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Selection of Novel DNA Aptamers against HPV16 Biomarker, E6: An In Silico Approach
Bonke Phathekile1, Darius Riziki Martin2,3, Nicole Remaliah Samantha Sibuyi2,4
1Organometallics and Nanomaterials, Department of Chemical Sciences, University of the Western Cape, Bellville, Cape Town 7535, South Africa.
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.
