Prediction of the responsiveness to pharmacological chaperones: lysosomal human alpha-galactosidase, a case of study

Abstract

BackgroundThe pharmacological chaperones therapy is a promising approach to cure genetic diseases. It relies on substrate competitors used at sub-inhibitory concentration which can be administered orally, reach difficult tissues and have low cost. Clinical trials are currently carried out for Fabry disease, a lysosomal storage disorder caused by inherited genetic mutations of alpha-galactosidase. Regrettably, not all genotypes respond to these drugs.ResultsWe collected the experimental data available in literature on the enzymatic activity of ninety-six missense mutants of lysosomal alpha-galactosidase measured in the presence of pharmacological chaperones. We associated with each mutation seven features derived from the analysis of 3D-structure of the enzyme, two features associated with their thermo-dynamic stability and four features derived from sequence alone. Structural and thermodynamic analysis explains why some mutants of human lysosomal alpha-galactosidase cannot be rescued by pharmacological chaperones: approximately forty per cent of the non responsive cases examined can be correctly associated with a negative prognostic feature. They include mutations occurring in the active site pocket, mutations preventing disulphide bridge formation and severely destabilising mutations. Despite this finding, prediction of mutations responsive to pharmacological chaperones cannot be achieved with high accuracy relying on combinations of structure- and thermodynamic-derived features even with the aid of classical and state of the art statistical learning methods.We developed a procedure to predict responsive mutations with an accuracy as high as 87%: the method scores the mutations by using a suitable position-specific substitution matrix. Our approach is of general applicability since it does not require the knowledge of 3D-structure but relies only on the sequence.ConclusionsResponsiveness to pharmacological chaperones depends on the structural/functional features of the disease-associated protein, whose complex interplay is best reflected on sequence conservation by evolutionary pressure. We propose a predictive method which can be applied to screen novel mutations of alpha galactosidase. The same approach can be extended on a genomic scale to find candidates for therapy with pharmacological chaperones among proteins with unknown tertiary structures.

α-Galactosidase Aggregation Is a Determinant of Pharmacological Chaperone Efficacy on Fabry Disease Mutants

“…These MASS plots show that certain disease mutations are spread through the aggregation spectrum, suggesting that they might affect the intrinsic aggregation propensity of the protein as well as reduce its thermodynamic stability, which could lead to protein aggregation. tion, and using aggregation propensity as a classifier we can predict DGJ response with an accuracy that is equivalent to the most performing predictor algorithms using sequence information from ␣-Gal homologs (17,18). This demonstrates that the aggregation propensity of ␣-Gal mutants is an important determinant for DGJ response, although it is clear that other factors certainly also participate.…”

“…Structural analysis reveals that the most disruptive mutants are on average associated with the most severe forms of the disease, and they are also on average the least responsive to DGJ treatment (43,44). However, it remains very difficult to predict DGJ response from structure only, as only 40% of the nonresponsive mutants can be identified in this manner (17,18). Clearly, thermodynamic destabilization and thus severity of misfolding alone are not sufficient to characterize the therapeutic response (16).…”

“…Still, it remains very difficult to rationalize DGJ response solely from structural information (16) as only approximately 40% of nonresponsive mutants can be correctly predicted from structure alone (17). More robust prediction has been achieved recently by combining structural information with sequence conservation scoring (17,18).…”

Identification of an Allosteric Binding Site on Human Lysosomal Alpha-Galactosidase Opens the Way to New Pharmacological Chaperones for Fabry Disease

“…We tested the effect of DTP on the mutant A230T [47], which is non-responsive to DGJ [36], but eligible for PC therapy [48]. …”

Identification of mutations in Colombian patients affected with Fabry disease

“…Given that this therapy can only be effective in patients with misfolding mutations, the decision of using it depends on an adequate genotyping based on a case-by-case scenario (Andreotti et al, 2010). In order to see which of these patients would be candidates for this kind of therapy we used the Fabry_CEP program.…”