title: Synergistic inhibitor binding to the papain-like protease of human SARS coronavirus: mechanistic and inhibitor design implications.
abstract: We previously developed two potent chemical classes that inhibit the essential papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus. In this study, we applied a novel approach to identify small fragments that act synergistically with these inhibitors. A fragment library was screened in combination with four previously developed lead inhibitors by fluorescence-based enzymatic assays. Several fragment compounds synergistically enhanced the inhibitory activity of the lead inhibitors by approximately an order of magnitude. Surface plasmon resonance measurements showed that three fragments bind specifically to the PLpro enzyme. Mode of inhibition, computational solvent mapping, and molecular docking studies suggest that these fragments bind adjacent to the binding site of the lead inhibitors and further stabilize the inhibitor-bound state. We propose potential next-generation compounds based on a computational fragment-merging approach. This approach provides an alternative strategy for lead optimization for cases in which direct co-crystallization is difficult.
authors.affiliation: Center for Pharmaceutical Biotechnology and Department of Medicinal Chemistry & Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA.
authors.forename: Hyun
authors.initials: H
authors.lastname: Lee
authors.forename: Shuyi
authors.initials: S
authors.lastname: Cao
authors.forename: Kirk E
authors.initials: KE
authors.lastname: Hevener
authors.forename: Lena
authors.initials: L
authors.lastname: Truong
authors.forename: Joseph L
authors.initials: JL
authors.lastname: Gatuz
authors.forename: Kavankumar
authors.initials: K
authors.lastname: Patel
authors.forename: Arun K
authors.initials: AK
authors.lastname: Ghosh
authors.forename: Michael E
authors.initials: ME
authors.lastname: Johnson
mesh_terms: D000998:Antiviral Agents / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D000086782:Coronavirus 3C Proteases; D003546:Cysteine Endopeptidases / Q000378:metabolism; D015195:Drug Design; D004357:Drug Synergism; D006801:Humans; D007700:Kinetics; D062105:Molecular Docking Simulation; D011480:Protease Inhibitors / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D045473:Severe acute respiratory syndrome-related coronavirus / Q000201:enzymology*; D054852:Small Molecule Libraries / Q000737:chemistry / Q000378:metabolism; D020349:Surface Plasmon Resonance; D014764:Viral Proteins / Q000037:antagonists & inhibitors* / Q000378:metabolism
chemical_list: D000998:Antiviral Agents; D011480:Protease Inhibitors; D054852:Small Molecule Libraries; D014764:Viral Proteins; D003546:Cysteine Endopeptidases; D000086782:Coronavirus 3C Proteases
keywords: fragments; human SARS coronavirus; inhibitors; papain-like protease; small molecules