Artificial intelligence paradigm for ligand-based virtual screening on the drug discovery of type 2 diabetes mellitus

Alhadi Bustamam, Haris Hamzah, Nadya A. Husna, Sarah Syarofina, Nalendra Dwimantara, Arry Yanuar, Devvi Sarwinda

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


Background: New dipeptidyl peptidase-4 (DPP-4) inhibitors need to be developed to be used as agents with low adverse effects for the treatment of type 2 diabetes mellitus. This study aims to build quantitative structure-activity relationship (QSAR) models using the artificial intelligence paradigm. Rotation Forest and Deep Neural Network (DNN) are used to predict QSAR models. We compared principal component analysis (PCA) with sparse PCA (SPCA) as methods for transforming Rotation Forest. K-modes clustering with Levenshtein distance was used for the selection method of molecules, and CatBoost was used for the feature selection method. Results: The amount of the DPP-4 inhibitor molecules resulting from the selection process of molecules using K-Modes clustering algorithm is 1020 with logP range value of -1.6693 to 4.99044. Several fingerprint methods such as extended connectivity fingerprint and functional class fingerprint with diameters of 4 and 6 were used to construct four fingerprint datasets, ECFP_4, ECFP_6, FCFP_4, and FCFP_6. There are 1024 features from the four fingerprint datasets that are then selected using the CatBoost method. CatBoost can represent QSAR models with good performance for machine learning and deep learning methods respectively with evaluation metrics, such as Sensitivity, Specificity, Accuracy, and Matthew’s correlation coefficient, all valued above 70% with a feature importance level of 60%, 70%, 80%, and 90%. Conclusion: The K-modes clustering algorithm can produce a representative subset of DPP-4 inhibitor molecules. Feature selection in the fingerprint dataset using CatBoost is best used before making QSAR Classification and QSAR Regression models. QSAR Classification using Machine Learning and QSAR Classification using Deep Learning, each of which has an accuracy of above 70%. The QSAR RFC-PCA and QSAR RFR-PCA models performed better than QSAR RFC-SPCA and QSAR RFR-SPCA models because QSAR RFC-PCA and QSAR RFR-PCA models have more effective time than the QSAR RFC-SPCA and QSAR RFR-SPCA models.

Original languageEnglish
Article number74
JournalJournal of Big Data
Issue number1
Publication statusPublished - Dec 2021


  • CatBoost
  • Deep neural network
  • Fingerprint
  • K-modes clustering
  • principal component analysis
  • Quantitative structure-activity relationship
  • Rotation Forest
  • Sparse principal component analysis


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