# Inhibiting Viral Macrodomains Using Structure-Based Design

> **NIH NIH U19** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2022 · $2,988,130

## Abstract

PROJECT 5: INHIBITING VIRAL MACRODOMAINS USING STRUCTURE-BASED DESIGN
SUMMARY
Viral macrodomains counter the host immune response by removing ADP-ribosylation modifications from host
proteins, with important consequences for interferon and many other signaling pathways. Previous experiments
in cell and animal models that use wild type and catalytically dead SARS-CoV and chikungunya virus (CHIKV)
macrodomains validate these proteins as potential drug targets. However, no inhibitors exist for viral
macrodomains. Using an integration of high throughput X-ray based fragment screen and docking, we have
identified over 200 binders to the SARS-CoV-2 macrodomain (Mac1). Our subsequent assays guided the
development of the first structurally characterized tool compounds that are more potent than the substrate ADP-
ribose. In addition, we have leveraged the chemical knowledge to uncover additional scaffolds by docking. In
this proposal, we advance compounds through a structure-based design approach, using biochemical assays
against peptide binding and catalytic function. To identify starting points against the CHIKV macrodomain, we
will perform a new X-ray crystallography-based fragment screen and perform an Ultra-large docking campaign
(Screening Core). Our plan is to design compounds with low potency against human macrodomains and to
leverage medicinal chemistry to drive potency against viral macrodomains. Our early activities will identify
multiple alternative scaffolds with high potency in vitro to progress to target engagement in cells. Our cell-based
aims will use cellular thermal shift and immunofluorescence of interferon treated cells as early markers of target
engagement (Proteomics Core, In Vitro Virology Core). We will identify biomarkers by comparing RNAseq,
proteomics, phosphoproteomics and ADP-Ribosylation AP-MS of compound treated cells to mutant
macrodomains (both as a transgene and in the context of virus). During these activities, we will continue
addressing aspects of permeability, off target effects, and other liabilities with the Medicinal Chemistry Core.
We will progress to animal models compounds with cellular effects on replication with validated target
engagement. Lead molecules with validated target engagement and minimal pharmacokinetic liabilities will allow
us to test the effectiveness of candidate molecules in animal models of SARS-CoV-2 and CHIKV (In Vivo
Virology Core). Based on previous studies in animal models with catalytically inactive macrodomain mutant
viruses, we will prioritize molecules that drop viral load by at least 100-fold. Our work will generate a target
package for further development by our industrial partner, Roche. The lessons of targeting SARS-CoV-2 and
CHIKV macrodomains will be applicable to developing future agents against macrodomains in other viruses and
those implicated in human disease.

## Key facts

- **NIH application ID:** 10512631
- **Project number:** 1U19AI171110-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** James Solomon Fraser
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $2,988,130
- **Award type:** 1
- **Project period:** 2022-05-16 → 2026-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10512631

## Citation

> US National Institutes of Health, RePORTER application 10512631, Inhibiting Viral Macrodomains Using Structure-Based Design (1U19AI171110-01). Retrieved via AI Analytics 2026-06-01 from https://api.ai-analytics.org/grant/nih/10512631. Licensed CC0.

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