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

Diffraction data collection, structure elucidation and refinement. Diffraction data from the crystal of the SARS-CoV M pro in complex with 11a were collected at 100 K at synchrotron beamline PXI-X06SA (PSI, Villigen, Switzerland) using a Pilatus 6M detector (DECTRIS). A diffraction data set from the SARS-CoV M pro crystal with compound 11s was collected at 100 K at beamline P11 of PETRA III (DESY, Hamburg, Germany), using the same type of detector. All diffraction data sets of HCoV-NL63 M pro complex structures and of the complex of CVB3 3C pro with 11a were collected at synchrotron beamline BL14.2 of BESSY (Berlin, Germany), using an MX225 CCD detector (Rayonics). All data sets were processed by the program XDSAPP and scaled by SCALA from the CCP4 suite. [50] [51] [52] The structure of SARS-CoV M pro with 11a was determined by molecular replacement with the structure of the complex between SARS-CoV M pro and SG85 (PDB entry 3TNT; Zhu et al., unpublished) as search model, employing the MOLREP program (also from the CCP4 suite). 52, 53 The complex structures of HCoV-NL63 M pro with 11a, 11f, and 11n were also determined with MOLREP, using as a search model the structure of the free enzyme determined by us (LZ et al., unpublished) . The complex structure between CVB3 3C pro and 11a was determined based on the search model of the free-enzyme structure (PDB entry 3ZYD; Tan et al., unpublished) . Geometric restraints for the compounds 11a, 11f, 11n, and 11s were generated by using JLIGAND 52, 54 and built into Fo-Fc difference density using the COOT software. 55 Refinement of the structures was performed with REFMAC version 5.8.0131 (ref. 52, 56, 57) .