Functional and pharmacological evaluation of novel GLA variants in Fabry disease identifies six (two de novo ) causative mutations and two amenable variants to the chaperone DGJ

GLA Mutations Suppress Autophagy and Stimulate Lysosome Generation in Fabry Disease

Fabry disease (FD) is an X-linked recessive inheritance lysosomal storage disorder caused by pathogenic mutations in the GLA gene leading to a deficiency of the enzyme alpha-galactosidase A (α-Gal A). Multiple organ systems are implicated in FD, most notably the kidney, heart, and central nervous system. In our previous study, we identified four GLA mutations from four independent Fabry disease families with kidney disease or neuropathic pain: c.119C>A (p.P40H), c.280T>C (C94R), c.680G>C (p.R227P) and c.801+1G>A (p.L268fsX3). To reveal the molecular mechanism underlying the predisposition to Fabry disease caused by GLA mutations, we analyzed the effects of these four GLA mutations on the protein structure of α-galactosidase A using bioinformatics methods. The results showed that these mutations have a significant impact on the internal dynamics and structures of GLA, and all these altered amino acids are close to the enzyme activity center and lead to significantly reduced enzyme activity. Furthermore, these mutations led to the accumulation of autophagosomes and impairment of autophagy in the cells, which may in turn negatively regulate autophagy by slightly increasing the phosphorylation of mTOR. Moreover, the overexpression of these GLA mutants promoted the expression of lysosome-associated membrane protein 2 (LAMP2), resulting in an increased number of lysosomes. Our study reveals the pathogenesis of these four GLA mutations in FD and provides a scientific foundation for accurate diagnosis and precise medical intervention for FD.

A theoretical study on binding and stabilization of galactose and novel galactose analogues to the human α-galactosidase A variant causing Fabry disease

α-galactosidase A (α-Gal A) catalyzes the hydrolysis of terminal α-galactosyl moieties from globotriaosylceramide, and mutations in this enzyme lead to the lipid metabolism disorder "Fabry disease". Mutation in α-Gal A possibly causes the protein misfolding, which reduces catalytic activity and stability of the enzyme. A recent study demonstrated that the binding of galactose on the α-Gal A catalytic site significantly increases its stability. Herein, the effect of mutation on secondary structure, structural energy, and galactose affinity of α-Gal A (wild type and A143T variant) was investigated using molecular dynamics simulations and free energy calculations based on MM/GBSA method. The results showed that A143T mutation caused the formation of unusual H-bonds that induced the change in secondary structure and binding affinities toward galactose. The amino acid residues involved in galactose binding were identified. The molecular binding mechanism obtained from this study could be helpful for optimizations and designs of new galactose analogs as pharmacological chaperones against Fabry disease.

Functional characterization of novel variants found in patients with suspected Fabry disease

The deficiency or absence of the lysosomal hydrolase α-Galactosidase A results in Fabry disease (FD), a rare and underdiagnosed X-linked disorder. The symptoms caused by FD have a direct relation with the variant present in the gene coding α-Galactosidase A (GLA) and enzyme residual activity, and it can vary drastically between men and women of the same family. Here, we present four novel variants found in patients with suspicion of FD. The patients were screened for FD by enzymatic activity and/or DNA sequencing, which showed four novel GLA missense variants. To confirm the potential pathogenicity of these variants, we employed site-directed mutagenesis. GLA wild-type and mutant plasmids were transfected into mammalian cells; RNA and proteins were extracted for expression and enzymatic activity analysis. The patients presented the variants p.Ile133Asn, p.Lys140Thr, p.Lys168Gln and p.Pro323Thr in the GLA. In vitro analysis showed pathogenic potential of three variants and one tolerated variant. The variants p.Ile133Asn and p.Lys168Gln showed no residual activity and, therefore, leading to classical phenotype, and the variant p.Lys140Thr, which presented 22% of residual activity, was considered a mild variant leading to non-classical phenotype. The variant p.Pro323Thr presented 66.7% of residual activity and alone, it is not enough to cause FD.

Identification of dual active sites in Caenorhabditis elegans GANA-1 protein: an ortholog of the human α-GAL a and α-NAGA enzymes

Fabry disease (FD) is caused by a defective α-galactosidase A (α-GAL A) enzyme responsible for breaking down globotriaosylceramide (Gb₃). To develop affordable therapeutics, more effort is needed to obtain insights into the underlying mechanism of FD and understanding human α-GAL A structure and function in related animal models. We adopted C. elegans as a model to elucidate the sequence and 3D structure of its GANA-1 enzyme and compared it to human α-GAL A. We constructed GANA-1 3D structure by homology modelling and validated the quality of the predicted GANA-1 structure, followed by computational docking of human ligands. The GANA-1 protein shared sequence similarities up to 42.1% with the human α-GAL A in silico and had dual active sites. GANA-1 homology modelling showed that 11 out of 13 amino acids in the first active site of GANA-1 protein overlapped with the human α-GAL A active site, indicating the prospect for substrate cross-reaction. Computational molecular docking using human ligands like Gb₃ (first pocket)_, 4-nitrophenyl-α-D-galactopyranoside (second pocket), α-galactose (second pocket), and N-acetyl-D-galactosamine (second pocket) showed negative binding energy. This revealed that the ligands were able to bind within both GANA-1 active sites, mimicking the human α-GAL A and α-NAGA enzymes. We identified human compounds with adequate docking scores, predicting robust interactions with the GANA-1 active site. Our data suggested that the C. elegans GANA-1 enzyme may possess structural and functional similarities to human α-GAL A, including an intrinsic capability to metabolize Gb₃ deposits.Communicated by Ramaswamy H. Sarma.

Fabry Disease in Slovakia: How the Situation Has Changed over 20 Years of Treatment

Fabry disease (FD, OMIM#301500) is a rare inborn error of the lysosomal enzyme α-galactosidase (α-Gal A, EC 3.2.1.22) and results in progressive substrate accumulation in tissues with a wide range of clinical presentations. Despite the X-linked inheritance, heterozygous females may also be affected. Hemizygous males are usually affected more severely, with an earlier manifestation of the symptoms. Rising awareness among health care professionals and more accessible diagnostics have positioned FD among the most-common inherited metabolic diseases in adults. An early and correct diagnosis of FD is crucial with a focus on personalised therapy. Preventing irreversible destruction of vital organs is the main goal of modern medicine. The aim of this study was to offer a complex report mapping the situation surrounding FD patients in Slovakia. A total of 48 patients (21 males, 27 females) with FD are registered in the Centre for Inborn Errors of Metabolism in Bratislava, Slovakia. In our cohort, we have identified three novel pathogenic variants in five patients. Three patients presented with the frameshift mutation c.736delA, and two others presented with the missense mutations c.203T>C, c.157A>C. Moreover, we present a new clinical picture of the pathogenic variant c.801+1G>A, which was previously described and associated with the renal phenotype.

Fabry's Disease: The Utility of a Multidisciplinary Screening Approach

(1) Background: As a lysosomal storage disorder, Fabry’s disease (FD) shows variable clinical manifestations. We applied our multidisciplinary approach to identify any organ damage in a sample of adult patients with different pathogenic variants. (2) Methods: 49 participants (mean age 44.3 ± 14.2 years; 37 females), underwent a multidimensional clinical and instrumental assessment. (3) Results: At diagnosis, mean enzymatic activity was 5.2 ± 4.6 nM/mL/h in females and 1.4 ± 0.5 nM/mL/h in males (normal values > 3.0), whereas globotriaosylsphingosine was 2.3 ± 2.1 nM/L in females and 28.7 ± 3.5 nM/L in males (normal values < 2.0). Overall, cardiovascular, neurological, and audiological systems were the most involved, regardless of the variant detected. Patients with classic variants (10) showed typical multiorgan involvement and, in some cases, prevalent organ damage (cardiovascular, neurological, renal, and ocular). Those with late-onset variants (39) exhibited lower occurrence of multiorgan impairment, although some of them affected the cardiovascular and neurological systems more. In patients with lower enzymatic activity, the most frequent involvement was neurological, followed by peripheral vascular disease. (4) Conclusions: FD patients exhibited wide phenotypic variability, even at single-organ level, likely due to the individual genetic mutation, although other factors may contribute. Compared to the conventional management, a multidisciplinary approach, as that prompted at our Center, allows one to achieve early clinical detection and management.

High-Risk Screening for Fabry Disease: A Nationwide Study in Japan and Literature Review

Fabry disease (FD) is an X-linked inherited disorder caused by mutations in the GLA gene, which encodes the lysosomal enzyme α-galactosidase A (α-Gal A). FD detection in patients at an early stage is essential to achieve sufficient treatment effects, and high-risk screening may be effective. Here, we performed high-risk screening for FD in Japan and showed that peripheral neurological manifestations are important in young patients with FD. Moreover, we reviewed the literature on high-risk screening in patients with renal, cardiac, and central neurological manifestations. Based on the results of this study and review of research abroad, we believe that FD can be detected more effectively by targeting individuals based on age. In recent years, the methods for high-risk screening have been ameliorated, and high-risk screening studies using GLA next-generation sequencing have been conducted. Considering the cost-effectiveness of screening, GLA sequencing should be performed in individuals with reduced α-Gal A activity and females with certain FD manifestations and/or a family history of FD. The findings suggest that family analysis would likely detect FD patients, although GLA sequencing of asymptomatic family members requires adequate genetic counseling.

Multicenter evaluation of use of dried blood spot compared to conventional plasma in measurements of globotriaosylsphingosine (LysoGb3) concentration in 104 Fabry patients

OBJECTIVES

Fabry disease (FD) is an X-linked lysosomal storage disorder, resulting from a deficiency of the enzyme α-galactosidase A, responsible for breaking down glycolipids such as globotriaosylceramide and its deacylated derivative, globotriaosylsphingosine (LysoGb3). Here, we compare the levels of LysoGb3 in dried blood spots (DBS) and plasma in patients with classic and late-onset phenotypes.

METHODS

LysoGb3 measurements were performed in 104 FD patients, 39 males and 65 females. Venous blood was collected. A portion was spotted onto filter paper and another portion separated to obtain plasma. The LysoGb3 concentrations in DBS and plasma were determined by highly sensitive electrospray ionization liquid chromatography tandem mass spectrometry. Agreement between different matrices was assessed using linear regression and Bland Altman analysis.

RESULTS

The method on DBS was validated by evaluating its precision, accuracy, matrix effect, recovery, and stability. The analytical performances were verified by comparison of a total of 104 paired DBS and plasma samples from as many FD patients (representing 46 GLA variants). There was a strong correlation between plasma and the corresponding DBS LysoGb3 concentrations, with few exceptions. Discrepancies were observed in anemic patients with typically low hematocrit levels compared to the normal range.

CONCLUSIONS

The method proved to be efficient for the rapid analysis of LysoGb3. DBS provides a convenient, sensitive, and reproducible method for measuring LysoGb3 levels for diagnosis, initial phenotypic assignment, and therapeutic monitoring in patients with FD.

Affinity purification of human alpha galactosidase utilizing a novel small molecule biomimetic of alpha-D-galactose

Alpha galactosidase (a-Gal) is an acidic hydrolase that plays a critical role in hydrolyzing the terminal alpha-galactoyl moiety from glycolipids and glycoproteins. There are over a hundred mutations reported for the GLA gene that encodes a-Gal that result in reduced protein synthesis, protein instability, and reduction in function. The deficiencies of a-Gal can cause Fabry disease, a rare lysosomal storage disorder (LSD) caused by the failure to catabolize alpha-d-galactoyl glycolipid moieties. The current standard of care for Fabry disease is enzyme replacement therapy (ERT) where the purified recombinant form of human a-Gal is given to patients. The manufacture of a-Gal is currently performed utilizing traditional large-scale chromatography processes. Developing an affinity resin for the purification of a-Gal would reduce the complexity of the manufacturing process, reduce costs, and potentially produce a higher quality a-Gal. After the evaluation of many small molecules, a commercially available small molecule biomimetic, N-5-Carboxypentyl-1-deoxygalactonojirimycin (N5C-DGJ), was utilized for the development of a novel small molecule biomimetic affinity resin for a-Gal. Affinity purified a-Gal demonstrated a purity greater than 90%, exhibited expected thermal stability and specific activity. Complementing this affinity purification is the development of an elution buffer system that confers an increased thermal stability to a-Gal. The N5C-DGJ affinity resin tolerated sodium hydroxide sanitization with no loss of binding capacity, making it amenable to large scale purification processes and potential use in manufacturing. This novel method for purifying the challenging a-Gal enzyme can be extended to other enzyme replacement therapies.

Hot topics in Fabry disease

Fabry disease is a rare inborn error of the enzyme α-galactosidase (α-Gal) and results in lysosomal substrate accumulation in tissues with a wide range of clinical presentations. The disease has attracted a lot of interest over the last years, in particular since enzyme replacement therapy (ERT) has become widely available in 2001. With rising awareness and rising numbers of (diagnosed) patients, physicians encounter new challenges. Over 900 α-Gal gene mutations are currently known, some with doubtful clinical significance, posing diagnostic and prognostic difficulties for the clinician and a lot of uncertainty for patients. Another challenge are patients who develop neutralising antibodies to ERT, which possibly leads to reduced therapy effectiveness. In this article, we summarise the latest developments in the science community regarding diagnostics and management of this rare lysosomal storage disorder and offer an outlook to future treatments.

Homology modeling in drug discovery: Overview, current applications, and future perspectives

Homology modeling is one of the computational structure prediction methods that are used to determine protein 3D structure from its amino acid sequence. It is considered to be the most accurate of the computational structure prediction methods. It consists of multiple steps that are straightforward and easy to apply. There are many tools and servers that are used for homology modeling. There is no single modeling program or server which is superior in every aspect to others. Since the functionality of the model depends on the quality of the generated protein 3D structure, maximizing the quality of homology modeling is crucial. Homology modeling has many applications in the drug discovery process. Since drugs interact with receptors that consist mainly of proteins, protein 3D structure determination, and thus homology modeling is important in drug discovery. Accordingly, there has been the clarification of protein interactions using 3D structures of proteins that are built with homology modeling. This contributes to the identification of novel drug candidates. Homology modeling plays an important role in making drug discovery faster, easier, cheaper, and more practical. As new modeling methods and combinations are introduced, the scope of its applications widens.