, these results provide an important step in identification of a scaffold for the design of selective molecular probes to study molecular mechanisms of Rio1 kinases in vitro and in vivo. In addition, it provides a rationale for the future design of potent inhibitors with drug-like properties targeting an inactive form of the enzyme. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).
KW - Atypical
KW - Enzyme-inhibitor complex
KW - Inhibitor
KW - Molecular docking
KW - RIO kinase
KW - Ribosome biogenesis
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U2 - 10.1016/j.bbapap.2013.03.012
DO - 10.1016/j.bbapap.2013.03.012
M3 - Article
C2 - 23523885
AN - SCOPUS:84878881731
SN - 1570-9639
VL - 1834
SP - 1292
EP - 1301
JO - Biochimica et Biophysica Acta - Proteins and Proteomics
JF - Biochimica et Biophysica Acta - Proteins and Proteomics
IS - 7
ER -