Aromatic Foldamer Mimics of B-DNA: Targeting the Alpha-Helix

Project Information

FOLOF

Grant agreement ID: 101054289

DOI

10.3030/101054289

EC signature date 11 May 2022

Start date 1 January 2023

End date 31 December 2027

Funded under

• European Research Council (ERC)

Total cost

€ 2 500 000,00

EU contribution

€ 2 500 000,00

Coordinated by

LUDWIG-MAXIMILIANS-UNIVERSITAET MUENCHEN
Germany

Periodic Reporting for period 1 - FOLOF (Aromatic Foldamer Mimics of B-DNA: Targeting the Alpha-Helix)

Reporting period: 2023-01-01 to 2025-06-30

Summary of the context and overall objectives of the project

Protein-nucleic acid interactions (PNIs) play a central role in biology and their control would enable long-desired biological interventions and future therapeutic applications. However, synthetic molecules that reproduce the overall shape and surface features of nucleic acids to interfere with PNIs have been lacking because, up to now, it has not been possible to design such extended and complex abiotic interactions interfaces. Due to their distinct chemical composition, predictable shapes, large size and conformational stability, aromatic oligoamide foldamers (AOFs) are prime candidates for breaking new ground in this field. FOLOF aims to develop AOF-based surface mimics of the B-DNA double helix targeted to the large ensemble of sequence-selective PNIs mediated by alpha-helices.
FOLOF will proceed by 1) expanding the chemistry tool box to enable specific design objectives; 2) optimizing the automation of AOF synthesis for the fast delivery of long sequences; 3) identifying structural features of protein-foldamer complexes and specific foldamer features that make them outcompete DNA binding; 4) establishing protocols to iteratively improve protein binding affinity and selectivity for AOFs, and AOF-DNA covalent hybrids; and 5) developing computational tools for ab initio AOF-based DNA mimic design. Through a strategic combination of chemical synthesis, computational predictions, crystallographic structural analysis, binding studies, and screening tools, FOLOF will push the production of abiotic molecular mimics of nucleic acids to a completely new ensemble.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

In the first two years of project implementation, the chemistry tools box, i.e. AOFs structural variations, has been considerably expanded. In addition, the solid phase synthesis of DNA mimic AOFs has been automated which enabled the production of the longest helical AOFs known to date. The first foldamer-DNA hybrid molecules have been designed, synthesized and characterized. Altogether, a range of candidates is available for testing their binding to DNA binding proteins, and their ability to interfere with protein function. Several of these candidates have already been shown to outcompete DNA for protein recognition (see illustration). In parallel, efforts at screening proteins that may bind to AOFs and efforts at perfecting computational tools have been met with success. These developments provide important step stones for the next phase of the project.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

A major milestone has been the structural characterization by x-ray crystallography of a complex between a DNA mimic foldamer and a small chromosomal protein. Such detailed structural information provides a basis for further molecular design. Obtaining such structures was one of the key objectives of the project. It was therefore not unexpected. Nevertheless, such achievements can never be guaranteed.
After only two years of project implementation, three publications have already appeared in peer-reviewed journals and two other manuscripts are at an advanced stage of preparation.

Crystal structure of a complex between a protein and a DNA limic foldamer

DNA mimic foldamers compete with DNA from protein binding