8GIA

Crystal structure of SARS-CoV-2 (Covid-19) Nsp3 macrodomain in complex with TFMU-ADPr

8GIA の概要

• エントリーDOI: 10.2210/pdb8gia/pdb
• 分子名称: Non-structural protein 3, [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3S,4R,5R)-3,4-dihydroxy-5-{[2-oxo-4-(trifluoromethyl)-2H-1-benzopyran-7-yl]oxy}oxolan-2-yl]methyl dihydrogen diphosphate (3 entities in total)
• 機能のキーワード: macrodomain, sars-cov, viral protein
• 由来する生物種: Severe acute respiratory syndrome coronavirus 2
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 38094.42

構造登録者

Wallace, S.D.,Bagde, S.R.,Fromme, J.C. (登録日: 2023-03-13, 公開日: 2023-05-17, 最終更新日: 2023-10-25)

主引用文献

Anmangandla, A.,Jana, S.,Peng, K.,Wallace, S.D.,Bagde, S.R.,Drown, B.S.,Xu, J.,Hergenrother, P.J.,Fromme, J.C.,Lin, H.
A Fluorescence Polarization Assay for Macrodomains Facilitates the Identification of Potent Inhibitors of the SARS-CoV-2 Macrodomain.
Acs Chem.Biol., 18:1200-1207, 2023

PubMed Abstract: Viral macrodomains, which can bind to and/or hydrolyze adenine diphosphate ribose (ADP-ribose or ADPr) from proteins, have been suggested to counteract host immune response and be viable targets for the development of antiviral drugs. Therefore, developing high-throughput screening (HTS) techniques for macrodomain inhibitors is of great interest. Herein, using a novel tracer , an ADP-ribose compound conjugated with tetramethylrhodamine, we developed a robust fluorescence polarization assay for various viral and human macrodomains including SARS-CoV-2 Macro1, VEEV Macro, CHIKV Macro, human MacroD1, MacroD2, and PARP9 Macro2. Using this assay, we validated (IC 6.4 μM) and (IC 15.2 μM), two literature-reported small-molecule inhibitors of SARS-CoV-2 Macro1. Our data suggest that is highly selective for SARS-CoV-2 Macro1 over other human and viral macrodomains. Furthermore, using this assay, we identified (ADP-ribosylated -nitrophenol, IC 370 nM) and (ADP-ribosylated trifluoromethyl umbelliferone, IC 590 nM) as the most potent SARS-CoV-2 Macro1 binders reported to date. An X-ray crystal structure of SARS-CoV-2 Macro1 in complex with TFMU-ADPr revealed how the TFMU moiety contributes to the binding affinity. Our data demonstrate that this fluorescence polarization assay is a useful addition to the HTS methods for the identification of macrodomain inhibitors.

PubMed: 37126856
DOI: 10.1021/acschembio.3c00092

実験手法

X-RAY DIFFRACTION (1.86 Å)