Journal: PLOS Pathogens

Article Title: An intrinsic loop-mediated structural stability modulating inhibitor potency in the SADS-CoV and SARS-CoV-2 main proteases

doi: 10.1371/journal.ppat.1013981

Figure Lengend Snippet: (A) Overall structure of SADS-CoV M pro . Protomer A is shown as a surface colored according to B-factor values (max(red)–min(blue)). Protomer B is depicted as a cartoon overlaid with surface, where Domain I is colored pink, Domain II green, and Domain III purple. The catalytic residue Cys144 is displayed as a yellow sphere, and His41 as a blue sphere. The N- and C-termini of protomer B are marked. (B) The substrate-binding pocket of SADS-CoV M pro . Cys144 and His41 are shown in yellow and blue, respectively. The subsites of the M pro substrate pocket are labeled. (C and D) Structural alignment of SADS-CoV M pro (magenta, PDB code: 9VUT) Domain I, II (C) and Domain III (D) with seven HCoVs (gray), including SARS-CoV-2 (PDB code: 7MHH), SARS-CoV (PDB code: 1UJ1), MERS-CoV (PDB code: 4WME), HCoV-HKU1 (PDB code: 3D23), HCoV-OC43 (PDB code: 9C7W), HCoV-229E (PDB code: 2ZU2), and HCoV-NL63 (PDB code: 7E6M). The residues 40–53 and 240–249 regions are highlighted with red dashed boxes. The N- and C-termini are marked. (E–I) Inhibition evaluation of 27h and SY110 . Chemical structures of compounds 27h (E) and SY110 (F). P1’, P1, P2, and P3 are labeled. The warheads are marked with asterisks. (G) Dose-dependent inhibition of SADS-CoV M pro by 27h and SY110 in FRET assays. (H) The K i values of 27h and SY110 against SADS-CoV M pro were determined using the Morrison K i assays. Data of (G) and (H) are presented as mean ± SD from three independent experiments (n = 3). (I) Thermal stabilization of SADS-CoV M pro by 27h and SY110 in DSF assay. Curves represent the average values from three independent experiments (n = 3).

Article Snippet: SARS-CoV-2 M pro -del-Lys97Val crystals were obtained in Morpheus condition 1–44 (0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 37.5% v/v Precipitant Mix 4, MiTeGen).

Techniques: Residue, Binding Assay, Labeling, Inhibition

Journal: PLOS Pathogens

Article Title: An intrinsic loop-mediated structural stability modulating inhibitor potency in the SADS-CoV and SARS-CoV-2 main proteases

doi: 10.1371/journal.ppat.1013981

Figure Lengend Snippet: (A) Structural comparison of SADS-CoV M pro - 27h (PDB code: 9VUU) with SARS-CoV-2 M pro - 27h (PDB code: 8I30). SARS-CoV-2 M pro - 27h is colored wheat, with residue labels underlined. The shift of the Cα of Glu47 (SARS-CoV-2) relative to Thr47 (SADS-CoV) is highlighted. The H1 and H2 regions have been outlined. The H2 of SARS-CoV-2 M pro is shown in orange, and the residues 45–51 of SADS-CoV M pro are shown in cyan. (B) Structural comparison of SADS-CoV M pro - SY110 (PDB code: 9VUV, purple) with SARS-CoV-2 M pro - SY110 (PDB code: 8HHU, wheat). (C) The B-factor values of residues 45–51 for SARS-CoV-2 M pro (PDB code: 7MHH), M pro - 27h (PDB code: 8I30), M pro - SY110 (PDB code: 8HHU), and SADS-CoV M pro (PDB code: 9VUT), M pro - 27h (PDB code: 9VUU), M pro - SY110 (PDB code: 9VUV). (D) Sequence alignment of residues 40–54 from five β-CoV M pro s and residues 40–53 from three α-CoV M pro s. (E) Structural alignment of residues 40–54 from SARS-CoV-2 (PDB code: 7MHH), SARS-CoV (PDB code: 1UJ1), MERS-CoV (PDB code: 4WME), HCoV-HKU1 (PDB code: 3D23), HCoV-OC43 (PDB code: 9C7W), and residues 40–53 from HCoV-229E (PDB code: 2ZU2), HCoV-NL63 (PDB code: 7E6M), and SADS-CoV M pro (PDB code: 9VUT). The H1 and H2 helices are highlighted with cyan and red dashed boxes, respectively. (F) Backbone hydrogen bonds in the H2 helix of SARS-CoV-2 M pro . (G) Structural comparison of the effect of residue '51' on the H2 helix. (H) Substrate affinity of SARS-CoV-2 M pro WT and its mutants, along with inhibition of 27h . Data are presented as mean ± SD from three independent experiments (n=3). Loop SADS-CoV (and so on): SARS-CoV-2 M pro mutant in which its residues 40–54 was replaced by residues 40–53 of SADS-CoV M pro ; M pro -del: Asn51 was deleted in SARS-CoV-2 M pro ; M pro -TT: Glu47 and Asp48 in SARS-CoV-2 M pro were mutated to Thr47 and Thr48 in SADS-CoV M pro , as control.

Article Snippet: SARS-CoV-2 M pro -del-Lys97Val crystals were obtained in Morpheus condition 1–44 (0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 37.5% v/v Precipitant Mix 4, MiTeGen).

Techniques: Comparison, Residue, Sequencing, Inhibition, Mutagenesis, Control

Journal: PLOS Pathogens

Article Title: An intrinsic loop-mediated structural stability modulating inhibitor potency in the SADS-CoV and SARS-CoV-2 main proteases

doi: 10.1371/journal.ppat.1013981

Figure Lengend Snippet: (A–H) The K i values of 27h against M pro s of SARS-CoV-2 (A), SARS-CoV (B), MERS-CoV (C), HCoV-HKU1 (D), HCoV-OC43 (E), HCoV-229E (F), HCoV-NL63 (G), and SADS-CoV (H). The K i curves for α- and β-CoV M pro s are shown in orange and cyan, respectively. Data are presented as mean ± SD from three independent experiments (n = 3).

Article Snippet: SARS-CoV-2 M pro -del-Lys97Val crystals were obtained in Morpheus condition 1–44 (0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 37.5% v/v Precipitant Mix 4, MiTeGen).

Techniques: