Theoretical prediction of spectral biomarkers for Alzheimer's disease enabled by highly efficient and adaptable mutli-level response methods

Informacje na temat projektu

FreezeAlz

Identyfikator umowy o grant: 745906

DOI

10.3030/745906

Realizacja projektu zakończyła się 28 Lutego 2018

Data podpisania przez KE 9 Marca 2017

Data rozpoczęcia 1 Lipca 2017

Data zakończenia 30 Czerwca 2019

Finansowanie w ramach

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Koszt całkowity

€ 173 857,20

Wkład UE

€ 173 857,20

Koordynowany przez

KUNGLIGA TEKNISKA HOEGSKOLAN
Sweden

Periodic Reporting for period 1 - FreezeAlz (Theoretical prediction of spectral biomarkers for Alzheimer's disease enabled by highly efficient and adaptable mutli-level response methods)

Okres sprawozdawczy: 2017-07-01 do 2019-06-30

Podsumowanie kontekstu i ogólnych celów projektu

Luminescent conjugated oligothiophenes are highly promising candidates for biomarkers for amyloid misfolds and thereby for early-stage detection of neurodegenerative diseases such as Alzheimer’s and Parkinson's disease. The elucidation of the microscopic mechanism and design principles behind these biomarkers requires theoretical assistance. Finding suitable theoretical models that allow sufficiently accurate spectra calculations for such large, dynamic, and complex biomolecular systems is a highly challenging task. There is, hence, a great need for efficient and adaptive theoretical models capable of incorporating the essential factors in spectra calculations of biomolecular systems sufficiently accurately.
The aim of this project is to combine the advantages of several state-of-the-art computational methods and thereby to devise efficient and adaptable methodologies for assisting the interpretation of existing spectra and predicting the performance of new candidates for biomarkers with respect to spectral discrimination of amyloid protein misfolds leading to an improved early-stage detection and more nuanced diagnosis of diseases such as Alzheimer’s and Parkinson’s disease. Currently ca. 6.4 mio EU citizens suffer from dementia and this number is expected to increase significantly within the next decades. Thus, early and nuanced diagnosis of neurodegenerative diseases is of great interest to the European society as such: It will allow a well-tailored medical treatment and thereby increase the patients’ life quality, which will in turn reduce the economic burden.

Prace wykonane od początku projektu do końca okresu sprawozdawczego oraz najważniejsze dotychczasowe rezultaty

We have:

(i) for the first time, performed large-scale, non-biased molecular dynamics simulations of an amyloid fibril in the presence of luminescent biomarkers. In these simulations, we succeeded in finding a convincing binding site for a family of luminescent oligothiophene biomarkers, which is in agreement with current experimental results. This study has been published in Chem. Commun., 2018, 54, 3030-3033.

(ii) contributed to the development of a novel visualization program VIA-MD (Visual Interactive Analysis of Molecular Dynamics). A particular focus of this development lies on flexible and intuitive analysis of properties of individual molecules or a set of molecules along trajectories. This enables, for instance, the identification of structure-property relationships in dynamic systems. This work has been published in Workshop on Molecular Graphics and Visual Analysis of Molecular Data, The Eurographics Association, 2018, edited by Jan Byska, Michael Krone, and Björn Sommer (https://diglib.eg.org/handle/10.2312/molva20181102).

(iii) established a protocol for the calculation of vibrationally broadened optical spectra from truly anharmonic wave functions in reduced vibrational space. This protocol has proven very promising for oligothiophenes, which are the backbone of the biomarkers of interest. We are currently preparing a peer-reviewed publication presenting these results.

(iv) set up a researchers' network for a modular electronic structure program, which is well suited for the method developments in the FreezeAlz action.

Innowacyjność oraz oczekiwany potencjalny wpływ (w tym dotychczasowe znaczenie społeczno-gospodarcze i szersze implikacje społeczne projektu)

The proposal of a convincing binding site for the amyloid biomarkers from non-biased simulations is a major step towards reliable simulation of amyloid biomarkers and therefore also towards rational design of improved fluorescent probes. This may become a game changer for more nuanced diagnosis of neurodegenerative diseases and, hence, of large socio-economic interest to the European society. Moreover, our methodological advances go clearly beyond the previous state of the art and will be important for future research, requiring accurate modeling of optical spectra of biomolecular systems. These advances include an intuitive visualization and analysis tool for structure-property relationships in molecular dynamics simulations and a reliable protocol for anharmonic quantum-mechanical calculations of vibrational broadenings, applicable to medium-sized molecules. Both became only available through the FreezeAlz action.

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