9GCX

Crystal structure of bovine Cytochrome bc1 in complex with inhibitor F8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.188 

Starting Model: experimental
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Literature

Novel antimalarial 3-substituted quinolones isosteres with improved pharmacokinetic properties.

Ge, S.Jian, R.Xuan, Q.Zhu, Y.Ren, X.Li, W.Chen, X.Huang, R.K.Lee, C.S.Leung, S.C.Basilico, N.Parapini, S.Taramelli, D.Pinthong, N.Antonyuk, S.V.O'Neill, P.M.Sheng, Z.Hong, W.D.

(2024) Eur J Med Chem 284: 117228-117228

  • DOI: https://doi.org/10.1016/j.ejmech.2024.117228
  • Primary Citation of Related Structures:  
    9GCX

  • PubMed Abstract: 

    Aryl quinolone derivatives can target the cytochrome bc 1 complex of Plasmodium falciparum, exhibiting excellent in vitro and in vivo antimalarial activity. However, their clinical development has been hindered due to their poor aqueous solubility profiles. In this study, a series of bioisosteres containing saturated heterocycles fused to a 4-pyridone ring were designed to replace the inherently poorly soluble quinolone core in antimalarial quinolones with the aim to reduce π-π stacking interactions in the crystal packing solid state, and a synthetic route was developed to prepare these alternative core derivatives. One such novel derivate, F14, exhibited significant enhancements in both aqueous solubility (20 μM) and lipophilicity (LogD 2.7), whilst retaining nanomolar antimalarial activity against the W2 strain of P. falciparum (IC 50  = 235 nM). The pharmacokinetic studies reported, provide preliminary insights into the in vivo distribution and elimination of F14, while findings from single crystal X-ray diffraction experiment rationalized the enhanced solubility. Protein X-ray crystallography and in silico docking simulations provide insight into the potential mode of action within the cytochrome bc 1 complex. These findings demonstrated the viability of this bioisostere replacement strategy and provided support for further exploration of in vivo efficacy in preclinical animal models and valuable insights for new drug design strategies in the fight against malaria.


  • Organizational Affiliation

    School of Pharmacy and Food Engineering, Wuyi University, 529020, Jiangmen, China; Department of Chemistry, University of Liverpool, L69 7ZD, Liverpool, UK; Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong Special Administrative Region of China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrial480Bos taurusMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrial453Bos taurusMutation(s): 0 
UniProt
Find proteins for P23004 (Bos taurus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b379Bos taurusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrial325Bos taurusMutation(s): 0 
EC: 7.1.1.8
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrial
E, I
274Bos taurusMutation(s): 0 
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7111Bos taurusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 882Bos taurusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrial109Bos taurusMutation(s): 0 
UniProt
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UniProt GroupA0A452DIC1
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 964Bos taurusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1056Bos taurusMutation(s): 0 
UniProt
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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M [auth A],
Q [auth C],
W [auth D]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
PSC
Query on PSC

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Z [auth E](7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE
C42 H81 N O8 P
JLPULHDHAOZNQI-AUSZDXHESA-O
LOP
Query on LOP

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BA [auth G]
L [auth A]
P [auth C]
S [auth C]
T [auth C]
BA [auth G],
L [auth A],
P [auth C],
S [auth C],
T [auth C],
Y [auth E]
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
C35 H68 N O8 P
FUUNMZKPCMPCHT-ILGKRYBBSA-N
HEC
Query on HEC

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V [auth D]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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N [auth C],
O [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
LMT
Query on LMT

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U [auth C]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
A1IKG
Query on A1IKG

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R [auth C]2-methyl-3-(4-(4-(trifluoromethoxy)phenoxy)phenyl)-1,5,7,8-tetrahydro-4H-pyrano[4,3-b]pyridin-4-one
C22 H18 F3 N O4
KAKRHIRXYVSXMS-FQEVSTJZSA-N
FES
Query on FES

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X [auth E]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
SO4
Query on SO4

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AA [auth F],
CA [auth G],
DA [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.188 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.082α = 90
b = 210.082β = 90
c = 344.844γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release