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8 protocols using gs 441524

1

Synthesis and Characterization of SARS-CoV-2 Inhibitors

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ALG-097161, nirmatrelvir, and PF-00835231 were synthesized by Aligos Therapeutics and purified to >95% purity. The synthesis of ALG-097161 is described in Text S1. GS-441524 was obtained from MedChem Express (catalog [cat.] no. HY-103586). The African green monkey kidney VeroE6 cell line was purchased from ATCC (cat. no. CRL-1586) and maintained in Dulbecco’s modified Eagle’s medium (DMEM; Gibco cat. no. 41965-039) supplemented with 10% (vol/vol) heat-inactivated fetal calf serum (FCS).
The SARS-CoV-2 GHB-03021 (EPI ISL407976|2020-02-03) isolate was obtained from a Belgian patient returning from Wuhan in February 2020. The isolate was passaged 7 times on VeroE6 cells, which introduced two series of amino acid deletions in the spike protein (37 (link)).
SARS-CoV-2 3CLpro wild-type and mutant enzymes were produced as previously described (38 (link)). Peptide substrate (Dabcyl-KTSAVLQSGFRKM-E(Edans)-NH2) for FRET was sourced from Biopeptide (San Diego, CA) at >95% purity.
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2

Screening Small-Molecule Inhibitors of ISG15

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The SmartTM chemical library was purchased from Chemdiv (San Diego, USA), which contains 50,080 small-molecule compounds with enhanced diversity and drug-like properties. Remdesivir and its prodrug GS-441524, as well as GRL0617 were purchased from MedChemExpress (NJ, USA). Arg-Leu-Arg-Gly-Gly-AMC (RLRGG-AMC) was purchased from Bachem Bioscience (Bubendorf, Switzerland). ISG15-AMC, ubiquitin-AMC, and HA-Ub-VS were purchased from R&D systems (Minneapolis, USA). Cellular protease assay kit (Cat# 539125) was purchased from Sigma-Aldrich. CellTiter-Glo cell viability assay kit was purchased from Promega. Other chemicals were purchased from Sigma-Aldrich unless specified.
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3

Antiviral Compound Characterization Protocol

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Formic acid and LC-MS grade acetonitrile were obtained from Fisher Scientific (Pittsburgh, PA, United States). Isopropyl alcohol and LC-MS grade methanol and acetonitrile were obtained from Sigma-Aldrich (St. Louis, MO, United States). Deionized water was generated using a Milli-Q Ultrapure water purification system from EMD Millipore (Billerica, MA, United States). GS-442524 and 13C5-GS-441524 (SIL-internal standard, SIL-IS) were ordered from AK Scientific (Union City, CA) and Cambridge Isotope Laboratories, Inc. (Tewksbury, MA), respectively. Control male C57BL6 mouse, Sprague Dawley rat, Cynomolgus monkey and Beagle dog plasmas were ordered from Bioreclamation IVT (Westbury, NY, United States). For Vero E6 CPE assay and EpiAirway efficacy study, GS-441524 and remdesivir were purchased from MedChem Express (Monmouth Junction, NJ), and EIDD-2801 was purchased from Cayman Chemical (Ann Arbor, MI).
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4

Molecular Docking of DDI in SARS-CoV-2 RdRp

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DDI (2′,3′-dideoxyinosine,
CAS registry number 69655-05-6) and remdesivir (GS-5734, CAS registry
number 1809249-37-3) were purchased from Biosynth Carbosynth (Carbosynth
Ltd., Berkshire, U.K.) (for DDI, product code ND02929, purity ≥98%;
for remdesivir, product code AG170167, purity ≥98%), whereas
the other reference compound GS-441524 (CAS registry number 1191237-69-0)
was purchased from MedChemExpress (MCE, MedChemExpress LLC, New Jersey,
U.S.A.) (catalog number HY-103586, purity 99.77%). The ultrapure solvent
dimethyl sulfoxide (DMSO, CAS registry number 67-68-5) was purchased
from a local distributor, El-Gomhouria Company For Drugs (El-Gomhouria
Co. For Trading Drugs, Chemicals & Medical Supplies, Mansoura
Branch, Egypt) (purity ≥99.9% “anhydrous”). The
simple and direct illustrative molecular docking of DDI in SARS-CoV-2
RdRp was performed utilizing a validated web server called COVID-19
Docking Server. This server uses AutoDock Vina 1.2.0 software as the
docking engine; the 3D structure of the SARS-CoV-2 RdRp (nsp12/7/8)
protein cocrystallized in a complex with RNA as well as the triphosphate
form of remdesivir (RTP) was obtained from the Protein Data Bank (PDB)
database with the code of 7BV2, employing the validated remdesivir docking protocol
as the comparison protocol for the ligand DDI.45
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5

Mung Bean Extract Compound Characterization

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Vigna radiata (L.) R. Wilczek extract (VRE) was provided by King’s Ground Biotech Co., Ltd. (Pingtung, Taiwan), following the preparation process outlined in the previous study, and the major components of VRE are vitexin and isovitexin (Lo et al. 2020 (link)). VRE was dissolved in DMSO and stored at −20 °C until use. GS-441524 (MedChemExpress) and GC376 (AdooQ Bioscience) were dissolved in DMSO and stored at −20 °C until use.
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6

Antiviral Drug Preparation and Storage

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The antiviral drugs GS-441524, teriflunomide, ritonavir, and nirmatrelvir utilized in this study were purchased from MedChemExpress (Princeton, NJ, USA). Ruxolitinib was obtained from InvivoGen (San Diego, CA, USA), while molnupiravir was sourced from Sigma-Aldrich (St. Louis, MO, USA). The antiviral compounds were dissolved or resuspended in dimethyl sulfoxide to prepare stock solutions (5 mM) of all six drugs. The stock solutions of the drugs were stored at −20 °C for Ruxolitinib and −80 °C for GS-441524, molnupiravir, nirmatrelvir, ritonavir, and teriflunomide. The drugs were further diluted to working concentrations using EMEM medium for experimental use.
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7

Evaluating Antiviral Compound Efficacy

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Active components of remdesivir and molnupiravir (i.e., GS-441524 and EIDD-1931), and nirmatrelvir (PF-07321332) were purchased from MedChemExpress. S-217622 (ensitrelvir) was kindly provided by Shionogi Co., Ltd. Compounds were dissolved in dimethyl sulfoxide (in vitro) or 0.5% methylcellulose (in vivo) prior to use.
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8

Synthesis and Characterization of Anti-COVID-19 Compounds

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Remdesivir was either purchased from MedChemExpress (cat# HY-104077, batch# 46182) or synthesized at Gilead Sciences, Inc. GS-441524 was either purchased from MedChemExpress (cat# HY-103586, batch# 62110) or synthesized at Gilead Sciences Inc. GS-621763 was synthesized at Gilead Sciences Inc:2 1H NMR (300 MHz, CHCl3-d3) δ 11.15 (bs, 1H), 8.27 (bs, 1H), 7.95 (s, 1H), 7.32 (m, 1H), 7.07 (m, 1H), 6.05 (d, J = 6.0 Hz, 1H), 5.44 (t, J = 5.1 Hz, 1H), 4.66 (t, J = 3.6 Hz, 1H), 4.32 (m, 2H), 2.73–2.52 (m, 3H), 1.27–1.14 (m, 18H). LC-MS (B) m/z = 502.2 [M + H], 500.1 [M – H]. All EIDD-2801/molnupiravir used in this study was provided by Gilead Sciences Inc., sourced from MedChemExpress.
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