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

Abstract

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

Keywords:

• α-galactosidase A
• α-N-acetylgalactosaminidase
• Caenorhabditis elegans
• docking
• Fabry disease
• Schindler disease

Acknowledgments

We would like to thank Dr. Mark Edgley from the Moerman lab, University of British Columbia for the gift of C. elegans VC4679 strains. The GLA-KO HEK-293 cell line was developed in collaboration with Monash Genome Modification Platform, Monash University, Australia. This study was partly supported by a Fundamental Research Grant Scheme FRGS/1/2019/STG05/MUSM/02/2 by the Ministry of Education Malaysia to K.N. C.S.Y.C. is supported by a Graduate Research Merit Scholarship offered by Monash University Malaysia.

Disclosure statement

The authors declare no conflict of interest related to this study.

Geolocation information

This project was carried out in Monash University, Malaysia (3.0633 N 101.6019E).