Development of SARS-CoV-2 papain-like protease inhibitors with a thiadiazole and oxadiazole linker

Abstract

The ongoing prevalence of SARS-CoV-2 variations highlights the urgent need for novel antiviral agents targeting key viral proteins. The papain-like protease (PLpro) is pivotal in viral replication and immune evasion, rendering it a compelling therapeutic target. In the present study, a series of novel thiadiazole- and oxadiazole-based derivatives (12-g & 13a-g) were rationally designed based on the structural features of the known PLpro inhibitor GRL0617. Convergent synthetic strategy was employed to synthesize the target compounds involving the construction of 1,3,4-thiadiazole/oxadiazole intermediates followed by amide coupling with a naphthyl-containing scaffold. All compounds were characterized by ¹ H NHMR, ¹³ C NMR and mass spectrometry and evaluated for their in vitro SARS-CoV-2 PLpro inhibitory activity. Several compounds exhibited potent inhibition, surpassing the reference inhibitor GRL0617 (IC ₅₀  = 2.4 ± 1.1 µM). Among them, oxadiazole derivative (13c) featuring 3-cyanophenyl substitution emerged as the most potent inhibitor with IC ₅₀ value of 0.06 ± 0.8 µM, followed by compounds (12b, IC ₅₀  = 0.3 ± 0.3 µM), (12e, IC ₅₀  = 0.4 ± 1.6 µM) and (13e, IC ₅₀  = 0.6 ± 0.8 µM) respectively. Structure activity relationship (SAR) analysis revealed that electron-withdrawing substituents, particularly cyano group at meta position, significantly enhanced PLpro inhibition whereas methoxy/methyl groups resulted in reduced inhibition. Furthermore, molecular docking studies demonstrated favorable binding interactions of the compounds within the PLpro catalytic pocket through H-bonding, hydrophobic and π–π interactions. Moreover, molecular dynamic simulations confirmed the stability of the ligand-protein complexes throughout the simulation period supporting the experimental findings. The integrated rational design-based synthesis, biological evaluation, and computational investigations collectively identified thiadiazole/oxadiazole scaffolds as promising candidates for the development of SARS-CoV-2 inhibitors, offering valuable insights for next-generation antiviral agents targeting coronavirus proteases.