It is observed that majority of the drugs used to cure malaria have developed
resistance within a span of 20 years of their introduction [2]. Other limitations of
the drugs in market are compliance, safety, and cost. The drugs should be fast
acting, curative within 3 days, and safe in pregnancy/early infancy [3]. Vaccine
RTS,S has also been introduced for malaria but due to low efficacy (26–50%) is not
recommended for babies between 6 and 12 weeks age [4].
To overcome these limitations, an extensive research is underway to discover
new lead molecules with the potential of being introduced as new drug.
Structure-based drug design (SBDD) is one such approach to discover new leads
[5]. With the explosion of new information regarding the structure of many new
targets, it has become easier to study the detailed structural aspects of the target.
A thorough analysis of mechanism of their enzymatic activity, important amino
acids responsible for molecular recognition and selectivity, mutated amino acids
and their role in resistance as well as changes in enzyme efficiency due to mutations
are some of the questions which are observed and answered during this process.
Choosing appropriate drug hit/lead is based on this information along with the
synthetic feasibility of the designed molecules. This is followed by biological
activity analysis and selecting lead compounds. These leads can be further modified
to improve the activity along with bioavailability and several such cycles of drug
discovery process help in identifying molecules with improved target binding and
specificity/selectivity.
PfDihydrofolateReductase (PfDHFR) is a very widely studied target which
depicts an ideal example for SBDD approach. It was identified as the target for
drugs like cycloguanil and pyrimethamine. The enzyme soon showed resistance
within a span of 20 years of introduction of its inhibitors. It was then observed that
the resistance occurred due to the mutation of Ser108 in the active site of the
enzyme to Asn108, which shows steric clash with the p-chloro substitution at the
phenyl ring of cycloguanil and pyrimethamine. This caused the emergence of two
forms of double mutants and finally the most resistant quadruple mutant [6]. To
avoid this steric clash, a linker chain was proposed to provide flexibility to the
molecule and avoid close interaction with mutated amino acid Asn108. This led to
the identification of WR99210 as lead molecule for in vitro PfDHFR inhibition both
in wild type and mutant form of the enzyme but failed during in vivo studies due to
low bioavailability and toxicity [7]. It was further observed that due to high pKa of
triazine moiety, WR99210 showed bioavailability problems. Further SBDD
approach led to the identification of P218 as the lead molecule which was successful in both in vitro and in vivo studies and is currently undergoing clinical trials
[8]. Molecular modeling studies on this enzyme led to the identification of key
structural features that are essential for its selective inhibition. These include
(i) H-bond donor head group for molecular recognition site, (ii) hydrophobic tail,
and (iii) linker chain between the head group and tail [9]. These parameters were
applied during SBDD approach for identification of new chemical head groups for
PfDHFR inhibitor design [10]. S-substituted guanylthiourea were identified which
showed similar interactions as that of the WR99210 during molecular docking
studies and later molecular dynamics studies [11]. In this series, two compounds
Structure-Based Design of PfDHODH Inhibitors …
179
resistance within a span of 20 years of their introduction [2]. Other limitations of
the drugs in market are compliance, safety, and cost. The drugs should be fast
acting, curative within 3 days, and safe in pregnancy/early infancy [3]. Vaccine
RTS,S has also been introduced for malaria but due to low efficacy (26–50%) is not
recommended for babies between 6 and 12 weeks age [4].
To overcome these limitations, an extensive research is underway to discover
new lead molecules with the potential of being introduced as new drug.
Structure-based drug design (SBDD) is one such approach to discover new leads
[5]. With the explosion of new information regarding the structure of many new
targets, it has become easier to study the detailed structural aspects of the target.
A thorough analysis of mechanism of their enzymatic activity, important amino
acids responsible for molecular recognition and selectivity, mutated amino acids
and their role in resistance as well as changes in enzyme efficiency due to mutations
are some of the questions which are observed and answered during this process.
Choosing appropriate drug hit/lead is based on this information along with the
synthetic feasibility of the designed molecules. This is followed by biological
activity analysis and selecting lead compounds. These leads can be further modified
to improve the activity along with bioavailability and several such cycles of drug
discovery process help in identifying molecules with improved target binding and
specificity/selectivity.
PfDihydrofolateReductase (PfDHFR) is a very widely studied target which
depicts an ideal example for SBDD approach. It was identified as the target for
drugs like cycloguanil and pyrimethamine. The enzyme soon showed resistance
within a span of 20 years of introduction of its inhibitors. It was then observed that
the resistance occurred due to the mutation of Ser108 in the active site of the
enzyme to Asn108, which shows steric clash with the p-chloro substitution at the
phenyl ring of cycloguanil and pyrimethamine. This caused the emergence of two
forms of double mutants and finally the most resistant quadruple mutant [6]. To
avoid this steric clash, a linker chain was proposed to provide flexibility to the
molecule and avoid close interaction with mutated amino acid Asn108. This led to
the identification of WR99210 as lead molecule for in vitro PfDHFR inhibition both
in wild type and mutant form of the enzyme but failed during in vivo studies due to
low bioavailability and toxicity [7]. It was further observed that due to high pKa of
triazine moiety, WR99210 showed bioavailability problems. Further SBDD
approach led to the identification of P218 as the lead molecule which was successful in both in vitro and in vivo studies and is currently undergoing clinical trials
[8]. Molecular modeling studies on this enzyme led to the identification of key
structural features that are essential for its selective inhibition. These include
(i) H-bond donor head group for molecular recognition site, (ii) hydrophobic tail,
and (iii) linker chain between the head group and tail [9]. These parameters were
applied during SBDD approach for identification of new chemical head groups for
PfDHFR inhibitor design [10]. S-substituted guanylthiourea were identified which
showed similar interactions as that of the WR99210 during molecular docking
studies and later molecular dynamics studies [11]. In this series, two compounds
Structure-Based Design of PfDHODH Inhibitors …
179