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Highly specific ubiquitin-competing molecules effectively promote frataxin accumulation and partially rescue the aconitase defect in Friedreich ataxia cells.

Rufini A, Cavallo F, Condò I, Fortuni S, De Martino G, Incani O, Di Venere A, Benini M, Massaro DS, Arcuri G, Serio D, Malisan F, Testi R - Neurobiol. Dis. (2014)

Bottom Line: The underlying genetic defect leads to reduced expression of the mitochondrial protein frataxin.By extending our search for effective UCM, we identified a set of new and more potent compounds that more efficiently promote frataxin accumulation.Interestingly, these UCM are not effective on the ubiquitin-resistant frataxin mutant, indicating their specific action on preventing frataxin ubiquitination.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Signal Transduction, Department of Biomedicine and Prevention, University of Rome "Tor Vergata," Via Montpellier 1, Rome 00133, Italy; Fratagene Therapeutics Ltd., 22 Northumberland Rd., Dublin, Ireland.

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Docking model of UCM71 to frataxin.(A) Crystal structure of frataxin (gray cartoon) with solvent accessible molecular surface around the W155 pocket. Overall structure as grey cartoon, molecular surface colored by lipophilicity (hydrophilic in magenta, lipophilic in green). (B) Putative model of the interaction between W155 pocket and the ligand UCM71 (ball and stick, CPK colors): the solvent accessible ligand surface (light blue mesh) fits perfectly with the naphthyl moiety buried by W155, P163, and S157. The phenothiazine ring recognizes the flat region formed by N146 and K147 (label not shown for clarity) and delimited by side chains of V131, S129, T149 and Q148. (C) Putative selected interactions of UCM71 with frataxin. Hydrogen bonds are formed between the hydroxyl substituent of the naphthyl group and the side chain of N146 and between the carbonyl group of the carbonyl-hydrazone scaffold and the hydroxyl of S157. These interactions induce minor rearrangements in the involved side chains of N146 (flip of terminal amide) and S157. (D) The flexibility of the carbonyl-hydrazone scaffold permits the flip of phenothiazine moiety to point its central amino group toward Q148 possibly inducing the flip of the amide group of its side chain resulting in the formation of a strong hydrogen bond.
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f0005: Docking model of UCM71 to frataxin.(A) Crystal structure of frataxin (gray cartoon) with solvent accessible molecular surface around the W155 pocket. Overall structure as grey cartoon, molecular surface colored by lipophilicity (hydrophilic in magenta, lipophilic in green). (B) Putative model of the interaction between W155 pocket and the ligand UCM71 (ball and stick, CPK colors): the solvent accessible ligand surface (light blue mesh) fits perfectly with the naphthyl moiety buried by W155, P163, and S157. The phenothiazine ring recognizes the flat region formed by N146 and K147 (label not shown for clarity) and delimited by side chains of V131, S129, T149 and Q148. (C) Putative selected interactions of UCM71 with frataxin. Hydrogen bonds are formed between the hydroxyl substituent of the naphthyl group and the side chain of N146 and between the carbonyl group of the carbonyl-hydrazone scaffold and the hydroxyl of S157. These interactions induce minor rearrangements in the involved side chains of N146 (flip of terminal amide) and S157. (D) The flexibility of the carbonyl-hydrazone scaffold permits the flip of phenothiazine moiety to point its central amino group toward Q148 possibly inducing the flip of the amide group of its side chain resulting in the formation of a strong hydrogen bond.

Mentions: In order to design small molecules able to inhibit the ubiquitination of frataxin, an extended analysis of the protein's accessible surfaces has been performed, extending our previous work, by taking into account protein flexibility. This analysis allowed us to identify binding pockets on frataxin that were more accessible to drugs. By focusing our analysis on the areas more proximal to K147, and by using virtual screening of commercially available compound libraries, several thousand compounds were docked on available NMR and x-ray structures of human frataxin. Some of these molecules were predicted to interact with frataxin near to K147 (Fig. 1). Promising candidates were subjected to functional validation.


Highly specific ubiquitin-competing molecules effectively promote frataxin accumulation and partially rescue the aconitase defect in Friedreich ataxia cells.

Rufini A, Cavallo F, Condò I, Fortuni S, De Martino G, Incani O, Di Venere A, Benini M, Massaro DS, Arcuri G, Serio D, Malisan F, Testi R - Neurobiol. Dis. (2014)

Docking model of UCM71 to frataxin.(A) Crystal structure of frataxin (gray cartoon) with solvent accessible molecular surface around the W155 pocket. Overall structure as grey cartoon, molecular surface colored by lipophilicity (hydrophilic in magenta, lipophilic in green). (B) Putative model of the interaction between W155 pocket and the ligand UCM71 (ball and stick, CPK colors): the solvent accessible ligand surface (light blue mesh) fits perfectly with the naphthyl moiety buried by W155, P163, and S157. The phenothiazine ring recognizes the flat region formed by N146 and K147 (label not shown for clarity) and delimited by side chains of V131, S129, T149 and Q148. (C) Putative selected interactions of UCM71 with frataxin. Hydrogen bonds are formed between the hydroxyl substituent of the naphthyl group and the side chain of N146 and between the carbonyl group of the carbonyl-hydrazone scaffold and the hydroxyl of S157. These interactions induce minor rearrangements in the involved side chains of N146 (flip of terminal amide) and S157. (D) The flexibility of the carbonyl-hydrazone scaffold permits the flip of phenothiazine moiety to point its central amino group toward Q148 possibly inducing the flip of the amide group of its side chain resulting in the formation of a strong hydrogen bond.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4358773&req=5

f0005: Docking model of UCM71 to frataxin.(A) Crystal structure of frataxin (gray cartoon) with solvent accessible molecular surface around the W155 pocket. Overall structure as grey cartoon, molecular surface colored by lipophilicity (hydrophilic in magenta, lipophilic in green). (B) Putative model of the interaction between W155 pocket and the ligand UCM71 (ball and stick, CPK colors): the solvent accessible ligand surface (light blue mesh) fits perfectly with the naphthyl moiety buried by W155, P163, and S157. The phenothiazine ring recognizes the flat region formed by N146 and K147 (label not shown for clarity) and delimited by side chains of V131, S129, T149 and Q148. (C) Putative selected interactions of UCM71 with frataxin. Hydrogen bonds are formed between the hydroxyl substituent of the naphthyl group and the side chain of N146 and between the carbonyl group of the carbonyl-hydrazone scaffold and the hydroxyl of S157. These interactions induce minor rearrangements in the involved side chains of N146 (flip of terminal amide) and S157. (D) The flexibility of the carbonyl-hydrazone scaffold permits the flip of phenothiazine moiety to point its central amino group toward Q148 possibly inducing the flip of the amide group of its side chain resulting in the formation of a strong hydrogen bond.
Mentions: In order to design small molecules able to inhibit the ubiquitination of frataxin, an extended analysis of the protein's accessible surfaces has been performed, extending our previous work, by taking into account protein flexibility. This analysis allowed us to identify binding pockets on frataxin that were more accessible to drugs. By focusing our analysis on the areas more proximal to K147, and by using virtual screening of commercially available compound libraries, several thousand compounds were docked on available NMR and x-ray structures of human frataxin. Some of these molecules were predicted to interact with frataxin near to K147 (Fig. 1). Promising candidates were subjected to functional validation.

Bottom Line: The underlying genetic defect leads to reduced expression of the mitochondrial protein frataxin.By extending our search for effective UCM, we identified a set of new and more potent compounds that more efficiently promote frataxin accumulation.Interestingly, these UCM are not effective on the ubiquitin-resistant frataxin mutant, indicating their specific action on preventing frataxin ubiquitination.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Signal Transduction, Department of Biomedicine and Prevention, University of Rome "Tor Vergata," Via Montpellier 1, Rome 00133, Italy; Fratagene Therapeutics Ltd., 22 Northumberland Rd., Dublin, Ireland.

Show MeSH
Related in: MedlinePlus