Severe Acute Respiratory Syndrome Coronavirus Papain-like Novel Protease Inhibitors: Design, Synthesis, Protein−Ligand X-ray Structure and Biological Evaluation

Abstract

The design, synthesis, X-ray crystal structure, molecular modeling, and biological evaluation of a series of new generation SARS-CoV PLpro inhibitors are described. A new lead compound 3 (6577871) was identified via high-throughput screening of a diverse chemical library. Subsequently, we carried out lead optimization and structure-activity studies to provide a series of improved inhibitors that show potent PLpro inhibition and antiviral activity against SARS-CoV infected Vero E6 cells. Interestingly, the (S)-Me inhibitor 15h (enzyme IC50 = 0.56 μM; antiviral EC50 = 9.1 μM) and the corresponding (R)-Me 15g (IC50 = 0.32 μM; antiviral EC50 = 9.1 μM) are the most potent compounds in this series, with nearly equivalent enzymatic inhibition and antiviral activity. A protein-ligand X-ray structure of 15g-bound SARS-CoV PLpro and a corresponding model of 15h docked to PLpro provide intriguing molecular insight into the ligand-binding site interactions.

Inhibitor Recognition Specificity of MERS-CoV Papain-like Protease May Differ from That of SARS-CoV

“…Mechanism of inhibition studies revealed that these compounds are mixed-type inhibitors with α values greater than 1, indicating that they bind to an allosteric site other than its catalytic site, but behave as if they are competitive inhibitors 35 . As noted above, these lead inhibitors bind to the flexible BL2 region and induce conformational changes to block substrate access to the catalytic site of the enzyme 27, 28 . There have been no MERS-PLpro inhibitors published to date; we have identified one compound ( 4 ) that inhibits both SARS-PLpro and MERS-PLpro.…”

Synergistic Inhibitor Binding to the Papain‐Like Protease of Human SARS Coronavirus: Mechanistic and Inhibitor Design Implications

“…[10] Unlike 3CLpro, the development of PLpro inhibitors has been very limited until recently, despite its essential role in SARS viral replication. In addition to our own work, [11] two very different types of PLpro inhibitors have been reported in recent years. First, 6-Mercaptopurine (6MP) and 6-thioguanine (6TG) were identified from compound screening with IC 50 values of 5 – 20 µM.…”

“…[11] Inhibitor 1 (GRL-0068S) has shown an inhibitory activity (IC 50 value) of 0.29 µM and antiviral activity (EC 50 ) of 5.2 µM (See Table 1 for inhibitor structures). Inhibitors 2 (GRL-0617S), 3 (GRL-0667S) and 4 (GRL-0737S) have exhibited inhibitory activities of 1.32 µM, 0.64 µM and 1.36 µM, with antiviral activities of 15 µM, 9.1 µM and 9.1 µM, respectively.…”

Papain-Like Protease (PLpro) Inhibitory Effects of Cinnamic Amides from <i>Tribulus terrestris</i> Fruits

“…[8][9][10] Thus, PLpro so serves as a model for development of drugs against other deubiquitinating enzymes involved in human diseases. 11) Importantly, endogenous deubiquitinating enzymes are now strongly linked to cancer and neurological disease development and in spite of a huge research effort, no deubiquitinating enzyme inhibitors are as yet even in clinical trials. 12) Tribulus terrestris LINN belongs to the family Zygophyllaceae and is distributed in warm regions throughout India and the southern part of China.…”

“…17) Many synthetic amide derivatives have been prepared as potential PLpro inhibitors, but no natural amide compounds have yet been shown to exhibit PLpro inhibition. 10,11) This encouraged us to search for PLpro inhibitors from T. terrestris because although it is most well known as a source of saponins, it is also known to contain cinnamic amides. 15) In this study, we isolated six SARS-CoV PLpro inhibitors from the fruits of T. terrestris using bioactivity guided fractionation.…”