# Host Defense Small Molecule Development for COVID-19 Treatment by Targeting Lysosome

> **NIH NIH R01** · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · 2024 · $785,479

## Abstract

SARS-CoV-2 is the pathogenic coronavirus responsible for the ongoing outbreak of Coronavirus Disease
(COVID-19). Although multiple approved vaccines appear efficacious, rapidly evolving SARS-CoV-2 variants and
their resilience against antiviral drugs demonstrate the need to identify complementary host-targeted antiviral
approaches for current and future pandemics. Autophagy is critically involved in host defense through the
elimination of numerous pathogens via autophagic-lysosomal pathways, which serves as an intriguing drug
target. In an effort to develop novel host defense therapies for COVID-19, we observed that the protein levels of
TFEB, a master transcriptional activator of autophagy and lysosome biogenesis, rapidly declined following
human coronavirus (HCoV) infection. Utilizing affinity purification and mass spectrometry, we identified a largely
uncharacterized E3 ubiquitin ligase subunit, DCAF7, which eliminated TFEB protein through ubiquitination and
degradation. Through a structure-based in silico screen of a 3 million compound library, we discovered several
DCAF7 small molecule inhibitors, further developed a chemistry program and derived several lead compounds.
These DCAF7 inhibitors can remarkably preserve TFEB protein thus activating its target CLEAR gene network
to enhance lysosomal biogenesis and acidification. Compound treatment notably reduced viral load in both HCoV
challenged cells and SARS-CoV-2 infected K18-hACE2 transgenic mice. With the observations that small
molecules inhibiting DCAF7 can strengthen the host's lysosomal-based viral clearance, we hypothesize
that cellular levels of TFEB are exquisitely controlled by DCAF7 to maintain lysosomal homeostasis and
host defense responses. As a corollary to this hypothesis, we propose that DCAF7 small molecule
inhibition will attenuate COVID-19 by preserving TFEB protein levels and boosting lysosomal-dependent
pathogen clearance in the setting of SARS-CoV-2 infection. In this proposal, we will examine the interactive
regulation between DCAF7/TFEB and SARS-CoV-2 viral proteins to identify the mechanism of how DCAF7
inhibitors impact the viral life cycle (Aim 1). Further, we propose to initiate a robust drug discovery program and
further advance unique small molecule DCAF7 inhibitors that empower lysosome (Aim 2). Finally, we will test
the efficacy of these inhibitors to decrease lung viral load in K18-hACE2 transgenic mice infected with SARS-
CoV-2 variants of concern (Aim 3). The significance of this work stems from our discovery of a new molecular
model for COVID-19 using a unique small molecule inhibiting the CRL4-DCAF7 ubiquitin E3 ligase that can boost
the host's antiviral response by activating lysosomes. Our proposal combines innovative concepts and drug
discovery technology with cutting-edge COVID-19 animal models to develop novel therapeutic compounds
targeting conserved host pathways critical for defense against coronavirus infection. We anticipate that DCAF7
inhibito...

## Key facts

- **NIH application ID:** 10892269
- **Project number:** 5R01AI172935-02
- **Recipient organization:** UNIVERSITY OF PITTSBURGH AT PITTSBURGH
- **Principal Investigator:** Simon M Barratt-Boyes
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $785,479
- **Award type:** 5
- **Project period:** 2023-07-21 → 2027-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10892269

## Citation

> US National Institutes of Health, RePORTER application 10892269, Host Defense Small Molecule Development for COVID-19 Treatment by Targeting Lysosome (5R01AI172935-02). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10892269. Licensed CC0.

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