5VK0

Crystal structure of human MDM2 in complex with a 12-mer lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 

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:  

  • 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 ...

    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

    School of Pharmacy , Second Military Medical University , Shanghai 200433 , China.,Changhai Hospital , Second Military Medical University , Shanghai 200433 , China . Email: drsujiacan@163.com.,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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase Mdm2
A, C, E, G, I, K, M, O, Q, S, U, W
85Homo sapiensMutation(s): 0 
Gene Names: MDM2
EC: 2.3.2.27
Find proteins for Q00987 (Homo sapiens)
Go to Gene View: MDM2
Go to UniProtKB:  Q00987
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lysine-cysteine side chain dithiocarbamate stapled peptide inhibitor PMI
B, D, F, H, J, L, N, P, R, T, V, X
14N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
C, X
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
B, D, F, H, J, L, N, P, R, T, V, X
NON-POLYMERH2 N

--

9E7
Query on 9E7
B, D, F, H, J, L, N, P, R, T, V, X
L-peptide linkingC7 H16 N2 O2 SLYS
ACE
Query on ACE
B, D, F, H, J, L, N, P, R, T, V, X
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 90.838α = 90.00
b = 157.470β = 90.00
c = 196.650γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01AI116274

Revision History 

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