Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication

Linlin Zhang; Daizong Lin; Yuri Kusov; Yong Nian; Qingjun Ma; Jiang Wang; Albrecht von Brunn; Pieter Leyssen; Kristina Lanko; Johan Neyts; Adriaan de Wilde; Eric J. Snijder; Hong Liu; Rolf Hilgenfeld

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.10.936898 doi: bioRxiv preprint Table 3 . The thiohemiketal is in the R configuration, with its oxygen accepting two hydrogen bonds from the oxyanion-hole amides of Gly143 and Cys145. The amide oxygen accepts an H-bond from His41. The side-chains of Ser144 and Arg188 have been omitted for clarity. B. The P2-benzyl substituent of 11a cannot fully enter the S2 pocket of the HCoV-NL63 M pro , which is much smaller and has less plasticity than the corresponding pocket of SARS-CoV M pro (cf. A). The benzyl therefore binds above the pocket in the view shown here; this is probably the reason for the total inactivity (IC50 > 50 µM) of compound 11a against HCoV-NL63 M pro . The small size of the pocket is due to the replacement of the flexible Gln189 of the SARS-CoV M pro by the more rigid Pro189 in this enzyme. The stereochemistry of the thiohemiketal is R. The sidechains of Ala143 and Gln188 have been omitted for clarity. C. Binding of 11a to the CVB3 3C pro . The stereochemistry of the thiohemiketal is S, as the group accepts a hydrogen bond from His41, whereas the amide keto group accepts three H-bonds from the oxyanion hole (residues 145 -147). The side-chain of Gln146 has been omitted for clarity. D. The crystal structure of 11f in complex with HCoV-NL63 M pro shows that this short (inactive) compound lacking a P3 residue has its P2-Boc group inserted into the S2 pocket of the protease. The stereochemistry of the thiohemiketal is S. The sidechains of Ala143 and Gln188 have been omitted for clarity. E. In contrast to P2 = benzyl in 11a, the isobutyl group of 11n is small and flexible enough to enter into the narrow S2 pocket of the HCoV-NL63 M pro . The thiohemiketal is in the R configuration. The side-chains of Ala143 and Gln188 have been omitted for clarity. F. In spite of its small size, the cyclopropylmethyl side-chain in the P2 position of 11s can tightly bind to the S2 subsite of the SARS-CoV M pro , as this pocket exhibits pronounced plasticity due to the conformational flexibility of Gln189 (see also Fig. 4 ). The stereochemistry of the thiohemiketal is S. The side-chains of Ser144 and Arg188 have been omitted for clarity.