# Developing Antivirals Targeting Proteases and Polymerases of Coronaviruses, Picornaviruses and Bunyavirales

> **NIH NIH U19** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2022 · $5,168,269

## Abstract

PROJECT 2: DEVELOPING ANTIVIRALS TARGETING PROTEASES AND POLYMERASES OF
CORONAVIRUSES, PICORNAVIRUSES AND BUNYAVIRALES
SUMMARY
The goal of this Project is to develop drug-like inhibitors of coronavirus (CoV), picornavirus (PV) and Bunyavirales
(BV) replication by targeting essential protease (PR) and polymerase (Pol) enzymes encoded by the viruses.
Molecular targets of the CoVs being pursued are the main PR (MPro), the papain-like PR (PLP), and the RNA-
dependent RNA polymerase (RdRp). Molecular targets of the PVs are the enteroviral (EV) 2A and 3C PRs and
RdRp, and for BV PLP and RdRp. In Aims 1 and 2 we will identify hits and conduct lead optimization, for
proteases and RdRps, respectively. Mechanism of action and resistance potential will be explored for both aims,
especially for inhibitors that target novel sites. The close evolutionary relationship between CoVs and PVs may
also yield broad-spectrum inhibitors and feedback between both viral targets. The team of investigators have a
long and successful track record of structure-guided drug design, including extensive targeting of PRs and Pols.
We have established robust, scalable expression systems for producing reagent quantities of SARS-CoV-2 viral
enzymes. High-throughput, sensitive assays for measuring PR and RdRp activity have been developed for
SARS-CoV-2 MPro, PLP and EV 2A and have been used to discover both covalent and noncovalent low μM
inhibitors for MPro, μM inhibitors for PLP, and a biologic activator of 2A. A 100,000-compound biochemical
screen against Lassa virus RdRp has yielded numerous hits and a path to structure-guided optimization. We will
develop robust high-throughput (HTP) PR and RdRp assays for related CoVs, PVs, and BVs. The substrate
specificity of PRs will be profiled to inform substrate and inhibitor design, while cellular perturbations these
inhibitors confer will be explored by proteomics and cellular tomography to understand mechanism of action. We
will use large panels of recombinant viral and host PRs and Pols to rapidly evaluate hit and lead selectivity and
specificity. These efforts will be supported by the activities of the eight Technology Cores.
Efforts will focus on novel chemotypes, identified using a combination of structure-based docking, diverse and
multi-technique fragment screens, and HTS. Compounds will be optimized to minimize eventual resistance.
Mode of binding and quantitative structure-activity relationships (QSAR) will be established using X-ray
crystallography, NMR spectroscopy, cryo-electron microscopy and viral replication assays. PR inhibitors and
RdRp inhibitors will be tested together to identify additive or synergistic effects. This information will be used to
direct the next round of screening and inhibitor improvement.
Clinically relevant mutations identified in patients treated with PR or RdRp inhibitors will be introduced into the
wild-type enzymes and characterized for their sensitivity to our novel chemotypes. Emerging from th...

## Key facts

- **NIH application ID:** 10512628
- **Project number:** 1U19AI171110-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Charles Scott Craik
- **Activity code:** U19 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $5,168,269
- **Award type:** 1
- **Project period:** 2022-05-16 → 2026-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10512628

## Citation

> US National Institutes of Health, RePORTER application 10512628, Developing Antivirals Targeting Proteases and Polymerases of Coronaviruses, Picornaviruses and Bunyavirales (1U19AI171110-01). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/10512628. Licensed CC0.

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