# Small Molecule E6 Inhibitors to Treat Oropharyngeal Cancers Caused by HPV Infections

> **NIH NIH R43** · KOVINA THERAPEUTICS INC. · 2022 · $275,766

## Abstract

Oncogenic human papillomaviruses (HPV) such as HPV type 16 are the etiologic agent of 50-70% of cancers
of the oropharynx. In the USA, the incidence of HPV-associated oropharyngeal cancers is increasing. This is
partly because there is no established screening test for oral HPV. HPV-16 DNA is detected by PCR in 1-8% of
oral swabs depending on the surveyed populations, with the highest frequencies in HIV+ individuals. Only a
small fraction of these infections will progress to frank malignancy. Moreover, early lesions are difficult to locate
and patients are largely asymptomatic until they have advanced tumors.
 Kovina Therapeutics is developing anti-viral therapeutics that selectively bind to the HPV-16 E6 oncoprotein
and prevent interactions with its cellular targets. E6 is necessary for viral genome replication and maintenance
and is always expressed in HPV-associated dysplasia and malignancies. We performed in silico structural
screening of chemical libraries for molecules that fit the E6 docking site for several of its cellular partners. Our
assays focused on the E6 protein-protein interaction with E6AP, which transfers ubiquitin onto the tumor
suppressor protein p53 and leads to its destruction by the proteasome. We designed and synthesized
compounds that 1) bind to HPV-16 E6 and 2) form a covalent bond with a specific cysteine in HPV-16 E6 at its
protein-protein interface with E6AP as well as other cellular interacting proteins. The approach to identify
molecules equipped with reactive ‘warheads’ that mediate covalent and irreversible binding to cysteine has been
successful for several new clinically available drugs, and this field is rapidly progressing to target proteins that
were previously considered undruggable. We show that these compounds covalently bind to HPV-16 E6, block
E6 interaction with E6AP, restore P53 function, and drive the HPV infected cell to apoptosis. Multiple biochemical
analyses including X-ray crystallography prove these inhibitors occupy this E6 pocket and form a single adduct
with this cysteine. Iterative optimization guided by the co-crystal data resulted in the design and synthesis of
>200 novel chemotypes that resulted in increased activity. This one-year Phase I SBIR proposal will select leads
based on for pharmacokinetic characterization. The most promising E6 inhibitors will then be test in vivo proof
of concept experiments using human oropharyngeal cancer derived cells in a tumor xenograft model. Successful
results in these Phase I experiments will strongly position us for a Phase II SBIR grant to carry out IND-enabling
studies.

## Key facts

- **NIH application ID:** 10484043
- **Project number:** 1R43DE031495-01A1
- **Recipient organization:** KOVINA THERAPEUTICS INC.
- **Principal Investigator:** ELLIOT J. ANDROPHY
- **Activity code:** R43 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $275,766
- **Award type:** 1
- **Project period:** 2022-09-01 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10484043

## Citation

> US National Institutes of Health, RePORTER application 10484043, Small Molecule E6 Inhibitors to Treat Oropharyngeal Cancers Caused by HPV Infections (1R43DE031495-01A1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10484043. Licensed CC0.

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