A fragment-based approach leading to the discovery of inhibitors of CK2α with a novel mechanism of action

Paul Brear, Claudia De Fusco, Eleanor L. Atkinson, Jessica Iegre, Nicola J. Francis-Newton, Ashok R. Venkitaraman, Marko Hyvönen and David R. Spring

Journal volume: RSC Med. Chem., 2022, Advance Article
DOI: 10.1039/D2MD00161F


CK2 is a ubiquitous protein kinase with an anti-apoptotic role and is found to be overexpressed in multiple cancer types. To this end, the inhibition of CK2 is of great interest with regard to the development of novel anti-cancer therapeutics. ATP-site inhibition of CK2 is possible; however, this typically results in poor selectivity due to the highly conserved nature of the catalytic site amongst kinases. An alternative methodology for the modulation of CK2 activity is through allosteric inhibition. The recently identified αD site represents a promising binding site for allosteric inhibition of CK2α. The work presented herein describes the development of a series of CK2α allosteric inhibitors through iterative cycles of X-ray crystallography and enzymatic assays, in addition to both fragment growing and fragment merging design strategies. Continue reading →

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Functional metagenomic screening identifies an unexpected β-glucuronidase

Stefanie Neun, Paul Brear, Eleanor Campbell, Theodora Tryfona, Kamel El Omari, Armin Wagner, Paul Dupree, Marko Hyvönen, Florian Hollfelder

Nature Chemical Biology. Online ahead of print. 07 July 2022 Jul.
DOI: 10.1038/s41589-022-01071-x
Pubmed: 35799064

PDB coordinates:
7QE1 (3D view), 7QE2 (3D view), 7QEF (3D view), 7QEA (3D view), 7QG4 (3D view), 7QEE (3D view)


The abundance of recorded protein sequence data stands in contrast to the small number of experimentally verified functional annotation. Here we screened a million-membered metagenomic library at ultrahigh throughput in microfluidic droplets for β-glucuronidase activity. We identified SN243, a genuine β-glucuronidase with little homology to previously studied enzymes of this type, as a glycoside hydrolase 3 family member. This glycoside hydrolase family contains only one recently added β-glucuronidase, showing that a functional metagenomic approach can shed light on assignments that are currently ‘unpredictable’ by bioinformatics. Continue reading →

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The common H202D variant in GDF-15 does not affect its bioactivity but can significantly interfere with measurement of its circulating levels

Yanislava Karusheva, Matt Ratcliff, Audrey Melvin, Alexander Moerseburg, Naveed Sattar, Peter Barker, Keith Burling, Anna Backmark, Robert Roth, Lutz Jermutus, Esther Guiu-Jurado, Matthias Blueher, Paul Welsh, Marko Hyvönen, Stephen O’Rahilly

The Journal of Applied Laboratory Medicine, Advance Article 07 July 2022.
DOI: 10.1093/jalm/jfac055
MedRxiv preprint DOI:

GDF15 bioactivity


Genetic variants in proteins can interfere with measurement of their circulating concentrations. Given the growing biomedical importance of GDF-15, we wished to establish whether a common histidine to aspartate variant present in position 6 of the mature GDF-15 protein (H202D variant) interfered with its measurement by two commonly used immunoassays. We first examined the detectability of recombinant monomers, homodimers and heterodimers of GDF-15 by assays and/or reagents used in two widely used immunoassays (Roche Elecsys GDF-15 and the R&D antibody combinations used in their Quantikine and DuoSet ELISAs). The Roche assay detected the H and D containing peptides similarly but the assays based on the R&D reagents consistently underreported concentrations of the D-containing variant peptide. Measurements of plasma concentrations of GDF-15 in genotyped human participants showed that the R&D reagents reported values in heterozygotes were ~25% lower, and in homozygotes, 50% lower than the Roche assay. Continue reading →

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Divergent binding mode for a protozoan BRC repeat to RAD51

Teodors Pantelejevs and Marko Hyvönen

Biochemical Journal, 479: 1031–1043 (2022)
DOI: 10.1042/BCJ20220141
Pubmed: 35502837
BioRxiv preprint: 2022.01.25.477309v1

PDB coordinates:
7QV8 (3D view)
L.infantum RAD51 complexed with BRC repeat


Interaction of BRCA2 through ca. 30 amino acid residue motifs, BRC repeats, with RAD51 is a conserved feature of the double-strand DNA break repair by homologous recombination in eukaryotes. In humans the binding of the eight BRC repeats is defined by two sequence motifs, FxxA and LFDE, interacting with distinct sites on RAD51. Little is known of the interaction of BRC repeats in other species, especially in protozoans, where variable number of BRC repeats are found in BRCA2 proteins. Here we have studied in detail the interactions of the two BRC repeats in Leishmania infantum BRCA2 with RAD51. We show LiBRC1 is a high-affinity repeat and determine the crystal structure of its complex with LiRAD51. Continue reading →

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Development of small cyclic peptides targeting the CK2α/β interface

Eleanor L. Atkinson, Jessica Iegre, Claudio D’Amore, Paul Brear, Mauro Salvi, Marko Hyvönen and David R. Spring

Chemical Communications, 58:4791-4794 (2022)
DOI: 10.1039/D2CC00707J
Pubmed: 35343996

PDB coordinates:

6YZH (3D view)
6Q4Q (3D view)

TOC graphic


In this work, an iterative cycle of enzymatic assays, X-ray crystallography, molecular modelling and cellular assays were used to develop a functionalisable chemical probe for the CK2α/β PPI. The lead peptide, P8C9, successfully binds to CK2α at the PPI site, is easily synthesisable and functionalisable, highly stable in serum and small enough to accommodate further optimisation.

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Anthraquinone derivatives as ADP-competitive inhibitors of liver pyruvate kinase

Amalyn Nain-Pereza, Anders Foller Füchtbauera, Liliana Håversen, Aleksei Lulla, Chunxia Gao, Josipa Matic, Leticia, Monjasa Alexandra Rodríguez, Paul Brear, Woonghee Kim, Marko Hyvönen, Jan Borén, Adil Mardinoglu, Mathias Uhlen, Morten Grøtli

European Journal of Medicinal Chemistry 23:114270 (2021)
DOI: 10.1016/j.ejmech.2022.114270
Pubmed: 35290845

PDB coordinates:

5SCL (3D view), 5SDT (3D view), 5SC8 (3D view), 5SCB (3D view), 5SC9 (3D view), 5SCA (3D view), 5SCK (3D view), 7QZU (3D view), 5SCE (3D view), 5SCC (3D view), 5SCD (3D view), 5SCF (3D view), 5SCH (3D view), 5SCG (3D view), 5SCI (3D view), 5SCJ (3D view), 7QDN (3D view)

Liver Pyruvate Kinase


Liver pyruvate kinase (PKL) is a major regulator of metabolic flux and ATP production during liver cell glycolysis and is considered a potential drug target for the treatment of non-alcoholic fatty liver disease (NAFLD). In this study, we report the first ADP-competitive PKL inhibitors and identify several starting points for the further optimization of these inhibitors. Modeling and structural biology guided the optimization of a PKL-specific anthraquinone-based compound. A structure–activity relationship study of 47 novel synthetic derivatives revealed PKL inhibitors with half-maximal inhibitory concentration (IC50) values in the 200 nM range. Continue reading →

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Unraveling the Mechanics of a Repeat-Protein Nanospring: From Folding of Individual Repeats to Fluctuations of the Superhelix

Marie Synakewicz, Rohan S Eapen, Albert Perez-Riba, Pamela J E Rowling, Daniela Bauer, Andreas Weißl, Gerhard Fischer, Marko Hyvönen, Matthias Rief, Laura S Itzhaki, Johannes Stigler

ACS Nano, 2022 (online before print version)
DOI: doi: 10.1021/acsnano.1c09162
Pubmed: 35258937


Tandem-repeat proteins comprise small secondary structure motifs that stack to form one-dimensional arrays with distinctive mechanical properties that are proposed to direct their cellular functions. Here, we use single-molecule optical tweezers to study the folding of consensus-designed tetratricopeptide repeats (CTPRs), superhelical arrays of short helix-turn-helix motifs. We find that CTPRs display a spring-like mechanical response in which individual repeats undergo rapid equilibrium fluctuations between partially folded and unfolded conformations. We rationalize the force response using Ising models and dissect the folding pathway of CTPRs under mechanical load, revealing how the repeat arrays form from the center toward both termini simultaneously. Continue reading →

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Poxviruses and paramyxoviruses use a conserved mechanism of STAT1 antagonism to inhibit interferon signaling

Callum Talbot-Cooper, Teodors Pantelejevs, John P. Shannon, Christian R. Cherry, Marcus T. Au, Marko Hyvönen, Heather D. Hickman, Geoffrey L.Smith

Cell Host & Microbe, in press.
DOI: 10.1016/j.chom.2022.01.014
Pubmed: 35182467

PDB coordinates:: 7NUF (3D view)
STAT1 complexed with 018


The induction of interferon (IFN)-stimulated genes by STATs is a critical host defense mechanism against virus infection. Here, we report that a highly expressed poxvirus protein, 018, inhibits IFN-induced signaling by binding to the SH2 domain of STAT1, thereby preventing the association of STAT1 with an activated IFN receptor. Despite encoding other inhibitors of IFN-induced signaling, a poxvirus mutant lacking 018 was attenuated in mice. The 2.0 Å crystal structure of the 018:STAT1 complex reveals a phosphotyrosine-independent mode of 018 binding to the SH2 domain of STAT1. Moreover, the STAT1-binding motif of 018 shows similarity to the STAT1-binding proteins from Nipah virus, which, similar to 018, block the association of STAT1 with an IFN receptor. Overall, these results uncover a conserved mechanism of STAT1 antagonism that is employed independently by distinct virus families.

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Welcome to new members

Welcome to new lab members Emma, Gwen, Aleks and Miha!

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Improved RAD51 binders through motif shuffling based on the modularity of BRC repeats

Laurens H. Lindenburg, Teodors Pantelejevs, Fabrice Gielen, Pedro Zuazua-Villar, Maren Butz, Eric Rees, Clemens F. Kaminski, Jessica A. Downs, Marko Hyvönen, and Florian Hollfelder

Proceedings of the National Academy of Sciences of the USA 118:e2017708118 (2021)
DOI: 10.1073/pnas.2017708118
Pubmed: 34772801
PDB coordinates: 6HQU (3D view)


Exchanges of protein sequence modules support leaps in function unavailable through point mutations during evolution. Here we study the role of the two RAD51-interacting modules within the eight binding BRC repeats of BRCA2. We created 64 chimeric repeats by shuffling these modules and measured their binding to RAD51. We found that certain shuffled module combinations were stronger binders than any of the module combinations in the natural repeats. Surprisingly, the contribution from the two modules was poorly correlated with affinities of natural repeats, with a weak BRC8 repeat containing the most effective N-terminal module. Continue reading →

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