Comparative analysis of computational approaches for predicting Transthyretin (TTR) transcription activators and human dopamine D1 receptor antagonists

Abstract

The study expands the application of scikit-learn-based machine learning (ML) to the prediction of small biomolecule functionalities based on Carbon 13 isotope (13C) NMR spectroscopy data derived from Simplified Molecular Input Line Entry System (SMILES) notations. The methodology previously demonstrated by predicting dopamine D1 receptor antagonists was upgraded with the addition of new molecular features derived from the PubChem database. The enhanced ML model obtained 75.8% Accuracy, 84.2% Precision, 63.6% Recall, 72.5% F1-score and 75.8 % ROC, when is trained on 25,532 samples and tested on 5,466 samples. To evaluate the applicability of the methodology for a variety of case studies, a comparison was conducted between the prediction capabilities of the ML models based on the human dopamine D1 receptor antagonists and on the neuronal Transthyretin (TTR) transcription activators. Since the TTR bioassay did not contain the required number of samples for comparison, the results were obtained hypothetically. Gradient Boosting classifier was the optimal model for TTR transcription activators, achieving hypothetical 67.4% Accuracy, 74.0% Precision, 53.5% Recall, 62.1% F1-score, 67.4 % ROC, if it could be trained with 25,532 samples and tested with 5,466 samples. In addition to the main study, to the attention of those interested in neuronal TTR, the CID_SID ML model has been developed to predict whether a compound, initially designed for another purpose, possesses TTR transcription activation capabilities. This ML model was based solely on its PubChem CID and SID and achieved 81.5% Accuracy, 94.6% Precision, 66.8% Recall, 78.3% F1-score, 81.5 % ROC.