Uncovering Flexible Active Site Conformations of SARS-CoV-2 3CL Proteases through Protease Pharmacophore Clusters and COVID-19 Drug Repurposing
Journal
ACS nano
Journal Volume
15
Journal Issue
1
Date Issued
2021
Author(s)
Pathak, Nikhil
Chen, Yun-Ti
Hsu, Yen-Chao
Hsu, Nung-Yu
Kuo, Chih-Jung
Tsai, Hui Ping
Huang, Chih-Heng
Chang, Yu-Hsiu
Liang, Po-Huang
Yang, Jinn-Moon
JAW-JOU KANG
Abstract
The infectious SARS-CoV-2 causes COVID-19, which is now a global pandemic. Aiming for effective treatments, we focused on the key drug target, the viral 3C-like (3CL) protease. We modeled a big dataset with 42 SARS-CoV-2 3CL protease-ligand complex structures from ∼98.7% similar SARS-CoV 3CL protease with abundant complex structures. The diverse flexible active site conformations identified in the dataset were clustered into six protease pharmacophore clusters (PPCs). For the PPCs with distinct flexible protease active sites and diverse interaction environments, we identified pharmacophore anchor hotspots. A total of 11 "PPC consensus anchors" (a distinct set observed in each PPC) were observed, of which three "PPC core anchors" EHV2, HV1, and V3 are strongly conserved across PPCs. The six PPC cavities were then applied in virtual screening of 2122 FDA drugs for repurposing, using core anchor-derived "PPC scoring S" to yield seven drug candidates. Experimental testing by SARS-CoV-2 3CL protease inhibition assay and antiviral cytopathic effect assays discovered active hits, Boceprevir and Telaprevir (HCV drugs) and Nelfinavir (HIV drug). Specifically, Boceprevir showed strong protease inhibition with micromolar IC50 of 1.42 μM and an antiviral activity with EC50 of 49.89 μM, whereas Telaprevir showed moderate protease inhibition only with an IC50 of 11.47 μM. Nelfinavir solely showed antiviral activity with a micromolar EC50 value of 3.28 μM. Analysis of binding mechanisms of protease inhibitors revealed the role of PPC core anchors. Our PPCs revealed the flexible protease active site conformations, which successfully enabled drug repurposing.
Subjects
FDA drug repurposing; SARS-CoV-2 3CL protease; core and consensus anchors; flexible active site conformations; protease pharmacophore clusters
SDGs
Other Subjects
Anchors; Complexation; Pharmacodynamics; Antiviral activities; Binding mechanisms; Cytopathic effect; Experimental testing; Interaction environment; Protease inhibition; Protease inhibitor; Virtual Screening; Diseases; 3C-like proteinase, SARS-CoV-2; antivirus agent; coronavirus spike glycoprotein; nelfinavir; oligopeptide; proteinase inhibitor; spike protein, SARS-CoV-2; telaprevir; animal; chemistry; Chlorocebus aethiops; drug repositioning; drug therapy; enzyme active site; enzymology; human; IC50; preclinical study; protein conformation; Vero cell line; Animals; Antiviral Agents; Catalytic Domain; Chlorocebus aethiops; Coronavirus 3C Proteases; COVID-19; Drug Evaluation, Preclinical; Drug Repositioning; Humans; Inhibitory Concentration 50; Nelfinavir; Oligopeptides; Protease Inhibitors; Protein Conformation; SARS-CoV-2; Spike Glycoprotein, Coronavirus; Vero Cells
Type
journal article