Marko

Alexander V Strizhak, Oleg Babii, Sergii Afonin, Iuliia Bakanovic, Teodors Pantelejevs, Wenshu Xu, Elaine Fowler, Rohan Eapen, Krishna Sharma, Maxim O Platonov, Vasyl V Hurmach, Laura Itzhaki, Marko Hyvönen, Anne S Ulrich, David R Spring, Igor V Komarov

Organic and Biomolecular Chemistry, 2020 May 11, Advance article in press
DOI: 10.1039/d0ob00831a
Pubmed: 32390036

PDB coordinates: 6y4q (3D view)

Abstract

Analogs of the known inhibitor (peptide pDI) of the p53/MDM2 protein-protein interaction are reported, which are stapled by linkers bearing a photoisomerizable diarylethene moiety. The corresponding photoisomers possess significantly different affinities to the p53-interacting domain of the human MDM2. Apparent dissociation constants are in the picomolar-to-low nanomolar range for those isomers with diarylethene in the “open” configuration, but up to eight times larger for the corresponding “closed” isomers. Spectroscopic, structural, and computational studies showed that the stapling linkers of the peptides contribute to their binding. Continue reading →

Francesca Negrini , Kevin O’Grady, Marko Hyvönen, Kevin M Folta, Elena Baraldi

PLoS One 15(3):e0226448
DOI: 10.1371/journal.pone.0226448
Pubmed: 32214345

Abstract

Rapid Alkalinization Factors (RALFs) are cysteine-rich peptides ubiquitous within plant kingdom. They play multiple roles as hormonal signals in diverse processes, including root elongation, cell growth, pollen tube development, and fertilization. Their involvement in host-pathogen crosstalk as negative regulators of immunity in Arabidopsis has also been recognized. In addition, peptides homologous to RALF are secreted by different fungal pathogens as effectors during early stages of infection. Previous studies have identified nine RALF genes in the diploid strawberry (Fragaria vesca) genome. This work describes the genomic organization of the RALF gene families in commercial octoploid strawberry (Fragaria × ananassa) and the re-annotated genome of F. vesca, and then compares findings with orthologs in Arabidopsis thaliana. Continue reading →

Emma-Ruoqi Xu, Aleix Lafita, Alex Bateman, Marko Hyvönen

Acta Crystallographica Section D Structural Biology D76:124-134 (2020)
DOI: 10.1107/S2059798319016747
Pubmed: 32038043

PDB coordinates:

6RK1 (3D view)

Abstract

The members of the CCN (Cyr61/CTGF/Nov) family are a group of matricellular regulatory proteins that are essential to a wide range of functional pathways in cell signalling. Through interacting with extracellular matrix components and growth factors via one of their four domains, the CCN proteins are involved in critical biological processes such as angiogenesis, cell proliferation, bone development, fibrogenesis and tumorigenesis. Here, the crystal structure of the thrombospondin module 1 (TSP1) domain of CCN3 (previously known as Nov) is presented, which shares a similar three-stranded fold with the thrombo­spondin type 1 repeats of thrombospondin-1 and spondin-1, but with variations in the disulfide connectivity. Continue reading →

Pooja Sharma, Robert Mahen, Maxim Rossmann, Jamie E. Stokes, Bryn Hardwick, David J. Huggins, Amy Emery, Dominique L. Kunciw, Marko Hyvönen, David R. Spring, Grahame J. McKenzie & Ashok R. Venkitaraman

Scientific Reports, 9:15930 (2019)
DOI: s41598-019-50702-2
Pubmed: tbd
PDB coordinates: 5NMM (3D view), 5NEI (3D view)

Abstract

The human polo-like kinase PLK1 coordinates mitotic chromosome segregation by phosphorylating multiple chromatin- and kinetochore-binding proteins. How PLK1 activity is directed to specific substrates via phosphopeptide recognition by its carboxyl-terminal polo-box domain (PBD) is poorly understood. Here, we combine molecular, structural and chemical biology to identify a determinant for PLK1 substrate recognition that is essential for proper chromosome segregation. We show that mutations ablating an evolutionarily conserved, Tyr-lined pocket in human PLK1 PBD trigger cellular anomalies in mitotic progression and timing. Continue reading →

Manuela Urbischek, Helena Rannikmae, Thomas Foets, Katharina Ravn, Marko Hyvönen & Marc de la Roche

Scientific Reports 6193 (2019)
DOI: 0.1038/s41598-019-42604-0
Pubmed: 30996238

Abstract

The media formulations necessary for deriving and sustaining organoids from epithelial tissues such as prostate, colon, gastric, liver, pancreas, and others have been established. Critical components of organoid media are a set of growth factors that include R-spondins and BMP signalling antagonists such as Noggin or Gremlin 1. Currently, the practical limitations for formulating organoid media of reproducible potency and larger-scale media production that have hampered further technological applications of organoid technology include: the cost of growth factors such as R-spondins and Gremlin 1/Noggin and their production as defined specific activities free of contaminants that may affect organoid growth. Continue reading →

Jessica Iegre, Paul Brear, David J. Baker, Yaw Sing Tan, Eleanor L. Atkinson, Hannah F. Sore, Daniel H. O’ Donovan, Chandra S. Verma, Marko Hyvönen and David R. Spring

Chem. Sci., advance publication (2019)

DOI: 10.1039/C9SC00798A
Pubmed: TBC

PDB coordinates:

6Q38 (3D view)
6Q4Q (3D view)

Abstract

The discovery of new Protein–Protein Interaction (PPI) modulators is currently limited by the difficulties associated with the design and synthesis of selective small molecule inhibitors. Peptides are a potential solution for disrupting PPIs; however, they typically suffer from poor stability in vivo and limited tissue penetration hampering their wide spread use as new chemical biology tools and potential therapeutics. In this work, a combination of CuAAC chemistry, molecular modelling, X-ray crystallography, and biological validation allowed us to develop highly functionalised peptide PPI inhibitors of the protein CK2. Continue reading →

Bert van Loo, Christopher D. Bayer, Gerhard Fischer, Stefanie Jonas, Eugene Valkov, Mark F. Mohamed, Anastassia Vorobieva, Celine Dutruel, Marko Hyvönen and Florian Hollfelder

Journal of American Chemical Society 141:370-387 (2019)
DOI: 10.1021/jacs.8b10290
Pubmed: 30497259

PDB coordinates:
4UPH (3D view), 4UPI (3D view), 4UPL (3D view), 4UPK (3D view)

Abstract

Highly proficient, promiscuous enzymes can be springboards for functional evolution, able to avoid loss of function during adaptation by their capacity to promote multiple reactions. We employ a systematic comparative study of structure, sequence, and substrate specificity to track the evolution of specificity and reactivity between promiscuous members of clades of the alkaline phosphatase (AP) superfamily. Construction of a phylogenetic tree of protein sequences maps out the likely transition zone between arylsulfatases (ASs) and phosphonate monoester hydrolases (PMHs). Kinetic analysis shows that all enzymes characterized have four chemically distinct phospho- and sulfoesterase activities, with rate accelerations ranging from 1011- to 1017-fold for their primary and 109- to 1012-fold for their promiscuous reactions, suggesting that catalytic promiscuity is widespread in the AP-superfamily. Continue reading →

Stephen J. Walsh, Soleilmane Omarjee, Warren R. J. D. Galloway, Terence T.-L. Kwan, Hannah F. Sore, Jeremy S. Parker, Marko Hyvönen, Jason S. Carroll and David R. Spring

Chem. Sci., 2019,10, 694-700

DOI: 10.1039/C8SC04645J
Pubmed: 0774870

Abstract

<Antibody–drug conjugates (ADCs) are a class of targeted therapeutics that utilize the specificity of antibodies to selectively deliver highly potent cytotoxins to target cells. Although recent years have witnessed significant interest in ADCs, problems remain with the standard linkage chemistries used for cytotoxin-antibody bioconjugation. These typically (1) generate unstable constructs, which may lead to premature cytotoxin release, (2) often give a wide variance in drug–antibody ratios (DAR) and (3) have poor control of attachment location on the antibody, resulting in a variable pharmacokinetic profile. Herein, we report a novel divinylpyrimidine (DVP) linker platform for selective bioconjugation via covalent re-bridging of reduced disulfide bonds on native antibodies. Continue reading →

Charlotte M. Miton, Stefanie Jonas, Gerhard Fischer, Fernanda Duarte, Mark F. Mohamed, Bert van Loo, Bálint Kintses, Shina C. L. Kamerlin, Nobuhiko Tokuriki, Marko Hyvönen, and Florian Hollfelder

Proceedings of the National Academy of Sciences of the USA (2017)

DOI: 10.1073/pnas.1607817115
Pubmed: 30012610

PDB coordinates:

4CYR (3D view), 4CXS (3D view), 4CXU (3D view), 4CYS (3D view)
5AJ9 (3D view), 4CXK (3D view)

Abstract

The recruitment and evolutionary optimization of promiscuous enzymes is key to the rapid adaptation of organisms to changing environments. Our understanding of the precise mechanisms underlying enzyme repurposing is, however, limited: What are the active-site features that enable the molecular recognition of multiple substrates with contrasting catalytic requirements? To gain insights into the molecular determinants of adaptation in promiscuous enzymes, we performed the laboratory evolution of an arylsulfatase to improve its initially weak phenylphosphonate hydrolase activity. The evolutionary trajectory led to a 100,000-fold enhancement of phenylphosphonate hydrolysis, while the native sulfate and promiscuous phosphate mono- and diester hydrolyses were only marginally affected (≤50-fold). Continue reading →

Paul Brear, Andrew North, Jessica Iegre, Kathy Hadje Georgiou, Alexandra Lubin, Laura Carro, William Green, Hannah F.Sore, Marko Hyvönen, David R.Spring

Bioorganic & Medicinal Chemistry 26:3016-3020 (2018)
DOI: 10.1016/j.bmc.2018.05.011
Pubmed: 29759799

PDB coordinates:

Abstract

Increased CK2 levels are prevalent in many cancers. Combined with the critical role CK2 plays in many cell-signaling pathways, this makes it a prime target for down regulation to fight tumour growth. Herein, we report a fragment-based approach to inhibiting the interaction between CK2α and CK2β at the α-β interface of the holoenzyme. A fragment, CAM187, with an IC50 of 44 μM and a molecular weight of only 257 gmol-1 has been identified as the most promising compound. Importantly, the lead fragment only bound at the interface and was not observed in the ATP binding site of the protein when co-crystallised with CK2α. The fragment-like molecules discovered in this study represent unique scaffolds to CK2 inhibition and leave room for further optimisation.