Binder 8 peptide inhibitor computationally designed to target HPV E1-E2 interface with high affinity

Oncogenic progression of high-risk Human Papillomavirus (HPV) strains critically depends on the cooperative interaction between the E1 replicative helicase and the E2 origin-binding protein to initiate viral DNA amplification. Disrupting this protein-protein interaction (PPI) represents a promising, yet clinically unrealized, therapeutic strategy for treating established HPV infections before malignant transformation. Current standard-of-care often focuses on symptom management or surgical removal, lacking targeted antiviral options for the underlying viral replication, leaving a significant gap for novel therapeutic approaches.

Researchers developed a comprehensive computational pipeline for the de novo design and evaluation of peptide inhibitors targeting a conserved arginine triad on the solvent-exposed surface of the HPV E1 helicase. The process involved sequence discovery using AlphaProteo and complex structural prediction with AlphaFold 3 to generate a candidate library. This library was then subjected to dual-scale Molecular Dynamics (MD) simulations and MM/GBSA thermodynamic validation using GROMACS. Binder 8 emerged as the lead candidate, undergoing further physicochemical profiling via CSM-Toxin and AlgPred 2.0 for toxicity and allergenicity predictions.

The lead candidate, Binder 8, yielded a predicted binding free energy of -59.1 ± 0.7 kcal/mol against the HPV E1-E2 interface. This represents a statistically significant improvement over the native E1-E2 baseline interaction (Welch's t-test, p = 8.14e-19; Cohen's d = 2.21). Per-residue energy decomposition confirmed that binding is anchored through multi-point interactions with the targeted arginine triad on HPV E1. Physicochemical profiling predicted zero toxicity and non-allergenic properties for Binder 8. Sequence alignment across 183 oncogenic Alpha-papillomavirus genotypes demonstrated near-universal conservation of the targeted E1 arginine triad. This broad conservation supports Binder 8 as a potential scaffold for broad-spectrum antiviral development. While MM/GBSA overestimates absolute affinities due to being an implicit solvent method, the reported values provide robust relative rankings. These findings offer a strong computational blueprint for subsequent in vitro validation.

Binder 8 achieved a predicted binding free energy of -59.1 ± 0.7 kcal/mol, significantly outperforming native E1-E2 binding (p = 8.14e-19).