Peptide antagonists of the human papillomavirus type 11 (HPV-11) E2-DNA association were identified using a filamentous bacteriophage random peptide library. Synthetic peptides antagonized the E2-DNA interaction, effectively blocked E2-mediated transcriptional activation of a reporter gene in cell culture, and inhibited E1-E2-mediated HPV-11 DNA replication in vitro. These peptides may prove to be useful tools for characterizing E2 function and for exploring the effectiveness of E2-inhibitor-based treatments for HPVassociated diseases.Present estimates are that 24 million Americans are infected with human papillomavirus (HPV) and that 5 million new cases occur annually. As there are no specific antiviral therapies for HPV infection, there is a clear unmet need for the development of safe and effective therapies for HPV-associated disease.Papillomaviruses lack the enzymes generally targeted by most currently available antiviral agents (e.g., virus-encoded DNA polymerases, reverse transcriptases, and proteases). Papillomaviruses do encode E1, a helicase-ATPase, but it has so far proven a difficult enzyme to develop for classic drug screening. As such, successful development of anti-HPV therapies may require identification of novel antiviral targets, such as viral transcription factors and replication proteins (2, 21, 25) such as the HPV-encoded E2 protein.The 50-kDa E2 protein is comprised of three functional domains (19). The amino-terminal domain of E2 is necessary for viral trans-activation and for direct association with E1. The smaller carboxyl-terminal domain (E2C) encodes the DNA binding and dimerization functions. Linking the amino-and carboxyl-terminal domains is a small, poorly conserved hinge region. E2 function requires binding to a 12-bp palindromic nucleotide sequence, ACCN 6 GGT, that is present at several locations throughout the HPV genome and is repeated several times near the viral origin of replication. Once associated with DNA, E2 interacts with a variety of host cell transcription factors to modulate viral transcription. The papillomavirus E2 protein is also required for origin (ORI)-specific viral DNA replication. Because association of E1 with E2 enhances the affinity of both proteins for the viral ORI, DNA sequencespecific binding by E2 effectively mediates sequence-specific DNA binding by E1 (6).Since the E2-DNA interaction is central to the coordination of the essential papillomavirus transcription and replication processes, disruption of E2-DNA binding should inhibit HPV replication. To this end, we constructed a filamentous bacteriophage 10-mer random peptide library and screened for sequences that disrupted the E2-DNA association by binding to the E2 protein.Phage display selection of E2-DNA binding inhibitors. We used peptide phage display (reviewed in reference 16) to identify peptide binders to bio-E2C, a biotinylated E2 fusion protein consisting of 88 carboxyl-terminal amino acids of the HPV type 11 (HPV-11) E2 DNA binding domain fused to the 99-residue polypeptide substrate of Es...