VTP-50469 is a novel, orally-available Menin-MLL1 inhibitor effective against MLL-rearranged
and NPM1c+ leukemiaAndrei V. Krivtsov1, Jayant Y. Gadrey1, Hannah Uckelmann1, Benjamin K. Eschle1, Sayuri Kitajima1, Gerard M. McGeehan2 and Scott A. Armstrong1
1 Center for Pediatric Cancer Therapeutics, Dana-Farber Cancer Institute, Boston, MA2 Syndax Pharmaceuticals, Inc., Waltham, MA
Introduction:• MLL-rearrangements are found approximately 5-10% of AML and B-
ALL cases, also >70% of infant leukemias (Krivtsov and Armstrong2007). NPM1c+ mutations are found in about 25-30% of all adultAML (Ley T et al., 2013).
• Therapeutic targeting of MEN:MLL1/MLL-fusion interaction in MLL-rearranged and NPM1c+ AML inhibits cell proliferation. (Yokoyamaet al 2005; Borkin et al., 2015; Kuhn et al., 2015)
• Currently available MEN:MLL interaction inhibitors have modestdrug like properties. Therefore, VTP-50469 was developed as anovel orally available MEN:MLL1 inhibitor.
VTP-50469 selectively kills cell lines with MLL-rearrangements and NPM1c+ mutations
CELL LINE FUSION IC50 nMMV4;11 MLL-AF4 17SEM-K2 MLL-AF4, AF4-MLL 27RS4;11 MLL-AF4, AF4-MLL 25MOLM-13 MLL-AF9 13KOPN-8 MLL-ENL 15HB11;19 MLL-ENL 36REH NONE >>2000HL-60 NONE >>2000
1° 2° 3° 4° 1° 2° 3° 4°0
100
200
300
Col
ony
Num
ber
Transformed NPM1c+ Mouse LSK
DMSO VTP
ns ***
0.001 0.01 0.1 1 10 1000
3,000
6,000
9,000
12,000
15,000
18,000
VTP conc, uM
Cel
ls, a
bsol
ute
coun
ts HB11;19 (MLL-ENL)
Mv4;11 (MLL-AF4)
RS4;11 (MLL-AF4)
(10 nM)
Colony forming assay in semi-solid media
day 3CellTiter-Glo assay
0.001 0.01 0.1 10
10,000
20,000
30,000
VTP -50469, uM
Cel
ls, a
bsol
ute
coun
ts
OCI-AML3 (NPM1c+), day 6
IC50 18nM
VTP-50469 dissociates MEN from nuclear complexes, in cells
MOLM13 (MLL-AF9)
Freeprotein ~ 1 mDa ~ 2 mDa
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
MENDMSO
VTP0.3uM
Glycerol gradient (10%-20%) fractionation of nuclear extracts, 300mM NaCl
MEN
5 10 15 200123
91827364554
Fraction #
ME
N1,
%
DMSO
VTP
18%
82%
100%
Identical fractionation results obtained from RS4;11 (MLL-AF4), ML-2 (MLL-AF6) and OCI-AML3 (NPM1c+) Cells
Fraction#
Day 3
VTP-50469 treatment leads to MEN loss from TSS in MLL-rearranged cell lines
RS4;11, 2 days
MOLM13, 5 days
VTP-50469
VTP, 0.3 uMDMSO
appr
ox. 2
5.00
0 TS
S
Treatment with VTP-50469 suppresses MLL-fusion target and DOT1L inhibitor sensitive genes
VTP,
0.3
uM
DMSO
243
335
Gene lists:Tags > 10p-val < 0.05
RS4;11, 3 days
p-val <0.001FDR = 0.0
p-val <0.001FDR = 0.008
HOXA5HOXA9
MEF2C
HOXA10
MEIS1
MLL-AF4 targets
DOT1L inhibitor (EPZ4777)
VTP-50469 treatment changes expression of MLL-target and DOT1L inhibitor sensitive genes faster as compared to EPZ4777
VTP-50469 treatment reduces leukemia burden in PDX models of MLL-r and NPM1 mutant leukemia
0 30 60 90 1200
20
40
60
80
100
days
Perc
ent s
urvi
val
CTRL
VTP
VTP
NPM1c+ AML
CTRL VTP 0
25
50
75
100
BM
CD
45+
CD
11b+
, %
CTRL VTP0
25
50
75
100
BM
CD
45+,
%
1-10% Leukemiain PB
PDX (n=9) 0.1% VTP, 100 mpk (IC90)Plasma conc. 1-2 uM 100 1000
0.00
0.25
0.50
0.75
1.00
VTP in Plasma, nM
MEI
S1, a
u
R2=0.93
MLL-r B-ALL (n=3) and AML (n=2); NPM1c+ AML (n=4)0 7 14 21 28
0
20
40
60
80
100
days of dosing
PB
CD
45+,
%
CTRL
VTP
MLL-r B-ALL
Conclusions:• VTP-50469 specifically inhibits proliferation of cell lines carrying MLL-
rearrangements or NPM1c+ mutations with an IC50<40 nM.
• VTP-50469 facilitates dissociation of MEN from high molecular weightcomplexes and leads to eviction of MEN and reverses MLL-fusion drivengene expression.
• Treatment of MLL-r and NPM1c+ PDX models with VTP-50469 leads todifferentiation and significant reduction of leukemia burden.
• Similar results in MLL-r B-ALL PDX presented by our collaborators RichardLock, Malcolm Smith in abstract #3187
