Design of SARS-CoV-2 PLpro Inhibitors for COVID-19 Antiviral Therapy Leveraging Binding Cooperativity

Zhengnan Shen, Kiira Ratia, Laura Cooper, Deyu Kong, Hyun Lee, Youngjin Kwon, Yangfeng Li, Saad Alqarni, Fei Huang, Oleksii Dubrovskyi, Lijun Rong, Gregory R.J. Thatcher, Rui Xiong

Research output: Contribution to journalArticlepeer-review

97 Scopus citations


Antiviral agents that complement vaccination are urgently needed to end the COVID-19 pandemic. The SARS-CoV-2 papain-like protease (PLpro), one of only two essential cysteine proteases that regulate viral replication, also dysregulates host immune sensing by binding and deubiquitination of host protein substrates. PLpro is a promising therapeutic target, albeit challenging owing to featureless P1 and P2 sites recognizing glycine. To overcome this challenge, we leveraged the cooperativity of multiple shallow binding sites on the PLpro surface, yielding novel 2-phenylthiophenes with nanomolar inhibitory potency. New cocrystal structures confirmed that ligand binding induces new interactions with PLpro: by closing of the BL2 loop of PLpro forming a novel "BL2 groove"and by mimicking the binding interaction of ubiquitin with Glu167 of PLpro. Together, this binding cooperativity translates to the most potent PLpro inhibitors reported to date, with slow off-rates, improved binding affinities, and low micromolar antiviral potency in SARS-CoV-2-infected human cells.

Original languageEnglish (US)
Pages (from-to)2940-2955
Number of pages16
JournalJournal of Medicinal Chemistry
Issue number4
StatePublished - Feb 24 2022

ASJC Scopus subject areas

  • Molecular Medicine
  • Drug Discovery


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