8UAC

CATHEPSIN L IN COMPLEX WITH AC1115


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Olgotrelvir, a dual inhibitor of SARS-CoV-2 M pro and cathepsin L, as a standalone antiviral oral intervention candidate for COVID-19.

Mao, L.Shaabani, N.Zhang, X.Jin, C.Xu, W.Argent, C.Kushnareva, Y.Powers, C.Stegman, K.Liu, J.Xie, H.Xu, C.Bao, Y.Xu, L.Zhang, Y.Yang, H.Qian, S.Hu, Y.Shao, J.Zhang, C.Li, T.Li, Y.Liu, N.Lin, Z.Wang, S.Wang, C.Shen, W.Lin, Y.Shu, D.Zhu, Z.Kotoi, O.Kerwin, L.Han, Q.Chumakova, L.Teijaro, J.Royal, M.Brunswick, M.Allen, R.Ji, H.Lu, H.Xu, X.

(2024) Med 5: 42-61.e23

  • DOI: https://doi.org/10.1016/j.medj.2023.12.004
  • Primary Citation of Related Structures:  
    8UAB, 8UAC

  • PubMed Abstract: 

    Oral antiviral drugs with improved antiviral potency and safety are needed to address current challenges in clinical practice for treatment of COVID-19, including the risks of rebound, drug-drug interactions, and emerging resistance. Olgotrelvir (STI-1558) is designed as a next-generation antiviral targeting the SARS-CoV-2 main protease (M pro ), an essential enzyme for SARS-CoV-2 replication, and human cathepsin L (CTSL), a key enzyme for SARS-CoV-2 entry into host cells. Olgotrelvir is a highly bioavailable oral prodrug that is converted in plasma to its active form, AC1115. The dual mechanism of action of olgotrelvir and AC1115 was confirmed by enzyme activity inhibition assays and co-crystal structures of AC1115 with SARS-CoV-2 M pro and human CTSL. AC1115 displayed antiviral activity by inhibiting replication of all tested SARS-CoV-2 variants in cell culture systems. Olgotrelvir also inhibited viral entry into cells using SARS-CoV-2 Spike-mediated pseudotypes by inhibition of host CTSL. In the K18-hACE2 transgenic mouse model of SARS-CoV-2-mediated disease, olgotrelvir significantly reduced the virus load in the lungs, prevented body weight loss, and reduced cytokine release and lung pathologies. Olgotrelvir demonstrated potent activity against the nirmatrelvir-resistant M pro E166 mutants. Olgotrelvir showed enhanced oral bioavailability in animal models and in humans with significant plasma exposure without ritonavir. In phase I studies (ClinicalTrials.gov: NCT05364840 and NCT05523739), olgotrelvir demonstrated a favorable safety profile and antiviral activity. Olgotrelvir is an oral inhibitor targeting M pro and CTSL with high antiviral activity and plasma exposure and is a standalone treatment candidate for COVID-19. Funded by Sorrento Therapeutics.


  • Organizational Affiliation

    ACEA Therapeutics, Inc., San Diego, CA 92121, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin L
A, B
220Homo sapiensMutation(s): 0 
Gene Names: CTSL
EC: 3.4.22.15
UniProt & NIH Common Fund Data Resources
Find proteins for P07711 (Homo sapiens)
Explore P07711 
Go to UniProtKB:  P07711
PHAROS:  P07711
GTEx:  ENSG00000135047 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07711
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W28 (Subject of Investigation/LOI)
Query on W28

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
N-[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-1H-indole-2-carboxamide
C22 H30 N4 O4
GSGDUCVRBYFHMQ-BQFCYCMXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.88α = 90
b = 76.46β = 90
c = 102.73γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Structure summary