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on the three-dimensional structures of macromolecular to identify chemical entities
binding to the targets and to elicit potential biological mechanisms with the advan-
tages of speed, efficiency and high-throughput. The availability of the small molecular
lead-compound library and the modeled 3D target structure makes it possible to use
SBVS to screen out a limited number of promising candidates that can interrupt the
TCS signal transduction by interacting with the HKs substrate of
S. pneumoniae
.
The HKs, as novel antibacterial targets, have attracted many attentions due to their
essentiality in the viability of microbes and their defi ciency in animals. The HKs are
involved in the regulation of bacterial growth and virulence in many bacterial species.
Previously, a HK named VicK has been used to screen lead compound inhibitors in
B.
subtilis
and
S. epidermidis
. We here for the fi rst time obtained 105 candidate chemi-
cal compounds directly aiming at
S. pneumoniae
VicK by screening 200,000 possible
compounds in
silico
. Compounds that can bind to the purifi ed target protein VicK' and
compete with its substrate ATP were further verifi ed by
in vitro
and
in vivo
antibacte-
rial assays. Eventually, we obtained six compounds with antibacterial activity that may
be used as novel drug leads.
Commonly, the response regulator YycF and the histidine kinase YycG are the
only essential TCS for viability in
B. subtilis
and
S. aureus
[10, 12]. In
S. pneumoniae
,
the VicR/K TCS regulates the expression of several critical genes, such as those en-
coding surface proteins and virulence factors [21, 33]. However, only the response
regulator VicR was found to be essential [20, 34]. The signal transduction of VicK
was possibly bypassed by other TCS HKs [35]. VicK has conserved ATP-dependent
HATPase_c domains accounting for autophosphorylation. Even non-cognate HKs
from other bacteria can phosphorylate the purifi ed VicR from
S. pneumoniae
[18]. In
a previous study [36], the MIC values of the lead compounds screened out by SBVS
targeting the YycG of
S. epidermidis
were almost equal to the corresponding IC
50
(for
YycG) values, with a correlation coeffi cient of 0.959, which suggested that inhibition
of 50% the YycG protein activity would interfere with the growth of
S. epidermidis
.
If this case is true in
S. pneumoniae
, the result that the MIC values of the lead-com-
pounds were far less than the corresponding IC50 values may be explained as bypass
effects of these compounds on other HKs. In a word, these lead compounds are most
likely having a “cross-inhibition” on other HKs in
S. pneumoniae
, which can enhance
their antibacterial effects, although they were not verifi ed in this study.
Although, the VicK protein in
S. pneumoniae
can be homologous to YycG in other
gram-positive strains, such as
S. epidermidis
,
Enterococcus faecalis
and
S. aureus
,
different strains generally have different characteristics of the HATPase_c domain
structure of HKs. These characteristics will determine the binding specifi city of the
lead compounds screened out by SBVS. Moreover, a different template for homolo-
gous modeling and different parameters for SBVS were used, which can guarantee
the specifi city of the lead compounds binding to the VicK' discovered. What is more,
23 compounds can inhibit the purifi ed VicK' protein activity by more than 50%, 6 of
which displayed different degrees of antibacterial effects
in vitro
and
in vivo
. Regret-
fully, the
in vivo
activities of these compounds were not quite consistent with their
corresponding
in vitro
activity, and some compounds displayed obvious cytotoxicity,
