Joel Ricci López Abstract

Molecular modeling simulation studies reveal new potential inhibitors against HPV E6 protein

Joel Ricci López1,2, Abraham Vidal-Limon1, Matías Zuñiga3, Verónica A. Jiménez3, Joel B. Alderete4, Carlos A. Brizuela2, Sergio A. Aguila1

1Nanoscience & Nanotechnology Centre, UNAM
2Center for Scientific Research and Higher Education at Ensenada, CICESE
3Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello
4Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad de Concepción
Human papillomavirus (HPV) infection is one of the most common sexually transmitted diseases. High-risk strains of HPV have been identified as the etiologic agent of some anogenital tract, head, and neck cancers. Due to their oncogenic effect, some of the HPV strains have been identified as high-risk (HR) types, being the leading cause of cervical cancer and the etiologic agent of some anogenital tract and head and neck cancers. However, although prophylactic HPV vaccines have been approved, it is still necessary a drug-based treatment against the infection and its oncogenic effects. The E6 oncoprotein is one of the most studied therapeutic targets of HPV, it has been identified as a key factor in cell immortalization and tumor progression in HPV-positive cells. E6 can promote the degradation of p53, a tumor suppressor protein, through the interaction with the cellular ubiquitin ligase E6AP. Therefore, preventing the formation of the E6-E6AP complex is one of the main strategies to inhibit the viability and proliferation of infected cells. Herein, we propose an in silico pipeline to identify small-molecule inhibitors of the E6-E6AP interaction. First, 34,804 molecules were obtained from their structural similarity with 26 reference compounds that have shown some anti-HPV activity. Then, preliminary filtering was applied predicting the drug-likeness and the pharmacokinetic properties of each compound. The procedure leads to the selection of 19,119 molecules with favorable absorption, distribution, metabolism, and excretion (ADME) profiles, followed by its evaluation through Structure-based Virtual Screening (SBVS) against the E6AP binding pocket of the HPV-16 E6 protein. Thereby we combined homology modeling, molecular dynamics simulations, “essential dynamics” (through principal component analysis), and geometric hierarchical clustering to identify four E6 conformations to perform Ensemble-based docking simulations. These four structures represented the main conformational changes of the E6 pocket observed over the course of the trajectories. The results further support the idea of the E6 protein flexibility and suggest the pocket’s ability to open and close through side-chain fluctuations and backbone motions. After the SBVS stage, the binding modes to E6 of the 100 top-ranked ligands were rescoring employing the MM/PB(GB)SA methodologies. The procedure afforded the selection of three final candidate compounds to be further evaluated by molecular dynamics. Along the trajectories of the E6-ligand systems, the docked molecule remained in its pose and limited the protein flexibility, showing favorable affinity values when compared with luteolin, a previously evaluated compound. When taken together, these results represent a new starting point for the development of anti-HPV drugs based on the disruption of E6-E6AP interactions. Since this study has only contemplated computational analysis, it is still necessary the validation of the last hit molecules by in vitro experiments. But beyond this, the information obtained along SBVS and molecular dynamics provides new insights into the importance of the E6 protein dynamics and the leading interactions that could enhance the binding between the protein and its potential inhibitor. We suggest that further research should take these results into account in both discovery and lead optimization stages to achieve a successful development of anti-HPV drugs.