A tale of two drug targets: the evolutionary history of BACE1 and BACE2.

Christopher Southan,John M Hancock

doi:10.3389/fgene.2013.00293

Abstract

The beta amyloid (APP) cleaving enzyme (BACE1) has been a drug target for Alzheimer's Disease (AD) since 1999 with lead inhibitors now entering clinical trials. In 2011, the paralog, BACE2, became a new target for type II diabetes (T2DM) having been identified as a TMEM27 secretase regulating pancreatic β cell function. However, the normal roles of both enzymes are unclear. This study outlines their evolutionary history and new opportunities for functional genomics. We identified 30 homologs (UrBACEs) in basal phyla including Placozoans, Cnidarians, Choanoflagellates, Porifera, Echinoderms, Annelids, Mollusks and Ascidians (but not Ecdysozoans). UrBACEs are predominantly single copy, show 35–45% protein sequence identity with mammalian BACE1, are ~100 residues longer than cathepsin paralogs with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain. While multiple paralogs in Trichoplax and Monosiga pre-date the nervous system, duplication of the UrBACE in fish gave rise to BACE1 and BACE2 in the vertebrate lineage. The latter evolved more rapidly as the former maintained the emergent neuronal role. In mammals, Ka/Ks for BACE2 is higher than BACE1 but low ratios for both suggest purifying selection. The 5' exons show higher Ka/Ks than the catalytic section. Model organism genomes show the absence of certain BACE human substrates when the UrBACE is present. Experiments could thus reveal undiscovered substrates and roles. The human protease double-target status means that evolutionary trajectories and functional shifts associated with different substrates will have implications for the development of clinical candidates for both AD and T2DM. A rational basis for inhibition specificity ratios and assessing target-related side effects will be facilitated by a more complete picture of BACE1 and BACE2 functions informed by their evolutionary context.

Highlights

UrBACEs are predominantly single copy, show 35–45% protein sequence identity with mammalian Beta-site APP Cleaving Enzyme 1 (BACE1), are ∼100 residues longer than cathepsin paralogs with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain
The amino acid aggregates of Aβ peptides forming the major component of plaques characteristic of Alzheimer’s Disease (AD) result from N-terminal cleavage of the amyloid precursor protein (APP) (Goedert and Spillantini, 2006) mediated by an aspartyl protease referred to as Beta-site APP Cleaving Enzyme 1 (BACE1) (Hussain et al, 1999; Sinha et al, 1999; Vassar et al, 1999; Yan et al, 1999)
Because neurotoxic Aβ peptide production needs the combination of BACE1 and gamma secretase, both have been intensively pursued as AD drug targets for well over a decade (Durham and Shepherd, 2006; Olson and Albright, 2008; Karran et al, 2011)

Summary

Introduction

The amino acid aggregates of Aβ peptides forming the major component of plaques characteristic of Alzheimer’s Disease (AD) result from N-terminal cleavage of the amyloid precursor protein (APP) (Goedert and Spillantini, 2006) mediated by an aspartyl protease referred to as Beta-site APP Cleaving Enzyme 1 (BACE1) (Hussain et al, 1999; Sinha et al, 1999; Vassar et al, 1999; Yan et al, 1999). UrBACEs are predominantly single copy, show 35–45% protein sequence identity with mammalian BACE1, are ∼100 residues longer than cathepsin paralogs with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain.

Results

Conclusion