Inhibition Studies on Enzymes Involved in Isoprenoid Biosynthesis: Focus on Two Potential Drug Targets: DXR and IDI-2 Enzymes

Abstract

Isoprenoid compounds constitute an immensely diverse group of acyclic, monocyclic and polycyclic compounds that play important roles in all living organisms. Despite the diversity of their structures, this plethora of natural products arises from only two 5-carbon precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). This review will discuss the enzymes in the mevalonate (MVA) and methylerythritol phosphate (MEP) biosynthetic pathways leading to IPP and DMAPP with a particular focus on MEP synthase (DXR) and IPP isomerase (IDI), which are potential targets for the development of antibiotic compounds. DXR is the second enzyme in the MEP pathway and the only one for which inhibitors with antimicrobial activity at pharmaceutically relevant concentrations are known. All of the published DXR inhibitors are fosmidomycin analogues, except for a few bisphosphonates with moderate inhibitory activity. These far, there are no other candidates that target DXR. IDI was first identified and characterised over 40 years ago (IDI-1) and a second convergently evolved isoform (IDI-2) was discovered in 2001. IDI-1 is a metalloprotein found in Eukarya and many species of Bacteria. Its mechanism has been extensively studied. In contrast, IDI-2 requires reduced flavin mononucleotide as a cofactor. The mechanism of action for IDI-2 is less well defined. This review will describe how lead inhibitors are being improved by structure-based drug design and enzymatic assays against DXR to lead to new drug families and how mechanistic probes are being used to address questions about the mechanisms of the isomerases.

Keywords: DXR; IDI; MEP; MVA; isomerase; isopentenyl; isoprenoid; mevalonate; reductoisomerase.

Fig. 1

Biosynthetic pathways catalyzed by isoprenyl diphosphate synthases and the final reaction products. Adapted from Wang and Ohnuma [3].

Fig. 2

Overview of the well-described mevalonate pathway. The alternative route described by Grochowski et al. in Archae is represented in the box.

Fig. 3

Overview of the mevalonate-independent pathway. Interestingly, IPP (1) and DMAPP (2) are obtained in a kinetically controlled reaction.

Fig. 4

Representation of path A: α-ketol or path B retroaldol/aldol rearrangement mechanisms. This latter is preferred by Munos et al. [44].

Fig. 5

Chemical structures of selected compounds synthesized and evaluated by Ortman et al. Chemical structures of the reference inhibitors are represented in the box.

Fig. 6

Chemical structures of selected compounds synthesized and evaluated by Link et al.

Fig. 7

Chemical structures of selected compounds synthesized and evaluated by Deng et al. Compound 14 is strong, lipophilic inhibitor and has a distinct structure from fosmidomycin.

Fig. 8

Chemical structures of selected compounds synthesized and evaluated by Zinglé et al. (16–25) and by Behrendt et al. (26–28).

Fig. 9

Most recent chemical structures of selected compounds synthesized and evaluated against DXR.

Fig. 10

Elongation of isoprenoids in order to obtain complex and diverse essential molecules.

Fig. 11

Representation of the catalytic mechanism of IDI-1 via protonation of the IPP and deprotonation of the carbocationic transition state.

Fig. 12

Representation of the two putative IDI-2 mechanisms through a radical rearrangement (1) or through a protonation/deprotonation mechanism similar to IDI-1 (2).

Fig. 13

Representation of the radical mechanism suggested by Hemmi et al. and similar to the UDP-galactopyranose mutase mechanism.

Fig. 14

a. Representation of the inhibition mechanism of eIPP against IDI-2. First epoxide is activated by protonation and then an attack of a near-by nucleophilic group of the IDI-2 active centre form covalent bond. b. IDI-2 reaction is similar to IDI-1, which proceeds via carbocation-type intermediate. The FMNH₂ is acting as a nucleophilic group.

Fig. 15

Chemical structures of the studied IDI-2 inhibitors (substrate or product analogues).

Fig. 16

Latest suggested IDI-2 mechanism where the N5 nitrogen of FMN seems the most plausible candidate for the catalyst.