Zinc and SARS‑CoV‑2: A molecular modeling study of Zn interactions with RNA‑dependent RNA‑polymerase and 3C‑like proteinase enzymes

Figures

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  Figure 1. Phylogenetic trees and multiple sequence alignments of COVID-19 RdRp. (A) Phylogenetic tree using ClustalW software and (B) multiple sequence alignment using CLUSTAL 2.1 based on amino acid sequences of COVID-19 nsp 12 (GenBank accession no. YP_009725307.1), SARS rep (UniProtKB accession no. R1AB_CVHSA), influenza A PB1 (GenBank accession no. AAK18013.1) and T7 Bacteriophage (T7 Phage) PHA (PDB accession no. 4RNP_C). (C) Phylogenetic tree and (D) Multiple sequences alignment based on DNA sequences of COVID-19 RdRp (GenBank accession no. MT042778.1), SARS RdRp (GenBank accession no. AY340092.1), influenza A PB1 (GenBank accession no. AJ620348.2) and hepatitis C virus NS5B (GenBank accession no. AJ608785.1), calcivirus RdRp (GenBank accession no. Y13703.1) and T7 Phage RdRp (GenBank accession no. M3830s28.1). RdRp, RNA-dependent RNA polymerase; COVID-19, coronavirus disease 2019; SARS, severe acute respiratory syndrome.

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  Figure 2. Phylogenetic trees and multiple sequence alignments of COVID-19 3CLpro. (A) Phylogenetic tree using ClustalW software and (B) multiple sequence alignment using CLUSTAL 2.1 based on amino acid sequences of COVID-19 nsp5A_3CLpro and nsp5B_3CLpro (NCBI Reference Sequence acces-sion no. YP_009742612.1), SARS peptidase_C30 (PDB accession no. 3F9G_A), YHV peptidase_C62 (GenBank accession no. ABL96309.1), BQV 3C-like protease (GenBank accession no. AIW60925.1) and European brown hare syndrome virus 3CLpro (NCBI Reference Sequence accession no. NP_786901.1). (C) Phylogenetic tree and (D) multiple sequence alignment based on DNA sequences of COVID-19 orf1ab (GenBank accession no. MT049951.1), SARS 3CLpro (GenBank accession no. AY609081.1), BQV 3CLpro (GenBank accession no. KM232906.1), YHV 3CLpro (GenBank accession no. EU977577.1) and avian infectious bronchitis virus 3CLpro (GenBank accession no. Q157446.1). YHV, yellow head virus; BQV, black queen cell virus; 3CLpro; 3C-like protease; COVID-19, coronavirus disease 2019; SARS, severe acute respiratory syndrome.

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  Figure 3. Structural alignment between SARS-CoV (pink) and COVID-19 (cyan) of the RdRp. (A and B) The first zinc binding site and (C) overall structure. The white box indicates the area where zinc binds on the overall structure. The structures were aligned on PyMol using previously determined crystal structures for RdRp in SARS-CoV (PDB accession no. 6NUR) and COVID-19 (PDB accession no. 6M71). The alignment was performed iteratively five times with a cut-off of 2.0 Å and a resulting root-mean-square deviation value of 0.588 for 7,027 atoms aligned out of a total 8,040 atoms. RdRp, RNA-dependent RNA polymerase; SARS, severe acute respiratory syndrome; CoV, coronavirus; HIS, histidine; CYS, cysteine.

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  Figure 4. Structural alignment between SARS-CoV (pink) and COVID-19 (cyan) of the RdRp. (A and B) The second zinc binding site and (C) overall structural alignment. The white box indicates the area where zinc binds based on the overall structure. The structures were aligned on PyMol using previously determined crystal structures for RdRp in SARS-CoV (PDB accession no. 6NUR) and COVID-19 (PDB accession no. 6M71). The alignment was performed iteratively five times with a cut-off of 2.0 Å and a resulting root-mean-square deviation value of 0.588 for 7,027 atoms aligned out of a total 8,040 atoms. RdRp, RNA-dependent RNA polymerase; SARS, severe acute respiratory syndrome; CoV, coronavirus; HIS, histidine; CYS, cysteine.

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  Figure 5. Structural alignment between SARS-CoV (pink) and COVID-19 (cyan) of the 3CLpro bound to a zinc coordinating compound (TLD-902; TDT). Subtitle: The alignment and structures were modelled with PyMol using previously determined crystal structures for the 3CLpro of SARS-CoV bound to TDT (PDB accession no. 2Z94) and 3CLpro of COVID-19 (PDB accession no. 6W63). The alignment was performed iteratively five times with a cut-off of 2.0 Å and a resulting root-meansquare value of 0.621 for 1,985 atoms aligned out of a total 2,339 atoms. (A and B) Zinc is shown here to specifically target the catalytic dyad C145 and H41 for inhibition, which are unaltered between SARS-CoV and COVID-19. (C) The overall structural alignment is also displayed with a white box indicating the location of the zinc binding site in relation to the full protein. TDT, toluene-3,4-dithiolato zinc; 3C-like proteinase, 3CLpro; HIS, histidine; CYS, cysteine.