Crystal structure of the papain-like protease of MERS coronavirus reveals unusual, potentially druggable active-site features

Abstract

The Middle-East Respiratory Syndrome coronavirus (MERS-CoV) causes severe acute pneumonia and renal failure. The MERS-CoV papain-like protease (PL(pro)) is a potential target for the development of antiviral drugs. To facilitate these efforts, we determined the three-dimensional structure of the enzyme by X-ray crystallography. The molecule consists of a ubiquitin-like domain and a catalytic core domain. The catalytic domain displays an extended right-hand fold with a zinc ribbon and embraces a solvent-exposed substrate-binding region. The overall structure of the MERS-CoV PL(pro) is similar to that of the corresponding SARS-CoV enzyme, but the architecture of the oxyanion hole and of the S3 as well as the S5 specificity sites differ from the latter. These differences are the likely reason for reduced in vitro peptide hydrolysis and deubiquitinating activities of the MERS-CoV PL(pro), compared to the homologous enzyme from the SARS coronavirus. Introduction of a side-chain capable of oxyanion stabilization through the Leu106Trp mutation greatly enhances the in vitro catalytic activity of the MERS-CoV PL(pro). The unique features observed in the crystal structure of the MERS-CoV PL(pro) should allow the design of antivirals that would not interfere with host ubiquitin-specific proteases.

Inhibitor Recognition Specificity of MERS-CoV Papain-like Protease May Differ from That of SARS-CoV

“…Our structure contains the second loop (BL2) that was not defined in another recently solved apo structure of MERS-PLpro (PDB ID: 4P16). 25 That structure and our structure are almost identical except for our structure defining the BL2 loop and two different cysteine modifications. This BL2 loop plays a crucial role in SARS-PLpro inhibitor binding according to four currently available x-ray crystal structures in complex with four different inhibitors.…”

“…MERS-PLpro is composed of four distinct domains, an ubiquitin-like (Ubl)-domain, thumb, palm, and zinc fingers (Figure 2A). The overall structure of MERS-PLpro resembles that of SARS-PLpro 21, 25 with an α carbon RMSD of 1.2 Å. There are minor structural deviations of the Ubl, thumb and palm domains between MERS-PLpro and SARS-PLpro.…”

“…One is with a wild-type SARS-PLpro with an ubiquitin aldehyde, and the other is a C112S mutant SARS-PLpro with bovine ubiquitin as a substrate. 31, 33 Lei and colleagues compared the C112S mutant SARS-PLpro complex structure with the apo MERS-PLpro and reported that the S2 (P163 vs. L163), S3 (F269 vs. Y265, A162 vs. E162), and S5 (R168 vs. E168) subsites of MERS-PLpro exhibited different features from those of SARS-PLpro, 25 which could explain the significant catalytic efficiency difference between the two PLpro enzymes with the same substrate.…”

Molecular Dynamic Studies of Interferon and Innate Immunity Resistance in MERS CoV Non-Structural Protein 3

“…In this context, the L106W mutation of the MERS CoV Plpro resulted in a drastic increase in deubiquitinating activity. 10) In addition, the mutation of SARS Plpro to residues similar to MERS CoV amino acids resulted in the profound loss of deubiquitinating activity. 10,20) Therefore, MERS CoV Plpro naturally has lower deubiquitinating activity compared with SARS CoV Plpro.…”

“…The Ubl domain is conserved in most CoVs including MERS CoV and SARS CoV, while the transmissible gastroenteritis CoV lacks the Ubl domain. 10,11) In studies related to the SARS CoV, Ubl was found to interfere with the IRF3 and nuclear factor-kappaB (NF-κB) antiviral pathways.…”