non-competitive inhibitor at two different allosteric sites which were present close
to C-terminal domain, causing conformational changes in NADH binding region
that inhibits the binding of NADH to its pocket. These allosteric sites provide
potential selectivity with minimal side effects.
Yang et al. in 2017 also reported that a total of four molecules of RYL-552 bind
in the enzyme in homodimer state (PDB ID 5JWC). One molecule in each
monomer and two molecules at dimer interface with difference in their binding
poses. The first binding pose at the allosteric site between the two C-terminals of
the homodimer (dimer interface) showed that two hydrogen bonds were formed by
trifluoromethoxy group (with Tyr74 and Lys533), a hydrogen bond by carboxyl
group (with Asn92), a water-mediated hydrogen bond by 4-oxo-5-fluoro group of
quinolone with Gly87 and Lys523, and a hydrophobic interaction offered by bisaryl
part (with Leu174, Val91, Ile170, and Ile532) of RYL-552. The other binding pose
at the second allosteric pocket present in each monomer demonstrated that a
water-mediated hydrogen bond is formed by quinolone ring nitrogen with Glu218
and Arg529 residues, two hydrogen bonds by 4-oxo-fluoro group (with Lys501),
and two edge-to-face p-p stacking interaction by quinolone ring (with Trp500 and
Tyr475 residue) [25]. Other compounds like HDQ (1-Hydroxy-2-dodecyl-4(1H)quinolone), Aurachins A-D [26], RYL-552 [25], 7-chloro-3-methyl-2-(4-(4-(trifluoromethoxy) benzyl)phenyl) quinolin-4(1H)-one (CK-2-68) with IC 50 36 nM
[24], and quinolone NQO2 (p-fluoro substituent has IC 50 9.6 nM) [27] were also
reported as inhibitors of PfNDH2.
2.4 P. falciparum Aspartate Carbamoyltransferase (PfACT)
Aspartate carbamoyltransferase is an essential enzyme for the de novo pyrimidine
biosynthesis in intra-erythrocytic stage, and it catalyzes the formation of
N-carbamoyl-L-aspartate from carbamoyl phosphate and L-aspartate (Fig. 5). The
malaria parasite cannot utilize salvage pathway for pyrimidine biosynthesis, as in
the case of human cells, makes it a potential drug target for antimalarial drug design
[28].
Banerjee et al. in 2011 developed a homology model of aspartate carbamoyltransferase using amino acid sequence of the P. falciparum 3D7 (ID:
XP_001350162.1 of NCBI database) as the target sequence and aspartate carbamoyltransferase of Pyrococcus abyssi (PDB ID: 1ML4, Resolution: 1.8 Å) as
template structure, with 38% overall sequence identity. The modeled structure was
found to be stable during molecular dynamics studies performed using NAMD2.5
software. The validation of modeled structure was carried out using PROCHECK,
WHATCHECK, WHATIF, VERIFY 3D, PROSA, ERRAT programs which suggested high quality of the model. The Q-SiteFinder software was used to find the
possible active sites in the modeled protein. N-(phosphonacetyl)-L-aspartate
(PALA) was known to inhibit Escherichia coli aspartate transcarbamylase.
Therefore, PALA and its derivatives were selected for molecular docking in the
184
S. Bhagat et al.
to C-terminal domain, causing conformational changes in NADH binding region
that inhibits the binding of NADH to its pocket. These allosteric sites provide
potential selectivity with minimal side effects.
Yang et al. in 2017 also reported that a total of four molecules of RYL-552 bind
in the enzyme in homodimer state (PDB ID 5JWC). One molecule in each
monomer and two molecules at dimer interface with difference in their binding
poses. The first binding pose at the allosteric site between the two C-terminals of
the homodimer (dimer interface) showed that two hydrogen bonds were formed by
trifluoromethoxy group (with Tyr74 and Lys533), a hydrogen bond by carboxyl
group (with Asn92), a water-mediated hydrogen bond by 4-oxo-5-fluoro group of
quinolone with Gly87 and Lys523, and a hydrophobic interaction offered by bisaryl
part (with Leu174, Val91, Ile170, and Ile532) of RYL-552. The other binding pose
at the second allosteric pocket present in each monomer demonstrated that a
water-mediated hydrogen bond is formed by quinolone ring nitrogen with Glu218
and Arg529 residues, two hydrogen bonds by 4-oxo-fluoro group (with Lys501),
and two edge-to-face p-p stacking interaction by quinolone ring (with Trp500 and
Tyr475 residue) [25]. Other compounds like HDQ (1-Hydroxy-2-dodecyl-4(1H)quinolone), Aurachins A-D [26], RYL-552 [25], 7-chloro-3-methyl-2-(4-(4-(trifluoromethoxy) benzyl)phenyl) quinolin-4(1H)-one (CK-2-68) with IC 50 36 nM
[24], and quinolone NQO2 (p-fluoro substituent has IC 50 9.6 nM) [27] were also
reported as inhibitors of PfNDH2.
2.4 P. falciparum Aspartate Carbamoyltransferase (PfACT)
Aspartate carbamoyltransferase is an essential enzyme for the de novo pyrimidine
biosynthesis in intra-erythrocytic stage, and it catalyzes the formation of
N-carbamoyl-L-aspartate from carbamoyl phosphate and L-aspartate (Fig. 5). The
malaria parasite cannot utilize salvage pathway for pyrimidine biosynthesis, as in
the case of human cells, makes it a potential drug target for antimalarial drug design
[28].
Banerjee et al. in 2011 developed a homology model of aspartate carbamoyltransferase using amino acid sequence of the P. falciparum 3D7 (ID:
XP_001350162.1 of NCBI database) as the target sequence and aspartate carbamoyltransferase of Pyrococcus abyssi (PDB ID: 1ML4, Resolution: 1.8 Å) as
template structure, with 38% overall sequence identity. The modeled structure was
found to be stable during molecular dynamics studies performed using NAMD2.5
software. The validation of modeled structure was carried out using PROCHECK,
WHATCHECK, WHATIF, VERIFY 3D, PROSA, ERRAT programs which suggested high quality of the model. The Q-SiteFinder software was used to find the
possible active sites in the modeled protein. N-(phosphonacetyl)-L-aspartate
(PALA) was known to inhibit Escherichia coli aspartate transcarbamylase.
Therefore, PALA and its derivatives were selected for molecular docking in the
184
S. Bhagat et al.