Identification of a Papain-Like Protease Inhibitor with Potential for Repurposing in Combination with an M^pro Protease Inhibitor for Treatment of SARS-CoV-2

Abstract

SARS-CoV-2 requires two cysteine proteases for viral polypeptide processing to allow maturation and replication: the 3C-like protease also known as the Main protease (Mpro) and the papain-like protease (PLpro). In addition to its critical role in viral replication, PLpro removes post-translational modifications like ubiquitin and interferon-stimulated gene product 15 (ISG15) from host proteins through its deubiquitinase domain, leading to host immunosuppression and increased ability of the virus to evade the host antiviral immune response. Through screening of a custom clinical compound library, we identified eltrombopag (DDL-701), a thrombopoietin receptor agonist, as having PLpro inhibitory activity that is sustained in the presence of the Mpro inhibitor nirmatrelvir. DDL-701 also suppressed both the deubiquitinase and ISG15 cleavage activities of PLpro. In addition, DDL-701 partially restored interferon-β induction – an element of the host immune response - in an in vitro model system. Further, modeling and docking studies suggest DDL-701 interacts with the active site region of the PLpro enzyme and pilot pharmacokinetic studies indicate it is brain permeable. DDL-701 is already approved for treatment of thrombocytopenia and has previously been shown to achieve human plasma levels after oral dosing that is above the IC50 needed for it to exert its PLpro inhibitory activity in vivo. In addition, it has also been reported to have antiviral efficacy against SARS-CoV-2. DDL-701 thus represents a drug that can immediately be repurposed and undergo clinical evaluation as a PLpro inhibitor that may be most effectively used in a protease inhibitor cocktail with an Mpro inhibitor such as nirmatrelvir (Paxlovid) for the treatment of COVID-19.

Deubiquitylating Enzymes in Cancer and Immunity

“…[278] Another small molecule DDL-701 is also an effective SARS2 PLpro inhibitor which displayed sustained inhibitory activity. [279] Although certain progress has been made in the development of drug targets for DUBs, it is still challenging for researchers to overcome a variety of existing obstacles. First, multiple DUBs are tightly related in similar catalytic pockets, which makes it difficult to develop potent inhibitors that represent selectivity for individual DUBs.…”

“…Oncology [ 603] Oncology [ 603] Oncology [ 603] USP47 Compound 1 Non-selective Oncology [ 584] POH1 8-thioquinoline Capzimin phen Non-selective Highly selective Highly selective Oncology [ 604] Oncology [ 605] Oncology [ 606] UCHL1 LDN-57444 Highly selective Oncology [ 607] GK13S Highly selective Oncology [ 608] 6RK73 Highly selective, irreversible Oncology [ 169] (Continued) [594][595][596] b-AP15 VLX1570 WP1130 Auranofin Non-selective, reversible Non-selective, reversible Non-selective Non-selective Oncology [ 597,598] Oncology [ 599] Oncology [ 582] Oncology [ 600] Trabid NSC112200 Highly selective Inflammation and oncology [ 609,610] CYLD Subquinocin Non-selective Inflammation [ 611] SARS-CoV PLpro GRL0617 Highly selective, reversible Anti-infection [ 276] DDL-701 Highly selective, reversible Anti-infection [ 279]…”