Targeting the IspD Enzyme in the MEP Pathway: Identification of a Novel Fragment Class

Hirsch, Anna K. H.; Diamanti, Eleonora; Hamed, Mostafa M.; Lacour, Antoine; Bravo, Patricia Isabel K.; Illarionov, Boris; Fischer, Markus; Rottmann, Matthias; Witschel, Matthias

doi:10.1002/cmdc.202100679

Cited by 7 publications

(7 citation statements)

References 25 publications

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“…It has been suggested that high levels of transporters are involved in cell detoxification, nutrient recycling, and antibiotics and drug efflux, significantly affecting the survival and development of multiple drug-resistant strains in Mtb [58,59,62,63]. It should be noted that the unique genes identified 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase and Arylamine N-acetyltransferase were previously characterized as high-confidence drug targets [64][65][66].…”

Section: Discussionmentioning

confidence: 99%

Comparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador

et al. 2022

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Background Tuberculosis is a serious infectious disease affecting millions of people. In spite of efforts to reduce the disease, increasing antibiotic resistance has contributed to persist in the top 10 causes of death worldwide. In fact, the increased cases of multi (MDR) and extreme drug resistance (XDR) worldwide remains the main challenge for tuberculosis control. Whole genome sequencing is a powerful tool for predicting drug resistance-related variants, studying lineages, tracking transmission, and defining outbreaks. This study presents the identification and characterization of resistant clinical isolates of Mycobacterium tuberculosis including a phylogenetic and molecular resistance profile study by sequencing the complete genome of 24 strains from different provinces of Ecuador. Results Genomic sequencing was used to identify the variants causing resistance. A total of 15/21 isolates were identified as MDR, 4/21 as pre-XDR and 2/21 as XDR, with three isolates discarded due to low quality; the main sub-lineage was LAM (61.9%) and Haarlem (19%) but clades X, T and S were identified. Of the six pre-XDR and XDR strains, it is noteworthy that five come from females; four come from the LAM sub-lineage and two correspond to the X-class sub-lineage. A core genome of 3,750 genes, distributed in 295 subsystems, was determined. Among these, 64 proteins related to virulence and implicated in the pathogenicity of M. tuberculosis and 66 possible pharmacological targets stand out. Most variants result in nonsynonymous amino acid changes and the most frequent genotypes were identified as conferring resistance to rifampicin, isoniazid, ethambutol, para-aminosalicylic acid and streptomycin. However, an increase in the resistance to fluoroquinolones was detected. Conclusion This work shows for the first time the variability of circulating resistant strains between men and women in Ecuador, highlighting the usefulness of genomic sequencing for the identification of emerging resistance. In this regard, we found an increase in fluoroquinolone resistance. Further sampling effort is needed to determine the total variability and associations with the metadata obtained to generate better health policies.

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Section: Discussionmentioning

confidence: 99%

Comparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador

et al. 2022

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“…We observed that more electronwithdrawing substituents, such as a nitro (8) or nitrile group (10), had a pronounced effect on the potency, resulting in a factor 400 increase (e.g., 8, PfIspD IC50 = 41 ± 7 nM). While substituents with a less distinct electronwithdrawing effect, such as the trifluoromethyl (11) and the chloride (5), had a smaller effect on the potency (e.g, 11, PfIspD IC50 = 91 ± 19 nM). Lastly, weak donating groups, such as the methyl (6), had an even smaller increase in potency (e.g, 6, PfIspD IC50 = 370 ± 80 nM), but were still significantly better than the initial hit compound 4.…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, the MEP pathway is absent in human cells, mitigating the risk of off-target side effects, hence making it a source of promising drug targets. 4,5 Validation of the MEP pathway enzymes as drug target is based on fosmidomycin, an inhibitor of the second protein, IspC or DXR, of the MEP pathway. Currently in second-phase clinical trials as a combination treatment for malaria.…”

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confidence: 99%

“…Despite the potential of IspD as a drug target, the number of IspD inhibitors reported is rather low, furthermore, the reported inhibitors are rather elaborated to synthesize or lack whole-cell activity. 5,[8][9][10][11][12] A possible cause might be the lack of a crystal structure of PfIspD available in the Protein Data Bank (PDB). Here, we report the structure-activity relationship (SAR) study of a new urea-based compound class targeting PfIspD with low nanomolar activity in vitro.…”

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confidence: 99%

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Targeting Plasmodium falciparum IspD in the Methyl-D-Erythritol Phosphate Pathway: Urea-Based Compounds with Nanomolar Potency on target with low micromolar whole-cell activity

Willocx,

Bizzarri,

Alhayek

et al. 2024

Preprint

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The methyl-D-erythritol phosphate (MEP) pathway has emerged as an interesting target in the fight against antimicrobial resistance. The pathway is essential in many human pathogens, including Plasmodium falciparum (Pf), but is absent in human cells, reducing the risk of off-target side effects. In the present study, we conducted a high-throughput screening on the third enzyme of the pathway, IspD, and discovered a new chemical class for which we ran a structure–activity relationship investigation, resulting in low-nanomolar inhibitors of PfIspD. In addition, we determined the whole-cell activity (PfNF54 IC50 = 3.4 ± 1.0 μM), mode of inhibition, metabolic, and plasma stability of the new compound class. In vivo pharmacokinetic profiling of a selection of compounds demonstrated promising behavior for future development. Lastly, we disclosed a new MS-based enzymatic assay for direct IspD activity determination, circumventing the need for auxiliary enzymes. We used this assay to investigate the mode of inhibition of our new compound class. In summary, we have identified a readily synthesizable compound class, demonstrating excellent activity and a promising profile, positioning it as a valuable tool compound for advancing research on IspD.

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“…For most bacteria and Apicomplexa parasites, the MEP pathway is the only route for the biosynthesis of IPP and DMAPP and has therefore been identified as an interesting target for the development of new antibiotics and antiparasitic drugs [ 10 , 11 , 12 , 13 , 14 , 15 , 16 ]. The MEP pathway in Plasmodium starts with the condensation of pyruvate and glyceraldehyde 3-phosphate (G3P), which yields DXP as a key metabolite.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Domiphen Bromide as a New Fast-Acting Antiplasmodial Agent Inhibiting the Apicoplastidic Methyl Erythritol Phosphate Pathway

et al. 2022

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The evolution of resistance by the malaria parasite to artemisinin, the key component of the combination therapy strategies that are at the core of current antimalarial treatments, calls for the urgent identification of new fast-acting antimalarials. The apicoplast organelle is a preferred target of antimalarial drugs because it contains biochemical processes absent from the human host. Fosmidomycin is the only drug in clinical trials targeting the apicoplast, where it inhibits the methyl erythritol phosphate (MEP) pathway. Here, we characterized the antiplasmodial activity of domiphen bromide (DB), another MEP pathway inhibitor with a rapid mode of action that arrests the in vitro growth of Plasmodium falciparum at the early trophozoite stage. Metabolomic analysis of the MEP pathway and Krebs cycle intermediates in 20 µM DB-treated parasites suggested a rapid activation of glycolysis with a concomitant decrease in mitochondrial activity, consistent with a rapid killing of the pathogen. These results present DB as a model compound for the development of new, potentially interesting drugs for future antimalarial combination therapies.

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Targeting the IspD Enzyme in the MEP Pathway: Identification of a Novel Fragment Class

Cited by 7 publications

References 25 publications

Comparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador

Comparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador

Targeting Plasmodium falciparum IspD in the Methyl-D-Erythritol Phosphate Pathway: Urea-Based Compounds with Nanomolar Potency on target with low micromolar whole-cell activity

Characterization of Domiphen Bromide as a New Fast-Acting Antiplasmodial Agent Inhibiting the Apicoplastidic Methyl Erythritol Phosphate Pathway

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