8S4M

Crystal structure of Mycobacterium tuberculosis cytochrome P450 CYP125 in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.246 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Fragment-based development of small molecule inhibitors targeting Mycobacterium tuberculosis cholesterol metabolism.

Kavanagh, M.E.McLean, K.J.Gilbert, S.H.Amadi, C.Snee, M.Tunnicliffe, R.B.Arora, K.Boshoff, H.I.Fanourakis, A.Rebello-Lopez, M.J.Ortega-Muro, F.Levy, C.W.Munro, A.W.Leys, D.Abell, C.Coyne, A.G.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.10.28.620643
  • Primary Citation of Related Structures:  
    8S4M, 8S53

  • PubMed Abstract: 

    Mycobacterium tuberculosis ( Mtb ) is the world's most deadly infectious pathogen and new drugs are urgently required to combat the emergence of multi- (MDR) and extensively- (XDR) drug resistant strains. The bacterium specifically upregulates sterol uptake pathways in infected macrophages and the metabolism of host-derived cholesterol is essential for Mtb's long-term survival in vivo. Here, we report the development of antitubercular small molecules that inhibit the Mtb cholesterol oxidases CYP125 and CYP142, which catalyze the initial step of cholesterol metabolism. An efficient biophysical fragment screen was used to characterize the structure-activity relationships of CYP125 and CYP142, and identify a non-azole small molecule 1a that can bind to the heme cofactor of both enzymes. A structure-guided fragment-linking strategy was used to optimize the binding affinity of 1a , yielding a potent dual CYP125/142 inhibitor 5m (K D CYP125/CYP142 = 0.04/0.16 μM). Compound 5m potently inhibits the catalytic activity of CYP125 and CYP142 in vitro (K I values < 0.1 μM), and rapidly depletes Mtb intracellular ATP (IC 50 = 0.15 μM). The compound has antimicrobial activity against both drug susceptible and MDR Mtb ( MIC 99 values 0.4 - 1.5 μM ) in extracellular assays, and inhibits the growth of Mtb in human macrophages (MIC = 1.7 μM) with good selectivity over mammalian cytotoxicity (LD 50 ≥ 50 μM). The combination of small molecule inhibitors and structural data reported here provide useful tools to study the role of cholesterol metabolism in Mtb and are a promising step towards novel antibiotics targeting bioenergetic pathways, which could be used to help combat MDR-TB.


  • Organizational Affiliation

    Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Steroid C26-monooxygenase
A, B, C
418Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: cyp125cyp125A1Rv3545cMTCY03C7.11
EC: 1.14.15.29
UniProt
Find proteins for P9WPP1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPP1 
Go to UniProtKB:  P9WPP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPP1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B],
M [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
A1H47 (Subject of Investigation/LOI)
Query on A1H47

Download Ideal Coordinates CCD File 
N [auth C]~{N}-(1~{H}-indol-5-ylmethyl)-3-(pyridin-4-ylamino)benzamide
C21 H18 N4 O
SRUJVDMQDGZASI-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.246 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.899α = 90
b = 68.848β = 93.915
c = 144.124γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1H47Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release