A Methodology for the Prediction of Drug Target Interaction using CDK Descriptors

Abstract: Detecting probable Drug Target Interaction (DTI) is a critical task in drug discovery. Conventional DTI studies are expensive, labor-intensive, and take a lot of time, hence there are significant reasons to construct useful computational techniques that may successfully anticipate possible DTIs. Although certain methods have been developed for this cause, numerous interactions are yet to be discovered, and prediction accuracy is still low. To meet these challenges, we propose a DTI prediction model built on molecular structure of drugs and sequence of target proteins. In the proposed model, we use Simplified Molecular Input Line Entry System (SMILES) to create CDK descriptors, Molecular ACCess System (MACCS) fingerprints, Electrotopological state (Estate) fingerprints and amino acid sequences of targets to get Pseudo Amino Acid Composition (PseAAC). We target to evaluate performance of DTI prediction models using CDK descriptors. For comparison, we use benchmark data and evaluate models performance on two widely used fingerprints, MACCS fingerprints and Estate fingerprints. The evaluation of performances shows that CDK descriptors are superior at predicting DTIs. The proposed method also outperforms other previously published techniques significantly.