Synthesis and Characterization of Cytidine Derivatives that Inhibit the Kinase IspE of the Non‐Mevalonate Pathway for Isoprenoid Biosynthesis

Abstract

The enzymes of the non-mevalonate pathway for isoprenoid biosynthesis are attractive targets for the development of novel drugs against malaria and tuberculosis. This pathway is used exclusively by the corresponding pathogens, but not by humans. A series of water-soluble, cytidine-based inhibitors that were originally designed for the fourth enzyme in the pathway, IspD, were shown to inhibit the subsequent enzyme, the kinase IspE (from Escherichia coli). The binding mode of the inhibitors was verified by co-crystal structure analysis, using Aquifex aeolicus IspE. The crystal structures represent the first reported example of a co-crystal structure of IspE with a synthetic ligand and confirmed that ligand binding affinity originates mainly from the interactions of the nucleobase moiety in the cytidine binding pocket of the enzyme. In contrast, the appended benzimidazole moieties of the ligands adopt various orientations in the active site and establish only poor intermolecular contacts with the protein. Defined binding sites for sulfate ions and glycerol molecules, components in the crystallization buffer, near the well-conserved ATP-binding Gly-rich loop of IspE were observed. The crystal structures of A. aeolicus IspE nicely complement the one from E. coli IspE for use in structure-based design, namely by providing invaluable structural information for the design of inhibitors targeting IspE from Mycobacterium tuberculosis and Plasmodium falciparum. Similar to the enzymes from these pathogens, A. aeolicus IspE directs the OH group of a tyrosine residue into a pocket in the active site. In the E. coli enzyme, on the other hand, this pocket is lined by phenylalanine and has a more pronounced hydrophobic character.

Isoprenoid biosynthesis in bacterial pathogens

“…Sequence-structure comparisons revealed that the active site and ligand interactions are highly conserved for YchB and that A. aeolicus YchB represents a suitable model for the human pathogen M. tuberculosis . A. aeolicus IspE has proved invaluable for providing structural information in the structure-based design approach for the generation of IspE inhibitors for organisms such as Plasmodium falciparum and M. tuberculosis (Crane et al, 2008;Hirsch et al, 2008). Co-crystal structure analysis (Crane et al, 2008;Hirsch et al, 2008) and structure-activity relationships (SARs) of A. aeolicus IspE have validated the binding mode of several new inhibitors.…”

“…A. aeolicus IspE has proved invaluable for providing structural information in the structure-based design approach for the generation of IspE inhibitors for organisms such as Plasmodium falciparum and M. tuberculosis (Crane et al, 2008;Hirsch et al, 2008). Co-crystal structure analysis (Crane et al, 2008;Hirsch et al, 2008) and structure-activity relationships (SARs) of A. aeolicus IspE have validated the binding mode of several new inhibitors. Buetow et al (2007) determined the crystal structure of M. smegmatis YghB, which has a high degree of similarity to YghB of M. tuberculosis.…”

Identification of novel small molecule inhibitors of 4-diphosphocytidyl-2-C-methyl-d-erythritol (CDP-ME) kinase of Gram-negative bacteria

“…At a time when there is an urgent need for new antimicrobial agents against resistant organisms, some suggested that it might be useful to identify new structural classes heretofore not observed [26]. Despite attempts to design specific CDP-ME kinase inhibitors by synthesizing derivatives of cytidine/cytosine [27–29], there has been no documented experimental, random HTS of inhibitors for E. coli or other bacterial CDP-ME kinases. Although these proof-of-principle approaches are valid, the identified inhibitors shared closely similar chemotypes and in some cases, IC 50 values of mM (millimolar) range [27].…”

“…Despite attempts to design specific CDP-ME kinase inhibitors by synthesizing derivatives of cytidine/cytosine [27–29], there has been no documented experimental, random HTS of inhibitors for E. coli or other bacterial CDP-ME kinases. Although these proof-of-principle approaches are valid, the identified inhibitors shared closely similar chemotypes and in some cases, IC 50 values of mM (millimolar) range [27]. In this study, we took two different approaches to expand the repertoire and diversity of the bacterial CDP-ME kinase inhibitors.…”

Biochemistry of the non-mevalonate isoprenoid pathway

“…The structural and mechanistic information summarized above served as the basis for the rational design of inhibitors for IspE and IspF protein [83][84][85][86][87][88][89][90]. In both cases, the cytosine motif present in the substrate and/or product served as the basic template.…”