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Title: Identification of inhibitors for a family of human oxoglutarate-dependent oxygenases
Author: Nowak, Radosław Piotr
ISNI:       0000 0004 6346 7222
Awarding Body: University of Oxford
Current Institution: University of Oxford
Date of Award: 2015
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The family of human iron- and 2-oxoglutarate - dependent oxygenases encompasses over 60 members and a subclass of the enzymes, containing Jumonji C (JmjC) domain, is directly involved in epigenetic control of gene transcription, through demethylation of methyl marks present on histone tails. Recently, JmjC-type enzymes, namely MINA53, NO66 and OGFOD, were identified as ribosomal protein hydroxylases (ROXs), broadening the known substrate set and indicating a function in the control of mRNA translation. Oxygenases are frequently implicated as key regulatory factors in various types of cancers and targeted inhibition of this class of enzymes can lead to suppressed cancer cell proliferation, opening an epigenetic avenue for therapeutic intervention by small molecules. In order to identify novel chemical starting points for JmjC- type oxygenases we have profiled representative members of the family with two libraries of fragments by activity assays and used X-ray crystallography to explore the binding mode of identified inhibitors. The obtained X-ray crystal structure complexes with JARID1B demethylase represent 7 novel chemotypes exploring different regions of the catalytic binding site as well as a previously unidentified putative allosteric pocket. We have then focussed on the ribosomal hydroxylases NO66 and MINA53, and identified novel chemical lead compounds through a mass spectrometry based enzymatic activity assay and obtained X-ray crystal structure complexes with JARID1B demethylase of two active inhibitors of MINA53 and JARID1B (IC50 of 0.9-5 µM). The most active hydroxamic acid series has an IC50 of 900 nM towards JARID1B with a favourable selectivity profile and shows anti-proliferative effects in human myeloma cell lines. We anticipate that our comprehensive set of fragment library activity data together with X-ray crystal structure complexes identified in this thesis can be used as starting points for further structure-based inhibitor development programs for JmjC- type oxygenases.
Supervisor: Oppermann, Udo ; Johansson, Catrine ; Tumber, Anthony ; Owen, Dafydd Sponsor: Engineering and Physical Sciences Research Council
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: KDM ; epigenetics ; oxygenases ; lysine demethylases ; ribosomal hydroxylases ; fragment screening ; structural biology