predicted active site containing Ser107 using GOLD program. 3-(4-Hydroxyphenyl)-2-(2-phosphono-acetylamino)-propionic acid was found to be the most
suitable molecule docked in the predicted active site based on its good binding
affinity toward the enzyme [28].
Lunev et al. first reported the crystal structure of PfACT (or
PfAspartateTranscarbamoylase, PfATC) (PDB ID 5ILQ) in 2016 without any
bound ligand. In 2018, a comparative study was reported between the apo-form of
the enzyme, PfACT complexed with citric acid at the active site (PDB ID 5ILN)
and PfACT complexed with 2,3-naphthalenediol at the allosteric site (PDB ID
6FBA). The citrate-bound complex structure of the enzyme was found to be analogues to the liganded R-state of the enzyme. It was observed that the active site is
highly conserved in this enzyme which might reduce the usefulness of this enzyme
as a target using SBDD approach. The recently reported crystal structure with
PDB ID 6FBA showed the presence of an allosteric site in which the enzyme is
present in the T-state which is very similar to the apo-protein. Most of the amino
acids in the allosteric site are non-conserved, thus making this site a potential target
for SBDD [29].
2.5 P. falciparum Thioredoxin Reductase (PfTrxR)
Thioredoxin reductase (TrxR) is a flavoenzyme (i.e., NADPH dependent) that
maintains the enhanced oxidative stress in the erythrocytic stage of the parasite. It
catalyzes the reduction of disulfide bridge of oxidized thioredoxin (Trx-S 2 ) into the
thiol form, i.e., Trx-SH 2 . This enzyme system is present in the cytosol, parasitophorous vacuole, and endoplasmic reticulum of the parasite. The PfThioredoxin
(PfTrx1), a biological substrate for PfTrxR enzyme, is an important proton donor
for the vital proteins like ribonucleotide reductase and other sets of peroxiredoxins
[30]. P. falciparum lacks classical glutathione peroxidase and catalase enzymes
which are present in eukaryotes to manage oxidative stress. Therefore, this enzyme
plays an essential role for the survival of P. falciparum in the erythrocytic stages.
The disruption of the redox state leads to antimalarial activity [31].
It is a homodimer containing three redox active centers to balance the redox state
in P. falciparum (PfTrxR) [31]. These are: (1) FAD-binding domain (2) N-terminal
redox center near to the FAD-binding domain (Cys-88 and Cys-93), and
(3) C-terminal redox center located on the flexible and accessible arm of other
monomeric subunit (Cys-535 and Cys-540) which finally interacts with the thioredoxin substrate [30]. The homodimer is stabilized by Met105, Phe109, Ile108,
Trp118, Phe120, and Leu123 (aromatic and hydrophobic) residues present at the
interface. Met105 and Phe109, involved in the bending of interface helices, are
conserved in the plasmodium species but not in the mammals. It is also reported that
the buried interface of PfTrxR enzyme is stabilized by more polar contacts than that
of the human enzyme [32]. The PfTrxR shows up to 40–42% sequence identity to
the HsTrxR and 77–80% sequence identity with other five species of the malaria
Structure-Based Design of PfDHODH Inhibitors …
185
suitable molecule docked in the predicted active site based on its good binding
affinity toward the enzyme [28].
Lunev et al. first reported the crystal structure of PfACT (or
PfAspartateTranscarbamoylase, PfATC) (PDB ID 5ILQ) in 2016 without any
bound ligand. In 2018, a comparative study was reported between the apo-form of
the enzyme, PfACT complexed with citric acid at the active site (PDB ID 5ILN)
and PfACT complexed with 2,3-naphthalenediol at the allosteric site (PDB ID
6FBA). The citrate-bound complex structure of the enzyme was found to be analogues to the liganded R-state of the enzyme. It was observed that the active site is
highly conserved in this enzyme which might reduce the usefulness of this enzyme
as a target using SBDD approach. The recently reported crystal structure with
PDB ID 6FBA showed the presence of an allosteric site in which the enzyme is
present in the T-state which is very similar to the apo-protein. Most of the amino
acids in the allosteric site are non-conserved, thus making this site a potential target
for SBDD [29].
2.5 P. falciparum Thioredoxin Reductase (PfTrxR)
Thioredoxin reductase (TrxR) is a flavoenzyme (i.e., NADPH dependent) that
maintains the enhanced oxidative stress in the erythrocytic stage of the parasite. It
catalyzes the reduction of disulfide bridge of oxidized thioredoxin (Trx-S 2 ) into the
thiol form, i.e., Trx-SH 2 . This enzyme system is present in the cytosol, parasitophorous vacuole, and endoplasmic reticulum of the parasite. The PfThioredoxin
(PfTrx1), a biological substrate for PfTrxR enzyme, is an important proton donor
for the vital proteins like ribonucleotide reductase and other sets of peroxiredoxins
[30]. P. falciparum lacks classical glutathione peroxidase and catalase enzymes
which are present in eukaryotes to manage oxidative stress. Therefore, this enzyme
plays an essential role for the survival of P. falciparum in the erythrocytic stages.
The disruption of the redox state leads to antimalarial activity [31].
It is a homodimer containing three redox active centers to balance the redox state
in P. falciparum (PfTrxR) [31]. These are: (1) FAD-binding domain (2) N-terminal
redox center near to the FAD-binding domain (Cys-88 and Cys-93), and
(3) C-terminal redox center located on the flexible and accessible arm of other
monomeric subunit (Cys-535 and Cys-540) which finally interacts with the thioredoxin substrate [30]. The homodimer is stabilized by Met105, Phe109, Ile108,
Trp118, Phe120, and Leu123 (aromatic and hydrophobic) residues present at the
interface. Met105 and Phe109, involved in the bending of interface helices, are
conserved in the plasmodium species but not in the mammals. It is also reported that
the buried interface of PfTrxR enzyme is stabilized by more polar contacts than that
of the human enzyme [32]. The PfTrxR shows up to 40–42% sequence identity to
the HsTrxR and 77–80% sequence identity with other five species of the malaria
Structure-Based Design of PfDHODH Inhibitors …
185