4ZX3

X-ray crystal structure of PfA-M1 in complex with hydroxamic acid-based inhibitor 10b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions.

Drinkwater, N.Vinh, N.B.Mistry, S.N.Bamert, R.S.Ruggeri, C.Holleran, J.P.Loganathan, S.Paiardini, A.Charman, S.A.Powell, A.K.Avery, V.M.McGowan, S.Scammells, P.J.

(2016) Eur.J.Med.Chem. 110: 43-64

  • DOI: 10.1016/j.ejmech.2016.01.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Malaria remains a global health problem, and though international efforts for treatment and eradication have made some headway, the emergence of drug-resistant parasites threatens this progress. Antimalarial therapeutics acting via novel mechanisms a ...

    Malaria remains a global health problem, and though international efforts for treatment and eradication have made some headway, the emergence of drug-resistant parasites threatens this progress. Antimalarial therapeutics acting via novel mechanisms are urgently required. Plasmodium falciparum M1 and M17 are neutral aminopeptidases which are essential for parasite growth and development. Previous work in our group has identified inhibitors capable of dual inhibition of PfA-M1 and PfA-M17, and revealed further regions within the protease S1 pockets that could be exploited in the development of ligands with improved inhibitory activity. Herein, we report the structure-based design and synthesis of novel hydroxamic acid analogues that are capable of potent inhibition of both PfA-M1 and PfA-M17. Furthermore, the developed compounds potently inhibit Pf growth in culture, including the multi-drug resistant strain Dd2. The ongoing development of dual PfA-M1/PfA-M17 inhibitors continues to be an attractive strategy for the design of novel antimalarial therapeutics.


    Organizational Affiliation

    Discovery Biology, Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), Parkville, VIC 3052, Australia.,Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), Parkville, VIC 3052, Australia.,Dipartmento di Biologia e Biotecnologie "Charles Darwin", Sapienza Universita di Roma, 00185 Roma, Italy.,Biomedicine Discovery Institute and Department of Microbiology, Melbourne, VIC 3800, Australia; Department of Biochemistry and Molecular Biology Monash University (Clayton Campus), Melbourne, VIC 3800, Australia. Electronic address: Sheena.McGowan@monash.edu.,Biomedicine Discovery Institute and Department of Microbiology, Melbourne, VIC 3800, Australia; Department of Biochemistry and Molecular Biology Monash University (Clayton Campus), Melbourne, VIC 3800, Australia.,Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185 Roma, Italy.,Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), Parkville, VIC 3052, Australia. Electronic address: Peter.Scammells@monash.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
M1 family aminopeptidase
A
890Plasmodium falciparum (isolate FcB1 / Columbia)Mutation(s): 7 
EC: 3.4.11.-
Find proteins for O96935 (Plasmodium falciparum (isolate FcB1 / Columbia))
Go to UniProtKB:  O96935
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
4TK
Query on 4TK

Download SDF File 
Download CCD File 
A
N-[(1R)-1-(4-bromophenyl)-2-(hydroxyamino)-2-oxoethyl]-2,2-dimethylpropanamide
C13 H17 Br N2 O3
QSMFBPVNXFNEGF-SNVBAGLBSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4TKKi: 65 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.660α = 90.00
b = 109.090β = 90.00
c = 117.350γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
MOSFLMdata reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)Australia1063786

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Data collection, Database references, Derived calculations