9NIQ | pdb_00009niq

Structure of Candida albicans trehalose-6-phosphate synthase in complex with 4456


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 
    0.289 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.254 (Depositor) 

Starting Model: experimental
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Literature

Inhibitors of trehalose-6-phosphate synthase activity in fungal pathogens compromise thermal tolerance pathways.

Miao, Y.Yadav, V.Shadrick, W.Liu, J.Jenner, A.R.Nichols, C.B.Gee, C.Schafer, M.Tenor, J.L.Perfect, J.R.Lee, R.E.Brennan, R.G.Washington, E.J.

(2025) mBio : e0179525-e0179525

  • DOI: https://doi.org/10.1128/mbio.01795-25
  • Primary Citation of Related Structures:  
    9NIQ, 9NKB

  • PubMed Abstract: 

    Infections caused by fungal pathogens such as Candida and Cryptococcus are associated with high mortality rates, partly due to limitations in the current antifungal arsenal. This highlights the need for antifungal drug targets with novel mechanisms of action. The trehalose biosynthesis pathway is a promising antifungal drug target because trehalose biosynthesis is essential for virulence in Cryptococcus neoformans and Candida albicans and is also a mediator of fungal stress responses, such as thermotolerance. To exploit its untapped antifungal potentials, we screened the St. Jude 3-point pharmacophore library to identify small molecule inhibitors of the first enzyme in the trehalose biosynthesis pathway, trehalose-6-phosphate synthase (Tps1). Structure-guided optimization of a potent hit, SJ6675, yielded a water-soluble inhibitor named 4456dh. Employing biochemical, structural, and cell-based assays, we demonstrate that 4456dh inhibits Tps1 enzymatic activity, suppresses trehalose synthesis, and exerts a fungicidal effect. Notably, the structure of Tps1 in complex with 4456 reveals that 4456 occupies the substrate binding pocket. Importantly, 4456dh renders normally thermotolerant fungal pathogens unable to survive at elevated temperatures, which is critical as we investigate the emergence of fungi from the environment due to a warming climate. Overall, this work develops the water-soluble 4456dh as an early-stage antifungal drug that has a distinct mechanism of action compared to existing clinical antifungals.IMPORTANCEThe rise of fungal infections in recent years is alarming due to an increase in the vulnerable immunocompromised population, global temperature increase, and limited antifungal treatment options. One of the major hurdles in developing new drugs is the identification of fungal-specific antifungal drug targets due to highly conserved cellular machinery between fungi and humans. Here, we describe a small molecule inhibitor, 4456dh, of the trehalose biosynthesis pathway. This pathway is present in fungi but not in humans. Trehalose plays a critical role in stress responses such as thermotolerance in fungal pathogens and is essential for their virulence. We show that treatment with 4456dh blocks the production of trehalose and renders fungal cells inviable. Thus far, 4456dh is active against two fungal pathogens of critical importance, suggesting broad-spectrum activity.


  • Organizational Affiliation
    • Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha,alpha-trehalose-phosphate synthase [UDP-forming]497Candida albicans SC5314Mutation(s): 0 
Gene Names: TPS1CAALFM_CR05720WACaO19.13961CaO19.6640
EC: 2.4.1.15
UniProt
Find proteins for Q92410 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore Q92410 
Go to UniProtKB:  Q92410
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92410
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BYI (Subject of Investigation/LOI)
Query on A1BYI

Download Ideal Coordinates CCD File 
B [auth A]N-[(4M)-4-(1-methyl-1H-pyrazol-4-yl)-1,3-thiazol-2-yl]-2-(pyridin-2-yl)acetamide
C14 H13 N5 O S
WSCNLEAKCHOALM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free:  0.289 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 0.254 (Depositor) 
Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.553α = 90
b = 117.553β = 90
c = 134.011γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1P01AI104533

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references