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1 occupies the H3K27me3 peptide binding pocket, including that
of the trimethyllysine itself, thus confirming competitive binding
against the peptide. While the H3K27me3- and pyrrolidine-bound
structures are globally very similar, our structure reveals a remark-
able remodeling of the H3K27me3 binding pocket to accommodate
the pyrrolidine ligand. Substantial rotamer changes in Trp364,
Tyr365 and Arg367 (Fig. 2a) disrupt the aromatic cage which ordi-
narily accommodates the trimethyllysine ammonium to expose a
larger, more druggable binding pocket. This alternate rotamer ori-
entation of Tyr365 creates a new aromatic cage consisting of three
residues (Phe97, Tyr148, Tyr365) which now accommodates the
pyrrolidine core of 1 (Fig. 2b). The p-methoxybenzyl ring occupies
the space previously held by Tyr365 while Arg367 adjusts to make
a cation-p interaction; other key interactions include a hydrogen
bond from the dimethylamine to a highly-coordinated water as
well as highly optimized hydrophobic and van der Waals interac-
tions between the rings of the indole and protein (i.e., Phe97,
Tyr148, Tyr365, Arg414). This initial structure suggested to us that
the N-benzyl and indole moieties would be amenable to
modification.
Fig. 1. Structures of screening hit 1 and tool compound 212 with molecular weight,
EED binding potency and ligand efficiency (LE = 1.4 Â pKi/# of heavy atoms).
Compound 1 is racemic and compound 2 is a mixture of two diastereomers with
pyrrolidine stereochemistry as shown.
The SAR work began with a thorough survey of N-benzyl sub-
stituents and revealed a strong preference for 2,6-disubstitution
(Table 1). While the high throughput screening hit 1 and the
at the H3K27 binding site of EED (see below). We now disclose the
SAR and physicochemical characterization of this pyrrolidine series
which led to the identification of our tool compound 2,12 a novel
inhibitor of the PRC2 complex through disruption of EED/
H3K27me3 binding.13
N-benzyl analog
9 were only modest ligands for EED, the
2-bromo-6-fluorobenzyl compound 10 had double-digit nanomo-
lar binding potency as did the 2-chloro-6-fluorobenzyl (11) and
2-fluoro-6-methylbenzyl (12) analogs. The importance of 2,6-dis-
ubstitution was further demonstrated by the somewhat attenuated
binding potency of the 2-fluorobenzyl (13) and 2-fluoro-5-methyl-
benzyl (14) analogs although 2-fluoro substitution alone was
generally beneficial to potency (data not shown). Regarding the
pyrrolidine stereochemistry, The (3R,4S) single enantiomer 10
was 5-fold more potent than the (3S,4R) enantiomer (not shown)
and exemplified the modest but consistent preference of EED for
the (R)-dimethylamino pyrrolidine enantiomers.
In an attempt to restrict the conformational freedom of
the benzyl moiety and increase the ligand-receptor contact while
enforcing the favorable binding conformation observed with the
o-methoxybenzyl in the crystal structure of analog 1, we annulated
the o-methyl and benzyl methylene of 12 into an indane bicycle
(15). While this provided a compound that was an equipotent bin-
der with 12, this analog was substantially more potent cellularly;
whereas benzyl analogs 10, 11 and 12 are micromolar inhibitors
of H3K27 trimethylation and proliferation of the Pfeiffer cell line,
indane 15 is a submicromolar inhibitor of histone trimethylation
with modestly improved antiproliferative activity. The enhance-
ment of cellular activity was a robust benefit of replacing benzyl
with indane (see Table 5 below); the origin of this potency boost
is unclear and cannot be explained by cellular permeability as
compounds 10, 11, 12 and 15 are all highly permeable (1–
3 Â 10À6 cm/s) as measured in the parallel artificial membrane
permeability assay (PAMPA).
The synthesis of pyrrolidine 1 is shown in Scheme 1 and exem-
plifies the preparation of many of the compounds in this work. The
a,b-unsaturated nitro 3 was treated with azomethine ylide precur-
sor 4 in the presence of TFA to give pyrrolidine 5 via [3+2] dipolar
cycloaddition; the (E)-alkene exclusively provided racemic pyrro-
lidine with trans stereochemistry.14 Nitro reduction of 5 with
Raney-Ni/hydrogen and reductive amination of the resulting
amine 6 with formaldehyde/sodium triacetoxyborohydride pro-
vided dimethylamino pyrrolidine 7. Hydrogenolysis in the pres-
ence of palladium hydroxide gave pyrrolidine
8 which was
converted to compound 1 by reductive amination with o-methoxy-
benzaldehyde in the presence of sodium triacetoxyborohydride.
Modification of ylide precursor 4 allowed for the convenient prepa-
ration of substituted-benzyl intermediates while chiral supercriti-
cal fluid chromatography (SFC) of intermediates such as nitro 5 or
N-benzyl 7 provided analogs as single enantiomers. Intermediates
6 and 8 allowed for the rapid examination of amino substituents
while indole and pyrrolidine modification/replacement were the
most difficult as they required distinct syntheses.
New analogs were assessed for EED binding potency using a TR-
FRET assay with a pyrrolidine-based Oregon green (488) probe.15
Potent EED ligands were then simultaneously examined in cellular
assays that measured selective inhibition of H3K27 trimethylation
over six days in several human tumor cell lines (e.g., G-401,
OCILY19)15 and proliferation over ten days in multiple tumor cell
lines including Pfeiffer (human diffuse large B-cell lymphoma).15
These cell lines were chosen, in part, for their known phenotypic
sensitivity to EZH2 inhibitors and the selectivity of the antiprolifer-
ative activity was routinely counter-screened against cell lines
known to be insensitive to EZH2 inhibition (e.g., human RD). Com-
pounds were also evaluated in a primary ADME screen that
included mouse in vitro intrinsic clearance and microsomal protein
binding.
Regarding indane stereochemistry, comparison of binding
potencies of the single enantiomer 15, bearing an (S)-indane stere-
ocenter, and indane 16, bearing an (R)-indane stereocenter,
demonstrates the recurring preference for the (S)-indane stereo-
center. An overlay of the X-ray crystal structures of protein bound
benzyl 10 (PDB ID: 5U8A) and indane 15 (PDB ID: 5U8F) in Fig. 3
demonstrates the desired conformational restriction resulting from
the indane and while it’s not clear why a large enhancement in
binding potency was not observed, the preference for the (S)-
indane stereochemistry is readily understood.
As mentioned above, the structure of EED (residues
D
77-441-
hereafter referred to as
D
EED)4 complexed with pyrrolidine 1
(PDB ID: 5U69) was determined by co-crystallization;16 compar-
ison of this structure with a previously published structure of
EED binding an H3K27me3 peptide (PDB ID: 3JZG)4 revealed that
Physicochemically, this initial set of compounds was very lipo-
philic with cLogP’s of 4–5 and tPSA’s of 10–20 (3/75 rule fail); not
surprisingly, the intrinsic clearance in mouse microsomes of the