Marko

Teodors Pantelejevs, Pedro Zuazua-Villar, Oliwia Koczy, Stephen J Walsh, Naomi Stephanie Robertson, Andrew J. Counsell, David R Spring, Jessica A. Downs and Marko Hyvönen

Chemical Science, accepted manuscript (2023)
DOI: 10.1039/D3SC03331G

PDB coordinates: 8c3j (3D view), 8br9 (3D view), 8c3n (3D view)

Abstract

Stapling is a macrocyclisation method that connects amino acid side chains of a peptide to improve its pharmacological properties. We describe an approach for stapled peptide preparation and biochemical evaluation that combines recombinant expression of fusion constructs of target peptides and cysteine-reactive divinyl-heteroaryl chemistry as an alternative to solid-phase synthesis. We then employ this workflow to prepare and evaluate BRC-repeat-derived inhibitors of the RAD51 recombinase, showing that a diverse range of secondary structure elements in the BRC repeat can be stapled without compromising binding and function. Using X-ray crystallography, we elucidate the atomic-level features of the staple moieties. We then demonstrate that BRC-repeat-derived stapled peptides can disrupt RAD51 function in cells following ionising radiation treatment.

Maria Reinecke, Paul Brear, Larsen Vornholz, Benedict-Tilmann Berger, Florian Seefried, Stephanie Wilhelm, Patroklos Samaras, Laszlo Gyenis, David William Litchfield, Guillaume Médard, Susanne Müller, Jürgen Ruland, Marko Hyvönen, Mathias Wilhelm, Bernhard Kuster

Journal volume:pages (year)
DOI: 10.1038/s41589-023-01459-3
Pubmed: 37904048

PDB coordinates:
7zwe (3D view ), 7a4q (3D view ), 7zwg (3D view ).

Abstract

Medicinal chemistry has discovered thousands of potent protein and lipid kinase inhibitors. These may be developed into therapeutic drugs or chemical probes to study kinase biology. Because of polypharmacology, a large part of the human kinome currently lacks selective chemical probes. To discover such probes, we profiled 1,183 compounds from drug discovery projects in lysates of cancer cell lines using Kinobeads. The resulting 500,000 compound-target interactions are available in ProteomicsDB and we exemplify how this molecular resource may be used. For instance, the data revealed several hundred reasonably selective compounds for 72 kinases. Cellular assays validated GSK986310C as a candidate SYK (spleen tyrosine kinase) probe and X-ray crystallography uncovered the structural basis for the observed selectivity of the CK2 inhibitor GW869516X. Continue reading →

 Victor Bolsanelli Cioffi, Maria Fernanda de Castro‑Amarante, Aleksei Lulla, Robert Andreata‑Santos, Mario Costa Cruz, Ana Carolina Ramos Moreno, Mariângela de Oliveira Silva, Bianca de Miranda Peres, Lucio Holanda Gondim de Freitas Junior, Carolina Borsoi Moraes, Edison Luiz Durigon, Nicola Coker Gordon, Marko Hyvönen, Luís Carlos de Souza Ferreira & Andrea Balan

Scientific Reports 13: 16821 (2023)
DOI: 10.1038/s41598-023-43720-8
Pubmed: 37798298

Abstract

Amongst the potential contribution of protein or peptide-display systems to study epitopes with relevant immunological features, the RAD display system stands out as a highly stable scaffold protein that allows the presentation of constrained target peptides. Here, we employed the RAD display system to present peptides derived from the SARS-CoV-2 Spike (S) protein as a tool to detect specific serum antibodies and to generate polyclonal antibodies capable of inhibiting SARS-CoV-2 infectivity in vitro. 44 linear S-derived peptides were genetically fused with the RAD scaffold (RAD-SCoV-epitopes) and screened for antigenicity with sera collected from COVID-19-infected patients. In a second step, selected RAD-SCoV-epitopes were used to immunize mice and generate antibodies. Phenotypic screening showed that some of these antibodies were able to recognize replicating viral particles in VERO CCL-81 and most notably seven of the RAD-SCoV-epitopes were able to induce antibodies that inhibited viral infection. Continue reading →

Maximilian A J Harman, Steven J Stanway, Heather Scott, Yuliya Demydchuk, Gustavo Arruda Bezerra, Simone Pellegrino, Liuhong Chen, Paul Brear, Aleksei Lulla, Marko Hyvönen, Paul J Beswick, Michael J Skynner

Journal of Medicinal Chemistry 6(14):9881-9893(2023)
DOI: 0.1021/acs.jmedchem.3c00710
Pubmed: 37433017
PDB coordinates: 8b9p (3D view), 8bfw (3D view), 8bn1 (3D view), 8byj (3D view)

Abstract

Angiotensin-converting enzyme 2 (ACE2) is a metalloprotease that cleaves angiotensin II, a peptide substrate involved in the regulation of hypertension. Here, we identified a series of constrained bicyclic peptides, Bicycle, inhibitors of human ACE2 by panning highly diverse bacteriophage display libraries. These were used to generate X-ray crystal structures which were used to inform the design of additional Bicycles with increased affinity and inhibition of ACE2 enzymatic activity. This novel structural class of ACE2 inhibitors is among the most potent ACE2 inhibitors yet described in vitro, representing a valuable tool to further probe ACE2 function and for potential therapeutic utility.

Katherine U. Gaynor, Marina Vaysburd, Maximilian A. J. Harman, Anna Albecka, Phillip Jeffrey, Paul Beswick, Guido Papa, Liuhong Chen, Donna Mallery, Brian McGuinness, Katerine Van Rietschoten, Steven Stanway, Paul Brear, Aleksei Lulla, Katarzyna Ciazynska, Veronica T. Chang, Jo Sharp, Megan Neary, Helen Box, Jo Herriott, Edyta Kijak, Lee Tatham, Eleanor G. Bentley, Parul Sharma, Adam Kirby, Ximeng Han, James P. Stewart, Andrew Owen, John A. G. Briggs, Marko Hyvönen, Michael J. Skynner & Leo C. James

Nature Communications, 14:3583, (2023)
DOI: 10.1038/s41467-023-39158-1 
Pubmed: 37328472

PDB coordinates: 8AAA (3D view), 7Z8O (3D view)
Plasmids in Addgene: pExp-His-ZBasic-RBD,

Abstract

COVID-19 has stimulated the rapid development of new antibody and small molecule therapeutics to inhibit SARS-CoV-2 infection. Here we describe a third antiviral modality that combines the drug-like advantages of both. Bicycles are entropically constrained peptides stabilized by a central chemical scaffold into a bi-cyclic structure. Rapid screening of diverse bacteriophage libraries against SARS-CoV-2 Spike yielded unique Bicycle binders across the entire protein. Exploiting Bicycles’ inherent chemical combinability, we converted early micromolar hits into nanomolar viral inhibitors through simple multimerization. Continue reading →