Mitochondrial carriers
(MCs) are essential proteins that transport
metabolites across mitochondrial membranes and play a critical role
in cellular metabolism. ADP/ATP (adenosine diphosphate/adenosine triphosphate)
is one of the most important carriers as it contributes to cellular
energy production and is susceptible to the powerful toxin bongkrekic
acid. This toxin has claimed several lives; for example, a recent
foodborne outbreak in Taipei, Taiwan, has caused four deaths and sickened
30 people. The issue of bongkrekic acid poisoning has been a long-standing
problem in Indonesia, with reports as early as 1895 detailing numerous
deaths from contaminated coconut fermented cakes. In bioinformatics,
significant advances have been made in understanding biological processes
through computational methods; however, no established computational
method has been developed for identifying mitochondrial carriers.
We propose a computational bioinformatics approach for predicting
MCs from a broader class of secondary active transporters with a focus
on the ADP/ATP carrier and its interaction with bongkrekic acid. The
proposed model combines protein language models (PLMs) with multiwindow
scanning convolutional neural networks (mCNNs). While PLM embeddings
capture contextual information within proteins, mCNN scans multiple
windows to identify potential binding sites and extract local features.
Our results show 96.66% sensitivity, 95.76% specificity, 96.12% accuracy,
91.83% Matthews correlation coefficient (MCC), 94.63% F1-Score, and
98.55% area under the curve (AUC). The results demonstrate the effectiveness
of the proposed approach in predicting MCs and elucidating their functions,
particularly in the context of bongkrekic acid toxicity. This study
presents a valuable approach for identifying novel mitochondrial complexes,
characterizing their functional roles, and understanding mitochondrial
toxicology mechanisms. Our findings, that utilize computational methods
to improve our understanding of cellular processes and drug-target
interactions, contribute to the development of therapeutic strategies
for mitochondrial disorders, reducing the devastating effects of bongkrekic
acid poisoning.