# Targeting Viroporins and Coronavirus M Protein

> **NIH NIH U19** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2022 · $3,846,686

## Abstract

PROJECT 3: TARGETING VIROPORINS AND CORONAVIRUS M PROTEIN
SUMMARY
Coronaviruses express four structural proteins; spike (S), membrane (M), envelope (E) and nucleocapsid (N),
which are essential for efficient viral particle formation. We seek to understand and structurally characterize E
and M, and to use this information to design antiviral drugs. M is a molecular scaffold that brings together the
structural proteins, and E is a member of the viroporin family of proteins, which act as ion channels to control
ionic composition in the host and virus. Previously, Hong and DeGrado solved the structures of the viroporins
from influenza A virus, AM2, and used this information to design novel drugs that address the problem of
resistance. We now have turned our attention to the E protein of SARS-CoV-2. Furthermore, we will determine
structures of viroporins from a variety of other coronaviruses and alphaviruses of the Togaviridae family to enable
structure-based protein design. M is essential for virus particle assembly. We will structurally characterize M
alone and with its viral interacting partners in vesicles and virus-like particles (VLPs). This work will elucidate
their role in stabilizing the virus and generating membrane curvature required for budding. We will use this
information plus high-throughput screening (HTS) to discover drugs targeting M.
More specifically, in Aim 1, we will structurally characterize the E protein and drug complexes using X-ray
crystallography, Cryo-EM and solid-state NMR. We will also determine structures of E proteins from multiple
alphacoronavirus and betacoronavirus lineages that infect humans. In Aim 2, we will determine Cryo-EM and
crystal structures of M alone and in association with viral protein partners, in liposomes, VLPs and virions. The
high-resolution structures determined in this aim will enable structure-based drug design. In parallel, we will use
a convenient VLP assay to map residues in M and E that are essential for packaging and entry. The VLP assay
will also be configured for HTS. In Aim 3, we will expand our studies to viroporins of alphaviruses of the
Togaviridae family, which include the chikungunya (CHIKV), Sindbis (SINV), Semliki Forest (SFV), and Ross
River (RRV) viruses. These viruses have viroporins, which are essential for effective replication in vivo. Using
methods in Aim 1, we will explore their structures and develop inhibitors to facilitate drug discovery.
In Aim 4, we will develop Optimized Lead compounds targeting E and M for transfer to Roche. Current
compounds that show weak inhibition of E, which include amantadine and hexamethylene amiloride (HMA),
provide starting points for design of higher specificity and affinity compounds. In parallel, we will use HTS, based
on VLPs and a yeast screen of channel function to develop starting points for optimization of drug leads. In years
2.5 to 5, we will design small molecules to target M. Overall, we aim to develop orally bioavailable Optim...

## Key facts

- **NIH application ID:** 10512629
- **Project number:** 1U19AI171110-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** WILLIAM DEGRADO
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $3,846,686
- **Award type:** 1
- **Project period:** 2022-05-16 → 2026-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10512629

## Citation

> US National Institutes of Health, RePORTER application 10512629, Targeting Viroporins and Coronavirus M Protein (1U19AI171110-01). Retrieved via AI Analytics 2026-05-29 from https://api.ai-analytics.org/grant/nih/10512629. Licensed CC0.

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