Computational Competitive and Negative Design to Derive a Specific cJun Antagonist.

Basic leucine-zipper (bZIP) proteins reside at the end of cell-signalling cascades and function to modulate transcription of specific gene targets. bZIPs are recognised as important regulators of cellular processes that include cell growth, apoptosis and cell differentiation. One such validated transcriptional regulator, Activator Protein-1 is typically comprised of heterodimers of Jun and Fos family members, and is key in the progression and development of a number of different diseases. The best described component, cJun is upregulated in a variety of diseases that include cancer and osteoporosis and psoriasis. Towards our goal of inhibiting bZIP proteins implicated in disease pathways, we here describe the first use of a novel in silico peptide-library screening platform that facilitates the derivation of sequences exhibiting high affinity with cJun while disfavouring homodimer formation or formation of heterodimers with other closely related Fos sequences. In particular, using Fos as a template, we have computationally screened a peptide library of over 60 million members and ranked hypothetical on/off target complexes according to predicted stability. This resulted in the identification of a sequence that bound cJun, but displayed little homomeric stability or preference for cFos. The computationally selected sequence maintains similar interaction stability to a previous experimentally derived cJun antagonist, while providing much improved specificity. Our study provides new insight into the use of tandem in silico screening / in vitro validation and the ability to create a peptide that is capable of satisfying conflicting design requirements.