Aug 2026· Pure and Applied Chemistry· 0 citations· 62 references
TL;DR
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.
Abstract
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 1H NHMR, 13C 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 (IC50 = 2.4 ± 1.1 µM). Among them, oxadiazole derivative (13c) featuring 3-cyanophenyl substitution emerged as the most potent inhibitor with IC50 value of 0.06 ± 0.8 µM, followed by compounds (12b, IC50 = 0.3 ± 0.3 µM), (12e, IC50 = 0.4 ± 1.6 µM) and (13e, IC50 = 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.
The continuous evolution of SARS-CoV-2 and the emergence of drug-resistant variants underscore the urgent need for broad-spectrum antiviral agents targeting conserved viral proteins. The main protease (Mpro) represents a promising target due to its essential role in coronavirus replication. In this study, we report the discovery and optimization of a novel series of piperazine-based Mpro inhibitors using a multi-site binding strategy guided by analysis of conserved residues within the coronavirus Mpro active sites. Starting from the noncovalent lead GC-14, systematic optimization of substituents occupying the S1', S1, S2, and S4 subsites of Mpro led to the development of the noncovalent inhibitor GY-e2, which showed improved inhibitory efficacy against both SARS-CoV-2 and SARS-CoV Mpro. To further enhance its antiviral efficacy in cellular models, reactive warheads targeting C145 were incorporated into the scaffold to generate covalent inhibitors. This strategy yielded the isomeric compounds Y-U0-R and Y-U0-S, which displayed potent Mpro inhibition and markedly enhanced antiviral activity in SARS-CoV-2-infected Calu-3 cells. Moreover, both compounds exhibited broad-spectrum antiviral activity against other human coronaviruses, and notably remained effective against the two major Nirmatrelvir-resistant strains evaluated in this study. Mechanistic studies further confirmed kinetically stable binding and time-dependent inhibition of Y-U0-R, supporting the rationale of covalent inhibitor design. These findings highlight the utility of structure-based design for the development of promising broad-spectrum anti-coronavirus agents.
Bing Ye, M. Lee, Letian Song et al.· European journal of medicina...· 0 citations
This study provides binding details for the designed compounds and demonstrates the feasibility of the joint X-ray/neutron structure-assisted drug design approach to generate more potent noncovalent nonpeptidic SARS-CoV-2 MPro inhibitors.
Dipendra Bhandari, Katerina Kovalevskaya, L. Coates et al.· RSC Medicinal Chemistry· 0 citations
The main protease Mpro of SARS-CoV-2 is an important enzyme for the viral cycle and its inhibition affects replication and infection propagation. In this way, it has been reported as an excellent target for drug design. In this work, we discovered a low molecular weight non-peptide, heterocyclic inhibitor, that inactivates Mpro. Initially, we screened a focused chemical library of heterocyclic compounds against Mpro that included several cysteine protease inhibitors. A compound based on a 6-methoxypyrimidine scaffold was identified as an inhibitor of this enzyme and structure-activity relationship studies revealed all the important groups for Mpro inhibition. Optimization of the hit compound provided a small (306 g/mol) competitive inhibitor that inactivated Mpro activity, being non-promiscuous to other cysteine proteases such as PLpro, human CatL, and cruzain. PH521 (4f) presented increased potency against SARS-CoV-2 infection of cells being 20-fold more potent than the initial hit compound.
I. S. Fortes, M. Lopes, T. H. M. Fernandes et al.· Bioorganic chemistry (Print)· 0 citations
New SARS-CoV-2 Mpro small-molecule inhibitors endowed with a pyrimidine scaffold are designed and synthesized and the mechanism of action of the most promising compound was elucidated.
Salvatore Nieddu, Giuseppe Ruggieri, Riccardo De Santis et al.· ACS Infectious Diseases· 0 citations
This Account summarizes the group's effort to convert PLpro from a challenging target into a tractable antiviral drug-discovery platform and illustrates how integrated assay development, structural biology, medicinal chemistry, pharmacology, virology, and resistance analysis can transform a challenging viral deubiquitinase into a credible antiviral target.
Jun Wang, Kan Li, Bin Tan· Accounts of Chemical Researc...· 0 citations
Developing covalent inhibitors of the SARS-CoV-2 papain-like protease (PLpro) represents a promising therapeutic strategy, but translation of this approach into in vivo antiviral efficacy remains limited. A major challenge is the shallow and minimally druggable binding environment surrounding the catalytic cysteine, which reflects the enzyme's stringent requirement for P1 and P2 Gly-Gly recognition. In addition, many previously reported covalent PLpro inhibitors have relied on warheads or linker designs with limited metabolic stability or nonspecific thiol reactivity, restricting their progression toward in vivo efficacy. Here, we report the design and synthesis of a novel class of covalent PLpro inhibitors with low intrinsic GSH reactivity, enabled by a chloroalkyne warhead and an optimized linker strategy. The lead compound, ID3-77 (12), potently inhibits PLpro biochemically, demonstrates strong cellular antiviral activity, reduces viral load in a SARS-CoV-2 infection model, and exhibits minimal glutathione labeling. Jump-dilution experiments demonstrate reversible covalent inhibition, while profiling against the cysteine proteases cathepsin B and calpain demonstrates selectivity over these related proteases. Together, these findings establish chloroalkyne as a promising target-directed reversible covalent warhead for PLpro inhibition and provide in vivo proof-of-concept for this chemistry in antiviral drug discovery, with potential for broader application to other cysteine proteases.
Divakar Indukuri, J. G. Achi, Boopathi Sownthirarajan et al.· Bioorganic & Medicinal Chemi...· 0 citations
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