Synthesis of useful fragments in drug discovery: 2-Amino-5-tert- butylpyridine and its oxidised analogues

Article abstract of DOI:10.1016/j.bmcl.2011.05.066

A novel and robust synthesis of the fragment, 2-amino-5-tert-butylpyridine, has been described, which has been shown to have improved physicochemical properties over 4-tert-butylaniline, when considering drug-like properties. The synthesis also yields fra

Full text of DOI:10.1016/j.bmcl.2011.05.066

Bioorganic & Medicinal Chemistry Letters 21 (2011) 4281–4283
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis of useful fragments in drug discovery: 2-Amino-5-tert-butylpyridine
and its oxidised analogues
⇑
Christopher G. Thomson , John Reilly, David A. Sandham
Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis Horsham Research Centre, Wimblehurst Road, Horsham, West Sussex RH12 5AB, United Kingdom
a r t i c l e i n f o
a b s t r a c t
Article history:
A novel and robust synthesis of the fragment, 2-amino-5-tert-butylpyridine, has been described, which
has been shown to have improved physicochemical properties over 4-tert-butylaniline, when considering
drug-like properties. The synthesis also yields fragments containing more highly oxidised precursors to
the tert-butyl group as intermediates. These fragments can be incorporated into final target molecules,
yielding pharmaceutical compounds and their putative CYP-mediated oxidative metabolites, which can
aid in elucidation of metabolic clearance processes.
Received 13 April 2011
Revised 17 May 2011
Accepted 18 May 2011
Available online 25 May 2011
Keywords:
Fragments
Ó 2011 Elsevier Ltd. All rights reserved.
Drug discovery
Metabolic clearance
Drug-like properties
A number of biologically active compounds contain the tert-bu-
tyl phenyl moiety, such as BCTC1 and terfenadine2 (Fig. 1).
Whilst the inclusion of this lipophilic group often results in
compounds of higher affinity, especially when compared to its par-
ent phenyl derivative, it seldom leads to compounds which im-
prove the ‘drug-like’ or ‘lead-like’ properties3 across the chemical
series.
channel and hence avoids cardiac side-effects. This acid metabolite
of terfenadine is the active anti-histamine, fexofenadine, and is
now marketed as such.
Our approach to the synthesis of 2 centred on the enolate cou-
pling chemistry of Hartwig et al.7 2-Amino-5-bromopyridine (5)
was di-p-methoxy benzyl protected,8 as reductive cleavage of
Within the context of a recent drug discovery program, a lead
series contained the 4-tert-butylaniline (1) moiety, akin to BCTC.
In an attempt to improve drug-like properties, 2-amino-5-tert-
butylpyridine (2) was identified as a possible replacement frag-
ment (Fig. 2), the key observation being that the 2-pyridyl nitrogen
was tolerated by the target pharmacophore. Insertion of the nitro-
gen leads to a modest reduction in calculated log P of the fragment
(Fig. 2). 2-Amino-5-tert-butylpyridine is known in the literature,4
but a new route was sought that not only supplied the target com-
pound, but also yielded fragments 3 and 4, which could be used to
synthesize putative oxidative metabolites of the lead molecules.
The tert-butyl group is often oxidised quickly via CYP450 en-
zymes when exposed to metabolic processes in vivo, as in the well
documented case of the H1 antagonist, terfenadine. Terfenadine
can cause cardiac side-effects,5 such as QTc prolongation and
Torsades de Pointes,6 attributed to blockade of the hERG channel.
Terfenadine acts as a pro-drug—the tert-butyl group undergoing
initial in vivo metabolic oxidation, to the phenylisobutanol com-
pound, then further oxidation to the carboxylic acid (Fig. 3). The
acid containing compound shows reduced binding to the hERG
O
N
N
H
N
N
Cl
BCTC
TRPV1 antagonist
HO
OH
N
Terfenadine
H1 Antagonist
⇑
Corresponding author.
E-mail address: christopher.thomson@novartis.com (C.G. Thomson).
Figure 1. Pharmaceutically active compounds containing the tert-butylphenyl
group.
0960-894X/$ - see front matter Ó 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2011.05.066

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C. G. Thomson et al. / Bioorg. Med. Chem. Lett. 21 (2011) 4281–4283
H2N
N
PMB2N
N
i
N
Br
Br
H2N
H2N
6
5
1
2
clogP 2.7
clogP 2.1
ii
CO2H
OH
N
N
PMB2N
N
PMB2N
N
H2N
H2N
iii
O
3
4
OH
O
Figure 2. 2-Amino-5-tert-butylpyridine as a replacement for 4-tert-butylaniline,
and its putative oxidation products via CYP mediated metabolism of the tert-butyl
group.
8
7
iv, v
PMB2N
N
H2N
N
vi
HO
N
CYP3A4
[O]
HO
N
9
2
OH
OH
Scheme 1. Reagents and conditions: (i) PMBnBr, 60% NaH/mineral oil, DMA, 0 °C,
1 h, 76% yield8; (ii) methyl isobutyrate, LiNCy2, Pd(dba)2, P(t-Bu)3, toluene,
overnight at ambient temperature, 78% yield; (iii) LiBH4, THF, 2 days at ambient
temperature, quantitative; (iv) Dess-Martin Periodinane, DCM, 10 min at ambient
temperature, 87% yield; (v), Hydrazine hydrate, KOH, diethylene glycol, heated at
reflux, 72 h, 71% yield; (vi) TFA, 5 h at ambient temperature, 91% yield.
HO
Terfenadine
CYP3A4
[O]
N
HO
N
Compound
H2N
H2N
OH
1
2
HPLC %HSA*
78.5
38.9
HPLC CHI
IAM¥
OH
35.5
2.83
33.0
1.53
38.9
8.0
O
HPLC
LogD7.4
Fexofenadine
†
Figure 3. The metabolic fate of terfenadine.
PSA / Å2
26.0
Calculated pKa
5.2
benzyl groups could not be carried out at the end of the synthesis
without reduction of the pyridine core. The enolate coupling of 6
(Scheme 1) with methyl isobutyrate resulted in a good yield of es-
ter (7), and this was easily reduced to the alcohol (8).
HT-
sol.
pH 6.8
<0.005
0.059
/mM
FASSIF
<0.005
0.072
With 8 in hand, transformation to the desired tert-butyl com-
pound was attempted via conversion of the hydroxyl moiety to a
leaving group and subsequent reduction. Iodination or mesylation
reactions of 8 were poor yielding, and all attempts to reductively
remove the subsequent iodine or mesylate leaving groups resulted
in polymerisation. The successful approach to formation of 9 was
oxidation of the alcohol to the aldehyde, which was converted to
the tert-butyl group using Wolff–Kishner reduction.
* HPLC estimation of binding to human serum albumin.10
¥ HPLC estimation of partitioning into artificial membranes.11,12
† HPLC estimation of logD.13
Internal high throughput solubility assay, in pH6.8 buffer, or
simulated fasted intestinal fluid (FASSIF).14
Figure 4. Comparison of the physicochemical properties for fragments 1 and 2.
Finally, in order to gauge the success of the approach in improv-
ing physicochemical properties over 1, HPLC methods10–13 were
used to estimate the lipophilicity, membrane affinity and protein
binding of fragments 1 and 2. This showed estimated log D to be
reduced by approximately 1 unit (Fig. 4), and binding to human
serum albumin (HSA) to be significantly reduced. Membrane affin-
ity (CHI IAM) remained largely unchanged. Polar surface area (PSA)
of fragment 2 is increased by around 13 Å2 compared with 1. High
The ester (7), alcohol (8) and tert-butyl intermediate (9) could
be deprotected using TFA,9 and fragments 2, 3 and the methyl ester
of 4 incorporated into the final molecules via standard amine
derivatization. This gave the target molecule, along with putative
CYP-mediated oxidation products (following base hydrolysis of
the ester to acid in the case of 4). The synthesis is amenable to
scale, with 60 g of compound 2 being produced within Novartis
laboratories.

C. G. Thomson et al. / Bioorg. Med. Chem. Lett. 21 (2011) 4281–4283
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The physicochemical properties of the 2-amino-5-tert-butylpyr-
idine fragment have been shown to be superior to 4-tert-butylan-
iline when considering drug-like properties: as well as reducing
the estimated log D and increasing PSA, this fragment also shows
an estimated reduction in binding to human serum albumin and
improved solubility. In conclusion, a novel, robust and scalable
synthesis of 2-amino-5-tert-butylpyridine has been described; a
useful fragment for incorporation into final target molecules,
potentially leading to molecules with improved drug-like proper-
ties. The synthesis also yields intermediates containing the puta-
tive CYP-mediated oxidation products of the tert-butyl group, so
aiding the identification of metabolic and clearance processes of
parent molecules.
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J = 2.5 Hz).
Acknowledgements
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The authors would like to thank Dr. Jeff McKenna and Dr. Greg
Hollingworth of NIBR, Horsham for their time and thoughtful
advice, and Dr. Constanze Hartwieg of NIBR, Basel for details
around large scale synthesis of fragment 2.
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References and notes
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