Discovery of Immunoproteasome Inhibitors Using Large-Scale Covalent Virtual Screening

Abstract

Large-scale virtual screening of boronic acid derivatives was performed to identify nonpeptidic covalent inhibitors of the β5i subunit of the immunoproteasome. A hierarchical virtual screening cascade including noncovalent and covalent docking steps was applied to a virtual library of over 104,000 compounds. Then, 32 virtual hits were selected, out of which five were experimentally confirmed. Biophysical and biochemical tests showed micromolar binding affinity and time-dependent inhibitory potency for two compounds. These results validate the computational protocol that allows the screening of large compound collections. One of the lead-like boronic acid derivatives identified as a covalent immunoproteasome inhibitor is a suitable starting point for chemical optimization.

Keywords: covalent inhibitor; immunoproteasome; virtual screening; β5i selective inhibitor.

Figure 1

Hierarchical protocol used in the virtual screening of the boronic acid library.

Figure 2

Representative shift of the IC₅₀ curves for compound 1. The shift to the left is characteristic for the time-dependent type of enzyme inhibition.

Figure 3

Interactions of compound 1 docked into iCP, Protein Data Bank (PDB) code: 5M2B [16]; 1 is represented as a thick tube with carbon atoms in magenta. Interacting residues discussed in the text are in a thin tube, and other residues are in a wire representation. Interactions are shown with dashed lines: ionic interactions in magenta and hydrogen bonds in yellow.

Figure 4

X-ray structure of Ro19 (yellow) (PDB code: 5M2B [16]) and docked pose of compound 1 (magenta).