A Generalised Approach to Derive Functionally Active Peptide Inhibitors of Transcription Factor Activity

Lead Research Organisation: University of Kent
Department Name: Sch of Biosciences

Abstract

We will develop and test a new intracellular peptide-library screening assay that we have created to derive functional antagonists for a family of transcription factors (bZIP proteins) implicated in disease. Using a cancer causing member that binds DNA, Activator Protein-1 (AP-1), as an exemplar we have recently established a proof-of-principle for our approach. AP-1 is a major player in cancer that functions by binding specific DNA sites to control the expression of genes involved in cellular processes such as cell growth. A major strength of our screening technique is that it selects inhibitors by their ability to bind AP-1, but also ensures they shut down its function. This ability to distinguish between AP-1 binders and those that are capable of shutting down AP-1 function is unique and addresses a problem that has hampered the search for 'functionally active' inhibitors.

Since the assay is undertaken entirely inside living bacterial cells, it allows for additional benefits such as removal of library members that do not bind specifically to AP-1, as well as those that are unstable, insoluble, or degraded by enzymes. The project will generate understanding about how AP-1 binds to DNA and how its activity can be prevented, as well as creating peptides with excellent potential to be further developed into druggable molecules.

We will test the potency of our peptides and peptide-derived molecules using a range of biophysical, structural, and cell-based experiments, including high-resolution imaging techniques that will allow us to study how our inhibitors work by looking at individual molecules. These experiments will shed light on how our inhibitors work looking for their ability not only to bind to AP-1 but importantly to shut down its function, we will gain an understanding of dosages required, where the inhibitors bind and how quickly, if they are stable in biological fluids, can cross biological membranes, and how they behave in cancer cell cultures where AP-1 is known to play a major role. The importance of these experiments is that we can derive a rule set for the design of inhibitors, enabling us to enhance certain properties of the inhibitors at will. In addition, this rule set can then be applied to rationally design inhibitors for this and other transcription factors.

Technical Summary

AP-1 is a major player in cancer. We have developed a novel assay that screens peptide libraries inside bacterial cells to generate inhibitors that bind AP-1 and guarantee functional loss. Those that bind AP-1 but do not shut down function will be removed from the library. Additional selection pressures mitigate against non-selection by removing insoluble, unstable, aggregate prone and non-specific members; leaving excellent scaffolds for further refinement. We provide clear evidence for proof of concept in this proposal. Lastly, using a technique known as CANDI developed by Mason, inhibitors will be derived such that they can work together without cross-talk, providing potentially synergistic combinations capable of 'mopping-up' both Jun and Fos AP-1 components.

Peptides and their mimetics will be tested using a range of biophysical (ensemble and single molecule), structural, and cell-based approaches to determine how these peptides block AP-1 function. Biophysical/structural studies will characterise how effective the peptides/mimetics bind to AP-1 and shut down function. Single molecule studies will provide a direct understanding of the mechanism of inhibition to enable the design of more effective inhibitors. These studies will be complemented by cell biology experiments to verify function in cancer cells in which AP-1 is a major player in the disease (e.g. breast, colon and lung cancers where cJun is over-expressed). For the 2-3 most effective peptides we will create and test mimetics to create compounds that can be further developed into druggable molecules. These will bring drug-like properties such as stability and bioavailability while serving as constrained secondary structural mimics. These compounds will be fed back into the biophysical and cellular studies to ascertain if the mechanism of action is preserved.

Planned Impact

The results from this research will find application in a number of important areas. The principle users of our findings will be both the academic community and those involved in developing protein-protein inhibitors. Hence the longer term beneficiaries include the health sector, where inhibitors developed as a consequence of this research will find application.
Most proteins function through interaction with other proteins; therefore making the development of a rational approach to interfering with such interactions incredibly important, and timely. This proposal will developing an understanding of how protein interaction inhibitors work and therefore will open doors into new therapies for a variety of diseases. Our example system itself will find application in the development of anti-cancer treatments

By providing a pre-defined intracellular screen for efficacy this study has the potential to transform the approach used to derive new inhibitors. Therefore we expect that our research will lead to considerable benefits for academics attempting to generate inhibitors of protein interactions both for therapeutics and non-therapeutics. Furthermore, the acceleration of the drug design process gained by using TBS to generate novel inhibitors can serve as the starting point for therapeutics against many other disease processes involving protein-protein interactions. This has considerable potential commercial benefit and therefore would benefit both the economic and knowledge economies of the UK. To develop interactions with industry we will use with the Research Services and the Innovation & Enterprise offices of both institutions.

The proposal will support two PDRAs across two institutions. The training potential is excellent as we intend for both PDRAs to interact and work together synergistically. This will hone their team work, networking, seminar and report writing skills. The techniques that we will be applying are very broad, from cell biology through protein biophysics to single molecule microscopy and the exposure of trainee scientists to this high interdisciplinary environment will be hugely beneficial. Investment in such research will enable the UK to remain internationally competitive as a knowledge economy.

All findings will be published in high impact publications to disseminate with the wider scientific community. In addition, seminars will be hosted for scientists (invited seminars and meetings), the general public (e.g. cafe scientifique, schools days at Bath, Bath Tapsin2Science), as we have strived to do over previous years. Communications outside the university will be aided by the Communications Office at Bath and the Press Office at Kent who liaise with journalists for radio/television and other media pieces, and who also produce their own monthly publications.

Publications

10 25 50
 
Description 1. We have discovered that cFos binds to and diffuses on dsDNA
2. We have revealed how cFos, cFos:cJun and cJun:cJun locate their target sites on DNA
3. We have developed new analytical tools that we have shared on Github for the scientific community to use
4. We have developed a new inhibitor for the cFos:cJun interaction
Exploitation Route At present the award is still in place, but we forsee that the outcomes may be taken forward by drug researchers and anti-cancer specialists.
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description Our findings have been used to begin to develop inhibitors of transcription factor action. This is a sibstantial step forwrads that could be used to engage healthcare technologists in the future. We have also identified the mechanism by which the transcription factors investigated in this proposal locate their binding sites, thereby enabling other researchers to develop new inhibitors based upon this new knowledge.
First Year Of Impact 2020
Sector Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Societal

 
Description Studying the mechanism of inhibition with Jody Mason 
Organisation University of Bath
Department Department of Biology and Biochemistry
Country United Kingdom 
Sector Academic/University 
PI Contribution We have begun working with the Mason group to study the mechanism of inhibition of transcription factors. This was completely facilitated by this award. Our contribution is to provide imaging expertise.
Collaborator Contribution The Mason lab has provided expertise and reagents for the study.
Impact At this early stage of the award the outcomes are yet to emerge
Start Year 2018