| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| primary antibodies: convalescent IgG fraction | a convalescent COVID-19 individual, reference S1 | N/A |
| secondary antibody: goat polyclonal anti-human-IgG-Alexa Fluor 488 Fab fragment antibody | Jackson ImmunoResearch Laboratories, Inc | Cat#109-547-003; RRID: AB_2337854 |
| Texas Red™-X dye conjugated Phalloidin | Thermo Fisher Scientific | Cat#T7471 |
| Bacterial and virus strains | ||
| JPN/TY/WK-521 (SARS-CoV-2WK-521) | National Institute of Infectious Diseases (Tokyo, Japan) | GISAID Accession ID; EPI_ISL_408667 |
| B.1.1.7 (alpha) strain [hCoV-19/Japan/QHN001/2020 (SARS-CoV-2QHN001)] | clinically isolated, National Institute of Infectious Diseases | GISAID Accession ID; EPI_ISL_804007) |
| B.1.351 (beta) strain [hCoV-19/Japan/TY8-612-P0/2021 (SARS-CoV-2TY8-612)] | clinically isolated, National Institute of Infectious Diseases | GISAID Accession ID; EPI_ISL_1123289 |
| P.1 (gamma) strain [hCoV-19/Japan/TY7-501-P0/2021 (SARS-CoV-2TY7-501)] | clinically isolated, National Institute of Infectious Diseases | GISAID Accession ID; EPI_ISL_833366 |
| B.1.617.2 (delta) strain [hCoV-19/Japan/TKYK01734/2021 (SARS-CoV-2K1734)] | clinically isolated, Tokyo Metropolitan Institute of public Health | GISAID Accession ID; EPI_ISL_2080609 |
| B.1.617.1 (kappa) strain [TKYTK5356_2021 (SARS-CoV-25356)] | clinically isolated, Tokyo Metropolitan Institute of public Health | GISAID Accession ID; EPI_ISL_2378733 |
| BA.1.1.529 (omicron BA.1) strain [hCoV-19/Japan/TKYX00012/2021 (SARS-CoV-2000129)] | clinically isolated, Tokyo Metropolitan Institute of public Health | GISAID Accession ID; EPI_ISL_8559478 |
| BA.1.1.529 (omicron BA.2) strain [hCoV-19/Japan/TKYS02037/2022 (SARS-CoV-202037)] | clinically isolated, Tokyo Metropolitan Institute of public Health | GISAID Accession ID; EPI_ISL_9397331 |
| Biological samples | ||
| BL21-CodonPlus(DE3)-RIL strain | Agilent | Cat#230245 |
| Chemicals, peptides, and recombinant proteins | ||
| SARS-CoV-2 Mpro/3CLpro | Hattori et al.19 | Accession #: MN908947 |
| Nirmatrelvir | MedChemExpress | HY-138687 |
| Remdesivir | Selleck | S8932 |
| Critical commercial assays | ||
| 3CL Protease, Untagged (SARS-CoV-2) Assay Kit | BPS Bioscience | Cat#78042-1 |
| QIAamp Viral RNA Mini QIAcube Kit | Qiagen | Cat#52926 |
| One Step PrimeScript III RT-qPCR mix | TaKaRa Bio | Cat# RR600B |
| Cell Counting Kit-8 | Dojindo | Cat# 341-08001 |
| Deposited data | ||
| SARS-CoV-2 Mpro-compound 3 co-crystal structure | This paper | PDB: 8DOY |
| Experimental models: Cell lines | ||
| VeroE6 cell | ATCC https://www.atcc.org/products/crl-1586 | Cat# ATCC CRL-1586 |
| Experimental models: Organisms/strains | ||
| Jcl:ICR (ICR) female mice | CLEA Japan | Cat# Jcl:ICR https://www.clea-japan.com/products/outbred/item_a0340 |
| Oligonucleotides | ||
| 5′-AAATTTTGGGGACCAGGAAC-3′ (forward) | SARS-CoV-2 nucleocapsid | Shirato et al.52 |
| 5′- TGGCAGCTGTGTAGGTCAAC-3′ (reverse) | SARS-CoV-2 nucleocapsid | Shirato et al.52 |
| 5′-FAM-ATGTCGCGCATTGGCATGGA-black hole quencher 1 (BHQ1)-3′ | SARS-CoV-2 nucleocapsid | Shirato et al.52 |
| Recombinant DNA | ||
| pGEX-4T1 vector (cloned into SARS-CoV2 Mpro-encoding sequence) | https://www.genscript.com/ | The sequence of SARS-CoV 3CL Protease was optimized and synthesized at GensSript and cloned into PGEX-4T1 vectors for E. Coli expression |
| Software and algorithms | ||
| QuantAnalysis Ver2.2.1 | Bruker Daltonics | Cat#1836735 |
| R software (version 4.0.5) | R Foundation for Statistical Computing | https://www.r-project.org/ |
| MolRep | Vagin and Teplyakov56 | https://www.ccp4.ac.uk/html/molrep.html |
| REFMAC5 | Murshudov et al.57 | https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ |
| Dundee PRODRG2 server | Schüttelkopf and van Aalten58 | http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg |
| ChemDraw Professional 18.0 | PerkinElmer | https://www.perkinelmer.com/category/chemdraw |
| GraphPad Prism 9 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| Other | ||
| preparative HPLC: JASCO PU-2086 plus/UV-2075 plus | JASCO Corporation | https://www.jasco.co.jp/jpn/product/index.html#LC |
| preparative HPLC: JASCO PU-2087 plus/UV-2075 plus | JASCO Corporation | https://www.jasco.co.jp/jpn/product/index.html#LC |
| preparative HPLC: JASCO PU-4086-Binary/UV-4075 | JASCO Corporation | https://www.jasco.co.jp/jpn/product/index.html#LC |
| analytical HPLC: JASCO PU-2089 plus/UV-2075 plus | JASCO Corporation | https://www.jasco.co.jp/jpn/product/index.html#LC |
| automatic silica gel flash column chromatography system (Isolera One) | Biotage | https://www.biotage.com/isolera-1-flash-chromatography-instrument |
| Pure C-815 | Buchi | https://www.buchi.com/en/products/instruments/pure-chromatography-systems |
| NMR: Bruker AVANCE III 400 spectrometer | Bruker Daltonics | https://www.bruker.com/en/products-and-solutions/mr/nmr.html |
| NMR: Bruker AVANCE 500 | Bruker Daltonics | https://www.bruker.com/en/products-and-solutions/mr/nmr.html |
| NMR: JNM-ECA500 | JEOL | https://www.jeol.co.jp/en/products/category_nmr.html |
| SPring-8 BL41XU | SPring-8 | http://www.spring8.or.jp/wkg/BL41XU/instrument/lang-en/INS-0000000328?set_language=en&cl=en |
| MS: micrOTOF focus | Bruker Daltonics | https://www.bruker.com/en/products-and-solutions/mass-spectrometry.html |
| LC-MS/MS: impact II | Bruker Daltonics | https://www.bruker.com/en/products-and-solutions/mass-spectrometry.html |
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