Understanding intrinsically disordered proteins and their potential as new drug targets through novel measurement capabilities

Lead Research Organisation: University of Strathclyde
Department Name: Pure and Applied Chemistry


Research into the structure-function relationship of proteins has been a productive area of study over many decades, contributing to our understanding of biology and health and hence to the development of therapies. Intrinsically disordered proteins (IDPs) are a recently discovered class of proteins that are particularly important to study because of their overrepresentation in major diseases, including cancers and neurodegenerative diseases. Unlike most proteins that exist in a defined 3-dimensional structure, IDPs switch readily between multiple shapes. This renders them notoriously difficult to study. During this Fellowship novel methods will be developed to investigate IDPs, which will lead to deeper understanding of their behaviour, and will hence allow us to identify new drugs to manipulate them in disease states.
Nano-electrospray ionisation mass spectrometry (nESI-MS) is a powerful tool to probe protein dynamics, providing information on the range of shapes in which a protein exists. Furthermore, its low sample consumption, rapid data acquisition and low data processing positions MS as an effective tool in protein structure research. The hybrid technique of ion mobility-mass spectrometry (IMMS) provides further insights into the range of structural arrangements adopted by proteins and protein complexes, since here the ions are separated according to their size and their shape.
During the proposed research, state-of-the-art IMMS methods will be used to characterise specific IDPs that are involved in disease pathways. Proteins that are of timely significance will be chosen for these studies, and will include the disordered region of the androgen receptor that is heavily implicated in prostate cancer. The range of shapes that the IDPs exist in will be explored, and their interaction with other proteins that they're known to bind to in the cell will be described. If a small molecule has previously been identified as a potential drug, the influence that it has on the IDPs behaviour and its interaction with binding partners will be measured. Methods will be developed to test libraries of small molecules to find more potential drugs that affect the properties of the IDP in the appropriate manner. In-depth analysis of the protein-drug interactions will then be performed to assess their suitability as potential drug molecules.
Currently, IDP analysis is generally performed using techniques that require expensive instrumentation and specialist technological knowledge. Such approaches include nuclear magnetic resonance (NMR) and small angle scattering methods. This fellowship will enable analytical chemistry methods to be developed to create cost-effective, accessible systems for IDP characterisation by the scientific community. The applicability of various chromatographic methods, in which proteins are separated in solution according to properties such as their charge and shape, will be tested. Possibilities to develop low-cost, easy-to-use IMMS methods for protein characterisation will also be explored.
Improved care for our ageing society is currently an important research priority across many fields. This includes the development of novel therapeutics to keep people healthier for longer. The proposed research will help to address this need by developing tools for the scientific community to exploit an unexplored set of drug targets and, by using state-of-the-art technologies, to identify small molecules as drug leads for further testing. The proposed research is therefore likely to be highly beneficial for society.

Planned Impact

Biotechnological and pharmaceutical companies will benefit from the development of innovative methods to exploit a new class of proteins as therapeutic targets, and identify drug leads that target them. IDPs were previously thought to be undruggable, in part due to the lack of methods with which to study them. The methods developed within the proposed research will help to overcome this notion. Additional benefits for the companies will include drug leads identified during the research. To maximise impact in this area, important drug targets will be used as test cases during the method development stages. This will include the disordered region of Androgen Receptor, a protein heavily implicated in castration-resistant prostate cancer. GlaxoSmithKline (Stevenage) hosts a large drug discovery department and they are likely to have an interest in methodologies that allow exploitation of a new class of drug targets. Existing links between Strathclyde and GSK will facilitate this cooperation.
The IDP community will benefit from knowledge about the conformational landscape of IDPs, which is impossible to visualise with other techniques. They will also benefit from the research that will be facilitated as a result of novel techniques for the community to measure IDPs, which will lead to an increased understanding, and extend the reach of the community.
The IMMS community will benefit from chromatographic methods that will serve as appropriate complementary techniques with which to validate gas-phase findings. Innovative methods for screening small molecule libraries for IDP inhibitors is likely to open up new areas of high-impact research, since it facilitates the possibility of identifying novel drugs for the treatment of important diseases.
Successful drug candidates identified during the research, or as a result of the novel methods developed during the Fellowship, will be of high benefit to society since it will allow better treatment of diseases. The need for new medicines has never been greater due to our aging population, and the medicines developed against cancer and neurodegenerative diseases will increase the standard of living in later life.
MS vendors will benefit from the research due to potential commercialisation of the innovative drug-screening methodologies. The methods will be developed on a Synapt G2S (Waters, UK). Existing links between the Fellow and Waters will provide the necessary means for maximum exploitation of the methods. The research could be of economic benefit therein, due to increased purchase of instrumentation, consumables and materials from Waters by users wishing to use the methods.
Research will be conducted to assess the suitability of Owlstone ultraFAIMS for studying native protein structure, with a specific focus on IDPs. The long-term aim of this is to develop an accessible, cost-effective standalone IMS device, in the absence of MS, for analysing protein structure and for drug screening purposes. Users will benefit from having an easy-to-use IMS device to analyse complex mixtures of protein structures, and Owlstone will benefit from research during the Fellowship since a concept and product for future commercialisation will be developed with potential economic impact.
I will train the PDRAs in the application of IMMS to IDPs. They will be trained in research-related and transferrable aspects of academic life, which will help them to fulfil their potential as future leaders. This will enable them to continue to make impact in the future.


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Ahmed IMM (2023) Native mass spectrometry interrogation of complexes formed during targeted protein degradation. in Rapid communications in mass spectrometry : RCM

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Guo C (2022) Peroxidase Activity of Myoglobin Variants Reconstituted with Artificial Cofactors. in Chembiochem : a European journal of chemical biology

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Perieteanu MC (2022) Selective Anti-Leishmanial Strathclyde Minor Groove Binders Using an N-Oxide Tail-Group Modification. in International journal of molecular sciences

Description The core vision of this research was to develop ion mobility mass spectrometry (IM-MS) methods to understand and exploit intrinsically disordered proteins (IDPs) as potential new drug targets. This has been realised through characterising the disordered N-terminal domain of the Androgen Receptor (AR-NTD) and determining the conformational effects exerted by the binding of its inhibitor EPI-001. AR-NTD is an attractive drug target due to its important role in advanced forms of prostate cancer, but its structural heterogeneity renders it a challenging region of the protein to drug. We identified two binding sites for the inhibitor on AR-NTD, and a large conformational change upon binding EPI-001 was elucidated for a short protein construct containing only one of the binding sites. This new knowledge relating the binding mechanisms of this class of drug will be beneficial in the identification and development of a next generation of compounds with improved properties, potentially leading to better treatments for prostate cancer. It is expected that the IM-MS methods developed will be applicable to further intrinsically disordered drug targets, of which there are many. It also highlights the potential of IM-MS to be a useful screening tool in the identification of novel drug leads against IDPs, which we have begun to explore through the use of groups of small molecules that potentially target the AR-NTD. This project demonstrates excellent progress against objective 1 of the original proposal, which was 'to use state-of-the-art IM-MS technology to analyse the dynamic behaviour if IDPs for which new drugs are urgently needed'. The ability to use IDPs as drug targets will represent a new paradigm in drug discovery.
Exploitation Route Outcomes will be useful for others in two main ways: in terms for the molecules that we identify that can serve as drug leads for better therapies, which will benefit medicinal chemists. It is also useful in terms of the methods that we are developing to search for further drug leads, which will benefit drug discovery programmes as it is a novel way to search for molecules that elicit a specific conformational response in intrinsically disordered proteins.
Sectors Healthcare

Pharmaceuticals and Medical Biotechnology

Description We have demonstrated that ion mobility mass spectrometry (IMMS) has high potential as a screening tool to identify new drugs that target intrinsically disordered proteins. IMMS vendor Waters acknowledges this potential and is enthusiastic about showcasing the utility of their new equipment in this research area and have demonstrated their commitment by supporting the application of the renewal phase of my UKRI Future Leaders Fellowship. They will provide prototype instrumentation for us to test and demonstrate the applicability of this technology for an unmet need in drug discovery. Our research is therefore having impact in industry.
First Year Of Impact 2023
Sector Healthcare,Manufacturing, including Industrial Biotechology
Impact Types Economic

Description Analysis of protein S-acylation in growth factor signalling proteins
Amount £99,000 (GBP)
Organisation GlaxoSmithKline (GSK) 
Sector Private
Country Global
Start 09/2023 
End 03/2027
Description Astrazeneca iCase studentship
Amount £118,513 (GBP)
Organisation AstraZeneca 
Sector Private
Country United Kingdom
Start 09/2022 
End 09/2026
Description BMSS Summer Studentship
Amount £1,860 (GBP)
Organisation British Mass Spectrometry Society 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2021 
End 07/2021
Description Development of mass spectrometry methods to investigate conformations and complexes of proteins relating to health and disease
Amount £85,750 (GBP)
Funding ID EPSRC DTP REA 2946 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2023 
End 03/2027
Description EPSRC DTP REA 2249
Amount £85,750 (GBP)
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 01/2021 
End 06/2024
Description Studentship support- Waters
Amount £35,000 (GBP)
Organisation Waters Corporation 
Sector Private
Country United States
Start 09/2021 
End 03/2025
Description Androgen Receptor Collaboration 
Organisation University of Aberdeen
Department Institute of Medical Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution We have used ion mobility mass spectrometry (IMMS) to measure the conformational distributions of the N-terminal domain of the Androgen Receptor (AR-NTD). We have deciphered the conformational change of AR-NTD upon binding the small molecule EPI-001, and compared the effect on constructs corresponding to different regions of the protein.
Collaborator Contribution The collaborators have supplied protein samples necessary for the research.
Impact New methods for understanding intrinsically disordered drug targets and their potential for manipulation in drug discovery. This helps to address the need for new therapeutics to keep people healthier for longer by providing tools for the scientific community to exploit an unexplored set of drug targets. New knowledge about a key prostate cancer-related protein region, which is the intrinsically disordered N-terminal domain of the Androgen Receptor. This knowledge will guide the design of new drugs for advanced forms of the disease, thereby having strong societal and economic impacts. Novel applications for IM-MS. Innovation in the area of intrinsically disordered drug targets is expected to yield economic growth for IM-MS vendors. This collaboration brings together analytical chemists and molecular biologists. 10.26434/chemrxiv-2023-f42kl D O I: 10.26434/chemrxiv-2023-f42kl
Start Year 2021
Description Effect of phosphorylation of c-myc binding capabilities 
Organisation University of Zurich
Country Switzerland 
Sector Academic/University 
PI Contribution Developed novel measurement methods for measuring binding capability
Collaborator Contribution Provided proteins and peptides for measurement
Impact New information about the effects of phosphorylation on c-myc
Start Year 2022
Description UBQLN-2 collaboration 
Organisation Syracuse University
Country United States 
Sector Academic/University 
PI Contribution We have been conducting ion mobility mass spectrometry experiments to better understand the biophysical properties of the UBQLN2 protein. We have measured how the protein responds to different salt concentrations, as this is known to affect how the protein coalesces into droplets which in turn affects the proteins function. We have also investigated how the dynamics of UBQLN2 are altered when it binds to other proteins.
Collaborator Contribution Our collaborators have supplied us with protein samples necessary for the research, as well as expertise regarding the samples and help with interpretation of our results.
Impact A key outcome of this research is the development of new methods to interrogate how the shapes of dynamic proteins are affected by conditions that cause them to coalesce into droplets. This collaboration is multidisciplinary, as it involves analytical chemists and molecular biologists. Further funding- EPSRC studentship (EPSRC DTP REA 2946) https://doi.org/10.1021/jacs.3c00756
Start Year 2021