Potential Inhibitors Targeting Papain-Like Protease of SARS-CoV-2: Two Birds With One Stone

Abstract

Severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2), the pathogen of the Coronavirus disease-19 (COVID-19), is still devastating the world causing significant chaos to the international community and posing a significant threat to global health. Since the first outbreak in late 2019, several lines of intervention have been developed to prevent the spread of this virus. Nowadays, some vaccines have been approved and extensively administered. However, the fact that SARS-CoV-2 rapidly mutates makes the efficacy and safety of this approach constantly under debate. Therefore, antivirals are still needed to combat the infection of SARS-CoV-2. Papain-like protease (PLpro) of SARS-CoV-2 supports viral reproduction and suppresses the innate immune response of the host, which makes PLpro an attractive pharmaceutical target. Inhibition of PLpro could not only prevent viral replication but also restore the antiviral immunity of the host, resulting in the speedy recovery of the patient. In this review, we describe structural and functional features on PLpro of SARS-CoV-2 and the latest development in searching for PLpro inhibitors. Currently available inhibitors targeting PLpro as well as their structural basis are also summarized.

Keywords: COVID-19; SARS-CoV-2; crystal structure; inhibitor; papain-like protease.

FIGURE 1

Schematic representation of the production and function of SARS- CoV- 2 PLpro. The positive- strand RNA (numbers indicate nucleotide position) including the ORF 1a/b, structural proteins S (spike), E (envelope), M (membrane) and N (nucleocapsid) are shown. PLpro is encoded by part of nsp3. It is able to mature nsp1- 3 and preferentially cleave the ubiquitin- like protein ISG15 from IRF3 by recognizing specific cleavage sites.

FIGURE 2

Crystal structures of SARS-CoV-2 PLpro in apo and substrate-bound forms. (A) Crystal structure of SARS-CoV-2 PLpro (PDB ID: 6WZU). The four distinct subdomains are indicated. The catalytic triad is shown in the blue dashed circle. (B) Superposition of ubiquitin/PLpro complex (PDB ID: 6XAA) with mouse-ISG15/PLpro complex (PDB ID: 6YVA). The catalytic triad is shown in the blue dashed circle. The two ubiquitin binding sites are indicated. The ubiquitin is colored in cyan, while the mouse ISG15 is colored in orange.

FIGURE 3

Crystal structure of SARS-CoV-2 PLpro in complex with non-covalent inhibitors. (A) Superposition of PLpro (light blue; PDB ID: 6WZU) with GRL0617/PLpro (magentas; PDB ID: 7CMD), Jun9-72-2/PLpro (wheat; PDB ID: 7SDR), XR8-24/PLpro (orange; PDB ID: 7LBS), and YM155/PLpro (limon; PDB ID: 7D7L) complexes. The catalytic triad and the zinc-finger motif are shown in the blue dashed circle. The blocking loop 2 and the S2 ubiquitin binding site are indicated. (B) Surface presentation of GRL0617 binding pocket. PLpro is shown as gray surface, while GR0617 is shown as sticks. S3 and S4 pockets are labeled. (C) Surface presentation of Jun9-72-2 binding pocket. PLpro is shown as gray surface, while Jun9-72-2 is shown as sticks. S4 pocket is labeled. (D) Surface presentation of XR8-24 binding pocket. PLpro is shown as gray surface, while XR8-24 is shown as sticks. S4 pocket and BL2 groove are labeled. (E) Surface presentation of YM155 binding pocket. PLpro is shown as gray surface, while YM155 is shown as sticks. S4 pocket is labeled.

FIGURE 4

Crystal structures of SARS-CoV-2 PLpro in complex with covalent inhibitors. (A) Superposition of SARS-CoV-2 PLpro (light blue; PDB ID: 6WZU) with VIR250/PLpro (green; PDB ID: 6WUU) and VIR251/PLpro (cyan; PDB ID: 6WX4) complexes. The blocking loop 2 is indicated. (B) Surface presentation of VIR250 binding pocket. PLpro is shown as gray surface, while VIR250 is shown as sticks. The catalytic cysteine of PLpro forms a covalent bond with VIR250. The P2-P4 positions are labeled. (C) Surface presentation of VIR251 binding pocket. PLpro is shown as gray surface, while VIR251 is shown as sticks. The catalytic cysteine of PLpro forms a covalent bond with VIR251. The P2-P4 positions are labeled.