Jun13296 for COVID-19

ABSTRACT Antiviral drugs have been approved for the treatment of COVID‐19. However, they present pharmacological limitations, a mixed efficacy profile and target just two coronavirus proteins. To extend the range of druggable coronavirus proteins, researchers explored small molecule N‐glycan binders as inhibitors of SARS‐CoV‐2 spike protein interaction with the cell receptor. Other groups investigated lipopeptides as inhibitors of cell fusion by viral spikes. High throughput screening of chemical libraries yielded viral maturation inhibitors that targeted the viral M protein. Massive screening led to inhibitors of the non‐structural coronavirus protein NSP14, a methyltransferase involved in viral mRNA cap synthesis. Machine learning–driven scans of chemical space revealed inhibitors of non‐structural coronavirus protein NSP3, a papain‐like protease subverting innate immune response to viral infection. A chimera of a nucleotide analogue coupled to an RNase L attractor bound the RNA‐dependent RNA polymerase NSP12 and mediated degradation of the viral RNA. Several of these compounds showed comparable or even superior antiviral efficacy as approved COVID‐19 drugs in preclinical animal tests. Parallel efforts were made to develop chemical compounds targeting host proteins needed for viral multiplication. Peptidomimetic tetrapeptides acted as inhibitors of the host protease TMPRSS2 involved in cell fusion by the viral spike protein. A repurposed TMPRSS2 inhibitor was tested in COVID‐19 patients without demonstrating efficacy. A genetic screen demonstrated an enzyme involved in sphingomyelin synthesis and its inhibitor which impaired SARS‐CoV‐2 replication. A viral‐cell protein interactome study showed 332 cellular proteins interacting with 26 coronaviral proteins. A chemoinformatic search found inhibitors for the interaction of NSP9 with host elongation factor eIF4A and for NSP13 with elongation factor eEF1A. Plitidepsin, a clinically used eEF1A inhibitor, was tested in human clinical trials with COVID‐19 patients demonstrating in vivo antiviral activity and a trend for clinical amelioration in an underpowered phase 3 clinical trial.

Papain-like protease (PLpro), a crucial functional domain of the SARS-CoV-2 non-structural protein 3 (nsp3), plays a dual role in both hydrolyzing viral polyprotein precursors and modulating host immune responses. These critical functions position PLpro as a key target in the ongoing development of antiviral therapies for SARS-CoV-2. This review analyzes more than 100 PLpro-ligand co-crystal structures and summarizes the major binding modes between these ligands and PLpro. Most of these ligands bind to sites analogous to those targeted by the classical non-covalent inhibitor GRL0617, primarily involving the P3 and P4 subsites and the BL2 loop. Based on these structural insights, optimized inhibitors have expanded targeting beyond the canonical binding site to auxiliary regions such as the BL2 groove and the Val70 site, and in some cases toward the catalytic Cys111 buried within a narrow pocket. Certain ligands identified through various screening approaches bind to non-canonical or allosteric regions, such as the S1 and S2 sites or the zinc-finger domain, engaging PLpro through distinct interaction modes and thereby offering additional opportunities for PLpro inhibitor design. The review also discusses potential strategies for future PLpro inhibitor development informed by recent structural advances. Taken together, these structural and functional insights support ongoing efforts in the structure-guided design and optimization of PLpro inhibitors.