Selection of Novel DNA Aptamers against HPV16 Biomarker, E6: An In Silico Approach.

Authors

Bonke Phathekile, Darius Riziki Martin, Nicole Remaliah Samantha Sibuyi, Abram Madimabe Madiehe, Martin Opiyo Onani, Mervin Meyer

Published in

ACS omega. Volume 11. Issue 26. Pages 38706-38722. Jul 07, 2026. Epub Jun 24, 2026.

Abstract

HPV16 E6 oncoprotein is a critical driver of cervical cancer, necessitating high-specificity diagnostic and therapeutic agents. This study presents an in silico selection of DNA aptamers targeting the HPV16 E6 oncoprotein through a pipeline of structure-based virtual screening and 250 ns Molecular Dynamics (MD) simulations, performed with GROMACS 2019 and the CHARMM36M. Using AutoDock VinaXB and HADDOCK, eight candidates were evaluated against the F2 RNA benchmark. MM/PBSA calculations identified Apt 9 (-143.76 kcal/mol) as the most potent lead, surpassing the affinity of the F2 control (-142.80 kcal/mol). Apt 8 emerged as a key consensus lead, exhibiting superior structural stability (RMSD 0.23 nm) and the most robust interaction network (11.49 hydrogen bonds). Notably, these leads primarily target critical Histidine residues (His78, His118, and His126) on the E6 protein. These results designate Apt 9 and Apt 8 as high-priority candidates for experimental validation, providing a robust theoretical foundation for novel HPV16-targeted interventions.

PMID:
42428842
Bibliographic data and abstract were imported from PubMed on 10 Jul 2026.

Read full publication at:
Please sign in to see all details.

Stats

1-terrible, 9-excellent. How would you rate this publication? Sign in in to submit your rating.

Post a comment

You need to be signed in to post comments. You can sign in here.

Comments

There are no comments yet.