7E6Q

Crystal structure of influenza A virus neuraminidase N5 complexed with 4'-phenyl-1,2,3-triazolylated oseltamivir carboxylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

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


Literature

Structure-based design of 5'-substituted 1,2,3-triazolylated oseltamivir derivatives as potent influenza neuraminidase inhibitors.

Wang, P.Oladejo, B.O.Li, C.Fu, L.Zhang, S.Qi, J.Lv, X.Li, X.

(2021) RSC Adv 11: 9528-9541

  • DOI: https://doi.org/10.1039/d1ra00472g
  • Primary Citation of Related Structures:  
    7E6Q

  • PubMed Abstract: 

    Resistant viruses containing mutant neuraminidases (NAs) with diminished drug affinity continue to emerge, and new anti-influenza agents are urgently required. Several potent inhibitors targeting the hydrophobic 150-cavity of viral NAs have been developed by modifying the antiviral drugs, oseltamivir carboxylate (OSC) and zanamivir, with hydrophobic groups. Here, we describe a different strategy for exploring novel and efficient NA inhibitors by targeting the charged amino acid residues around the entrance to the 150-cavity. We synthesized a C5-substituted OSC derivative (1e) with a 4'-phenyl-1,2,3-triazolyl group capable of entering the 150-cavity, and solved the crystal structure of 1e in complex with influenza A virus N5 NA. Using the resulting structural information, we next designed and synthesized two series of OSC derivatives carrying various polar substituents at the triazolyl group of 1e and 2e, with 2e being a 5'-phenyl-1,2,3-triazole regioisomer of 1e. The NA inhibition assays demonstrated that the 2 series (2e-n) generally had superior activity compared with the 1 series (1e-n). Compound 2j, bearing a 3-phenylamino group on the triazole ring, was the most potent inhibitor of all tested NAs including an N2 NA containing the E119V OSC-resistant mutation. Moreover, 2j potently inhibited viral replication in vitro , and molecular docking studies revealed that its phenylamino group can form an additional strong hydrogen bond with residue D151 near the entrance of the 150-cavity. The design method described in this study provides useful insights into the development of novel NA inhibitors. Compound 2j warrants further structural optimization to obtain a candidate for clinical use.


  • Organizational Affiliation

    CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS) Chaoyang District Beijing 100101 China wslvxun@163.com lixb@im.ac.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuraminidase
A, B
395Influenza A virus (A/duck/Alberta/60/1976(H12N5))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for A1ILL9 (Influenza A virus (strain A/Duck/Alberta/60/1976 H12N5))
Explore A1ILL9 
Go to UniProtKB:  A1ILL9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1ILL9
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HZF
Query on HZF

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
(3R,4R,5S)-4-acetamido-3-pentan-3-yloxy-5-(4-phenyl-1,2,3-triazol-1-yl)cyclohexene-1-carboxylic acid
C22 H28 N4 O4
GPEBJEGIHZQYIK-PWRODBHTSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.064α = 90
b = 109.064β = 90
c = 71.149γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary