Integral membrane pyrophosphatases: a novel drug target for human pathogens?

Shah, Nita R.; Vidilaseris, Keni; Xhaard, Henri; Goldman, Adrian

doi:10.3934/biophy.2016.1.171

Cited by 16 publications

(30 citation statements)

References 101 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, atomistic MD simulations may be helpful in structure-based drug design, for assessing the magnitude of thermodynamically unfavourable changes both in conformational flexibility associated with binding and in the design of additional compounds with related chemical scaffolds. Since mPPases are not found in humans, targeting these proteins in human pathogens, such as protozoan parasites or Bacteroides species, is a viable option and would carry a reduced risk of human toxicity 29 . One strategy would be to combine structural data with computer modelling by first identifying the binding site of the initial hit compound by X-ray crystallography.…”

Section: Discussionmentioning

confidence: 99%

Insights into the mechanism of membrane pyrophosphatases by combining experiment and computer simulation

Shah

Wilkinson

Harborne

et al. 2017

Structural Dynamics

Self Cite

View full text Add to dashboard Cite

Membrane-integral pyrophosphatases (mPPases) couple the hydrolysis of pyrophosphate (PPi) to the pumping of Na+, H+, or both these ions across a membrane. Recently solved structures of the Na+-pumping Thermotoga maritima mPPase (TmPPase) and H+-pumping Vigna radiata mPPase revealed the basis of ion selectivity between these enzymes and provided evidence for the mechanisms of substrate hydrolysis and ion-pumping. Our atomistic molecular dynamics (MD) simulations of TmPPase demonstrate that loop 5–6 is mobile in the absence of the substrate or substrate-analogue bound to the active site, explaining the lack of electron density for this loop in resting state structures. Furthermore, creating an apo model of TmPPase by removing ligands from the TmPPase:IDP:Na structure in MD simulations resulted in increased dynamics in loop 5–6, which results in this loop moving to uncover the active site, suggesting that interactions between loop 5–6 and the imidodiphosphate and its associated Mg2+ are important for holding a loop-closed conformation. We also provide further evidence for the transport-before-hydrolysis mechanism by showing that the non-hydrolyzable substrate analogue, methylene diphosphonate, induces low levels of proton pumping by VrPPase.

show abstract

Section: Discussionmentioning

confidence: 99%

Insights into the mechanism of membrane pyrophosphatases by combining experiment and computer simulation

Shah

Wilkinson

Harborne

et al. 2017

Structural Dynamics

Self Cite

View full text Add to dashboard Cite

show abstract

“…16 For that, a simple, cheap, and sensitive method to determine the reaction product of mPPases is needed to screen drug candidates. Several methods have been reported for determining the phosphate released from the enzymatic reaction of pyrophosphatase, including colourimetric, 17-21 uoro-metric, 22,23 enzymatic, [24][25][26] and radiolabeling 27 methods.…”

mentioning

confidence: 99%

A high-throughput method for orthophosphate determination of thermostable membrane-bound pyrophosphatase activity

2018

Self Cite

View full text Add to dashboard Cite

Membrane-bound pyrophosphatases (mPPases) are homodimeric integral membrane proteins that hydrolyse pyrophosphate into orthophosphates coupled to the active transport of protons or sodium ions across membranes. They occur in bacteria, archaea, plants, and protist parasites. As they are essential in protist parasites and there are no homologous proteins in animals and humans, these enzymes represent an excellent drug target for treating protistal diseases. Experimental screening to find drug candidates is an important step to discover new hit compounds. For that, a cheap, simple, and robust assay is needed. Here we report the application of the molybdenum blue reaction method for a medium throughput microplate activity assay of the hyperthermophilic bacterium Thermotoga maritima mPPase and the possible application of the assay to screen inhibitors of membrane-bound pyrophosphatases.

show abstract

“…These helices form two concentric layers with six helices (TMH5-6, 11-12, and 15-16) forming the inner layer and the other ten (TMH 1-4, 7-10, and [13][14] forming the outer layer. Each monomer consists of four regions: a hydrolytic centre, a coupling funnel, an ion gate, and an exit channel 12 (Fig.…”

Section: Introductionmentioning

confidence: 99%

“…Protist parasites such as Plasmodium falciparum, Toxoplasma gondii, Trypanosoma brucei, and Leishmania donovani all possess mPPases 13 , two types (H + -pump K + -dependent and H + -pump K +independent mPPase) for Plasmodium 14 and one type (H + -pump K + -dependent) for the others 15,16,17 .…”

Section: Introductionmentioning

confidence: 99%

“…Non-hydrolysable PP i analogues are not viable mPPase drug candidates, as they will inhibit the many human enzymes that produce or hydrolyse PP i , from inorganic pyrophosphatases to polymerases and ectonucleotide pyrophosphatase/phosphodiesterases 20 . Our goal is thus the discovery of drug-like small molecular weight compounds that would specifically inhibit mPPases from protist parasites 13 . Here, we report the first non-phosphorous non-substrate analogue low…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Asymmetry in catalysis by Thermotoga maritima membrane-bound pyrophosphatase demonstrated by a non-phosphorous allosteric inhibitor

Vidilaseris

Kiriazis

Turku

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

Membrane-bound pyrophosphatases are homodimeric integral membrane proteins that hydrolyse pyrophosphate into orthophosphates, coupled to the active transport of protons or sodium ions across membranes. They are important in the life cycle of bacteria, archaea, plants, and protist parasites, but no homologous proteins exist in vertebrates, making them a promising drug target.Here, we report the first non-phosphorous allosteric inhibitor (K i of 1.8 ± 0.3 μM) of the thermophilic bacterium Thermotoga maritima membrane-bound pyrophosphatase and its bound structure at 3.7 Å resolution together with the substrate analogue imidodiphosphate. The unit cell contains two protein homodimers, each binding a single inhibitor dimer near the exit channel, creating a hydrophobic clamp that inhibits the movement of β-strand 1-2 during pumping, and thus preventing the hydrophobic gate from opening. This asymmetry of inhibitor binding with respect to each homodimer provide the first clear demonstration of asymmetry in the catalytic cycle of membrane-bound pyrophosphatases.

show abstract

Integral membrane pyrophosphatases: a novel drug target for human pathogens?

Cited by 16 publications

References 101 publications

Insights into the mechanism of membrane pyrophosphatases by combining experiment and computer simulation

Insights into the mechanism of membrane pyrophosphatases by combining experiment and computer simulation

A high-throughput method for orthophosphate determination of thermostable membrane-bound pyrophosphatase activity

Asymmetry in catalysis by Thermotoga maritima membrane-bound pyrophosphatase demonstrated by a non-phosphorous allosteric inhibitor

Contact Info

Product

Resources

About