Mechanistic insights on the effect of small molecule aggregation inhibitors on amyloid formation
Lead Research Organisation:
University of Oxford
Department Name: SABS CDT
Abstract
Protein misfolding diseases are becoming increasingly prevalent with the increase in life expectancy and lifestyle changes over the last century (Dobson, 2017) and constitute a health challenge at a global level. This project is concerned with understanding the mechanism by which proteins aggregate and form amyloid, and how molecular chaperones and small molecules can recognize aggregates and inhibit aggregation. Studying these interactions experimentally is immensely challenging due to a large number of aggregates of varying size in solution that interconvert rapidly. Prof. Baldwin's lab has developed a method for characterising the kinetics, thermodynamic and structural features of these processes using nuclear magnetic resonance spectroscopy (NMR) (Tkachenko et al., 2018). With this method it is possible to measure nucleation rates of aggregation and characterize the very short lived aggregation nuclei structurally. This data can be fitted using large systems of ODEs to derive models of aggregation. Work underpinning this proposed project has established that an important human chaperone, aB-crystallin, selectively recognizes and distorts these short lived states, revealing a mechanism that cells have evolved to inhibit amyloid formation. aB-crystallin, and other small heat-shock proteins, are the major focus of Prof. Benesch's lab, which has expertise in characterizing their assembly and dynamics by using cutting edge native mass spectrometry (MS) methods.
The short project led to the development of an algorithm prototype for automated building and testing of chemical kinetics models for protein aggregation, which was tested with aggregation data of a tau fragment (Adamcik et al., 2016). This prototype will be extended to incorporate explicit interactions of the protein with other molecules such as small molecules and chaperones, and will be tested with data from public domain small molecule inhibition of tau and a-synuclein aggregation.
Building on the initial studies outline above, the overall goal of the DPhil project is to apply the NMR method to study the aggregation of a range of proteins associated with ageing, including a-synuclein, tau and amyloid b peptides. MS studies on aB-crystallin and other chaperones will provide complementary insight into the assemblies formed. We will extend the study to examine the effects of aggregates on cell lines and investigate the effects of small molecule aggregation inhibitors, taking advantage of expertise and facilities at Lilly UK.
Appropriate facilities are in place. Solution and solid-state NMR spectrometers are available in Oxford (300-950 MHz) and Lilly UK (500-600 MHz). A cluster comprising 6 nodes (40 processors each) in Oxford will be available for data analysis, and time on the ARC super computer will be obtained when necessary. Oxford is the leading centre worldwide for native MS. Wet labs for protein production are available in Oxford and Surrey, and facilities for human cell growth and expertise are available in Surrey.
This project falls within the EPSRC Chemical Reaction Dynamics and Mechanisms, Computational & Theoretical Chemistry, Chemical Biology and Biological Chemistry and Biophysics and Soft Matter Physics research areas.
References
Adamcik J, et al. (2016) Microtubule-Binding R3 Fragment from Tau Self-Assembles into Giant Multistranded Amyloid Ribbons. Angewandte Chemie 128(2):628-632.
Dobson CM (2017) The amyloid phenomenon and its links with human disease. Cold Spring harb Perspect Biol a023648
Tkachenko O, Benesch JLP, Baldwin AJ (2018) a B-crystallin inhibits amyloidogenesis by disassembling aggregation nuclei. BioRxiv.
The short project led to the development of an algorithm prototype for automated building and testing of chemical kinetics models for protein aggregation, which was tested with aggregation data of a tau fragment (Adamcik et al., 2016). This prototype will be extended to incorporate explicit interactions of the protein with other molecules such as small molecules and chaperones, and will be tested with data from public domain small molecule inhibition of tau and a-synuclein aggregation.
Building on the initial studies outline above, the overall goal of the DPhil project is to apply the NMR method to study the aggregation of a range of proteins associated with ageing, including a-synuclein, tau and amyloid b peptides. MS studies on aB-crystallin and other chaperones will provide complementary insight into the assemblies formed. We will extend the study to examine the effects of aggregates on cell lines and investigate the effects of small molecule aggregation inhibitors, taking advantage of expertise and facilities at Lilly UK.
Appropriate facilities are in place. Solution and solid-state NMR spectrometers are available in Oxford (300-950 MHz) and Lilly UK (500-600 MHz). A cluster comprising 6 nodes (40 processors each) in Oxford will be available for data analysis, and time on the ARC super computer will be obtained when necessary. Oxford is the leading centre worldwide for native MS. Wet labs for protein production are available in Oxford and Surrey, and facilities for human cell growth and expertise are available in Surrey.
This project falls within the EPSRC Chemical Reaction Dynamics and Mechanisms, Computational & Theoretical Chemistry, Chemical Biology and Biological Chemistry and Biophysics and Soft Matter Physics research areas.
References
Adamcik J, et al. (2016) Microtubule-Binding R3 Fragment from Tau Self-Assembles into Giant Multistranded Amyloid Ribbons. Angewandte Chemie 128(2):628-632.
Dobson CM (2017) The amyloid phenomenon and its links with human disease. Cold Spring harb Perspect Biol a023648
Tkachenko O, Benesch JLP, Baldwin AJ (2018) a B-crystallin inhibits amyloidogenesis by disassembling aggregation nuclei. BioRxiv.
Planned Impact
The main impact of the SABS CDT will be the difference made by the scientists trained within it, both during their DPhils and throughout their future careers.
The impact of the students during their DPhil should be measured by the culture change that the centre engenders in graduate training, in working at the interface between mathematical/physical sciences and the biomedical sciences, and in cross sector industry/academia working practices.
Current SABS projects are already changing the mechanisms of industry academic collaboration, for example as described by one of our Industrial Partners
"UCB and Roche are currently supervising a joint DPhil project and have put in two more joint proposals, which would have not been possible without the connections and the operational freedom offered by SABS-IDC and its open innovation culture, a one-of-the-kind in UK's CDTs."
New collaborations are also being generated: over 25% of current research projects are entirely new partnerships brokered by the Centre. The renewal of SABS will allow it to continue to strengthen and broaden this effect, building new bridges and starting new collaborations, and changing the culture of academic industrial partnerships. It will also continue to ensure that all of its research is made publically available through its Open Innovation structure, and help to create other centres with similar aims.
For all of our partners however, the students themselves are considered to be the ultimate output: as one our partners describes it,
"I believe the current SABS-IDC has met our original goals of developing young research scientists in a multidisciplinary environment with direct industrial experience and application. As a result, the graduating students have training and research experience that is directly applicable to the needs of modern lifescience R&D, in areas such as pharmaceuticals and biotechnology."
However, it is not only within the industrial realm that students have impact; in the later years of their DPhils, over 40% of SABS students, facilitated by the Centre, have undertaken various forms of public engagement. This includes visiting schools, working alongside Zooniverse to develop citizen science projects, and to produce educational resources in the area of crystal images. In the new Centre all students will be required to undertake outreach activities in order to increase engagement with the public.
The impact of the students after they have finished should be measured by how they carry on this novel approach to research, be it in the sector or outside it. As our industrial letters of support make clear, though no SABS students have yet completed their DPhils, there is a clear expectation that they will play a significant role in shaping the UK economy in the future. For example, as one of our partners comments about our students
"UCB has been in constant search for such talents, who would thrive in pharmaceutical research, but they are rare to find in conventional postgraduate programmes. Personally I am interested in recruiting SABS-IDC students to my group once they are ready for the job market."
To demonstrate the type of impact that SABS alumni will have, we consider the impact being made by the alumni of the i-DTC programmes from which this proposal has grown. Examples include two start-up companies, both of which already have investment in the millions. Several students also now hold senior positions in industry and in research facilities and institutes. They have also been named on 30 granted or pending patents, 15 of these arising directly from their DPhil work.
The examples of past success given above indicate the types of impact we expect the graduates from SABS to achieve, and offer clear evidence that SABS students will become future research leaders, driving innovation and changing research culture.
The impact of the students during their DPhil should be measured by the culture change that the centre engenders in graduate training, in working at the interface between mathematical/physical sciences and the biomedical sciences, and in cross sector industry/academia working practices.
Current SABS projects are already changing the mechanisms of industry academic collaboration, for example as described by one of our Industrial Partners
"UCB and Roche are currently supervising a joint DPhil project and have put in two more joint proposals, which would have not been possible without the connections and the operational freedom offered by SABS-IDC and its open innovation culture, a one-of-the-kind in UK's CDTs."
New collaborations are also being generated: over 25% of current research projects are entirely new partnerships brokered by the Centre. The renewal of SABS will allow it to continue to strengthen and broaden this effect, building new bridges and starting new collaborations, and changing the culture of academic industrial partnerships. It will also continue to ensure that all of its research is made publically available through its Open Innovation structure, and help to create other centres with similar aims.
For all of our partners however, the students themselves are considered to be the ultimate output: as one our partners describes it,
"I believe the current SABS-IDC has met our original goals of developing young research scientists in a multidisciplinary environment with direct industrial experience and application. As a result, the graduating students have training and research experience that is directly applicable to the needs of modern lifescience R&D, in areas such as pharmaceuticals and biotechnology."
However, it is not only within the industrial realm that students have impact; in the later years of their DPhils, over 40% of SABS students, facilitated by the Centre, have undertaken various forms of public engagement. This includes visiting schools, working alongside Zooniverse to develop citizen science projects, and to produce educational resources in the area of crystal images. In the new Centre all students will be required to undertake outreach activities in order to increase engagement with the public.
The impact of the students after they have finished should be measured by how they carry on this novel approach to research, be it in the sector or outside it. As our industrial letters of support make clear, though no SABS students have yet completed their DPhils, there is a clear expectation that they will play a significant role in shaping the UK economy in the future. For example, as one of our partners comments about our students
"UCB has been in constant search for such talents, who would thrive in pharmaceutical research, but they are rare to find in conventional postgraduate programmes. Personally I am interested in recruiting SABS-IDC students to my group once they are ready for the job market."
To demonstrate the type of impact that SABS alumni will have, we consider the impact being made by the alumni of the i-DTC programmes from which this proposal has grown. Examples include two start-up companies, both of which already have investment in the millions. Several students also now hold senior positions in industry and in research facilities and institutes. They have also been named on 30 granted or pending patents, 15 of these arising directly from their DPhil work.
The examples of past success given above indicate the types of impact we expect the graduates from SABS to achieve, and offer clear evidence that SABS students will become future research leaders, driving innovation and changing research culture.