# Targeting SARS-CoV-2 PLpro for COVID-19 treatment

> **NIH NIH R01** · UNIVERSITY OF ARIZONA · 2023 · $600,292

## Abstract

ABSTRACT
The COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2), has caused profound socioeconomic challenges for humankind. Antiviral agents
blocking SARS-CoV-2 viral replication that complement vaccination are urgently needed to stop
the current pandemic and to avoid potential future outbreaks. The papain-like protease (PLpro),
an essential cysteine protease that regulates viral replication and host immune sensing, is a
promising antiviral target against SARS-CoV-2. However, the rapid development of potent PLpro
inhibitors has been hindered by limited draggable interactions at the active site due to restricted
P1 and P2 sites with glycine recognition. To address these challenges, we have investigated
novel, druggable binding sites, distal to the active site, using structure-guided design and X-ray
crystallography. These efforts led to a series of 2-phenylthiophene-based inhibitors with low
nanomolar potency. Crystal structures revealed that these potent SARS-CoV-2 PLpro inhibitors
engage with a novel ligand-binding site, the “BL2 groove”, leading to slower off-rates, improved
binding affinities, and low micromolar antiviral potency in SARS-CoV-2-infected human cells.
Moreover, these inhibitors showed good microsomal stability and in vivo exposure after
intraperitoneal (IP) administration. Building on these encouraging preliminary data, we propose in
this project to further optimize and develop these novel PLpro inhibitors to achieve in vivo antiviral
efficacy. We propose: Aim 1) to optimize our lead PLpro inhibitors for improved potency and drug-
likeness properties using structure-guided design; Aim 2) to evaluate and triage PLpro inhibitors
based on biochemical, ADME, and antiviral assays; Aim 3) to assess the PK/PD profile of top
inhibitors and to establish in vivo antiviral efficacy. Completion of the research will lead to small
molecules suitable for development as drug candidates to treat SARS-CoV-2.

## Key facts

- **NIH application ID:** 10577845
- **Project number:** 5R01AI168165-03
- **Recipient organization:** UNIVERSITY OF ARIZONA
- **Principal Investigator:** Rui Xiong
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $600,292
- **Award type:** 5
- **Project period:** 2022-02-22 → 2027-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10577845

## Citation

> US National Institutes of Health, RePORTER application 10577845, Targeting SARS-CoV-2 PLpro for COVID-19 treatment (5R01AI168165-03). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10577845. Licensed CC0.

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