Screening for Functional Peptide Inhibitors of Transcription Factor Activity


Transcription factor dysfunction leads to a range of detrimental outcomes including cancer, diabetes, and autoimmune and cardiovascular disease. Drug discovery is slow, costly and complex. Often, researchers are on a quest to find pharmaceutical molecules that can bind to sites on disease-causing proteins. But binding to a target site is not enough, a therapeutic molecule must also have the ability to shut down the dangerous protein. Most importantly, it must succeed in doing so in a live cell, without too many side effects.

In a new study by Universities of Bath and Kent scientists and led by Professor Jody Mason have developed a new technique to accelerate the discovery of cancer-fighting drugs. The technique identifies molecules that can shut down dangerous proteins before they wreak disease-triggering havoc, by blocking them from interacting with a cell’s DNA. The new drug-discovery platform, Transcription Block Survival (TBS) has the potential to dramatically accelerate the hunt for cures of deadly cancers. This breakthrough has wider implications too, as the proteins involved in cancer also play a central role in many other diseases, including osteoporosis and inflammatory diseases like rheumatoid arthritis and psoriasis., Professor Mason and his team screened over 130,000 different peptides to identify one that is functionally active (red and white in the image) in potently blocking AP-1 (blue) from binding to specific DNA sequences (yellow). This action effectively blocks AP-1’s ability to promote gene transcription. The original research article is now published in in JACS Au.

The research team used the TBS approach, and they were able to eliminate molecules that stick to the cell target but that ultimately fail to knock out the function of the disease-causing protein. By removing molecules from the screening process that ultimately have little or no therapeutic value, scientists can save money and time. TBS facilitates high-throughput genotype-to-phenotype screening and competition of peptide libraries to isolate those that result in functional loss of cJun DNA binding activity from those that bind but have little or no effect upon target activity. The authors focused in their new approach in finding molecules called peptides (short chains of amino acids—the building blocks of proteins) that permanently suppress the activity of a protein called Activator Protein-1 (AP-1). AP-1 is present naturally in the body and is important in ‘switching on’ genes involved in a number of cellular processes, but when out of control, it becomes a major player in cancer. Genes work by making copies of themselves in a process known as transcription. These copies, which take the form of messenger RNA (mRNA), then turn the genetic information into proteins—the building blocks of life that carry out the instructions encoded within the genes. AP-1 promotes the growth of cancerous cells first by binding to gene promotors in specific sections of a cell’s DNA, and then hijacking the expression of key genes by permanently switching them on. In other words, AP-1 forces a gene to make mRNA and corresponding proteins at the wrong times and amounts.

The researchers successfully found peptides that bind AP-1 without overstimulating cancer-related genes. These peptides can both block AP-1 from binding to DNA or kick AP-1 off genes it has already paired with, allowing them to turn off the cancerous signal in vulnerable cells.

According to the authors: A major strength and distinguishing feature of the new drug-screening technique, is that it allows scientists to identify peptides that have a dual function: for example, in their experiments, they can recognize/bind to AP-1 both before it has bound to DNA and when it is in a DNA-bound state, ultimately freeing AP-1 from DNA and shutting down its function altogether. Moreover, another advantage of the TBS method is that the screening technique happens within live cells and without modifying either the protein target or the peptide library with tags that may alter function, a common issue with other techniques, therefore avoid false positives.

The authors plan further TBS screening for a range of transcription factor targets with the aim to produce both nongenetic tools and probes of disease pathways, but there is also considerable potential for a new generation of optimized functional antagonists and clinical leads.

Screening for Functional Peptide Inhibitors of Transcription Factor Activity - Medicine Innovates

About the author

Jody M. Mason
Professor of Biochemistry
University of Bath
Department of Biology & Biochemistry
Bath, BA2 7AY, United Kingdom

Our research interests centre on protein-protein interactions, particularly helical, coiled coil and amyloid-based proteins, and understanding how key interactions achieve stability and specificity. We use the Protein-fragment Complementation Assay (PCA) to screen libraries and select peptides or proteins with significant improvements in stability over wild-type interactions. Specificity of protein-protein interactions can be further improved by using a Competitive And Negative Design Initiative (CANDI) which I have developed to maximize the energy barrier between desired and non-desired protein pairs. Work currently being undertaken includes:

  • Design and screening of peptide-based libraries, particularly for oncogenic transcriptional regulator proteins, to investigate the role of key residues in stability and specificity.
  • Monitoring the folding of natural and designed variants of protein-protein interactions to understand how stability and specificity is manifested.
  • Generating peptides to bind, reverse, and prevent amyloid fibril formation, particularly for beta-amyloid, the primary factor implicated in Alzheimer’s disease.
  • Development of our Wellcome Trust funded game ‘Cascade’ – being designed in collaboration with Fayju. Cascade seeks to increase Alzheimer’s disease awareness, understanding, empathy, and to highlight the desperate need for a cure.


Andrew Brennan, James T. Leech, Neil M. Kad, and Jody M. Mason. An Approach to Derive Functional Peptide Inhibitors of Transcription Factor Activity. JACS Au 2022