Robert K. Leśniak joined the Medicinal Chemistry Knowledge Center at Stanford ChEM-H in 2018 as a postdoctoral fellow. Prior to coming to Stanford, he worked with Professor Chris Schofield at the University of Oxford, as a postdoctoral research associate, designing novel antibiotics for the European gram-negative antibacterial engine (ENABLE) and UK Medical Research Council (MRC). Dr Leśniak also completed his DPhil under the guidance of Professor Schofield as a BHF-CRE studentship recipient, which involved the design and implementation of small molecules targeting Fe(II), 2-oxoglutarate dependent oxygenase enzymes involved in carnitine biosynthesis and hypoxic response as a means to treat cardiovascular disease. In addition, work on small-molecule modulation of bacterial metallo-beta-lactamases to combat antibiotic resistance was also carried out. Dr Leśniak completed his undergraduate at the University of Bristol, and worked at GlaxoSmithKline, North Carolina, developing inhibitors of bromodomains and histone acetyl-transferases. He is currently working with Professor Thomas Montine at the Stanford School of Medicine on the design of neurotransmitter prodrugs.
MSci, University of Bristol, MSci in Chemistry (2012)
DPhil, Oxford University, Chemical Biology (2017)
F-19 NMR studies on gamma-butyrobetaine hydroxylase provide mechanistic insights and suggest a dual inhibition mode
2019; 55 (98): 14717–20
The final step in the biosynthesis of l-carnitine in humans is catalysed by the 2-oxoglutarate and ferrous iron dependent oxygenase, γ-butyrobetaine hydroxylase (BBOX). 1H and 19F NMR studies inform on the BBOX mechanism including by providing evidence for cooperativity between monomers in substrate/some inhibitor binding. The value of the 19F NMR methods is demonstrated by their use in the design of new BBOX inhibitors.
View details for DOI 10.1039/c9cc06466d
View details for Web of Science ID 000501305100032
View details for PubMedID 31702759
View details for PubMedCentralID PMC6927413
Small-molecules that covalently react with a human prolyl hydroxylase - towards activity modulation and substrate capture
2019; 55 (8): 1020–23
We describe covalently binding modulators of the activity of human prolyl hydroxylase domain 2 (PHD2) and studies towards a strategy for photocapture of PHD2 substrates. Reversible active site binding of electrophile bearing compounds enables susbsequent covalent reaction with a lysine residue (K408) in the flexible C-terminal region of PHD2 to give a modified protein that retains catalytic activity.
View details for DOI 10.1039/c8cc07706a
View details for Web of Science ID 000458544800038
View details for PubMedID 30452037
View details for PubMedCentralID PMC6350621
The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases (vol 14, pg 688, 2018)
NATURE CHEMICAL BIOLOGY
2018; 14 (10): 988
In the version of this article initially published, authors Sarah E. Wilkins, Charlotte D. Eaton, Martine I. Abboud and Maximiliano J. Katz were incorrectly included in the equal contributions footnote in the affiliations list. Footnote number seven linking to the equal contributions statement should be present only for Suzana Markolovic and Qinqin Zhuang, and the statement should read "These authors contributed equally: Suzana Markolovic, Qinqin Zhuang." The error has been corrected in the HTML and PDF versions of the article.
View details for PubMedID 29950663
The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases
NATURE CHEMICAL BIOLOGY
2018; 14 (7): 688-+
Biochemical, structural and cellular studies reveal Jumonji-C (JmjC) domain-containing 7 (JMJD7) to be a 2-oxoglutarate (2OG)-dependent oxygenase that catalyzes (3S)-lysyl hydroxylation. Crystallographic analyses reveal JMJD7 to be more closely related to the JmjC hydroxylases than to the JmjC demethylases. Biophysical and mutation studies show that JMJD7 has a unique dimerization mode, with interactions between monomers involving both N- and C-terminal regions and disulfide bond formation. A proteomic approach identifies two related members of the translation factor (TRAFAC) family of GTPases, developmentally regulated GTP-binding proteins 1 and 2 (DRG1/2), as activity-dependent JMJD7 interactors. Mass spectrometric analyses demonstrate that JMJD7 catalyzes Fe(II)- and 2OG-dependent hydroxylation of a highly conserved lysine residue in DRG1/2; amino-acid analyses reveal that JMJD7 catalyzes (3S)-lysyl hydroxylation. The functional assignment of JMJD7 will enable future studies to define the role of DRG hydroxylation in cell growth and disease.
View details for PubMedID 29915238
View details for PubMedCentralID PMC6027965
Crystallographic analyses of isoquinoline complexes reveal a new mode of metallo-beta-lactamase inhibition
2017; 53 (43): 5806–9
Crystallographic analyses of the VIM-5 metallo-β-lactamase (MBL) with isoquinoline inhibitors reveal non zinc ion binding modes. Comparison with other MBL-inhibitor structures directed addition of a zinc-binding thiol enabling identification of potent B1 MBL inhibitors. The inhibitors potentiate meropenem activity against clinical isolates harboring MBLs.
View details for DOI 10.1039/c7cc02394d
View details for Web of Science ID 000402296200003
View details for PubMedID 28470248
View details for PubMedCentralID PMC5516270
Human carnitine biosynthesis proceeds via (2S, 3S)-3-hydroxy-N-epsilon-trimethyllysine
2017; 53 (2): 440–42
Nε-Trimethyllysine hydroxylase (TMLH) catalyses the first step in mammalian biosynthesis of carnitine, which plays a crucial role in fatty acid metabolism. The stereochemistry of the 3-hydroxy-Nε-trimethyllysine product of TMLH has not been defined. We report enzymatic and asymmetric synthetic studies, which define the product of TMLH catalysis as (2S,3S)-3-hydroxy-Nε-trimethyllysine.
View details for DOI 10.1039/c6cc08381a
View details for Web of Science ID 000391736100035
View details for PubMedID 27965989
View details for PubMedCentralID PMC5644716
Discovery and Characterization of GSK2801, a Selective Chemical Probe for the Bromodomains BAZ2A and BAZ2B
JOURNAL OF MEDICINAL CHEMISTRY
2016; 59 (4): 1410–24
Bromodomains are acetyl-lysine specific protein interaction domains that have recently emerged as a new target class for the development of inhibitors that modulate gene transcription. The two closely related bromodomain containing proteins BAZ2A and BAZ2B constitute the central scaffolding protein of the nucleolar remodeling complex (NoRC) that regulates the expression of noncoding RNAs. However, BAZ2 bromodomains have low predicted druggability and so far no selective inhibitors have been published. Here we report the development of GSK2801, a potent, selective and cell active acetyl-lysine competitive inhibitor of BAZ2A and BAZ2B bromodomains as well as the inactive control compound GSK8573. GSK2801 binds to BAZ2 bromodomains with dissociation constants (KD) of 136 and 257 nM for BAZ2B and BAZ2A, respectively. Crystal structures demonstrated a canonical acetyl-lysine competitive binding mode. Cellular activity was demonstrated using fluorescent recovery after photobleaching (FRAP) monitoring displacement of GFP-BAZ2A from acetylated chromatin. A pharmacokinetic study in mice showed that GSK2801 had reasonable in vivo exposure after oral dosing, with modest clearance and reasonable plasma stability. Thus, GSK2801 represents a versatile tool compound for cellular and in vivo studies to understand the role of BAZ2 bromodomains in chromatin biology.
View details for DOI 10.1021/acs.jmedchem.5b00209
View details for Web of Science ID 000371103600012
View details for PubMedID 25799074
View details for PubMedCentralID PMC4770311
Cation-pi Interactions Contribute to Substrate Recognition in gamma-Butyrobetaine Hydroxylase Catalysis
CHEMISTRY-A EUROPEAN JOURNAL
2016; 22 (4): 1270–76
γ-Butyrobetaine hydroxylase (BBOX) is a non-heme Fe(II) - and 2-oxoglutarate-dependent oxygenase that catalyzes the stereoselective hydroxylation of an unactivated C-H bond of γ-butyrobetaine (γBB) in the final step of carnitine biosynthesis. BBOX contains an aromatic cage for the recognition of the positively charged trimethylammonium group of the γBB substrate. Enzyme binding and kinetic analyses on substrate analogues with P and As substituting for N in the trimethylammonium group show that the analogues are good BBOX substrates, which follow the efficiency trend N(+) >P(+) >As(+). The results reveal that an uncharged carbon analogue of γBB is not a BBOX substrate, thus highlighting the importance of the energetically favorable cation-π interactions in productive substrate recognition.
View details for DOI 10.1002/chem.201503761
View details for Web of Science ID 000368922500013
View details for PubMedID 26660433
View details for PubMedCentralID PMC4736438
- Development and application of ligand-based NMR screening assays for gamma-butyrobetaine hydroxylase MEDCHEMCOMM 2016; 7 (5): 873–80