Developing drugs for brain infection by
Naegleria
fowleri
is an unmet medical need. We used a combination
of cheminformatics, target-, and phenotypic-based drug discovery methods
to identify inhibitors that target an essential
N.
fowleri
enzyme, sterol 14-demethylase (NfCYP51). A
total of 124 compounds preselected
in silico
were
tested against
N. fowleri
. Nine primary
hits with EC
50
≤ 10 μM were phenotypically
identified. Cocrystallization with NfCYP51 focused attention on one
primary hit, miconazole-like compound
2a
. The
S
-enantiomer of
2a
produced a 1.74 Å cocrystal
structure. A set of analogues was then synthesized and evaluated to
confirm the superiority of the
S
-configuration over
the
R
-configuration and the advantage of an ether
linkage over an ester linkage. The two compounds,
S
-
8b
and
S
-
9b
, had an improved
EC
50
and
K
D
compared to
2a
. Importantly, both were readily taken up into the brain.
The brain-to-plasma distribution coefficient of
S
-
9b
was 1.02 ± 0.12, suggesting further evaluation
as a lead for primary amoebic meningoencephalitis.