Druggability of the enzymes of the non-mevalonate-pathway

Masini, Tiziana; Kroezen, Blijke S.; Hirsch, Anna K. H.

doi:10.1016/j.drudis.2013.07.003

Cited by 55 publications

(81 citation statements)

References 62 publications

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“…The presence of two conformers of TMBPP in the E. coli IspH:TMBPP complex is puzzling and might be related to the selectivity of the protonation. The IspH enzyme was recently predicted to contain a spacious druggable pocket, formed by binding sites for the substrate and neighboring sites, which might accommodate larger inhibitors than the substrate . Due to the large size of the IspH active site, many conformers of 10 might be accommodated, and the two conformers observed in the structure of the IspH:TMBPP complex might represent the two most stable conformers when substrate 10 is replaced by 11 .…”

Section: Resultsmentioning

confidence: 99%

“…The IspH enzyme was recently predicted to contain as pacious druggable pocket, formed by bindings ites for the substrate and neighboring sites, which might accommodate larger inhibitors than the substrate. [18] Due to the large size of the IspH active site, many conformers of 10 might be accommodated, and the two conformers observed in the structure of the IspH:TMBPPc omplex might represent the two mosts table conformers when substrate 10 is replaced by 11.I th as been proposed that the hydrogen required for the final protonation could be provided by the b-phosphate of the allyl anion intermediate. [11,19] As the distance between the C4 atom of TMBPPa nd the b-phosphate differs in both conformers by more than 1 ,i ti sa ttractive to propose that protonation at C4 is disfavored if HMBPP adopts the non-regular conformation, leading instead to protonation at C2 and, hence,o nly to product, 1.T he factt hat IspH seems to accommodate more than one substrate conformer might explain the origin of the two products,b ut this hypothesis needs confirmation.…”

Section: Resultsmentioning

confidence: 99%

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Further Insight into Crystal Structures of Escherichia coli IspH/LytB in Complex with Two Potent Inhibitors of the MEP Pathway: A Starting Point for Rational Design of New Antimicrobials

et al. 2017

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IspH, also called LytB, a protein involved in the biosynthesis of isoprenoids through the methylerythritol phosphate pathway, is an attractive target for the development of new antimicrobial drugs. Here, we report crystal structures of Escherichia coli IspH in complex with the two most potent inhibitors: (E)-4-mercapto-3-methylbut-2-en-1-yl diphosphate (TMBPP) and (E)-4-amino-3-methylbut-2-en-1-yl diphosphate (AMBPP) at 1.95 and 1.7 Å resolution, respectively. The structure of the E. coli IspH:TMBPP complex exhibited two conformers of the inhibitor. This unexpected feature was exploited to design and evolve new antimicrobial candidates in silico.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Further Insight into Crystal Structures of Escherichia coli IspH/LytB in Complex with Two Potent Inhibitors of the MEP Pathway: A Starting Point for Rational Design of New Antimicrobials

et al. 2017

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“…The MEP pathway, therefore, represents a platform for the development of novel herbicides, antimalarials, and antibiotics to aid the treatment of human disease. [13–16]…”

Section: Introductionmentioning

confidence: 99%

Mechanistic binding insights for 1-deoxy-d-Xylulose-5-Phosphate synthase, the enzyme catalyzing the first reaction of isoprenoid biosynthesis in the malaria-causing protists, Plasmodium falciparum and Plasmodium vivax

Battistini

Shoji

Handa

et al. 2016

Protein Expression and Purification

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We have successfully truncated and recombinantly-expressed 1-deoxy-D-xylulose-5-phosphate synthase (DXS) from both P. vivax and P. falciparum. We elucidated the order of substrate binding for both of these ThDP-dependent enzymes using steady-state kinetic analyses, dead-end inhibition, and intrinsic tryptophan fluorescence titrations. Both enzymes adhere to a random sequential mechanism with respect to binding of both substrates: pyruvate and D-glyceraldehyde-3-phosphate. These findings are in contrast to other ThDP-dependent enzymes, which exhibit classical ordered and/or ping-pong kinetic mechanisms. A better understanding of the kinetic mechanism for these two Plasmodial enzymes could aid in the development of novel DXS-specific inhibitors that might prove useful in treatment of malaria.

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“…Despite the low lipophilic character of the TDP pocket with respect to the average for druggable pockets, 32 it obtained a rather high Dscore when analysed with the programme DogSiteScore. 33 The fragments were designed so that they could be further grown either towards the diphosphate pocket or ideally towards the substrate-binding pocket, where selectivity could be gained.…”

Section: Resultsmentioning

confidence: 99%

De novo fragment-based design of inhibitors of DXS guided by spin-diffusion-based NMR spectroscopy

et al. 2014

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We applied for the first time an innovative ligand-based NMR methodology (STI) to a medicinal-chemistry project aimed at the development of inhibitors for the enzyme 1-deoxy-D-xylulose-5-phosphate synthase (DXS). DXS is the first enzyme of the 2C-methyl-D-erythritol-4-phosphate (MEP) pathway, present in most bacteria (and not in humans) and responsible for the synthesis of the essential isoprenoid precursors. We designed de novo a first generation of fragments, using Deinococcus radiodurans DXS as a model enzyme, targeting the thiamine diphosphate (TDP) pocket of DXS whilst also exploring the putative substrate-binding pocket, where selectivity over other human TDP-dependent enzymes could be gained. The STI methodology -suitable for weak binders -was essential to determine the binding mode in solution of one of the fragments, circumventing the requirement for an X-ray co-crystal structure, which is known to be particularly challenging for this specific enzyme and in general for weak binders. Based on this finding, we carried out fragment growing and optimisation, which led to a threefold more potent fragment, about as potent as the well-established thiamine analogue deazathiamine.The STI methodology proved therefore its strong potential as a tool to support medicinal-chemistry projects in their early stages, especially when dealing with weak binders.

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Druggability of the enzymes of the non-mevalonate-pathway

Cited by 55 publications

References 62 publications

Further Insight into Crystal Structures of Escherichia coli IspH/LytB in Complex with Two Potent Inhibitors of the MEP Pathway: A Starting Point for Rational Design of New Antimicrobials

Further Insight into Crystal Structures of Escherichia coli IspH/LytB in Complex with Two Potent Inhibitors of the MEP Pathway: A Starting Point for Rational Design of New Antimicrobials

Mechanistic binding insights for 1-deoxy-d-Xylulose-5-Phosphate synthase, the enzyme catalyzing the first reaction of isoprenoid biosynthesis in the malaria-causing protists, Plasmodium falciparum and Plasmodium vivax

De novo fragment-based design of inhibitors of DXS guided by spin-diffusion-based NMR spectroscopy

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