7SDA | pdb_00007sda

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Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

(2023) J Med Chem 66: 11040-11055

PubMed Abstract:
SARS-CoV-2, the COVID-19 pathogen, relies on its main protease (M ^Pro) for replication and pathogenesis. M ^Pro is a demonstrated target for the development of antivirals for SARS-CoV-2. Past studies have systematically explored tripeptidyl inhibitors such as nirmatrelvir as M ^Pro inhibitors. However, dipeptidyl inhibitors especially those with a spiro residue at their P2 position have not been systematically investigated. In this work, we synthesized about 30 dipeptidyl M ^Pro inhibitors and characterized them on enzymatic inhibition potency, structures of their complexes with M ^Pro, cellular M ^Pro inhibition potency, antiviral potency, cytotoxicity, and in vitro metabolic stability. Our results indicated that M ^Pro has a flexible S2 pocket to accommodate inhibitors with a large P2 residue and revealed that dipeptidyl inhibitors with a large P2 spiro residue such as ( S )-2-azaspiro [4,4]nonane-3-carboxylate and ( S )-2-azaspiro[4,5]decane-3-carboxylate have favorable characteristics. One compound, MPI60, containing a P2 ( S )-2-azaspiro[4,4]nonane-3-carboxylate displayed high antiviral potency, low cellular cytotoxicity, and high in vitro metabolic stability.

Organizational Affiliation

Department of Chemistry, Texas A&M Drug Discovery Laboratory, Texas A&M University, College Station, Texas 77843, United States.

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
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Reference Sequence

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8UI (Subject of Investigation/LOI) Query on 8UI Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4,4-dimethyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide C₂₄ H₃₄ N₄ O₅ TTZNYKDOBZQMLD-DOXZYTNZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]