Design and structure-activity relationships of 2-alkyl-3-aminomethyl-6-(3-methoxyphenyl)-7-methyl-8-(2-fluorobenzyl) imidazolo[1,2-α]pyrimid-5-ones as potent GnRH receptor antagonists

Article abstract of DOI:10.1021/jm0205402

SAR studies of 7-phenylpyrrolo[1,2-α]pyrimid-4-ones 1 and 2, and 2-phenylimidazolo[1,2-α]-pyrimidines 3 and 4, as nonpeptide human GnRH receptor antagonists, lead us to believe that the aromatic ring at position-2 of 4 is no longer crucial for the binding

Full text of DOI:10.1021/jm0205402

J . Med. Chem. 2003, 46, 1769-1772
1769
Design a n d Str u ctu r e-Activity Rela tion sh ip s of 2-Alk yl-3-a m in om eth yl-6-
(3-m eth oxyp h en yl)-7-m eth yl-8-(2-flu or oben zyl)im id a zolo[1,2-a ]p yr im id -5-on es a s
P oten t Gn RH Recep tor An ta gon ists
Yun-Fei Zhu,*,† Zhiqiang Guo,† Timothy D. Gross,† Yinghong Gao,† Patrick J . Connors, J r.,† R. Scott Struthers,‡
Qiu Xie,‡ Fabio C. Tucci,† Greg J . Reinhart,‡ Dongpei Wu,† J ohn Saunders,† and Chen Chen*,†
Department of Medicinal Chemistry and Department of Exploratory Discovery, Neurocrine Biosciences, Inc.,
10555 Science Center Drive, San Diego, California 92121
Received November 27, 2002
SAR studies of 7-phenylpyrrolo[1,2-a]pyrimid-4-ones 1 and 2, and 2-phenylimidazolo[1,2-a]-
pyrimidines 3 and 4, as nonpeptide human GnRH receptor antagonists, lead us to believe that
the aromatic ring at position-2 of 4 is no longer crucial for the binding once an aryl group is
incorporated at postion-6. We report here the use of a 2-alkyl group on the imidazolo[1,2-a]-
pyrimidone core to generate potent GnRH receptor antagonists. This discovery enabled us to
obtain smaller but equally potent GnRH receptor antagonists.
In tr od u ction
Targeting gonadotropin-releasing hormone (GnRH),
also known as luteinizing hormone-releasing hormone
(LHRH), receptor for the suppression of sex hormone
levels has led to the successful clinical applications of
peptide agonists and antagonists for a variety of dis-
eases.1,2 However, small molecule GnRH receptor an-
tagonists could possess advantages over the existing
peptidyl therapeutics due to their potential for oral
administration.
F igu r e 1. The general structures of 1-4.
To date, several classes of small molecule GnRH
antagonists have been described in the literature.3-6
and 9 (based on LC-MS data). N-Benzylation of 7a was
accomplished by using 2-fluorobenzyl bromide in THF
containing tetra-n-butylammonium fluoride (TBAF) to
afford the desired product 10a and a N1-alkylation
byproduct 11a , which can be separated by flash column
chromatography. However, in the case of 7b, alkylation
gave 10b as the only isolated product (58% yield). The
assignment of regioisomers 10a and 11a was confirmed
by NOE NMR experiments. A clear NOE was observed
between the 7-methyl group and the 8-benzylic protons
for 10a , while this effect was not seen for 11a . Com-
pounds 10a ,b were then subjected to Suzuki coupling
conditions with 3-methoxylphenylboronic acid to give
12a ,b. Finally, Mannich reactions of 12a ,b with a
variety of secondary amines (R2R3NH) yielded the
desired products 13-31. Alternatively, 12a was formyl-
ated under Vilsmeier conditions (POCl3/DMF) to afford
the corresponding aldehyde 32 as described in Scheme
2. Reductive aminations of 32 with primarily amines
(R2NH2) and NaBH(OAc)3 gave 33-37 as the final
products. Compound 12b, in which R1 was a 1-methyl-
1-methoxycarbonylethyl group, was further modified as
depicted in Scheme 3. Ester 12b was hydrolyzed with
KOH in a mixture of water and methanol at 50 ° C to
give 38, which was reduced with borane to yield the cor-
responding alcohol 39. 39 was reacted with 2-(methyl-
aminomethyl)pyridine and formaldehyde in acetic acid
to give the amino product 40. As shown in Scheme 4,
39 was also subjected to a Swern oxidation to give the
Our group has discovered a series of 7-phenylpyrrolo-
[1,2-a]pyrimid-4-ones 1 and 25 and 2-phenylimidazolo-
[1,2-a]pyrimidines 3 and 46 (Figure 1) as nonpeptide
human GnRH (hGnRH) receptor antagonists. In our
efforts to optimize the biological activity of molecules,
we found that the aromatic ring at position-2 of the
imidazolo[1,2-a]pyrimidone 4 can be replaced with an
alkyl group to generate potent GnRH antagonists. In
this paper we report the synthesis and the SAR of
2-alkylimidazolo[1,2-a]pyrimidones as GnRH antago-
nists.
Ch em istr y
The synthesis of the 2-alkylimidazolo[1,2-a]pyrimid-
5-one core structure was outlined in Scheme 1. 2-Amino-
5-bromo-4-hydroxy-6-methylpyrimidine 5 was reacted
with R-bromoketones (R1COCH2Br, 6) in the presence
of NaH in DMF to give the bicyclic products 7a ,b in good
yield. This reaction required a bulky R1 group, such as
tert-butyl, to produce the sole desired products 7. A
small R1 group, such as methyl, led to the formation of
a mixture of unreacted 5 and overalkylated products 8
* To whom correspondence should be addressed. Y.-F. Zhu: phone
(858) 658-7745; fax (858) 658-7601; e-mail fzhu@neurocrine.com. C.
Chen: phone (858) 658-7634; fax (858) 658-7601; e-mail cchen@
neurocrine.com.
† Department of Medicinal Chemistry.
‡ Department of Exploratory Discovery.
10.1021/jm0205402 CCC: $25.00 © 2003 American Chemical Society
Published on Web 03/28/2003

1770 J ournal of Medicinal Chemistry, 2003, Vol. 46, No. 9
Brief Articles
Sch em e 1a
a
(a): R1COCH2Br (6), NaH, DMF; (b): 2-fluorobenzyl bromide, TBAF, THF; (c): 3-methoxyphenylboronic acid, Pd(PPh3)4, Na2CO3,
toluene, H2O; (d): R2R3NH, CH2O in water, HOAc.
Sch em e 2a
Sch em e 4a
a
(a): POCl3, DMF; (b): R2NH2, NaBH(OAc)3, ClCH2CH2Cl.
a
(a): Swern oxidation, then 2-(2-aminoethyl)pyridine, NaBH-
Sch em e 3a
(OAc)3, ClCH2CH2Cl; (b) CH2O in water, HOAc.
Resu lts a n d Discu ssion s
Our earlier SAR studies had indicated that the para-
substitution of a small lipophilic group with hydrogen
bond acceptor such as isobutyramido (i-PrCONH) or
isobutoxy group on the 7-phenyl of the pyrrolo[1,2-a]-
pyrimidone or the 2-phenyl of the imidazolo[1,2-a]-
pyrimidone (Figure 1) core was a crucial feature for
obtaining highly potent GnRH antagonists.5 However,
the most recent SAR data6 implied that when 3-meth-
oxyphenyl was incorporated to position-6 of the imid-
azolo[1,2-a]pyrimidone core structure to replace the
ester or amide group, the para-substituent at the
2-phenyl of imidazolo[1,2-a]pyrimidone played a much
less important role in binding. We then further postu-
lated that the phenyl may not be optimal for high
potency since the 3-methoxyphenyl at position-6 may
now have subtly reoriented the molecule so that further
optimization may be beneficial. To test this hypothesis,
a tert-butyl moiety was initially introduced at position-2
of the imidazolo[1, 2-a]pyrimidone core to replace the
phenyl group. The binding affinities of such analogues
are shown in Table 1. For easy comparison, the binding
data of 4a was also included in Table 1. Compound 13
having dimethylaminomethyl group at position-3 was
only weakly active. As observed previously, replacement
a
(a): KOH, MeOH, H2O, 50°C; (b): BH3, THF; (c): CH2O/H2O,
2-(N-methylaminomethyl)pyridine, HOAc.
corresponding aldehyde which, without further purifica-
tion, reacted with 2-(2-aminoethyl)pyridine in the pres-
ence of NaBH(OAc)3 to give the amine compound 41.
An intramolecular Mannich reaction with formaldhyde
yielded the tricyclic product 42.

Brief Articles
J ournal of Medicinal Chemistry, 2003, Vol. 46, No. 9 1771
Ta ble 1. Binding Affinities of 2-tert-Butyl-6-
(3-methoxyphenyl)-8-(2-fluorobenzyl)imidazolo[1,2-a]pyrimid-5-
ones 13-20
F igu r e 2. The hypothetical model for the interaction between
compounds 14 or 19 with an acidic residue and an aromatic
residue on the receptor.
Ta ble 2. Binding Affinities of 2-(1-Methyl-1-
methoxycarbonyl)ethyl-6-(3-methoxyphenyl)-8-
(2-fluorobenzyl)imidazolo[1,2-a]pyrimid-5-ones 25-35
a
Ki values for human GnRH receptor were the means ( SEM,
determined from at least three independent experiments meas-
ured.
of one of the two N-methyl groups of 13 with a 2-(2-
pyridyl)ethyl group resulted in a highly potent molecule
(14, Ki ) 5.2 nM), which is equally potent to 4a , a
4-methoxyphenyl analogue. To determine whether the
pyridyl nitrogen was responsible for higher binding
affinity by acting as a second basic center, a simple
diamine analogue 15 was prepared, but it was much
less potent than 14 with a Ki value of 260 nM. Having
a hydrogen bond acceptor in the same side chain (16)
also failed to induce high potency. The binding data of
15 and 16 suggested the importance of the aromatic ring
for binding. Introduction of a phenyl ring (17), a close
analogue of 14 without the hydrogen bonding capability
of the pyridine, also caused a loss in potency, although
the benzyl substituent (18) was marginally more potent
than 17 (Ki ) 72 nM). Thus, the 2-pyridyl analogue 19
was prepared and proved to be a potent antagonist (Ki
) 11 nM). Enhancement of the binding affinity by
2-pyridine in 14 and 19 may be explained by a hypo-
thetical model shown in Figure 2. The nitrogen on the
pyridine ring could enhance the interaction of the basic
amine with an acidic residue of the GnRH receptor by
forming a “five- or six-membered ring”. At the same time
a
Ki values for human GnRH receptor were the means ( SEM,
determined from at least 3 independent experiments.
the pyridine ring itself could provide aromatic π-π
interaction with a phenyl residue on the receptor.7
Clearly none of the other less potent analogues could
provide such dual interactions. Extension of the N-
methyl group of 14 to N-ethyl (compound 20) had no
effect on binding affinity (Ki ) 7.9 nM for 20 vs 5.2 nM
for 14). Table 2 summarizes the binding data for com-
pounds 21-31 with the 1-methyl-1-methoxycarbonyl-
ethyl group as the substituent at position-2 of the
bicyclic core. SAR of these compounds is generally
paralleled to the corresponding 2-tert-butyl series, al-
though compounds in this series were more potent than
their counterpart. As an interesting note, 25 was nearly

1772 J ournal of Medicinal Chemistry, 2003, Vol. 46, No. 9
Brief Articles
ability to inhibit Ca2+ influx induced by GnRH. The
result indicates that 14 is a potent functional antagonist
with IC50 ) 27 nM (Figure 3, in Supporting Informa-
tion).
Ta ble 3. Binding Affinities of 2-tert-butyl-6-
(3-methoxyphenyl)-8-(2-fluorobenzyl)-imidazolo[1,2-a])-
pyrimid-5-ones 33-37
Con clu sion
We have discovered that once an optimal 3-methoxy-
phenyl was attached at position-6, position-2 of the
imidazolo[1, 2-a]pyrimidone did not require a para-
substituted aromatic ring such as p-butyramidophenyl
or p-methoxyphenyl to achieve high binding affinity to
the receptor. This modification led to potent compounds
with reduced molecular weights. The SAR results also
implied that even the alkyl group at this position might
not be required since the modifications with several
different alkyl groups produced similarly potent com-
pounds. This hypothesis has been investigated, and the
results will be published elsewhere.
Ack n ow led gm en t. This work was supported, in
part, by National Institutes of Health grants 1-R43-
HD38625-01 and 2-R44-HD38625-02.
Su p p or tin g In for m a tion Ava ila ble: Binding assay and
functional assay; synthetic procedures and characterization of
all compounds; molecular modeling of compounds 14 and 42.
This material is available free of charge via the Internet at
http://pubs.acs.org.
a
Ki values for human GnRH receptor were the means ( SEM,
determined from at least three independent experiments.
Ta ble 4. Binding Affinities of 3-Aminomethyl-8-
(2-fluorobenzyl)imidazolo[1,2-a]pyrimid-5-ones 40-43
Ki (nM)a
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350 ( 17
12000 ( 1600
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C. Initial Structure-Activity Relationship Studies of a Novel
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a
Ki values for human GnRH receptor were the means (SEM,
determined from at least 3 independent experiments.
100-fold less potent than its 2-pyridyl analogue 22. Once
again all these data again support the dual interaction
model shown in Figure 2. Attempt to use 2-hydroxy-
phenyl as possible replacement of 2-pyridyl failed since
compound 27 displayed only a modest binding affinity.
Obviously the oxygen of 28 played no role in hydrogen
bonding since compound 29 was equally potent to 28.
Attempts to constrain the phenyl ring caused a large
reduction in potency (compounds 30 and 31). Surpris-
ingly, the N-desmethyl analogue of 14, 33 (Ki ) 160 nM)
lost about 30-fold potency while the N-desmethyl ana-
logues of 18 and 19, 34 and 35 lost about 3-fold potency
(Table 3). The reason for the decreased potencies of 33,
34, and 35 is not clear, but it could be attributed to the
conformational difference in the side chains between the
secondary amines and the corresponding tertiary amines.
Furthermore, saturated cycloalkyl compounds 36 and
37 proved to be only weak binders. As shown in Table
4, the alcohol 40 was as potent as 19. The cyclic
derivative 42 lost binding affinity completely, presum-
ably due to the relative orientation of the basic amine
and pyridine side chain resulting in an undesired
conformation for interaction with the receptor. These
results offer us some hints about the required conforma-
tion for high potent antagonists.
To ensure that these potent molecules were functional
antagonists, compound 14 was selected for testing its
J M0205402