Dynamic Substrate Enhancement for the Identification of Specific, Second‐Site‐Binding Fragments Targeting a Set of Protein Tyrosine Phosphatases

Schmidt, Marco F.; Groves, Matthew R.; Rademann, Jörg

doi:10.1002/cbic.201100414

Cited by 28 publications

(23 citation statements)

References 31 publications

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“…Most protein tyrosine phosphatase (PTP) inhibitors compete with the phosphate substrate for the active site of the enzymes and thus contain phosphate bioisosteres, which can be developed to highly specific inhibitors by extension with fragments targeting specific secondary binding sites . Bioisosteres of the phosphotyrosine residue include benzyl phosphonates, difluorobenzyl phosphonates, sulfonates, triflylamides, carboxylic acids, and isothiazolidinones . Recently, benzoyl phosphonates were discovered as photoactivated phosphotyrosine bioisosteres and have been used for the specific deactivation and covalent labeling of phosphotyrosine recognition domains and photo‐deactivation of PTP .…”

Section: Introductionmentioning

confidence: 99%

Benzyl Mono‐P‐Fluorophosphonate and Benzyl Penta‐P‐Fluorophosphate Anions Are Physiologically Stable Phosphotyrosine Mimetics and Inhibitors of Protein Tyrosine Phosphatases

Wagner

Accorsi

Rademann

2017

Chemistry A European J

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α,α-Difluoro-benzyl phosphonates are currently the most popular class of phosphotyrosine mimetics. Structurally derived from the natural substrate phosphotyrosine, they constitute classical bioisosteres and have enabled the development of potent inhibitors of protein tyrosine phosphatases (PTP) and phosphotyrosine recognition sites such as SH2 domains. Being dianions bearing two negative charges, phosphonates, however, do not permeate membranes and thus are often inactive in cells and have not been a successful starting point toward therapeutics, yet. In this work, benzyl phosphonates were modified by replacing phosphorus-bound oxygen atoms with phosphorus-bound fluorine atoms. Surprisingly, mono-P-fluorophosphonates were fully stable under physiological conditions, thus enabling the investigation of their mode of action toward PTP. Three alternative scenarios were tested and mono-P-fluorophosphonates were identified as stable reversible PTP1B inhibitors, despite of the loss of one negative charge and the replacement of one oxygen atom as an H-bond donor by fluorine. In extending this replacement strategy, α,α-difluorobenzyl penta-P-fluorophosphates were synthesized and found to be novel phosphotyrosine mimetics with improved affinity to the phosphotyrosine binding site of PTP1B.

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Section: Introductionmentioning

confidence: 99%

Benzyl Mono‐P‐Fluorophosphonate and Benzyl Penta‐P‐Fluorophosphate Anions Are Physiologically Stable Phosphotyrosine Mimetics and Inhibitors of Protein Tyrosine Phosphatases

Wagner

Accorsi

Rademann

2017

Chemistry A European J

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“…This sensitizing effect results from the templated assembly of protein ligands on the protein surface. As a consequence, standard biochemical assays can be applied for the detection of low-affinity fragments, for example, the enzymatic conversion of a fluorogenic substrate or fluorescence polarization for a binding assay 19 . DLS provides fewer hits than biophysical assays, as only fragments with a fitting spatial orientation in the ligation product are detected as actives.…”

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confidence: 99%

Catalytic activation of pre-substrates via dynamic fragment assembly on protein templates

Burda

Rademann

2014

Nat Commun

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Sensitive detection of small molecule fragments binding to defined sites of biomacromolecules is still a considerable challenge. Here we demonstrate that protein-binding fragments are able to induce enzymatic reactions on the protein surface via dynamic fragment ligation. Fragments binding to the S1 pocket of serine proteases containing a nitrogen, oxygen or sulphur nucleophile are found to activate electrophilic pre-substrates through a reversible, covalent ligation reaction. The dynamic ligation reaction positions the pre-substrate molecule at the active site of the protein thereby inducing its enzymatic cleavage. Catalytic activation of pre-substrates is confirmed by fluorescence spectroscopy and by high-performance liquid chromatography. The approach is investigated with 3 pre-substrates and 14 protein-binding fragments and the specific activation and the templating effect exerted by the enzyme is quantified for each protease-fragment-pre-substrate combination. The described approach enables the site-specific identification of protein-binding fragments, the functional characterization of enzymatic sites and the quantitative analysis of protein template-assisted ligation reactions.

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“…[1][2][3] In addition, phthalimides have also successfully been used as key components in materials and polymers, [4][5][6][7] as catalysts, [8,9] and as fluorescent probes. [1,[13][14][15][16] A straightforward protocol with a 1:1 molar ratio of phthalic acid and amine or aniline that could be performed in high concentration and without any additives would be both economic and simplify the purification of the target compounds. Phthalimides are normally synthesized from phthalic acids in more than one step by using high temperatures and long reaction times or by using various additives such as coupling reagents or catalysts, which often require additional purification steps.…”

Section: Introductionmentioning

confidence: 99%

Efficient Synthesis of 2‐Substituted Phthalimides from Phthalic Acids in One Step

Chorell

2013

Eur J Org Chem

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Efficient procedures for synthesizing 2‐substituted phthalimide (isoindole‐1,3‐dione) analogues starting from phthalic acids have been developed by using experimental design. The phthalimide central fragment frequently appears in biologically active compounds, materials, catalysts, and fluorescent probes, and therefore the development of general, fast, and convenient synthetic methods to this scaffold under neutral, acidic, and basic conditions would be attractive. After an initial screening, the use of acetonitrile, acetic acid, or pyridine in combination with microwave heating proved most promising. Experimental design was applied to these conditions to optimize the time, temperature, and concentration. This strategy has successfully generated synthetic methods that have been used to synthesize a series of phthalimides from phthalic acids and various amines or anilines in excellent yields. The developed methods have proven to be general, fast, convenient, and economic, and thus are expected to have broad utility to efficiently construct novel compounds for future biological and chemical applications.

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Dynamic Substrate Enhancement for the Identification of Specific, Second‐Site‐Binding Fragments Targeting a Set of Protein Tyrosine Phosphatases

Cited by 28 publications

References 31 publications

Benzyl Mono‐P‐Fluorophosphonate and Benzyl Penta‐P‐Fluorophosphate Anions Are Physiologically Stable Phosphotyrosine Mimetics and Inhibitors of Protein Tyrosine Phosphatases

Benzyl Mono‐P‐Fluorophosphonate and Benzyl Penta‐P‐Fluorophosphate Anions Are Physiologically Stable Phosphotyrosine Mimetics and Inhibitors of Protein Tyrosine Phosphatases

Catalytic activation of pre-substrates via dynamic fragment assembly on protein templates

Efficient Synthesis of 2‐Substituted Phthalimides from Phthalic Acids in One Step

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