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Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro.

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Researchers elucidated the cleavage order of the SARS-CoV-2 nsp7-11 polyprotein by the main protease (Mpro). This study reveals how Mpro binds and processes its substrate, crucial for understanding viral replication and developing inhibitors.

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Area of Science:

  • Virology
  • Structural Biology
  • Biochemistry

Background:

  • Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes COVID-19.
  • Viral polyprotein processing by proteases like main protease (Mpro) is critical for SARS-CoV-2 replication.
  • The precise mechanism of Mpro-mediated cleavage of the nsp7-11 polyprotein remains incompletely understood.

Purpose of the Study:

  • To determine the order of Mpro-mediated cleavages within the nsp7-11 polyprotein.
  • To structurally and functionally characterize the interaction between Mpro and its nsp7-11 substrate.
  • To investigate potential Mpro inhibitors using the nsp7-11 polyprotein.

Main Methods:

  • Integrative modeling combining mass spectrometry (hydrogen-deuterium exchange, cross-linking) and x-ray scattering.
  • Proteolysis assays to study Mpro activity and inhibition.
  • Structural analysis of Mpro-nsp7-11 complexes.

Main Results:

  • The sequential order of Mpro-mediated cleavages in the nsp7-11 polyprotein was identified.
  • An ensemble structure of the nsp7-11 polyprotein was determined, showing conserved secondary structures.
  • Mpro preferentially binds to polyprotein junction sites, with transient contacts aiding substrate orientation for cleavage.

Conclusions:

  • The study provides a detailed mechanistic understanding of Mpro's role in SARS-CoV-2 polyprotein processing.
  • Structural insights into Mpro-substrate interactions can inform the design of antiviral drugs.
  • The nsp7-11 polyprotein serves as a valuable substrate for evaluating Mpro inhibitors.