6NE5

Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors that Demonstrate in vivo Activity in Mouse Xenograft Models of Human Cancer

  • Classification: APOPTOSIS
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli K-12

  • Deposited: 2018-12-17 Released: 2019-04-17 
  • Deposition Author(s): Zhao, B.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors That Demonstrate in Vivo Activity in Mouse Xenograft Models of Human Cancer.

Lee, T.Christov, P.P.Shaw, S.Tarr, J.C.Zhao, B.Veerasamy, N.Jeon, K.O.Mills, J.J.Bian, Z.Sensintaffar, J.L.Arnold, A.L.Fogarty, S.A.Perry, E.Ramsey, H.E.Cook, R.S.Hollingshead, M.Davis Millin, M.Lee, K.M.Koss, B.Budhraja, A.Opferman, J.T.Kim, K.Arteaga, C.L.Moore, W.J.Olejniczak, E.T.Savona, M.R.Fesik, S.W.

(2019) J.Med.Chem. 62: 3971-3988

  • DOI: 10.1021/acs.jmedchem.8b01991

  • PubMed Abstract: 
  • Overexpression of myeloid cell leukemia-1 (Mcl-1) in cancers correlates with high tumor grade and poor survival. Additionally, Mcl-1 drives intrinsic and acquired resistance to many cancer therapeutics, including B cell lymphoma 2 family inhibitors, ...

    Overexpression of myeloid cell leukemia-1 (Mcl-1) in cancers correlates with high tumor grade and poor survival. Additionally, Mcl-1 drives intrinsic and acquired resistance to many cancer therapeutics, including B cell lymphoma 2 family inhibitors, proteasome inhibitors, and antitubulins. Therefore, Mcl-1 inhibition could serve as a strategy to target cancers that require Mcl-1 to evade apoptosis. Herein, we describe the use of structure-based design to discover a novel compound (42) that robustly and specifically inhibits Mcl-1 in cell culture and animal xenograft models. Compound 42 binds to Mcl-1 with picomolar affinity and inhibited growth of Mcl-1-dependent tumor cell lines in the nanomolar range. Compound 42 also inhibited the growth of hematological and triple negative breast cancer xenografts at well-tolerated doses. These findings highlight the use of structure-based design to identify small molecule Mcl-1 inhibitors and support the use of 42 as a potential treatment strategy to block Mcl-1 activity and induce apoptosis in Mcl-1-dependent cancers.


    Organizational Affiliation

    Department of Cell and Molecular Biology , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 , United States.,Chemical Synthesis Core, Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37232 , United States.,Department of Hematology and Oncology , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States.,Leidos Biomedical Research , Frederick National Laboratory for Cancer Research , Frederick , Maryland 21701 , United States.,National Cancer Institute , Bethesda , Maryland 20892 , United States.,Department of Medicine , Vanderbilt-Ingram Cancer Center , Nashville , Tennessee 37232 , United States.,Department of Biochemistry , Vanderbilt University School of Medicine , 2215 Garland Avenue, 607 Light Hall , Nashville , Tennessee 37232-0146 , United States.,Department of Cell and Developmental Biology , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Induced myeloid leukemia cell differentiation protein Mcl-1
A, B, C, D
159Homo sapiensMutation(s): 0 
Gene Names: MCL1 (BCL2L3)
Find proteins for Q07820 (Homo sapiens)
Go to Gene View: MCL1
Go to UniProtKB:  Q07820
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KJP
Query on KJP

Download SDF File 
Download CCD File 
A, B, C, D
3-[(4R)-7-chloro-10-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-4-methyl-1-oxo-6-(1,3,5-trimethyl-1H-pyrazol-4-yl)-3,4-dihydropyrazino[1,2-a]indol-2(1H)-yl]-1-methyl-1H-indole-5-carboxylic acid
C39 H39 Cl2 N5 O4
BSAYHBZFNXDOIJ-JOCHJYFZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.332α = 90.00
b = 135.942β = 95.95
c = 60.051γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-12-17 
  • Released Date: 2019-04-17 
  • Deposition Author(s): Zhao, B.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesHHSN261200800001E
National Institutes of Health/National Cancer InstituteUnited StatesP50CA098131

Revision History 

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-08
    Type: Data collection, Database references