5VK1

Crystal structure of human MDM4 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.281 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Dithiocarbamate-inspired side chain stapling chemistry for peptide drug design.

Li, X.Tolbert, W.D.Hu, H.G.Gohain, N.Zou, Y.Niu, F.He, W.X.Yuan, W.Su, J.C.Pazgier, M.Lu, W.

(2019) Chem Sci 10: 1522-1530

  • DOI: 10.1039/c8sc03275k
  • Primary Citation of Related Structures:  
    5VK1, 5VK0

  • PubMed Abstract: 
  • Two major pharmacological hurdles severely limit the widespread use of small peptides as therapeutics: poor proteolytic stability and membrane permeability. Importantly, low aqueous solubility also impedes the development of peptides for clinical use. Various elaborate side chain stapling chemistries have been developed for α-helical peptides to circumvent this problem, with considerable success in spite of inevitable limitations ...

    Two major pharmacological hurdles severely limit the widespread use of small peptides as therapeutics: poor proteolytic stability and membrane permeability. Importantly, low aqueous solubility also impedes the development of peptides for clinical use. Various elaborate side chain stapling chemistries have been developed for α-helical peptides to circumvent this problem, with considerable success in spite of inevitable limitations. Here we report a novel peptide stapling strategy based on the dithiocarbamate chemistry linking the side chains of residues Lys( i ) and Cys( i + 4) of unprotected peptides and apply it to a series of dodecameric peptide antagonists of the p53-inhibitory oncogenic proteins MDM2 and MDMX. Crystallographic studies of peptide-MDM2/MDMX complexes structurally validated the chemoselectivity of the dithiocarbamate staple bridging Lys and Cys at ( i , i + 4) positions. One dithiocarbamate-stapled PMI derivative, DTC PMI, showed a 50-fold stronger binding to MDM2 and MDMX than its linear counterpart. Importantly, in contrast to PMI and its linear derivatives, the DTC PMI peptide actively traversed the cell membrane and killed HCT116 tumor cells in vitro by activating the tumor suppressor protein p53. Compared with other known stapling techniques, our solution-based DTC stapling chemistry is simple, cost-effective, regio-specific and environmentally friendly, promising an important new tool for the development of peptide therapeutics with improved pharmacological properties including aqueous solubility, proteolytic stability and membrane permeability.


    Organizational Affiliation

    Institute of Human Virology and Department of Biochemistry and Molecular Biology , University of Maryland , School of Medicine , Baltimore , MD , USA . Email: mpazgier@ihv.umaryland.edu ; Email: wlu@ihv.umaryland.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein Mdm4 ACEGIKMO85Homo sapiensMutation(s): 3 
Gene Names: MDM4MDMX
Find proteins for O15151 (Homo sapiens)
Explore O15151 
Go to UniProtKB:  O15151
NIH Common Fund Data Resources
PHAROS:  O15151
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI BDFHJLNP14synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
9E7
Query on 9E7
B,D,F,H,J,L,N,PL-PEPTIDE LINKINGC7 H16 N2 O2 SLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.281 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.294α = 76.72
b = 47.73β = 89.92
c = 93.394γ = 72.6
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.2: 2019-03-13
    Changes: Data collection, Database references