Discovery of Novel Inhibitors of Streptococcus pneumoniae - Recent Advances in Microbiology - page 91

( S. aureus ) [10-13], and thus received attention as potential targets for antimicrobials
[9, 14-17]. In S. pneumoniae , although at least 13 TCSs were identifi ed, only TCS02
(also designated as VicR/K [18], MicA/B [19] or 492 hk/rr [20]) is essential for bac-
teria viability, which can be a potential target for antimicrobial intervention. To be
detailed, in TCS02, only functional VicR appears to be essential for S. pneumoniae [21],
without which S. pneumoniae can not grow or act as a pathogen [22]. However, the
crystal structure of VicR is unsuitable for SBVS because the active site is too shal-
low to dock a small molecule [22, 23]. The reason that VicK does not seem to be es-
sential for S. pneumoniae viability, was supposed to be that some currently unknown
HKs also participate in the activation of VicR by phosphorylation [24, 25]. However,
among these HKs, VicK it is best-known one with defi nite action on VicR. More-
over, recent researches showed a high-degree homology in the catalytic domain of
these HKs [14-17]. Thus theoretically, selective inhibitors to VicK, a representative
of HKs, can interrupt the phosphorylation of VicR and ultimately reduce the viability
of S. pneumoniae .
The SBVS, an approach used widely in drug design and discovery, possesses
many advantages, such as rapidness, economization, effi ciency, and high-through-
put. In the recent years, SBVS has attracted great attention in developing innovative
antimicrobial agents. A case in point is the discovery of a lead-compound named
diarylquinoline against Mycobacterium tuberculosis [26]. Our study here was de-
signed to search the compound database for potential inhibitors targeting the VicK
protein of S. pneumoniae by using in silico and experimental methods, which may
provide much valuable information to develop new antibiotics against pneumococ-
cal infection.
Sequence Analysis of the VicK TCS in S. pneumoniae
Domain analysis [http://smart.embl.de/smart/show_motifs.pl?ID=Q9S1J9] indicat-
ed that the VicK protein of S. pneumoniae contained one transmembrane segment
and several domains: PAS, PAC, HisKA, and HATPase_c. Multi-alignment of the
HATPase_c domain sequences showed that in most bacteria the sequences around the
ATP binding site of VicK HKs are similar and have four conserved motifs: the N box,
G1 box, F box, and G2 box [27]. This high homology of ATP binding domain of HKs
in bacteria makes it reasonable to screen antibacterial agents by using this domain as
a potential target [16].
Compared with VicK HATPase_c domain in S. pneumoniae (GenBank accession
number: AAK75332.1), the most homologous sequence in the structural Protein Data
Bank (PDB) was the similar domain of Thermotoga maritime (PDB entry: 2c2a) [28],
a TCS molecule, with 33% sequence identity and 57% conservative replacements
(Figure 1). This domain is the entire cytoplasmic portion of a sensor HK protein. The
X-ray crystal structure of the domain of Thermotoga maritima was therefore used
as a template for modeling the 3D structure of the VicK HATPase_c domain of S.
pneumoniae .