Logo image
Back
Discovery of SARS-CoV-2 PLpro covalent inhibitors enabled by a novel reversible covalent chloroalkyne warhead
Journal article   Peer reviewed

Discovery of SARS-CoV-2 PLpro covalent inhibitors enabled by a novel reversible covalent chloroalkyne warhead

Divakar Indukuri, Jazmin Galván Achi, Boopathi Sownthirarajan, Malla Reddy Gannarapu, Omar Lozano Ramos, Kiira Ratia, Priyajit Kaur, Rishi Vardhan Chunduru, Zuohuang Qi, Paulina Anguiano, …
Bioorganic & medicinal chemistry, Vol.143(December 2026), 118792
08/29/2026
DOI: 10.1016/j.bmc.2026.118792
PMID: 42710463

View Online

Abstract

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. [Display omitted] •Chlorine substitution converts an irreversible terminal alkyne into a reversible covalent warhead with low GSH reactivity.•Structure-guided linker optimization yielded potent covalent PLpro inhibitors.•ID3–77 covalently labels catalytic Cys111 and shows strong cellular antiviral activity.•ID3–77 shows selectivity over the cysteine proteases cathepsin B and calpain 1.•ID3–77 reduces SARS-CoV-2 lung viral load in vivo.•Chloroalkyne provides a promising reversible covalent warhead for broader cysteine-targeted drug design.
 Antiviral agent Chloroalkyne Covalent inhibitors Cysteine protease PLpro SARS

Details

Metrics

3 Record Views
Logo image