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Structure paper

TitleC-2 Thiophenyl Tryptophan Trimers Inhibit Cellular Entry of SARS-CoV-2 through Interaction with the Viral Spike (S) Protein.
Journal, issue, pagesJ Med Chem, Vol. 66, Issue 15, Page 10432-10457, Year 2023
Publish dateAug 10, 2023
AuthorsMarta Gargantilla / Clara Francés / Anmol Adhav / Alicia Forcada-Nadal / Belén Martínez-Gualda / Olaia Martí-Marí / María Luisa López-Redondo / Roberto Melero / Clara Marco-Marín / Nadine Gougeard / Carolina Espinosa / Antonio Rubio-Del-Campo / Rafael Ruiz-Partida / María Del Pilar Hernández-Sierra / Laura Villamayor-Belinchón / Jerónimo Bravo / José-Luis Llacer / Alberto Marina / Vicente Rubio / Ana San-Félix / Ron Geller / María-Jesús Pérez-Pérez /
PubMed AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, by infecting cells via the interaction of its spike protein (S) with the primary cell receptor angiotensin-converting ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, by infecting cells via the interaction of its spike protein (S) with the primary cell receptor angiotensin-converting enzyme (ACE2). To search for inhibitors of this key step in viral infection, we screened an in-house library of multivalent tryptophan derivatives. Using VSV-S pseudoparticles, we identified compound as a potent entry inhibitor lacking cellular toxicity. Chemical optimization of rendered compounds and , which also potently inhibited genuine SARS-CoV-2 cell entry. Thermofluor and microscale thermophoresis studies revealed their binding to S and to its isolated receptor binding domain (RBD), interfering with the interaction with ACE2. High-resolution cryoelectron microscopy structure of S, free or bound to , shed light on cell entry inhibition mechanisms by these compounds. Overall, this work identifies and characterizes a new class of SARS-CoV-2 entry inhibitors with clear potential for preventing and/or fighting COVID-19.
External linksJ Med Chem / PubMed:37471688 / PubMed Central
MethodsEM (single particle)
Resolution3.4 - 4.3 Å
Structure data

17576

8p99

EMDB-17576, PDB-8p99:
SARS-CoV-2 S-protein:D614G mutant in 1-up conformation
Method: EM (single particle) / Resolution: 3.4 Å

17578

8p9y

EMDB-17578, PDB-8p9y:
SARS-CoV-2 S protein S:D614G mutant in 3-down with binding site of an entry inhibitor
Method: EM (single particle) / Resolution: 4.3 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-NA:
Unknown entry

ChemComp-XIO:
[(2~{S})-2-[[4-(2-azanylethanoylamino)-7-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-4-[3-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-3-oxidanylidene-propyl]-7-oxidanylidene-heptanoyl]amino]-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]propanoyl]oxysodium

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / Spike / SARS COV-2 / Inhibitor

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