Trapping a non-cognate nucleotide upon initial binding for replication fidelity control in SARS-CoV-2 RNA dependent...

Area of Science:

• Molecular Biology
• Virology
• Computational Chemistry

Background:

• The SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is crucial for viral replication and transcription.
• Understanding RdRp's nucleotide selectivity mechanism is key to controlling viral fidelity.

Purpose of the Study:

• To computationally investigate SARS-CoV-2 RdRp's nucleotide selectivity during elongation.
• To elucidate the mechanisms of cognate vs. non-cognate nucleotide binding and insertion.

Main Methods:

• Microsecond ensemble equilibrium all-atom molecular dynamics (MD) simulations.
• Enhanced sampling methods (e.g., umbrella sampling) to calculate free energy profiles.
• Analysis of nucleotide binding and conformational changes in the RdRp active site.

Main Results:

• Non-cognate dATP and GTP exhibit stability in the open active site but are prevented from insertion.
• Cognate ATP and the antiviral drug analogue RDV-TP favor stabilization in the closed active site for insertion.
• SARS-CoV-2 RdRp intrinsically rejects non-cognate nucleotides through distinct binding pathways.

Conclusions:

• The study reveals the intrinsic nucleotide selectivity mechanism of SARS-CoV-2 RdRp.
• This selectivity mechanism contributes to viral genome replication fidelity.
• Findings provide insights for designing novel antiviral drugs targeting RdRp function.