Interaction Suppression of SFXN1 and ABAD may Impair Aβ-ABAD Associated Toxicity and Assist in Alzheimer’s Treatment

Abstract

Mitochondria play a pivotal role in eukaryotic cells by generating metabolic energy. Recently, downregulation of two mitochondrial proteins, Amyloid Binding Alcohol Dehydrogenase (ABAD) and Sideroflexin 1 (SFXN1) involved in mitochondrial transport and catalysis have been observed in Alzheimer's disease (AD). AD is a debilitating neurodegenerative disorder characterized by amyloid-beta (Aβ) peptide accumulation and mitochondrial dysfunction. Thus, mitochondrial proteins have been scrutinized as targets for Aβ, as it interacts with various mitochondrial proteins, causing dysfunction. Here in this study, we performed comprehensive sequence and structural analyses of ABAD and SFXN1 to explore their critical functions in AD. Given these complex interactions, our study aimed to uncover the interplay between ABAD, Aβ, and SFXN1. Moreover, through structure-based virtual screen, we isolated multiple lead compounds that may disrupt Aβ ABAD interactions and restore ABAD-SFXN1 binding. Molecular docking analysis unveiled the binding mode of ABAD and SFXN1, suggesting a shared interaction site at the LD loop, where Aβ is known to bind. Common residues in both ABAD-SFXN1 and ABAD-Aβ complexes were Leu103, Phe114, Leu118, Ala158, Gly161, Val163, Ser169, Gly173, and Gly174 of ABAD. This implies that these two proteins may compete for the same binding site required for Aβ binding. Aβ interference with ABAD SFXN1 interaction corroborates the intricate involvement of these proteins in AD pathophysiology. This competition may further compromise SFXN1 functionality, leading to the mitochondrial dysfunction, an impaired heme biosynthesis, and eventual cell deterioration. Interestingly, virtual screening identified the top three small molecules with high binding affinities. These lead compounds, including [(N-[3-[4-[[(2,3-dimethylbenzoyl)amino]methyl] 5-methyl-1,3-oxazol-2-yl]phenyl]-5-methylthiophene-2-carboxamide)] (-10.1 kcal/mol), [(2 [3-(4-ethylphenyl)-1H-indazol-1-yl]-N-(2-methyl-2H-1,2,3-triazol-4-yl)acetamide)] (-9.6 kcal/mol), and [(2-[3-(2-Methoxyphenyl)-1,2,4-oxadiazol-5-yl]imidazo[1,2-a]pyrimidine)] ( 7.55 kcal/mol) exhibit promising pharmacokinetic properties and may effectively prevent Aβ binding to potentially restore proper ABAD and SFXN1 function. By disrupting this interaction, the proposed lead compounds may offer a way to mitigate these effects. Molecular dynamics simulations demonstrated an overall stability in small molecule-bound ABAD complexes and facilitate in the exploration of potential conformational changes that Interaction Suppression of SFXN1 and ABAD may Impair Aβ-ABAD Associated Toxicity and Assist in Alzheimer’s Treatment vii Abstract may hinder Aβ-ABAD interaction via LD loop targeting. This may prevent Aβ binding and restore ABAD-SFXN1 interactions. Notably, [(2-[3-(4-ethylphenyl)-1H-indazol-1-yl]-N-(2 methyl-2H-1,2,3-triazol-4-yl)acetamide)] exhibited a consistent interaction pattern throughout simulations. Molecular docking analysis revealed a competitive site for Aβ and SFXN1 binding. However, inhibitors that bind to ABAD show displacement of the LD loop to a position that inhibits only the binding of Aβ. Additionally, the MD simulation revealed that the inhibitors moved to the loop region, where stable binding was demonstrated. This loop region is directly involved in binding to Aβ. Therefore, we propose that these inhibitors may not target the SFXN1 and ABAD interaction and may potentially be helpful in AD treatment. Collectively, these findings underscore a competitive nature of Aβ and SFXN1 for ABAD binding. Keeping in view that the proposed novel small molecules bind at the ABAD site (LD loop) that is required for the crosslinking of Aβ; it is plausible that targeting of LD loop may uncover ABAD interface for SFXN1 leading to prevention of AD phenotype. Overall, this study proposes a novel mechanism to comprehend the intricate network involving complex molecular interactions of mitochondrial proteins and characterizes a structural-functional framework that may offer a better therapeutic option for AD treatment