Peptide-assisted direct detection of HPV nucleic acids from liquid-based cytology samples without extraction
High-risk human papillomavirus remains the causal agent of nearly all cervical cancers. And we need tools for rapid detection that work in routinely taken samples (e.g., PreservCyt®) that can speed up, facilitate or simplify the extraction process. Conventional workflows rely on nucleic-acid extraction, a cost- and labor-intensive step that restricts scalability in both high-throughput and resource-limited settings. Here, we introduce MDP-1, a rationally designed peptide that represents the prototype of a new class of capsid-targeted diagnostic enhancers. Unlike antimicrobial peptides historically developed for therapeutic membrane lysis, MDP-1 was engineered to bind the HPV L1 major capsid protein, interfere with L1-L1 interactions, and promote partial capsid destabilization to enhance genome accessibility. In silico docking demonstrated favorable binding (HADDOCK score -173.4 ± 6.2; BSA 1958 ± 83.9 Ų; RMSD 1.8 ± 0.1 Å) with extensive electrostatic and hydrophobic complementarity. When integrated into a direct-to-PCR workflow, MDP-1 enabled robust amplification from unextracted PreservCyt® specimens, maintaining efficiencies within 90-110 % and achieving a limit of detection of 1.25 copies/µL. Analytical specificity testing confirmed no cross-reactivity, while interference studies showed tolerance to common clinical inhibitors. In a feasibility cohort (n = 53), the MDP-1 workflow achieved 93.5 % sensitivity (95 % CI: 78.6-99.2) and 99.3 % specificity (95 % CI: 85.4-99.9) for the detection of high-risk HPV DNA, with an overall accuracy of 98.5 % compared to extraction-based qPCR and strongly correlated Ct values (R² = 0.772). This proof-of-concept positions MDP-1 as a first-in-class tool that recasts HPV diagnostics by leveraging peptide-virion interactions to bypass inhibitors and eliminate timely and costly extraction workflows.