Advancing Synthethic Supramolecular chemical biology

Project Information

ASSEMBLY

Grant agreement ID: 844872

DOI

10.3030/844872

Project terminated on 30 September 2021

EC signature date 11 April 2019

Start date 1 August 2019

End date 23 December 2021

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 175 572,48

EU contribution

€ 175 572,48

Coordinated by

TECHNISCHE UNIVERSITEIT EINDHOVEN
Netherlands

Periodic Reporting for period 1 - ASSEMBLY (Advancing Synthethic Supramolecular chemical biology)

Reporting period: 2019-08-01 to 2021-07-31

Summary of the context and overall objectives of the project

The use of cucurbituril as supramolecular tool to develop novel chemical biologically relevant interactions was explored. More robuust and elaborate systems are essential for the development of personalized medicine, advancement of the field of biosensors and development of more complex Logic gates and molecular diagnostics.

To start to tackle these issues a better understanding signaling networks is required. Split proteins offer great advantages when designing supramolecular synthetic signalling networks. When combined with our cucurbituril-bases molecular recognition system they have great promise to function in parallel with any natural signalling systems, thus having the potential to limit its biological interference, while still effecting the desired interactions.

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

By attaching cucurbituril-selective guests to the novel split luciferase NanoLuc a powerful tool was created for signal readout allowing of finetuning of the ongoing interactions. To increase the stability of the system over time and to mitigate substrate depletion a secondary ratiometric system was developed that allows for a direct and fair calibration in the system, using the Nanoluc-mNeonGreen BRET pair.

The formed supramolecular assembly between the cucurbituril and its guests can be modulated via competitor systems. The development of a light-sensitive peptidic inhibitor allows for the direct assembly of the splitprotein-cucurbituril complex in the aqueous media. Additionally a light-sensitive peptidic inhibitor was developed that, after being exposed to light facilitated the direct, irreversible de-assembly of the reformed splitprotein-cucurbituril complex in aqueous media.

To increase the understanding of the multi-complex equilibria that are formed in the model systems, the use of computational modeling proved valuable. However, as every system is different it was found time-consuming to have to develop and mathematically derive all the elaborate thermodynamic equations by hand. To facilitate this, the error prone method was replaced by an automated derivitization process. The model builder program was designed to be easy to use and modular. Stress tests show that the novel developed algorithm can cope with very large multi-component complexes with ease.

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)

The manuscript for the development of the cucurbituril-controlled the split nanoluciferase with the ratiometric calibrator with competitor controlled modulation is under construction. This project offers a reliable and robuust system that can be implemented in synthetic signalling systems, biosensors.
The manuscript detailing the novel approach to construct computational models based on multi-component complex equilibria is currently under review. The program is already been shared and tested by different research groups within the department and has been useful in the creation of several models. The developed models help provide key insights into the molecular mechanisms that are underlying many of the processes that are studied in the department. As soon as the project clear review and the full program and coding will be publicly available.

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