The Structure of the Porcine Deltacoronavirus Main Protease Reveals a Conserved Target for the Design of Antivirals

Abstract

The existing zoonotic coronaviruses (CoVs) and viral genetic variants are important microbiological pathogens that cause severe disease in humans and animals. Currently, no effective broad-spectrum antiviral drugs against existing and emerging CoVs are available. The CoV main protease (Mpro) plays an essential role in viral replication, making it an ideal target for drug development. However, the structure of the Deltacoronavirus Mpro is still unavailable. Porcine deltacoronavirus (PDCoV) is a novel CoV that belongs to the genus Deltacoronavirus and causes atrophic enteritis, severe diarrhea, vomiting and dehydration in pigs. Here, we determined the structure of PDCoV Mpro complexed with a Michael acceptor inhibitor. Structural comparison showed that the backbone of PDCoV Mpro is similar to those of alpha-, beta- and gamma-CoV Mpros. The substrate-binding pocket of Mpro is well conserved in the subfamily Coronavirinae. In addition, we also observed that Mpros from the same genus adopted a similar conformation. Furthermore, the structure of PDCoV Mpro in complex with a Michael acceptor inhibitor revealed the mechanism of its inhibition of PDCoV Mpro. Our results provide a basis for the development of broad-spectrum antivirals against PDCoV and other CoVs.

Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses

“…Prior to analysis, data quality assessment was completed using Xtriage [ 18 ]. The structures were solved by molecular replacement using PHASER [ 19 ] with 7L0D [ 20 ] for the SARS-CoV-2 M pro –PF-00835231 structure, SW1 apo M pro (8FWX) to solve the SW1 M pro –GC376 structure, and 7WKU [ 16 ] to solve the HKU15 M pro –PF-00835231 structure. In each case, models for molecular replacement were prepared by removing ligands, structural and bulk solvent waters, and cryoprotectant molecules.…”

“…The M pro amino acid sequence of HKU15 and SW1 are less than 50% identical to those from beta-CoVs as well as to each other ( Figure S2 ). The crystal structure of HKU15 M pro has recently been determined with a relatively large peptidomimetic inhibitor [ 16 ]. However, how potential pan-CoV inhibitors bind to HKU15 is not known.…”

Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses

“…Prior to analysis, data quality assessment was done using Xtriage [18]. The structures were solved by molecular replacement using PHASER [19] with 7L0D [20] for the SARS-CoV-2 M pro –PF-00835231 structure, SW1 apo M pro (8FWX) to solve the SW1 M pro –GC376 structure, and 7WKU [16] to solve the HKU15 M pro –PF-00835231 structure. In each case, models for molecular replacement were prepared by removing ligands, structural and bulk solvent waters, and cryoprotectant molecules.…”

“…The M pro amino acid sequence of HKU15 and SW1 are less than 50% identical to those from beta-CoVs as well as to each other (Figure S1). The crystal structure of HKU15 M pro has recently been determined with a relatively large peptidomimetic inhibitor [16] but how potential pan-CoV inhibitors bind to HKU15 is not known. Additionally, apart from the avian infectious bronchitis virus (IBV) [17], structural characterization of M pro from gamma-CoVs is severely lacking.…”

In Silico Identification of Natural Compounds Against SARS-CoV-2 Main Protease From Chinese Herbal Medicines

“…These nsps contribute to the production of four main structural proteins that play an important role in the invasion and spread of SARS-CoV-2 in the human body [ 6 , 7 ]. In addition, the structures of Mpros were revealed to be relatively conserved among CoVs, especially in the substrate-binding pockets [ 8 ]. Correspondingly, Mpro sequences also show a low mutation frequency across known SARS-CoV-2 variants [ 9 ].…”