9RHO

Structure of SARS-coV-2 NSP3 macrodomain in complex with ligand

This is a non-PDB format compatible entry.

Summary for 9RHO

• Entry DOI: 10.2210/pdb9rho/pdb
• Descriptor: Papain-like protease nsp3, [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] methyl hydrogen phosphate (3 entities in total)
• Functional Keywords: sars-cov-2, nsp3, macrodomain, viral protein, virus
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2)
• Total number of polymer chains: 2
• Total formula weight: 37367.94

Authors

Ruiz Carrillo, D.,Sander, S.,Tidow, H.,Garcia-Alai, M. (deposition date: 2025-06-09, release date: 2026-06-24, Last modification date: 2026-08-19)

Primary citation

Sandmann, M.,Tajdar, S.,Sander, S.,Ruiz Carrillo, D.,Ganter, B.,Fischer, C.,Ocenas, M.,Etzold, S.,Pekarek, N.,Berger, J.,Meister, T.L.,Selisko, B.,Canard, B.,Watt, J.M.,Baszczynski, O.,Potter, B.V.,Garcia Alai, M.,Henning, T.,Susanne, P.,Meier, C.,Fliegert, R.
Design, structure-based optimization and antiviral evaluation of potent inhibitors for the macrodomain Mac1 of SARS-CoV-2.
Nat Commun, 17:-, 2026

PubMed Abstract: Enzymatically active macrodomains of (+)ss-RNA viruses mediate immune evasion by countering ADP-ribosylation and are therefore promising druggable targets. Here we report testing of ADP / ADP-ribose analogues for their ability to inhibit Mac1 of SARS-CoV-2, measurement of the affinity of active compounds and characterization of their binding mode by cocrystallization, uncovering critical molecular determinants of protein-ligand interaction. Key findings of the resulting structure-activity relationship (SAR) include that inhibitory potency is improved by either replacing the distal ribose of ADP-ribose by a small alkyl group or the adenine N7 by carbon. Based on insights from the SAR, we show β-methyl-GS-441524-diphosphate as nanomolar inhibitor that exhibits >1000-fold selectivity over human MacroD1 and MacroD2. Addition of C-acyloxybenzyl (AB)-masking groups yields a membrane permeable, lipophilic prodrug that inhibits SARS-CoV-2 in cell culture (EC 0.06 µM) while exhibiting low cytotoxicity (CC > 50 µM). Replacement of the terminal methyl phosphate with an ethyl phosphonate increases stability of the prodrug with little effect on toxicity and antiviral potency (EC = 0.03 µM), making it a membrane-permeable nucleotide-based prodrug against viral macrodomains.

PubMed: 42509248
DOI: 10.1038/s41467-026-75835-7

Experimental method

X-RAY DIFFRACTION (1.6 Å)