Shailendra Kumar Sharma

Crystal structure of dimeric FabZ of Plasmodium falciparum reveals conformational switching to active hexamers by peptide flips

The crystal structure of β‐hydroxyacyl acyl carrier protein dehydratase of Plasmodium falciparum (PfFabZ) has been determined at a resolution of 2.4 Å. PfFabZ has been found to exist as a homodimer (d‐PfFabZ) in the crystals of the present study in contrast to the reported hexameric form (h‐PfFabZ) which is a trimer of dimers crystallized in a different condition. The catalytic sites of this enzyme are located in deep narrow tunnel‐shaped pockets formed at the dimer interface. A histidine residue from one subunit of the dimer and a glutamate residue from the other subunit lining the tunnel form the catalytic dyad in the reported crystal structures. While the position of glutamate remains unaltered in the crystal structure of d‐PfFabZ compared to that in h‐PfFabZ, the histidine residue takes up an entirely different conformation and moves away from the tunnel leading to a His‐Phe cis–trans peptide flip at the histidine residue. In addition, a loop in the vicinity has been observed to undergo a similar flip at a Tyr–Pro peptide bond. These alterations not only prevent the formation of a hexamer but also distort the active site geometry resulting in a dimeric form of FabZ that is incapable of substrate binding. The dimeric state and an altered catalytic site architecture make d‐PfFabZ distinctly different from the FabZ structures described so far. Dynamic light scattering and size exclusion chromatographic studies clearly indicate a pH‐related switching of the dimers to active hexamers.

Mass Spectrometry-Based Systems Approach for Identification of Inhibitors of Plasmodium falciparum Fatty Acid Synthase

ABSTRACT The emergence of strains of Plasmodium falciparum resistant to the commonly used antimalarials warrants the development of new antimalarial agents. The discovery of type II fatty acid synthase (FAS) in Plasmodium distinct from the FAS in its human host (type I FAS) opened up new avenues for the development of novel antimalarials. The process of fatty acid synthesis takes place by iterative elongation of butyryl-acyl carrier protein (butyryl-ACP) by two carbon units, with the successive action of four enzymes constituting the elongation module of FAS until the desired acyl length is obtained. The study of the fatty acid synthesis machinery of the parasite inside the red blood cell culture has always been a challenging task. Here, we report the in vitro reconstitution of the elongation module of the FAS of malaria parasite involving all four enzymes, FabB/F (β-ketoacyl-ACP synthase), FabG (β-ketoacyl-ACP reductase), FabZ (β-ketoacyl-ACP dehydratase), and FabI (enoyl-ACP reductase), and its analysis by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS). That this in vitro systems approach completely mimics the in vivo machinery is confirmed by the distribution of acyl products. Using known inhibitors of the enzymes of the elongation module, cerulenin, triclosan, NAS-21/91, and (−)-catechin gallate, we demonstrate that accumulation of intermediates resulting from the inhibition of any of the enzymes can be unambiguously followed by MALDI-TOF MS. Thus, this work not only offers a powerful tool for easier and faster throughput screening of inhibitors but also allows for the study of the biochemical properties of the FAS pathway of the malaria parasite.

Benzothiophene carboxamide derivatives as inhibitors of Plasmodium falciparum enoyl-ACP reductase.

Benzothiophene derivatives like benzothiophene sulphonamides, biphenyls, or carboxyls have been synthesized and have found wide pharmacological usage. Here we report, bromo‐benzothiophene carboxamide derivatives as potent, slow tight binding inhibitors of Plasmodium enoyl‐acyl carrier protein (ACP) reductase (PfENR). 3‐Bromo‐N‐(4‐fluorobenzyl)‐benzo[b]thiophene‐2‐carboxamide (compound 6) is the most potent inhibitor with an IC50 of 115 nM for purified PfENR. The inhibition constant (Ki) of compound 6 was 18 nM with respect to the cofactor and 91 nM with respect to crotonoyl‐CoA. These inhibitors showed competitive kinetics with cofactor and uncompetitive kinetics with the substrate. Thus, these compounds hold promise for the development of potent antimalarials.

β‐Ketoacyl‐ACP synthase I/II from Plasmodium falciparum (PfFabB/F)—Is it B or F?

Condensing enzymes play an important and decisive role in terms of fatty acid composition of any organism. They can be classified as condensing enzymes involved in initiating the cycle and enzymes involved in elongating the initiated fatty acyl chain. In E. coli, two isoforms for the elongation condensing enzymes (FabB and FabF) exists whereas Plasmodium genome contains only one isoform. By in vitro complementation studies in E. coli CY244 cells, we show that PfFabB/F functions like E. coli FabF as the growth of the mutant cells could be rescued only in the presence of oleic acid. But unlike bacterial enzyme, PfFabB/F does not increase the cis‐vaccenic acid content in the mutant cells upon lowering the growth temperature. This study thus highlights the distinct properties of P. falciparum FabF which sets it apart from E. coli and most other enzymes of this family described so far.

Crystallization and preliminary crystallographic analysis of beta-hydroxyacyl ACP dehydratase (FabZ) from Plasmodium falciparum.

The malarial parasite Plasmodium falciparum synthesizes fatty acids by the type II mechanism. In this cycle, the dehydration of the beta-hydroxyacyl acyl carrier protein is catalyzed by FabZ. Purified FabZ has been crystallized using the hanging-drop vapour-diffusion and microbatch techniques. The crystals are orthorhombic, with space group I222 or I2(1)2(1)2(1) and unit-cell parameters a = 71.78, b = 81.99, c = 97.49 A. A complete data set to a resolution of 2.5 A has been collected under cryoconditions (100 K) using a MAR imaging-plate detector system mounted on a rotating-anode X-ray generator.

Packing and loop-structure variations in non-isomorphous crystals of FabZ from Plasmodium falciparum.

The crystals obtained from various batches of crystallization trials of FabZ from Plasmodium falciparum exhibited non-isomorphism. The c axis of the I222 cell showed a large variation of about 16 A, from c = 81 A to c = 97 A. Complete data sets were collected for three crystal forms with varying lengths of the c axis (form 1, c = 97 A; form 2, c = 92 A; form 3, c = 81 A). The crystal structure of form 1 has been reported previously. Here, the crystal structures of the other two crystal forms are reported and a detailed structural comparison is made of the three crystal forms in order to explore the possible reasons for the existence of non-isomorphism. The conformations of three loops vary between the three crystal forms. The disposition of the loops affects the crystal packing and hence the unit-cell parameter. The crystallization condition and crystallization method employed, which change the evaporation rate, determine the crystal form of the enzyme. The present analysis shows that pH-induced intrinsic conformational changes in the protein play a key role in the observed differences.