EPSP analogs were retrieved from

EPSP analogs were retrieved from PubChem database and docking procedure yielded about eight best binding analogs (Fig. 10). The selected molecules were further assessed for their theoretical Ki values using AUTODOCK software version 4. The predicted binding efficiency of retrieved analogs was estimated based on the values of dissociation constant Ki, docking score, docking nk1 receptor antagonist and extent of interactions with active site residues. The comparative study of eight different analogs with highest predicted binding efficiency into active site of PfCS, HpCS and ScCS was made and corresponding docking results along with interacting residues of PfCS are shown in Table 1. Thomas et al. has described a series of analogs of benzofuran-3[2H]-one as inhibitors of SpCS with varying degree of potency [34]. We retrieved the submitted structures of these analogs from the Binding Database (www.bindingdb.org) and studied their binding capability in active site pockets of SpCS, HpCS and PfCS (Fig. 11). Six of these inhibitors with highest predicted binding efficiency along with corresponding docking parameters and interacting residues are shown in Table 2. In our study, 6,7-dihydroxy-2-[1-(4-morpholin-4-yl-phenyl)-meth-(E)-ylidene]-benzofuran-3-one (ChEBI ID: 323325), with reported experimental IC50 value 50μM with SpCS, was found to be most potent molecule binding into the active site of PfCS (Ki=2.66μM). In the docked structure of this inhibitor with PfCS, the 6,7 hydroxyl groups of catechol is found to interact with Thr54 and Gln59. It also interacts with Gln50 and Ser486 using its furan ring. The catechol and the furan ring are found to be present in the same binding pocket as that of EPSP (figure not shown).
Conclusion In present study, the molecular model of PfCS was generated using the crystal structure of HpCS as template. The modeled structure of PfCS monomer shows a three layered “β–α–β sandwich fold” which is a characteristic feature of CS family. We have also proposed the modified signature sequence that satisfies the conserved motif of apicomplexa CS. The model also facilitated the recognition of conserved residues in active site pocket. As all the CS mainly exists in dimeric form, the dimeric PfCS was generated to recognize all the interface residues involved in dimerization. The reliable model also permitted the study of binding efficiency of substrate analogs as well as previously reported inhibitors of SpCS. The study yielded a small highly focused virtual subset of EPSP analogs, with speculated inhibitory capacity against PfCS and having binding efficiency in nanomolar range. This study can thus help to direct the focus of synthetic chemists, designing the next generation of antimalarial agents.
Acknowledgments This work was supported by financial aid from the Department of Science and Technology, New Delhi, India. We thank Dr. Shailly Tomar for helpful discussions. We also acknowledge Macromolecular Crystallographic Unit (MCU) for providing computational facilities. Satya thanks AICTE, Abhinav thanks DBT, Sonali thanks MHRD and Preeti thanks CSIR for financial support.
Introduction Malaria is one of the most widespread infectious diseases in the world. Every year about 500 million people are infected and over 2.7 million people die, most of them are children [1]. Because of the rapidly developing resistance of the malaria parasite Plasmodium falciparum to currently used alkaloidal drugs such as quinine and chloroquine, new non alkaloidal artemisinin type antimalarial drugs (artemisinin and its derivatives) have become increasingly important. Artemisinin is a sesquiterpene endoperoxide (Fig. 1) which is isolated from the herb of the Chinese medicinal plant Artemisia annua[2]. Artemisinin is a potent antimalarial drug against the resistant strains of P. falciparum[3], [4]. Though the mechanism of action of the artemisinin type antimalarial drugs is not completely understood, there is growing evidence supporting the idea jejunum the initial key step is the reductive cleavage of O–O bond of the endoperoxide group. This reaction presumably works by hemin, leading to oxygen and then carbon-centred radicals that subsequently lead to the biologically relevant damage to the malarial parasite [5], [6], [7].