Periodic Reporting for period 2 - TubInTrain (Tuning Tubulin Dynamics and Interactions to Face Neurotoxicity: a Multidisciplinary Approach for Training and Research)
Okres sprawozdawczy: 2021-10-01 do 2023-09-30
The improvements in life expectancy in the Western societies have turned neurodegenerative diseases and cancer into the most common health problems of the European Union. It is therefore of outmost importance to find and optimize tools that can contribute to the full comprehension of the molecular mechanisms involved in the progression of these pathologies.
Microtubules a) are formed by polymerization of the globular proteins alpha- and beta-tubulin; b) present a structure that is regulated by a polymerization-depolymerization dynamic process; c) are biological entities that play an important role in a number of cellular processes including also cell division; d) interact with other proteins and this interaction is relevant for different cellular functionalities such as neuronal activity. Changes in the behaviour and organization of microtubules are emerging as relevant events associated with many neurodegenerative diseases.
Deciphering the very basic biological mechanisms of neuronal damage linked to tubulin/microtubule perturbation is a challenge for facing neurodegeneration and in particular for the design of possible compounds that could reduce the effect of the neurological diseases.
The aim of TubInTrain was to investigate the role of microtubules in neuron functionality through an interdisciplinary approach that is mandatory for a better comprehension of microtubules involvement in the pathogenic mechanisms of neurodegeneration. TubInTrain involved research groups that belongs to different scientific area such as chemistry, biology and computer science (Fig.1). All the scientific progresses in this subject, are giving important information for the design of therapeutic interventions, thus making this project in line with the aim of Horizon 2020 programme [Challenge “Health, demographic change and wellbeing”].
In particular, we investigated different strategies for tuning tubulin dynamics and the interactions of microtubules with other proteins with the aim to:
i) model and evaluate the impact of different classes of small molecules (obtained by chemical synthesis or extracted by natural sources as secondary metabolites) on tubulin/microtubules at atomic level in cell free system,
ii) model and evaluate the impact of two tubulin interacting proteins (Tau and alpha-Synuclein) on tubulin/microtubules at atomic level in cell free system,
iii) determine the effects of the above compounds on microtubule dynamics, protein-microtubule interaction, protein aggregation and metabolism in peripheral neurons and in cellular models of neurodegeneration.
The research activities were articulated into three Work Packages (WP1-WP2-WP3 - Fig.2)
Microtubules a) are formed by polymerization of the globular proteins alpha- and beta-tubulin; b) present a structure that is regulated by a polymerization-depolymerization dynamic process; c) are biological entities that play an important role in a number of cellular processes including also cell division; d) interact with other proteins and this interaction is relevant for different cellular functionalities such as neuronal activity. Changes in the behaviour and organization of microtubules are emerging as relevant events associated with many neurodegenerative diseases.
Deciphering the very basic biological mechanisms of neuronal damage linked to tubulin/microtubule perturbation is a challenge for facing neurodegeneration and in particular for the design of possible compounds that could reduce the effect of the neurological diseases.
The aim of TubInTrain was to investigate the role of microtubules in neuron functionality through an interdisciplinary approach that is mandatory for a better comprehension of microtubules involvement in the pathogenic mechanisms of neurodegeneration. TubInTrain involved research groups that belongs to different scientific area such as chemistry, biology and computer science (Fig.1). All the scientific progresses in this subject, are giving important information for the design of therapeutic interventions, thus making this project in line with the aim of Horizon 2020 programme [Challenge “Health, demographic change and wellbeing”].
In particular, we investigated different strategies for tuning tubulin dynamics and the interactions of microtubules with other proteins with the aim to:
i) model and evaluate the impact of different classes of small molecules (obtained by chemical synthesis or extracted by natural sources as secondary metabolites) on tubulin/microtubules at atomic level in cell free system,
ii) model and evaluate the impact of two tubulin interacting proteins (Tau and alpha-Synuclein) on tubulin/microtubules at atomic level in cell free system,
iii) determine the effects of the above compounds on microtubule dynamics, protein-microtubule interaction, protein aggregation and metabolism in peripheral neurons and in cellular models of neurodegeneration.
The research activities were articulated into three Work Packages (WP1-WP2-WP3 - Fig.2)
The work performed by the network could briefly summarized as subsequently reported:
1) The computational studies based on the simulation of the possible interaction between small molecules and proteins allowed to a) define a fruitful strategy to virtually screen large collection of chemical compounds and to design new promising compounds able to interact with tubulin/microtubules and b) face the behaviour of the mutated forms of alpha-synuclein in comparison to the behaviour of the one of native alpha-synuclein
2) The research groups involved in the chemical synthesis prepared some de-novo designed small molecules and some putative α-Synuclein-microtubules binding peptides
3) X-Ray crystallography demonstrated the effective interaction with tubulin of some of the prepared small molecules and the biological evaluation demonstrated for some of the obtained small molecules an interesting biological activity
4) A protocol to determine microtubule dynamics by quantitative live cell imaging in axon-like processes of model neurons was established and validated
5) A protocol for the matabolomic studies was defined and used for some of the upon mentioned small molecules
6) 13 early stage researchers were trained in the subsequents aspects: fruitful collaboration, scientific writing, complementary experimental skills, team working ability. They are using the acquired expertise to continue their activity as researchers in academy or private companies
6) 14 papers were published. One of them (doi.org/10.1002/chem.202103520 - Fig.3) perfectly described the results obtained for a group of compounds according to the described points 1,2 and 3.
The network defined the way in which it’s possible to move from computational studies regarding the interactions that involve tubulin, microtubules, Tau and designed small molecules to the study of the effect on neurons with some unsolved problems about alpha-synuclein.
The obtained compounds and the subsequent cristallographic studies gave further details about the design of new tubulin binders in maitansin, taxane and pironetin binding site.
For a detailed description of the performed work, see Technical Report file Part. B
1) The computational studies based on the simulation of the possible interaction between small molecules and proteins allowed to a) define a fruitful strategy to virtually screen large collection of chemical compounds and to design new promising compounds able to interact with tubulin/microtubules and b) face the behaviour of the mutated forms of alpha-synuclein in comparison to the behaviour of the one of native alpha-synuclein
2) The research groups involved in the chemical synthesis prepared some de-novo designed small molecules and some putative α-Synuclein-microtubules binding peptides
3) X-Ray crystallography demonstrated the effective interaction with tubulin of some of the prepared small molecules and the biological evaluation demonstrated for some of the obtained small molecules an interesting biological activity
4) A protocol to determine microtubule dynamics by quantitative live cell imaging in axon-like processes of model neurons was established and validated
5) A protocol for the matabolomic studies was defined and used for some of the upon mentioned small molecules
6) 13 early stage researchers were trained in the subsequents aspects: fruitful collaboration, scientific writing, complementary experimental skills, team working ability. They are using the acquired expertise to continue their activity as researchers in academy or private companies
6) 14 papers were published. One of them (doi.org/10.1002/chem.202103520 - Fig.3) perfectly described the results obtained for a group of compounds according to the described points 1,2 and 3.
The network defined the way in which it’s possible to move from computational studies regarding the interactions that involve tubulin, microtubules, Tau and designed small molecules to the study of the effect on neurons with some unsolved problems about alpha-synuclein.
The obtained compounds and the subsequent cristallographic studies gave further details about the design of new tubulin binders in maitansin, taxane and pironetin binding site.
For a detailed description of the performed work, see Technical Report file Part. B
The scientific results are not exhaustively in shedding light on the topic of the faced research but they contributed in focusing the attention of the scientific community through publication and of the entire society through social media to biological implications of some neurodegenerative diseases. In particular, we are confident that the use of social media transferred to the entire society the message that neurodegenerative diseases are faced by different kind of scientists and the European Commission is trusting and helping them in pursuing new advances to make a better life expectancy. Along this way a further relevant message transferred to the society is that science is not limited by the borders that divide different countries and that the cooperation gives us a special hope for the future. We retain relevant for the socio-economic impact the training of the fellows and their human and professional growth.
The Consortium trained 13 PhD students, also during the COVID-19 pandemic, to give them the basis for independence and resourcefulness of the research activity. Living in a such international and interdisciplinary environment allowed the fellows to reach outstanding levels of professionalism, collaboration and empathy.
During the last year of TubInTrain the fellows went to several conferences making posters and oral presentations with a high impact on the scientific community. The ESRs recorded also two videos explaining their research activity and impact to the society. These videos are shared on the social media and website.
It was surprising seeing that in the last part of the project the discussions about the research topics were mainly held by the fellows. It means they gained skills and confidence to become main protagonist of the network.
To confirm the relevance of the training they received, the ESRs are finding relevant jobs as researchers or managers in academy and in companies
The Consortium trained 13 PhD students, also during the COVID-19 pandemic, to give them the basis for independence and resourcefulness of the research activity. Living in a such international and interdisciplinary environment allowed the fellows to reach outstanding levels of professionalism, collaboration and empathy.
During the last year of TubInTrain the fellows went to several conferences making posters and oral presentations with a high impact on the scientific community. The ESRs recorded also two videos explaining their research activity and impact to the society. These videos are shared on the social media and website.
It was surprising seeing that in the last part of the project the discussions about the research topics were mainly held by the fellows. It means they gained skills and confidence to become main protagonist of the network.
To confirm the relevance of the training they received, the ESRs are finding relevant jobs as researchers or managers in academy and in companies