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Structural Basis of RNA Polymerase of SARS-CoV-2 with RNA and Remdesivir


The COVID-19 pandemic caused by the SARS-CoV-2 virus has become an unprecedented global crisis, with so far over 4.1 million infections and 283,000 deaths reported. SARS-CoV-2 is a positive strand RNA virus, and its replication is dependent on RNA polymerase (RdRp) consisting of nsp12, nsp7, and nsp8. However, the lack of structure of RdRp in complex with an RNA or with nucleotide inhibitors hampers drug development. Recently, a joint research group from China successfully determined the cryo-EM structure of the SARS-CoV-2 RdRp complex with a template-primer RNA and the antiviral drug Remdesivir, which was recently received the Emergency Use Authorization (EUA) status for COVID-19 from the FDA.
In the co-structure, the template-RTP RdRp complex contains one nsp12, one nsp7 and one nsp8, and the template-primer RNA consisting of a 14-base RNA in the template strand, a 11-base RNA in the primer strand held by the finger-palm-thumb subdomains (Figure 1A). The template-primer RNA forms extensive protein-RNA interactions with a total of 29 residues in nsp12 (Figure. 1B). In contrast, no protein-RNA interaction is formed with nsp7 or nsp8, although these two proteins are required for RNA binding by RdRp. No base pairs of the template-primer RNA are in contact with nsp12. The RNA phosphate-ribose backbones and the 2′-OH groups of the primer strand contribute to most of the protein-RNA interactions. The nucleotides at the +2 and +3 positions of the template strand interact with residues from the back of the finger subdomain (Figure 1C). This structural information is consistent with the fact that no specific sequence is required for the enzymatic activity of RdRp during the elongation process.
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B:
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Figure 1: Cryo-EM Structure of the Remdesivir and RNA bound RdRp complex
The inhibitor Remdesivir monophosphate (RMP) is covalently linked to the 3′ end of the primer strand of RNA and locates in the center of the catalytic active site. The adenosine of RMP forms either base-stacking interactions with the upstream base from the primer strand or two hydrogen bonds with the uridine base from the template strand (Figure 2A, B).  Two magnesium ions and a pyrophosphate locate near the bound RMP and magnesium ions play as part of catalytic active site, while the pyrophosphate blocks the entry of nucleotide triphosphate to the active side.
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B:

Figure 2: A diagram of interactions of the bound Remdesivir in a monophosphate form with surrounding residues and nucleotide bases.
The catalytic active site of the nsp12 RdRp is constructed by seven conserved motifs from A to G. The residues involved in RNA binding as well as residues comprising the catalytic active site are highly conserved (Figure 3), which could explain the broad-spectrum antiviral inhibitors, such as Remdesivir and Galidesivir, are also effective for SARS-CoV-2.
The revealed co-structure of template-RTP RdRp complex displayed the Remdesivir binding modeling with the SARS-CoV-2 RdRp and structurally clarified the inhibitory mechanism of Remdesivir for SARS-CoV-2. Moreover, this structure provided a solid template for modeling and design even more potent inhibitors to combat the vicious infection of SARS-CoV-2.
Figure 3: Sequence alignment of six coronavirus nsp12

Reference: Eric Xu, et.al. Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir. Science. 2020. doi: 10.1126/science.abc1560.

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