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
  • Mutation(s): No 

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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
  • Primary Citation of Related Structures:  
    6NE5

  • 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, proteasome inhibitors, and antitubulins ...

    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 Biochemistry , Vanderbilt University School of Medicine , 2215 Garland Avenue, 607 Light Hall , Nashville , Tennessee 37232-0146 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1A, B, C, D159Homo sapiensMutation(s): 0 
Gene Names: MCL1BCL2L3
UniProt & NIH Common Fund Data Resources
Find proteins for Q07820 (Homo sapiens)
Explore Q07820 
Go to UniProtKB:  Q07820
PHAROS:  Q07820
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KJP (Subject of Investigation/LOI)
Query on KJP

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
KJP Binding MOAD:  6NE5 Ki: 0.06 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.332α = 90
b = 135.942β = 95.95
c = 60.051γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



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 Institute (NIH/NCI)United StatesHHSN261200800001E
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP50CA098131

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence