Potential dual purpose molecular probe for HPV16 E6: a computational and experimental approach

Abstract

The goal of this project is to find a molecular probe for HPV variant 16 protein E6. This goal is accomplished using a combination of Virtual Ligand Screening (VLS) and experimental ligand binding assays. Protein E6 is a protein that is expressed in all individuals with the human papillomavirus (HPV) virus. A number of HPV 16 protein E6 genetic variants have been associated with increased risk for cervical cancer. Currently, there is no fast and reliable method for testing for the presence of these high-risk protein variants. We want to develop a method that is both fast and reliable for detecting the presence of this protein using molecular probes. These molecular probes could potentially be used for optical or PET diagnostic imaging, for risk-assessment and to guide early intervention. Using virtual ligand screening, we have identified a number of molecular probe candidates with affinity for the binding site of prototype E6. This affinity is assessed using binding energy scores. Compounds possessing favorable calculated binding energy scores and other desirable molecular properties are identified as potential molecular probes. Selected candidates include: O-succinyl-L-homoserine (-46 kcal/mol), paclitaxel (-70 kcal/mol), and 3- Amino-5-fluorobenzo [E] [1,2,4] Triazine 1, 4 dioxide (-47kcal/mol), for 3-Chloro-2-(2-[(3-oxo- 2-Benzfuran-1 (3H)-Yliden] methyl) Hydrazino)-5-(Trifluoromethyl) Pyridinum Acetate (- 68.33kcal/mol), 3-Chloro-2-(3-[1-(Phenyl sulfonyl)-(H-pyrazol-3-YL] Phenoxy)-5- (Trifluoromethyl) Pyridine (-66.12kcal/mol), and N-(2,4-dinitrophenyl)-L-arginine ) (- 78.58kcal/mol). We have performed experimental ligand-binding assays of the potential molecular probes against purified prototype protein E6. Both intrinsic tryptophan fluorescence and fluorescence polarization assays have been performed. One of our compounds 3-Amino-5-fluorobenzo [E] [1,2,4] Triazine 1, 4 dioxide (AFTD) was shown to have affinity for our target protein (EC50 6M). Due to its intrinsic fluorescence and the presence of a fluorine atom, this molecule could potentially be used for either PET or optical imaging modalities. Cell based assays have also been conducted to further characterize AFTD's potential as an in vivo imaging probe. Results indicate that AFTD is cytotoxic at 25M, although it appears to be cell permeable. Further experiments need to be conducted to assess its potential use as in-vivo imaging probe. An alternative use for this molecule as a probe in biochemical assay tracking E6 protein-protein interactions is suggested. This is demonstrated using a monoclonal antibody (6F4) that is specific to HPV16 E6. These results set the stage for future work to further characterize this potential dual-purpose probe which may aid our understanding of the link between HPV infection and cancer.