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

Date Published: March 15, 2019

Publisher: Public Library of Science

Author(s): Joel Ricci-López, Abraham Vidal-Limon, Matías Zunñiga, Verónica A. Jimènez, Joel B. Alderete, Carlos A. Brizuela, Sergio Aguila, Francesca Spyrakis.


High-risk strains of human papillomavirus (HPV) have been identified as the etiologic agent of some anogenital tract, head, and neck cancers. 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. Virtual screening was carried out by predicting the ADME properties of the molecules and performing ensemble-based docking simulations to E6 protein followed by binding free energy estimation through MM/PB(GB)SA methods. Finally, the top-three compounds were selected, and their stability in the E6 docked complex and their effect in the inhibition of the E6-E6AP interaction was corroborated by molecular dynamics simulation. Therefore, this pipeline and the identified molecules represent a new starting point in the development of anti-HPV drugs.

Partial Text

Human papillomavirus (HPV) infection is one of the most common sexually transmitted diseases. 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 [1]. Epidemiologically, HPV-16 is the most prevalent type in cervical cancer, accounting for approximately 55% of all cases [2]. Nowadays prophylactic vaccines, Cervarix [3] and Gardasil [4], have been approved and effectively applied for the prevention of HPV infection. However, for people already infected, current therapies consist of the use of chemotherapeutic agents or the application of surgical and ablative techniques to eliminate developed tumors [5]. These treatments are invasive, non-specific, and tend to be expensive, difficulting their availability to millions of patients, particularly in developing countries. Hence, one of the main alternatives to treat HPV-related diseases is the development of accessible drug-based therapies directed against the virus.

In the present study, we conducted an in silico methodology combining ADME prediction, SBVS, and MD to identify new compounds able to inhibit 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 leds to the selection of 19,119 molecules with favorable ADME profiles, followed by its evaluation through SBVS against the LxxLL binding pocket of the HPV-16 E6 protein. Thereby we combined homology modelling, MD, PCA, and geometric 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.