ZINC1797251, a novel natural product small molecule targets viral oncoprotein E6 in human papillomavirus-16 positive cervical cancer cells
Creators: name: Kumar, Ashish
Publisher: name: Taylor & Francis
Year: 2025
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Hematology

description: Cervical cancer burden due to recurrent human papillomavirus (HPV) infections necessitates the urgent need to impede viral proliferation targeting the oncogene E6 of the high-risk serotype HPV16. This study aims to identify a small molecule from a natural product library that could prevent a tumorigenic complex of E6 with p53 in HPV16-positive cervical cancer cells. <i>In silico</i> methods such as high-throughput virtual screening (HTVS) of natural product like library ZINC database followed by atomistic molecular dynamics (MD) simulations were performed to identify lead natural compound. This was validated with <i>in vitro</i> analysis using HPV16 positive SiHa cells and CaSki cells by MTT and flow cytometry assays. Virtual screening identified top 10 compounds with high affinity for HPV16 E6. The docking scores, Protein-Ligand Interaction Profiler analysis, MD simulation and molecular mechanics Poisson Boltzmann surface area-based binding energy estimation narrowed down the search to ZINC1797251, a molecule with stable binding, low energy scores and consistent H-bonds, establishing that it could prevent interaction of p53 and E6. ZINC1797251 inhibited the proliferation of SiHa and CaSki cells with a G<sub>I50</sub> values of 615.40 and 417.30 nM, respectively. The compound reduced HPV16 E6, while increased p53 positive populations in SiHa and CaSki cells. Treatment with ZINC1797251 induced the G<sub>1</sub> cell phase arrest and promoted early and late phase apoptosis in these cells. The restoration of tumor inhibitory activity of p53 in HPV-infected cervical cancer cells to promote apoptosis could be achieved using the ZINC molecule—ZINC1797251. However, further studies are deemed essential for further developments. High-throughput virtual screening of small molecules against the ‘hot-spot’ region of E6 protein High-throughput virtual screening and molecular dynamics simulation along with MMPBSA-based binding energy estimation identified ZINC1797251 binds stably and avidly to the oncoprotein E6.The lead molecule identified targets the hydrophobic pocket of E6, which harbors crucial amino acids for eliciting the activity of E6 protein.Further evaluations indicate the inhibitive property of ZINC1797251 against HPV16 E6, to inhibit HPV16 positive SiHa and CaSki cervical cancer cells.The natural product molecule upregulated p53 to induce G1 cell phase arrest and apoptosis in these cells. High-throughput virtual screening and molecular dynamics simulation along with MMPBSA-based binding energy estimation identified ZINC1797251 binds stably and avidly to the oncoprotein E6. The lead molecule identified targets the hydrophobic pocket of E6, which harbors crucial amino acids for eliciting the activity of E6 protein. Further evaluations indicate the inhibitive property of ZINC1797251 against HPV16 E6, to inhibit HPV16 positive SiHa and CaSki cervical cancer cells. The natural product molecule upregulated p53 to induce G1 cell phase arrest and apoptosis in these cells.