Periodic Reporting for period 1 - ProteoKnot (Entangled tertiary folds)
Période du rapport: 2023-06-01 au 2025-11-30
ProteoKnot tackles a fundamental challenge in molecular design: the current inability to create synthetic molecules with dynamic, protein-like tertiary structures. In nature, the functions of biomolecules such as proteins rely on their ability to adopt complex, flexible three-dimensional conformations. In contrast, synthetic systems are typically limited to simpler, rigid secondary structures, like single helices. To overcome this limitation, ProteoKnot introduces a novel approach that uses molecular entanglements to control both the shape and flexibility of synthetic macromolecules.
The project is structured around three main objectives. First, we are developing design principles for constructing multiply entangled molecular architectures, referred to as “entangled tertiary folds”. These principles are tested on multi-stranded helices (WP1), then applied to more complex structures including entangled macromolecules (WP2) and polymers (WP3). Second, we are incorporating photoswitchable elements (azobenzene units) into these systems to enable remote, reversible control over their conformations (WP4). At a later stage of the project, we will demonstrate the functional potential of these dynamic structures by developing multi-responsive catalysts that mimic key aspects of protein behavior (WP5).
ProteoKnot aims to significantly advance the fields of synthetic foldamers and molecular topology by enabling the synthesis of dynamic, programmable tertiary structures. The outcomes of this project could open new avenues for designing adaptive molecular machines, smart catalysts, and functional materials, offering a powerful alternative to current bioinspired approaches and expanding the toolbox of molecular nanotechnology.
The project is structured around three main objectives. First, we are developing design principles for constructing multiply entangled molecular architectures, referred to as “entangled tertiary folds”. These principles are tested on multi-stranded helices (WP1), then applied to more complex structures including entangled macromolecules (WP2) and polymers (WP3). Second, we are incorporating photoswitchable elements (azobenzene units) into these systems to enable remote, reversible control over their conformations (WP4). At a later stage of the project, we will demonstrate the functional potential of these dynamic structures by developing multi-responsive catalysts that mimic key aspects of protein behavior (WP5).
ProteoKnot aims to significantly advance the fields of synthetic foldamers and molecular topology by enabling the synthesis of dynamic, programmable tertiary structures. The outcomes of this project could open new avenues for designing adaptive molecular machines, smart catalysts, and functional materials, offering a powerful alternative to current bioinspired approaches and expanding the toolbox of molecular nanotechnology.
During the reporting period, significant progress was made towards the development of “entangled tertiary folds” and their functional applications.
We developed a reliable method to synthesize specialized molecular strands that can assemble into double and triple helical structures in water. These strands include a variety of side groups that influence the stability of the resulting helices. Systematic studies showed how changes in these side groups affect helix formation under different conditions such as pH, concentration, and temperature. This work helped us better understand how the sequence of these strands determines their ability to form specific types of helices.
Using these strands as building blocks, we created more complex, entangled molecular architectures. A major achievement was making a molecule known as a [3]catenane, composed of three interlinked rings, with six crossings, formed by linking strand ends through specific chemical bonds in mild water-based conditions. We are also working on the synthesis a more complex knotted molecule with eight crossings, which includes light-responsive parts that could change shape when exposed to light. Additionally, strands modified with chemical groups that promote gel formation were made, with preliminary gelation tests currently ongoing.
An alternative approach to entangled macromolecules was pursued by designing simpler systems capable of forming topologically complex structures. This led to the successful synthesis of a doubly entangled catenane (Solomon link) featuring an internal cavity with high sulfate-binding affinity (K ≈ 10⁵ M⁻¹) in water, an impressive result given the challenges of anion recognition in aqueous environments. This system has been further modified with functional groups such as benzothiadiazole, which may enable singlet oxygen generation. Spectroscopic evaluation of these derivatives is ongoing in collaboration with external partners.
Additionally, an unexpected discovery was made when a synthetic intermediate spontaneously crystallized on surfaces, forming nanocubes approximately 200 nm in edge length. These nanostructures have been characterized using SEM, TEM, and various spectroscopic techniques.
We developed a reliable method to synthesize specialized molecular strands that can assemble into double and triple helical structures in water. These strands include a variety of side groups that influence the stability of the resulting helices. Systematic studies showed how changes in these side groups affect helix formation under different conditions such as pH, concentration, and temperature. This work helped us better understand how the sequence of these strands determines their ability to form specific types of helices.
Using these strands as building blocks, we created more complex, entangled molecular architectures. A major achievement was making a molecule known as a [3]catenane, composed of three interlinked rings, with six crossings, formed by linking strand ends through specific chemical bonds in mild water-based conditions. We are also working on the synthesis a more complex knotted molecule with eight crossings, which includes light-responsive parts that could change shape when exposed to light. Additionally, strands modified with chemical groups that promote gel formation were made, with preliminary gelation tests currently ongoing.
An alternative approach to entangled macromolecules was pursued by designing simpler systems capable of forming topologically complex structures. This led to the successful synthesis of a doubly entangled catenane (Solomon link) featuring an internal cavity with high sulfate-binding affinity (K ≈ 10⁵ M⁻¹) in water, an impressive result given the challenges of anion recognition in aqueous environments. This system has been further modified with functional groups such as benzothiadiazole, which may enable singlet oxygen generation. Spectroscopic evaluation of these derivatives is ongoing in collaboration with external partners.
Additionally, an unexpected discovery was made when a synthetic intermediate spontaneously crystallized on surfaces, forming nanocubes approximately 200 nm in edge length. These nanostructures have been characterized using SEM, TEM, and various spectroscopic techniques.
ProteoKnot has made significant progress in advancing the design of dynamic, entangled tertiary folds. Key scientific achievements to date include:
• The development of oligo(m-phenylene ethynylene) strands that self-assemble into double and triple helices in water, with a variety of side chains and functional groups.
• The successful synthesis of a [3]catenane with six crossings, and ongoing efforts toward the construction of an 8-crossing molecular knot incorporating photoswitchable azobenzenes.
• The design and synthesis of a Solomon link with high affinity for sulfate in water, demonstrating the functional potential of entangled architectures.
• Initial progress on polymeric hydrogels based on these foldamer scaffolds.
• The serendipituous discovery of self-assembled nanocubes during intermediate synthesis, currently under characterization.
These results establish the feasibility of constructing programmable, multiply entangled molecular systems and lay the groundwork for exploring their functional applications.
To ensure the continued success and broader relevance of these findings, further research is essential. In the second period of the grant, we will focus on completing the synthesis and characterization of the 8-crossing photoswitchable molecular knot and the entangled hydrogels. Particular attention will be given to initiating WP5, which aims to develop multi-responsive switchable catalysts based on these entangled architectures. In parallel, we will seek to establish additional collaborations, particularly in functional testing and materials characterization, which will be key to advancing these systems toward real-world applications.
• The development of oligo(m-phenylene ethynylene) strands that self-assemble into double and triple helices in water, with a variety of side chains and functional groups.
• The successful synthesis of a [3]catenane with six crossings, and ongoing efforts toward the construction of an 8-crossing molecular knot incorporating photoswitchable azobenzenes.
• The design and synthesis of a Solomon link with high affinity for sulfate in water, demonstrating the functional potential of entangled architectures.
• Initial progress on polymeric hydrogels based on these foldamer scaffolds.
• The serendipituous discovery of self-assembled nanocubes during intermediate synthesis, currently under characterization.
These results establish the feasibility of constructing programmable, multiply entangled molecular systems and lay the groundwork for exploring their functional applications.
To ensure the continued success and broader relevance of these findings, further research is essential. In the second period of the grant, we will focus on completing the synthesis and characterization of the 8-crossing photoswitchable molecular knot and the entangled hydrogels. Particular attention will be given to initiating WP5, which aims to develop multi-responsive switchable catalysts based on these entangled architectures. In parallel, we will seek to establish additional collaborations, particularly in functional testing and materials characterization, which will be key to advancing these systems toward real-world applications.