Andre Schutzer Godoy / Aline Minalli Nakamura / Alice Douangamath / Yun Song / Gabriela Dias Noske / Victor Oliveira Gawriljuk / Rafaela Sachetto Fernandes / Humberto D Muniz Pereira / Ketllyn Irene Zagato Oliveira / Daren Fearon / Alexandre Dias / Tobias Krojer / Michael Fairhead / Alisa Powell / Louise Dunnet / Jose Brandao-Neto / Rachael Skyner / Rod Chalk / Dávid Bajusz / Miklós Bege / Anikó Borbás / György Miklós Keserű / Frank von Delft / Glaucius Oliva /
PubMed Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and plays a critical role in the ability of the virus to evade the immune system. NendoU is a promising target for the development of new antiviral drugs. However, the complexity of the enzyme's structure and kinetics, along with the broad range of recognition sequences and lack of structural complexes, hampers the development of inhibitors. Here, we performed enzymatic characterization of NendoU in its monomeric and hexameric form, showing that hexamers are allosteric enzymes with a positive cooperative index, and with no influence of manganese on enzymatic activity. Through combining cryo-electron microscopy at different pHs, X-ray crystallography and biochemical and structural analysis, we showed that NendoU can shift between open and closed forms, which probably correspond to active and inactive states, respectively. We also explored the possibility of NendoU assembling into larger supramolecular structures and proposed a mechanism for allosteric regulation. In addition, we conducted a large fragment screening campaign against NendoU and identified several new allosteric sites that could be targeted for the development of new inhibitors. Overall, our findings provide insights into the complex structure and function of NendoU and offer new opportunities for the development of inhibitors.
EMDB-24392, PDB-7rb2: Cryo-EM structure of SARS-CoV-2 NSP15 NendoU in BIS-Tris pH 6.0 Method: EM (single particle) / Resolution: 3.27 Å
PDB-5s6x: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z2889976755 Method: X-RAY DIFFRACTION / Resolution: 2.32 Å
PDB-5s6y: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z56900771 Method: X-RAY DIFFRACTION / Resolution: 2.32 Å
PDB-5s6z: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with PB2255187532 Method: X-RAY DIFFRACTION / Resolution: 2.28 Å
PDB-5s70: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with EN300-181428 Method: X-RAY DIFFRACTION / Resolution: 2.327 Å
PDB-5s71: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with FUZS-5 Method: X-RAY DIFFRACTION / Resolution: 1.941 Å
PDB-5s72: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with BBL029427 Method: X-RAY DIFFRACTION / Resolution: 2.512 Å
PDB-5sa4: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z239136710 Method: X-RAY DIFFRACTION / Resolution: 2.046 Å
PDB-5sa5: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z1530301542 Method: X-RAY DIFFRACTION / Resolution: 2.09 Å
PDB-5sa6: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z2856434783 Method: X-RAY DIFFRACTION / Resolution: 2.517 Å
PDB-5sa7: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z1673618163 Method: X-RAY DIFFRACTION / Resolution: 2.222 Å
PDB-5sa8: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z68299550 Method: X-RAY DIFFRACTION / Resolution: 2.298 Å
PDB-5sa9: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z2697514548 Method: X-RAY DIFFRACTION / Resolution: 1.92 Å
PDB-5saa: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z319891284 Method: X-RAY DIFFRACTION / Resolution: 2.239 Å
PDB-5sab: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z31504642 Method: X-RAY DIFFRACTION / Resolution: 2.486 Å
PDB-5sac: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z59181945 Method: X-RAY DIFFRACTION / Resolution: 2.029 Å
PDB-5sad: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z425449682 Method: X-RAY DIFFRACTION / Resolution: 1.961 Å
PDB-5sae: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z3219959731 Method: X-RAY DIFFRACTION / Resolution: 2.12 Å
PDB-5saf: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with EN300-321461 Method: X-RAY DIFFRACTION / Resolution: 2.11 Å
PDB-5sag: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with EN300-1605072 Method: X-RAY DIFFRACTION / Resolution: 1.881 Å
PDB-5sah: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with EN300-100112 Method: X-RAY DIFFRACTION / Resolution: 2.16 Å
PDB-5sai: PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z1424343998 Method: X-RAY DIFFRACTION / Resolution: 2.022 Å
PDB-5sbf: PanDDA analysis group deposition of ground-state model of SARS-CoV-2 NendoU Method: X-RAY DIFFRACTION / Resolution: 1.64 Å
PDB-7keg: Crystal structure from SARS-COV2 NendoU NSP15 Method: X-RAY DIFFRACTION / Resolution: 2.9 Å
PDB-7keh: Crystal structure from SARS-CoV-2 NendoU NSP15 Method: X-RAY DIFFRACTION / Resolution: 2.59 Å
PDB-7kf4: Crystal structure from SARS-CoV-2 NendoU NSP15 Method: X-RAY DIFFRACTION / Resolution: 2.61 Å
PDB-7n7r: Crystal Structure of SARS-CoV-2 NendoU in complex with Z2472938267 Method: X-RAY DIFFRACTION / Resolution: 2.01 Å
PDB-7n7u: Crystal Structure of SARS-CoV-2 NendoU in complex with LIZA-7 Method: X-RAY DIFFRACTION / Resolution: 2.06 Å
PDB-7n7w: Crystal Structure of SARS-CoV-2 NendoU in complex with CSC000178569 Method: X-RAY DIFFRACTION / Resolution: 2.42 Å
PDB-7n7y: Crystal Structure of SARS-CoV-2 NendoU in complex with Z18197050 Method: X-RAY DIFFRACTION / Resolution: 2.09 Å
PDB-7n83: Crystal Structure of SARS-CoV-2 NendoU in complex with Z2443429438 Method: X-RAY DIFFRACTION / Resolution: 1.91 Å
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HYDROLASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / nsp15 / nendoU / 
