8TBE

Co-crystal structure of SARS-CoV-2 Mpro with Pomotrelvir

PDB DOI: https://doi.org/10.2210/pdb8TBE/pdb

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-06-28 Released: 2023-08-09
Deposition Author(s): Olland, A., Fontano, E., White, A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.299
R-Value Work: 0.229
R-Value Observed: 0.232

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Evaluation of in vitro antiviral activity of SARS-CoV-2 M pro inhibitor pomotrelvir and cross-resistance to nirmatrelvir resistance substitutions.

Tong, X., Keung, W., Arnold, L.D., Stevens, L.J., Pruijssers, A.J., Kook, S., Lopatin, U., Denison, M., Kwong, A.D.

(2023) Antimicrob Agents Chemother 67: e0084023-e0084023

PubMed: 37800975 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/aac.00840-23
Primary Citation of Related Structures:
8TBE

PubMed Abstract:
The unprecedented scale of the COVID-19 pandemic and the rapid evolution of SARS-CoV-2 variants underscore the need for broadly active inhibitors with a high barrier to resistance. The coronavirus main protease (M ^pro) is an essential cysteine protease required for viral polyprotein processing and is highly conserved across human coronaviruses. Pomotrelvir is a novel M ^pro inhibitor that has recently completed a phase 2 clinical trial. In this report, we demonstrated that pomotrelvir is a potent competitive inhibitor of SARS-CoV-2 M ^pro with high selectivity against human proteases. In the enzyme assay, pomotrelvir is also active against M ^pro proteins derived from human coronaviruses CoV-229E, CoV-OC43, CoV-HKU1, CoV-NL63, MERS, and SARS-CoV. In cell-based SARS-CoV-2 replicon and SARS-CoV-2 infection assays, pomotrelvir has shown potent inhibitory activity and is broadly active against SARS-CoV-2 clinical isolates including Omicron variants. Many resistance substitutions of the M ^pro inhibitor nirmatrelvir confer cross-resistance to pomotrelvir, consistent with the finding from our enzymatic analysis that pomotrelvir and nirmatrelvir compete for the same binding site. In a SARS-CoV-2 infection assay, pomotrelvir is additive when combined with remdesivir or molnupiravir, two nucleoside analogs targeting viral RNA synthesis. In conclusion, our results from the in vitro characterization of pomotrelvir antiviral activity support its further clinical development as an alternative COVID-19 therapeutic option.

Organizational Affiliation

Pardes Biosciences, Inc. , Carlsbad, California, USA.

Macromolecule Content

Total Structure Weight: 68.57 kDa
Atom Count: 5,098
Modelled Residue Count: 610
Deposited Residue Count: 612
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZQB (Subject of Investigation/LOI) Query on ZQB Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	Pomotrelvir bound form C₂₃ H₂₈ Cl N₅ O₃ IOEBZYOQTDUOBG-UZWGZPNFSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]