Unlocking the MEP/DOXP Pathway: Enzymatic Secrets Fueling Next-Gen Therapeutics (2025)

Unlocking the MEP/DOXP Pathway: Enzymatic Secrets Fueling Next-Gen Therapeutics (2025)

Caleb Johnson

The Enzymology of the Non-Mevalonate (MEP/DOXP) Pathway: Unraveling Biochemical Innovations and Their Impact on Drug Discovery. Explore How This Alternative Isoprenoid Pathway is Shaping the Future of Antimicrobial and Antimalarial Strategies. (2025)

Introduction to the MEP/DOXP Pathway: Historical Context and Discovery

The non-mevalonate pathway, also known as the methylerythritol phosphate (MEP) or 1-deoxy-D-xylulose 5-phosphate (DOXP) pathway, represents a crucial alternative to the classical mevalonate pathway for isoprenoid biosynthesis. Discovered in the late 1990s, the MEP/DOXP pathway was first elucidated through studies in Escherichia coli and various plant species, revealing a previously unrecognized route for the production of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), the universal precursors of isoprenoids. This pathway is now known to be present in most bacteria, algae, and the plastids of higher plants, but absent in animals, making it a significant target for antimicrobial and antiparasitic drug development.

The historical context of the MEP/DOXP pathway’s discovery is rooted in the search for alternative isoprenoid biosynthesis routes in organisms where the mevalonate pathway was not detected. Early biochemical and genetic studies in the 1990s, particularly in E. coli, led to the identification of DOXP as a key intermediate, followed by the characterization of the enzymes responsible for its conversion to MEP and subsequent metabolites. The pathway’s full enzymatic sequence was mapped by the early 2000s, with the identification of seven core enzymes: DXS, DXR, IspD, IspE, IspF, IspG, and IspH.

In the years leading up to 2025, research has increasingly focused on the detailed enzymology of the MEP/DOXP pathway, leveraging advances in structural biology, genomics, and metabolomics. The availability of high-resolution crystal structures for several pathway enzymes has enabled a deeper understanding of their catalytic mechanisms and regulatory features. For example, the enzyme IspH, which catalyzes the final step in the pathway, has been extensively studied due to its unique iron-sulfur cluster and its potential as a drug target against pathogens such as Plasmodium falciparum and Mycobacterium tuberculosis.

The significance of the MEP/DOXP pathway extends beyond basic science. Its absence in humans and presence in many pathogens has spurred international research initiatives, including those coordinated by organizations such as the National Institutes of Health and the World Health Organization, to develop selective inhibitors as novel antibiotics and antimalarials. As of 2025, the pathway remains a focal point for drug discovery, synthetic biology, and metabolic engineering, with ongoing efforts to exploit its unique enzymology for both therapeutic and industrial applications.

Key Enzymes and Their Mechanisms in the MEP/DOXP Pathway

The non-mevalonate pathway, also known as the MEP/DOXP pathway, is a crucial metabolic route for isoprenoid biosynthesis in many bacteria, apicomplexan parasites, and plant plastids. Unlike the mevalonate pathway found in animals and fungi, the MEP/DOXP pathway is absent in humans, making its enzymes attractive targets for antimicrobial and antiparasitic drug development. As of 2025, research continues to elucidate the detailed enzymology of this pathway, with a focus on the structure, function, and inhibition of its key enzymes.

The pathway initiates with the condensation of pyruvate and glyceraldehyde-3-phosphate, catalyzed by 1-deoxy-D-xylulose-5-phosphate synthase (DXS), forming 1-deoxy-D-xylulose-5-phosphate (DOXP). DXS is a thiamine diphosphate-dependent enzyme, and recent structural studies have provided insights into its active site dynamics and regulation. The subsequent step, catalyzed by 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), converts DOXP to 2-C-methyl-D-erythritol 4-phosphate (MEP). DXR is a validated drug target, with the antibiotic fosmidomycin acting as a potent inhibitor; ongoing research in 2025 is focused on developing next-generation DXR inhibitors with improved pharmacokinetic properties and resistance profiles.

Further downstream, the pathway involves a series of unique enzymes: MEP cytidylyltransferase (IspD), CDP-ME kinase (IspE), MEcPP synthase (IspF), HMBPP synthase (IspG), and HMBPP reductase (IspH). Each enzyme catalyzes a distinct transformation, often involving unusual cofactors such as iron-sulfur clusters (notably in IspG and IspH). Recent advances in cryo-electron microscopy and X-ray crystallography have enabled high-resolution visualization of these enzymes, revealing mechanistic details that are guiding rational drug design efforts. For example, the iron-sulfur cluster-dependent enzymes IspG and IspH have been shown to undergo complex electron transfer reactions, and their inhibition is being explored as a strategy against multidrug-resistant pathogens.

The European Bioinformatics Institute and RCSB Protein Data Bank continue to serve as key repositories for structural and functional data on MEP pathway enzymes, supporting global research efforts. Additionally, organizations such as the National Institutes of Health are funding projects aimed at exploiting the pathway for novel antimicrobial therapies. Looking ahead, the next few years are expected to see the translation of enzymological insights into clinical candidates, particularly for diseases like malaria and tuberculosis, where the MEP/DOXP pathway is essential for pathogen survival.

Comparative Analysis: MEP/DOXP vs. Mevalonate Pathways

The non-mevalonate pathway, also known as the MEP (2-C-methyl-D-erythritol 4-phosphate) or DOXP (1-deoxy-D-xylulose 5-phosphate) pathway, is a crucial metabolic route for isoprenoid biosynthesis in many bacteria, apicomplexan parasites, and plant plastids. In contrast, animals and fungi predominantly utilize the mevalonate (MVA) pathway. Comparative enzymology between these two pathways has become a focal point for both fundamental research and applied biotechnology, especially in the context of antimicrobial drug development and metabolic engineering.

The MEP/DOXP pathway comprises seven enzymatic steps, beginning with the condensation of pyruvate and glyceraldehyde-3-phosphate to form DOXP, catalyzed by DOXP synthase (DXS). This is followed by a series of transformations involving enzymes such as DOXP reductoisomerase (DXR), MEP cytidylyltransferase (IspD), and others, ultimately yielding isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP)—the universal isoprenoid precursors. In contrast, the MVA pathway starts from acetyl-CoA and proceeds through mevalonate, involving enzymes like HMG-CoA reductase.

Recent structural and mechanistic studies, particularly those employing cryo-electron microscopy and X-ray crystallography, have elucidated the active sites and catalytic mechanisms of several MEP pathway enzymes. For example, the structure of DXR has been resolved in complex with its substrate and inhibitors, providing a template for rational drug design. These advances are significant because the MEP pathway is absent in humans, making its enzymes attractive targets for novel antibiotics and antimalarials. The World Health Organization (World Health Organization) and research consortia have highlighted the urgent need for new antimicrobial strategies, and the MEP pathway remains a top candidate for such interventions.

Comparative analyses have revealed that while both pathways converge on the production of IPP and DMAPP, their regulatory mechanisms and enzyme sensitivities differ markedly. For instance, feedback inhibition in the MVA pathway is tightly linked to cholesterol biosynthesis in mammals, whereas the MEP pathway is regulated by substrate availability and feedback from downstream isoprenoid products in bacteria and plants. This divergence is being exploited in synthetic biology, with organizations such as the European Molecular Biology Laboratory and National Institutes of Health supporting research into pathway engineering for sustainable production of isoprenoids, including pharmaceuticals and biofuels.

Looking ahead to 2025 and beyond, the integration of high-throughput enzyme screening, computational modeling, and synthetic biology is expected to accelerate the discovery of selective MEP pathway inhibitors and the optimization of isoprenoid biosynthesis in engineered organisms. The continued comparative enzymology of the MEP and MVA pathways will be central to both drug discovery and industrial biotechnology, with global health and sustainability implications.

Structural Biology of MEP/DOXP Pathway Enzymes

The structural biology of enzymes involved in the non-mevalonate pathway, also known as the MEP/DOXP pathway, has become a focal point for research in infectious disease and antimicrobial drug discovery as of 2025. This pathway, absent in humans but essential in many bacteria, apicomplexan parasites, and plant plastids, offers a suite of unique enzymatic targets for selective inhibition. The pathway comprises seven core enzymes: 1-deoxy-D-xylulose-5-phosphate synthase (DXS), DXP reductoisomerase (DXR), 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD), 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE), 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF), 4-hydroxy-3-methylbut-2-enyl diphosphate synthase (IspG), and 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (IspH).

Recent advances in cryo-electron microscopy (cryo-EM) and X-ray crystallography have enabled high-resolution structural elucidation of several MEP pathway enzymes. For instance, the structure of Plasmodium falciparum DXR, a validated antimalarial target, has been resolved at sub-2.5 Å resolution, revealing key active site residues and conformational dynamics critical for inhibitor design. Similarly, bacterial IspH and IspG, both iron-sulfur cluster-containing enzymes, have been structurally characterized, providing insights into their unique catalytic mechanisms and potential allosteric sites. These findings are being leveraged by academic consortia and public health organizations to accelerate the development of novel antibiotics and antiparasitics.

The RCSB Protein Data Bank, a global repository for macromolecular structures, has seen a marked increase in deposited MEP pathway enzyme structures since 2022, reflecting the growing interest and technical feasibility in this area. Structural data are being integrated with computational modeling and fragment-based drug discovery approaches, as supported by initiatives from organizations such as the National Institutes of Health and the European Bioinformatics Institute. These efforts are expected to yield new chemical scaffolds with high specificity for MEP pathway enzymes, minimizing off-target effects in humans.

Looking ahead, the next few years are likely to witness further breakthroughs in the structural biology of the MEP/DOXP pathway. Advances in time-resolved crystallography and in situ structural studies are anticipated to provide dynamic views of enzyme catalysis and inhibitor binding. Such insights will be crucial for rational drug design, particularly in the context of rising antimicrobial resistance. Collaborative projects between structural biologists, chemists, and infectious disease specialists, often coordinated by international bodies such as the World Health Organization, are poised to translate these structural discoveries into tangible therapeutic advances.

Regulation and Genetic Control of the MEP/DOXP Pathway

The regulation and genetic control of the MEP/DOXP pathway, a crucial route for isoprenoid biosynthesis in bacteria, algae, and plant plastids, remains a dynamic area of research as of 2025. This pathway, distinct from the mevalonate pathway found in animals and fungi, is tightly regulated at multiple enzymatic and genetic levels to ensure cellular homeostasis and adaptability to environmental cues.

Recent studies have highlighted the central role of 1-deoxy-D-xylulose 5-phosphate synthase (DXS), the first committed enzyme of the pathway, as a major regulatory node. DXS activity is modulated both transcriptionally and post-translationally, with feedback inhibition by downstream isoprenoid intermediates such as IPP and DMAPP. Advances in transcriptomics and proteomics have revealed that DXS gene expression is responsive to light, developmental stage, and stress conditions, particularly in model plants like Arabidopsis thaliana and economically important crops. The plastidial localization of the pathway adds another layer of regulation, involving transporters and compartmentalized metabolite pools.

Genetic control of the MEP/DOXP pathway is orchestrated by a network of nuclear-encoded genes, many of which are subject to coordinated regulation with other plastidial metabolic processes. In 2024–2025, CRISPR/Cas9-mediated genome editing has enabled precise manipulation of key pathway genes, such as dxs, dxr (encoding 1-deoxy-D-xylulose 5-phosphate reductoisomerase), and ispD, in both model and non-model organisms. These interventions have provided insights into gene redundancy, essentiality, and the impact of gene dosage on isoprenoid output. For instance, overexpression of dxs and dxr in transgenic plants has led to increased accumulation of valuable terpenoids, while knockouts have confirmed their essential roles in viability and development.

At the systems level, regulatory cross-talk between the MEP/DOXP pathway and other metabolic networks, such as the shikimate and carotenoid pathways, is being elucidated through integrative omics approaches. The identification of transcription factors and small RNAs that modulate pathway gene expression is a current focus, with the aim of engineering plants and microbes for enhanced production of pharmaceuticals, biofuels, and industrial isoprenoids.

Looking ahead, the next few years are expected to see the deployment of synthetic biology tools for fine-tuned pathway regulation, including inducible promoters and synthetic regulatory circuits. These advances, supported by international collaborations and initiatives such as those coordinated by the European Molecular Biology Organization and National Science Foundation, are poised to accelerate both fundamental understanding and biotechnological exploitation of the MEP/DOXP pathway.

Pharmacological Targeting: Inhibitors and Drug Development

The non-mevalonate pathway, also known as the methylerythritol phosphate (MEP) or 1-deoxy-D-xylulose 5-phosphate (DOXP) pathway, is a crucial metabolic route for isoprenoid biosynthesis in many bacteria, apicomplexan parasites (including Plasmodium spp.), and plant plastids, but is absent in humans. This unique distribution makes its enzymes attractive pharmacological targets, particularly for the development of novel antibiotics and antimalarials. As of 2025, research and drug development efforts are intensifying, with a focus on both established and emerging enzymatic targets within the pathway.

The MEP/DOXP pathway comprises seven enzymatic steps, each catalyzed by a distinct enzyme: DXS, DXR (also known as IspC), IspD, IspE, IspF, IspG, and IspH. Among these, DXR has been the most extensively studied, with the antibiotic fosmidomycin and its analogs serving as prototypical inhibitors. Fosmidomycin, originally developed as an antibacterial, has demonstrated potent antimalarial activity by inhibiting DXR, and is currently under clinical evaluation in combination therapies for malaria. However, resistance and limited spectrum have prompted the search for next-generation inhibitors targeting other enzymes in the pathway.

Recent structural and mechanistic studies, supported by organizations such as the National Institutes of Health and the Helmholtz Association, have elucidated the active sites and catalytic mechanisms of downstream enzymes like IspD, IspE, IspF, IspG, and IspH. These advances have enabled structure-based drug design, with several small-molecule inhibitors now in preclinical development. Notably, IspH, which catalyzes the final step of the pathway, has emerged as a particularly promising target due to its unique [4Fe-4S] cluster and absence in humans. Inhibitors of IspH are being explored for their broad-spectrum antibacterial and antiparasitic potential.

In 2025, collaborative initiatives involving academic consortia, public health agencies, and pharmaceutical companies are accelerating the translation of MEP pathway inhibitors into clinical candidates. The World Health Organization has highlighted the need for new antimalarial agents with novel mechanisms, and the MEP pathway remains a priority. Additionally, the European Medicines Agency and U.S. Food and Drug Administration are providing regulatory guidance for the development of anti-infectives targeting this pathway.

Looking ahead, the next few years are expected to see the advancement of MEP pathway inhibitors into early-phase clinical trials, particularly for multidrug-resistant bacterial infections and malaria. The integration of high-throughput screening, computational modeling, and chemical biology will likely yield new classes of selective inhibitors, further expanding the pharmacological arsenal against pathogens reliant on the non-mevalonate pathway.

Role in Pathogenic Microorganisms and Implications for Antimicrobial Therapy

The non-mevalonate pathway, also known as the methylerythritol phosphate (MEP) or 1-deoxy-D-xylulose 5-phosphate (DOXP) pathway, is a crucial metabolic route for isoprenoid biosynthesis in many pathogenic bacteria and apicomplexan parasites, including Plasmodium falciparum, the causative agent of malaria. Unlike humans and other mammals, which utilize the mevalonate pathway, these pathogens rely exclusively on the MEP/DOXP pathway, making its enzymes attractive targets for novel antimicrobial therapies.

Recent enzymological studies have elucidated the structure, function, and inhibition mechanisms of key enzymes in the MEP/DOXP pathway, such as DOXP synthase (DXS), DOXP reductoisomerase (DXR), and IspG/IspH. Advances in X-ray crystallography and cryo-electron microscopy have provided high-resolution structures of these enzymes, enabling rational drug design efforts. For instance, the antibiotic fosmidomycin, a potent inhibitor of DXR, has demonstrated efficacy against P. falciparum and several Gram-negative bacteria in both in vitro and clinical settings. However, resistance and limited spectrum have prompted the search for next-generation inhibitors with improved pharmacokinetic properties and broader activity.

In 2025, research is increasingly focused on the development of dual- or multi-target inhibitors that simultaneously block multiple enzymes within the MEP/DOXP pathway, aiming to reduce the likelihood of resistance development. Structure-guided approaches, supported by computational modeling and high-throughput screening, are accelerating the identification of novel scaffolds. Additionally, the essentiality of the MEP/DOXP pathway in pathogens but not in humans continues to drive interest in these enzymes as selective drug targets, minimizing potential host toxicity.

Collaborative efforts between academic institutions, public health organizations, and pharmaceutical companies are intensifying. For example, the National Institutes of Health and the World Health Organization are supporting research into MEP/DOXP pathway inhibitors as part of broader antimicrobial resistance (AMR) strategies. The European Medicines Agency and U.S. Food and Drug Administration are also monitoring the clinical development of such agents, given their potential to address unmet needs in infectious disease treatment.

Looking ahead, the next few years are expected to yield further insights into the regulation and dynamics of the MEP/DOXP pathway in pathogenic microorganisms, as well as the emergence of preclinical and clinical candidates targeting its enzymes. These advances may pave the way for new classes of antimicrobials, crucial in the fight against drug-resistant infections and diseases like malaria.

Biotechnological Applications: Synthetic Biology and Metabolic Engineering

The non-mevalonate pathway, also known as the MEP/DOXP pathway, is a crucial metabolic route for isoprenoid biosynthesis in bacteria, algae, and plant plastids. Its unique enzymology has made it a focal point for synthetic biology and metabolic engineering, especially as the demand for sustainable production of isoprenoids—key precursors for pharmaceuticals, fragrances, and biofuels—continues to rise. In 2025, advances in the characterization and engineering of MEP pathway enzymes are accelerating the development of microbial cell factories and plant systems with enhanced isoprenoid yields.

Recent years have seen significant progress in elucidating the structure-function relationships of the seven core enzymes of the MEP pathway, from 1-deoxy-D-xylulose-5-phosphate synthase (DXS) to 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR). High-resolution structural data, enabled by cryo-electron microscopy and X-ray crystallography, have provided new insights into enzyme mechanisms and regulatory sites, facilitating rational design and directed evolution approaches. For example, engineering of DXS and DXR (1-deoxy-D-xylulose-5-phosphate reductoisomerase) has led to variants with improved catalytic efficiency and reduced feedback inhibition, directly impacting isoprenoid titers in engineered Escherichia coli and Synechocystis strains.

Synthetic biology platforms are increasingly leveraging modular pathway assembly and CRISPR-based genome editing to optimize flux through the MEP pathway. In 2025, several research groups are employing multiplexed gene editing to fine-tune expression levels of MEP pathway enzymes, balancing precursor supply and minimizing metabolic bottlenecks. Additionally, the integration of dynamic regulatory circuits—such as metabolite-responsive promoters and riboswitches—enables real-time adjustment of pathway activity in response to cellular or environmental cues.

Biotechnological applications are not limited to microbial systems. Plant metabolic engineering, particularly in crops and medicinal plants, is harnessing MEP pathway manipulation to boost the production of high-value terpenoids. The use of genome editing tools, such as CRISPR/Cas9, is facilitating precise modifications of endogenous MEP pathway genes, with several proof-of-concept studies demonstrating increased accumulation of target compounds in plastids.

Looking ahead, the next few years are expected to bring further integration of computational modeling, machine learning, and high-throughput screening to accelerate enzyme optimization and pathway balancing. Collaborative initiatives, such as those coordinated by the U.S. Department of Energy Joint Genome Institute and the European Bioinformatics Institute, are providing open-access genomic and enzymatic data, supporting global efforts in pathway engineering. As the enzymology of the MEP pathway becomes increasingly well-understood, its biotechnological exploitation is poised to expand, driving innovation in sustainable chemical production and synthetic biology.

The market and public interest in the enzymology of the non-mevalonate pathway (MEP/DOXP pathway) are poised for significant growth in 2025 and the following years, driven by advances in antimicrobial drug discovery, synthetic biology, and agricultural biotechnology. The MEP/DOXP pathway, essential for isoprenoid biosynthesis in many bacteria, apicomplexan parasites, and plant plastids, remains absent in humans, making its enzymes attractive targets for selective therapeutics and metabolic engineering.

Recent years have seen a surge in research funding and collaborative initiatives focused on elucidating the structure, function, and inhibition of key MEP pathway enzymes such as DXS, DXR, IspD, IspE, IspF, IspG, and IspH. This trend is expected to intensify through 2025, as organizations like the National Institutes of Health and the World Health Organization continue to prioritize antimicrobial resistance and malaria eradication. The MEP pathway’s role in pathogens such as Plasmodium falciparum and Mycobacterium tuberculosis has led to increased investment in high-throughput screening and structure-based drug design targeting these enzymes.

On the industrial front, the demand for sustainable production of isoprenoids—used in pharmaceuticals, flavors, fragrances, and biofuels—is catalyzing interest in engineering microbial hosts via the MEP pathway. Companies and research consortia are leveraging advances in enzyme engineering and synthetic biology to optimize flux through the MEP pathway, aiming to enhance yields and reduce costs. The Synthetic Biology Leadership Council and similar bodies are supporting public-private partnerships to accelerate commercialization of MEP pathway-based bioprocesses.

Market forecasts for 2025 anticipate a compound annual growth rate (CAGR) in the high single digits for MEP pathway enzyme research tools, reagents, and related services. This is underpinned by the expanding pipeline of MEP-targeted drug candidates and the growing adoption of pathway engineering in industrial biotechnology. Public interest is also expected to rise, particularly as new antibiotics and antimalarials targeting the MEP pathway progress into clinical trials, and as sustainable isoprenoid production aligns with global climate and health goals.

Looking ahead, the next few years will likely see increased cross-sector collaboration, further integration of AI-driven enzyme design, and the emergence of novel MEP pathway modulators. Regulatory agencies such as the European Medicines Agency are anticipated to play a key role in shaping the translational landscape, ensuring safety and efficacy of new therapeutics and bioproducts derived from MEP pathway enzymology.

Challenges, Knowledge Gaps, and Emerging Research Directions

The non-mevalonate pathway, also known as the MEP/DOXP pathway, is a crucial metabolic route for isoprenoid biosynthesis in many bacteria, apicomplexan parasites, and plant plastids. Despite significant advances in elucidating the enzymology of this pathway, several challenges and knowledge gaps persist as of 2025, shaping the direction of current and near-future research.

A primary challenge remains the structural and mechanistic characterization of several MEP pathway enzymes, particularly in pathogenic organisms. While crystal structures for enzymes such as DXS (1-deoxy-D-xylulose-5-phosphate synthase) and DXR (1-deoxy-D-xylulose-5-phosphate reductoisomerase) have been resolved for model species, high-resolution structures from clinically relevant pathogens (e.g., Plasmodium falciparum and Mycobacterium tuberculosis) are still limited. This impedes rational drug design efforts targeting these enzymes for novel anti-infective therapies. Recent advances in cryo-electron microscopy and AI-driven protein structure prediction are expected to accelerate progress in this area over the next few years, as highlighted by initiatives from organizations such as the European Bioinformatics Institute and RCSB Protein Data Bank.

Another significant knowledge gap involves the regulation and integration of the MEP pathway with other metabolic networks. The pathway’s flux control points, feedback mechanisms, and cross-talk with the mevalonate pathway in plants and engineered microbes remain incompletely understood. This limits the ability to optimize isoprenoid production in synthetic biology applications. Ongoing research, supported by entities like the National Science Foundation and National Institutes of Health, is increasingly focused on systems biology approaches, including metabolomics and fluxomics, to map these regulatory networks in detail.

Emerging research directions also include the discovery of novel MEP pathway variants and enzyme isoforms in extremophiles and uncultured microorganisms, facilitated by advances in metagenomics and single-cell sequencing. These efforts, championed by consortia such as the Joint Genome Institute, are expected to reveal new biocatalysts with unique properties for industrial biotechnology.

Finally, the development of selective inhibitors for MEP pathway enzymes remains a high priority, particularly for combating antimicrobial resistance. However, challenges persist in achieving specificity and cell permeability, especially for Gram-negative bacteria and apicomplexan parasites. Collaborative initiatives between academic groups and pharmaceutical companies, as coordinated by organizations like the World Health Organization, are anticipated to drive translational research in this area through 2025 and beyond.

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