Drug Res (Stuttg) 2024; 74(05): 208-219
DOI: 10.1055/a-2306-8311
Review

Artificial Intelligence in Drug Identification and Validation: A Scoping Review

Mukhtar Lawal Abubakar
1   School of Applied Sciences, Suresh Gyan Vihar University, Jaipur, Rajasthan, India
,
Neha Kapoor
1   School of Applied Sciences, Suresh Gyan Vihar University, Jaipur, Rajasthan, India
,
Asha Sharma
2   Department of Zoology, Swargiya P. N. K. S. Govt. PG College, Dausa, Rajasthan, India
,
Lokesh Gambhir
3   School of Basic and Applied Sciences, Shri Guru Ram Rai University, Dehradun, Uttarakhand, India
,
Nakuleshwar Dutt Jasuja
4   School of Basic and Applied Sciences, Nirwan University, Jaipur, Rajasthan India
,
Gaurav Sharma
1   School of Applied Sciences, Suresh Gyan Vihar University, Jaipur, Rajasthan, India
› Author Affiliations

Abstract

The end-to-end process in the discovery of drugs involves therapeutic candidate identification, validation of identified targets, identification of hit compound series, lead identification and optimization, characterization, and formulation and development. The process is lengthy, expensive, tedious, and inefficient, with a large attrition rate for novel drug discovery. Today, the pharmaceutical industry is focused on improving the drug discovery process. Finding and selecting acceptable drug candidates effectively can significantly impact the price and profitability of new medications. Aside from the cost, there is a need to reduce the end-to-end process time, limiting the number of experiments at various stages. To achieve this, artificial intelligence (AI) has been utilized at various stages of drug discovery. The present study aims to identify the recent work that has developed AI-based models at various stages of drug discovery, identify the stages that need more concern, present the taxonomy of AI methods in drug discovery, and provide research opportunities. From January 2016 to September 1, 2023, the study identified all publications that were cited in the electronic databases including Scopus, NCBI PubMed, MEDLINE, Anthropology Plus, Embase, APA PsycInfo, SOCIndex, and CINAHL. Utilising a standardized form, data were extracted, and presented possible research prospects based on the analysis of the extracted data.



Publication History

Received: 22 January 2024

Accepted: 02 April 2024

Article published online:
03 June 2024

© 2024. Thieme. All rights reserved.

Georg Thieme Verlag KG
Rüdigerstraße 14, 70469 Stuttgart, Germany

 
  • References

  • 1 Verma P, Thakur AS, Deshmukh K, Jha AK, Verma S. Routes of drug administration. Int J Pharm Sci Res 2010; 1: 54-59
  • 2 Ouyang B, Gu X, Holford P. Plant genetic engineering and biotechnology: a sustainable solution for future food security and industry. Plant Growth Regul 2017; 83: 171-173
  • 3 Atanasov AG, Waltenberger B, Pferschy-Wenzig EM, Linder T, Wawrosch C, Uhrin P, Temml V, Wang L, Schwaiger S, Heiss EH, Rollinger JM, Schuster D. et al. Discovery and resupply of pharmacologically active plant-derived natural products: A review. Biotechnol Adv 2015; 33: 1582-1614
  • 4 Sinha S, Vohora D. Drug discovery and development: An overview. In: Pharmaceutical medicine and translational clinical research. 2018: 19-32
  • 5 Mohs RC, Greig NH. Drug discovery and development: Role of basic biological research. Alzheimers Dement (N Y) 2017; 3: 651-657
  • 6 Hughes JP, Rees S, Kalindjian SB, Philpott KL. Principles of early drug discovery. Br J Pharmacol 2011; 162: 1239-1249
  • 7 Deore AB, Dhumane JR, Wagh R, Sonawane R. The stages of drug discovery and development process. AJPRD 2019; 7: 62-67
  • 8 Fox S, Farr-Jones S, Sopchak L, Boggs A, Nicely HW, Khoury R, Biros M. High-throughput screening: update on practices and success. J Biomol Screen 2006; 11: 864-869
  • 9 Boppana K, Dubey PK, Jagarlapudi SA, Vadivelan S, Rambabu G. Knowledge based identification of MAO-B selective inhibitors using pharmacophore and structure based virtual screening models. Eur J Med Chem 2009; 44: 3584-3590
  • 10 Law R, Barker O, Barker JJ, Hesterkamp T. et al. The multiple roles of computational chemistry in fragment-based drug design. J Comput Aid Mol Des 2009; 23: 459-473
  • 11 Guido RV, Oliva G, Andricopulo AD. Modern drug discovery technologies: opportunities and challenges in lead discovery. Comb Chem High Throughput Screen 2011; 14: 830-839
  • 12 Sashidhara KV, Rosaiah JN. Various Dereplication Strategies Using LC-MS for Rapid Natural Product Lead Identification and Drug Discovery. Nat Prod Comm. 2007 2. 2
  • 13 Zhou SF, Zhong WZ. Drug Design and Discovery: Principles and Applications. Molecules 2017; 22: 279
  • 14 Yoo J, Kim TY, Joung I, Song SO. Industrializing AI/ML during the end-to-end drug discovery process. Curr Opin Struct Biol 2023; 79: 102528
  • 15 Zeng X, Zhu S, Lu W, Liu Z, Huang J, Zhou Y. et al. Target identification among known drugs by deep learning from heterogeneous networks. Chem Sci 2020; 11: 1775-1797
  • 16 Najm M, Azencott CA, Playe B, Stoven V. Drug target identification with machine learning: How to choose negative examples. Int J Mol Sci 2021; 22: 5118
  • 17 Tang D, Cao D, Zhao J. Predicting Drug-target Interaction using Support Vector Machine and Invasive Tumor Growth Optimization. Int J Hybrid Inf Technol 2017; 10: 41-50
  • 18 Rayhan F, Ahmed S, Mousavian Z, Farid DM, Shatabda S. FRnet-DTI: Deep convolutional neural network for drug-target interaction prediction. Heliyon. 2020
  • 19 Svensson E, Hoedt PJ, Hochreiter S, Klambauer G. Robust task-specific adaption of models for drug-target interaction prediction. NeurIPS 2022 AI for Science: Progress and Promises. October 2022
  • 20 Dehghan A, Razzaghi P, Abbasi K, Gharaghani S. TripletMultiDTI: Multimodal Representation Learning in Drug-Target Interaction Prediction. Expert Syst Appl. 2023 120754.
  • 21 Monteiro NR, Ribeiro B, Arrais JP. Drug-target interaction prediction: end-to-end deep learning approach. IEEE/ACM Trans Comput Biol Bioinform 2020; 18: 2364-2374
  • 22 Singh R, Sledzieski S, Cowen L, Berger B. Learning the drug-target interaction lexicon. bioRxiv. 2022
  • 23 Zhijian L, Shaohua J, Yigao L, Min G. GDGRU-DTA: Predicting Drug-Target Binding Affinity Based on GNN and Double GRU. arXiv preprint arXiv. 2204.1 1857
  • 24 Zhijian L, Shaohua J, Yonghao T. DSAGLSTM-DTA: Prediction of Drug-Target Affinity Using Dual Self-Attention And LSTM. MLAIJ 2022; 9: 2
  • 25 Bahi M, Batouche M. Drug-target interaction prediction in drug repositioning based on deep semi-supervised learning. In: Computational Intelligence and Its Applications: 6th IFIP TC 5 International Conference, CIIA 2018, Oran, Algeria, May 8-10, 2018, Proceedings 6. Springer International Publishing; 2018. 6. 302-313
  • 26 Kamuntavičius G, Prat A, Paquet T, Bastas O, Aty HA, Sun Q. et al. Accelerated Hit Identification with Target. Evaluation, Deep Learning and Automated Labs: Prospective Validation in IRAK1. 2023
  • 27 Zhao Q, Duan G, Yang M, Cheng Z, Li Y, Wang J. AttentionDTA: Drug–target binding affinity prediction by sequence-based deep learning with attention mechanism. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2022; 20: 852-863
  • 28 Brereton AE, MacKinnon S, Safikhani Z, Reeves S, Alwash S, Shahani V. et al. Predicting drug properties with parameter-free machine learning: pareto-optimal embedded modeling (POEM). Machine Learning: Science and Technology 2020; 1: 025008
  • 29 Li F, Zhang Z, Guan J, Zhou S. Effective drug–target interaction prediction with mutual interaction neural network. Bioinformatics 2022; 38: 3582-3589
  • 30 Moon S, Zhung W, Yang S, Lim J, Kim WY. PIGNet: a physics-informed deep learning model toward generalized drug–target interaction predictions. Chem Sci 2022; 13: 3661-3673
  • 31 Ezzat A, Zhao P, Wu M, Li XL, Kwoh CK. Drug-target interaction prediction with graph regularized matrix factorization. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2016; 14: 646-656
  • 32 Barkat MR, Moussa SM, Badr NL. Drug target interaction [DTI] and prediction using machine learning. Int J Res Appl Sci Eng Technol 2022; 10: 116-122
  • 33 Srivastava D, Soni D, Sharma V, Kumar P, Singh AK. An Artificial Intelligence Based Recommender System to analyze Drug Target Indication for Drug Repurposing using Linear Machine Learning Algorithm. J Algebraic Statistics 2022; 13: 790-797
  • 34 Boezer M, Tavakol M, Sajadi Z. Fast DTI: Drug-Target Interaction Prediction using Multimodality and Transformers. Proceedings of the Northern Lights Deep Learning Workshop. 2023: 4
  • 35 Liu X, Ye K, van Vlijmen HW, Emmerich MT, IJzerman AP, van Westen GJ. DrugEx v2: de novo design of drug molecules by Pareto-based multi-objective reinforcement learning in polypharmacology. J Cheminformatics 2021; 13: 85
  • 36 Du Y, Wang J, Wang X, Chen J, Chang H. Predicting drug-target interaction via wide and deep learning. Proceedings of the 2018 6th International Conference on Bioinformatics and Computational Biology. 2018: 128-132
  • 37 Abbasi M, Pereira T, Santos BP, Ribeiro B, Arrais J. Multiobjective Reinforcement Learning in Optimized Drug Design. ESANN. 2021
  • 38 Ezzat A, Wu M, Li XL, Kwoh CK. Drug-target interaction prediction via class imbalance-aware ensemble learning. BMC Bioinf 2016; 17: 267-276
  • 39 Lee I, Keum J, Nam H. DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences. PLoS Comput Biol 2019; 15: e1007129
  • 40 Wang Q, Feng Y, Huang J, Wang T, Cheng G. A novel framework for the identification of drug target proteins: Combining stacked auto-encoders with a biased support vector machine. PloS ONE 2017; 12: e0176486
  • 41 Wang H, Wang J, Dong C, Lian Y, Liu D, Yan Z. A novel approach for drug-target interactions prediction based on multimodal deep autoencoder. Fron Pharmacol 2020; 10: 1592
  • 42 Wang J, Shi Y, Wang X, Chang H. A drug target interaction prediction based on LINE-RF learning. Curr Bioinform 2020; 15: 750-757
  • 43 Lan W, Wang J, Li M, Liu J, Li Y, Wu FX, Pan Y. Predicting drug–target interaction using positive-unlabeled learning. Neurocomputing 2016; 206: 50-57
  • 44 Nascimento AC, Prudêncio RB, Costa IG. A multiple kernel learning algorithm for drug-target interaction prediction. BMC bioinf 2016; 17: 1-16
  • 45 Yang J, He S, Zhang Z, Bo X. NegStacking: Drug− Target Interaction Prediction Based on Ensemble Learning and Logistic Regression. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2020; 18: 2624-2634
  • 46 Rodríguez-Pérez R, Bajorath J. Interpretation of machine learning models using Shapley values: application to compound potency and multi-target activity predictions. J Comput Aided Mol Des 2020; 34: 1013-1026
  • 47 Dezső Z, Ceccarelli M. Machine learning prediction of oncology drug targets based on protein and network properties. BMC Bioinf 2020; 21: 1-12
  • 48 Peng J, Li J, Shang X. A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network. BMC Bioinf 2020; 21: 1-13
  • 49 Wang YB, You ZH, Yang S, Yi HC, Chen ZH, Zheng K. A deep learning-based method for drug-target interaction prediction based on long short-term memory neural network. BMC Med Inform Decis Mak 2020; 20: 1-9
  • 50 Liu G, Singha M, Pu L, Neupane P, Feinstein J, Wu HC, Brylinski M. GraphDTI: a robust deep learning predictor of drug-target interactions from multiple heterogeneous data. J Cheminform 2021; 13: 1-17
  • 51 Madhukar NS, Khade PK, Huang L, Gayvert K, Galletti G, Stogniew M, Elemento O. A Bayesian machine learning approach for drug target identification using diverse data types. Nat Commun 2019; 10: 5221
  • 52 Ye Q, Hsieh CY, Yang Z, Kang Y, Chen J, Cao D, Hou T. A unified drug–target interaction prediction framework based on knowledge graph and recommendation system. Nat Commun 2021; 12: 6775
  • 53 Sadegh S, Skelton J, Anastasi E, Bernett J, Blumenthal DB, Galindez G, Kacprowski T. Network medicine for disease module identification and drug repurposing with the NeDRex platform. Nat Commun 2021; 12: 6848
  • 54 Masoudi-Sobhanzadeh Y, Omidi Y, Amanlou M, Masoudi-Nejad A. Trader as a new optimization algorithm predicts drug-target interactions efficiently. Sci Rep 2019; 9: 9348
  • 55 Rohani N, Eslahchi C. Drug-drug interaction predicting by neural network using integrated similarity. Sci Rep 2019; 9: 13645
  • 56 Mei S, Zhang K. A machine learning framework for predicting drug–drug interactions. Sci Rep 2021; 11: 17619
  • 57 Rahman MM, Vadrev SM, Magana-Mora A, Levman J, Soufan O. A novel graph mining approach to predict and evaluate food-drug interactions. Sci Rep 2022; 12: 1061
  • 58 Thafar MA, Alshahrani M, Albaradei S, Gojobori T, Essack M, Gao X. Affinity2Vec: drug-target binding affinity prediction through representation learning, graph mining, and machine learning. Sci Rep 2022; 12: 4751
  • 59 Wei B, Zhang Y, Gong X. DeepLPI: a novel deep learning-based model for protein–ligand interaction prediction for drug repurposing. Sci Rep 2022; 12: 18200
  • 60 Shin B, Park S, Kang K, Ho JC. Self-attention-based molecule representation for predicting drug-target interaction. Mach Learn Healthc Conf 2019; 230-248
  • 61 Kavipriya G, Manjula D. Drug–Target Interaction Prediction Model Using Optimal Recurrent Neural Network. Intell Autom Soft Comput. 2023 35.
  • 62 Wang L, You ZH, Chen X, Xia SX, Liu F, Yan X, Zhou Y. Computational methods for the prediction of drug-target interactions from drug fingerprints and protein sequences by stacked auto-encoder deep neural network. In: Bioinformatics Research and Applications: 13th International Symposium, ISBRA 2017. Springer International Publishing; 2017: 46-58
  • 63 Wang L, You ZH, Chen X, Xia SX, Liu F, Yan X, Song KJ. A computational-based method for predicting drug–target interactions by using stacked autoencoder deep neural network. J Comput Biol 2018; 25: 361-373
  • 64 Wen M, Zhang Z, Niu S, Sha H, Yang R, Yun Y, Lu H. Deep-learning-based drug–target interaction prediction. J Proteome Res 2017; 16: 1401-1409
  • 65 Ye Q, Zhang X, Lin X. Drug-target interaction prediction via multiple output deep learning. 2020 IEEE International Conference on Bioinformatics
  • 66 Zhang J, Zhu M, Chen P, Wang B. DrugRPE: random projection ensemble approach to drug-target interaction prediction. Neurocomputing 2017; 228: 256-262
  • 67 Zhao Q, Xiao F, Yang M, Li Y, Wang J. AttentionDTA: prediction of drug–target binding affinity using attention model. In: 2019 IEEE Int Conf Bioinforma Biomed (BIBM). IEEE; 2019: 64-69
  • 68 Zheng Y, Wu Z. A Machine Learning-Based Biological Drug–Target Interaction Prediction Method for a Tripartite Heterogeneous Network. ACS Omega 2021; 6: 3037-3045
  • 69 Fu G, Ding Y, Seal A, Chen B, Sun Y, Bolton E. Predicting drug target interactions using meta-path-based semantic network analysis. BMC Bioinf 2016; 17: 1-10
  • 70 Gao KY, Fokoue A, Luo H, Iyengar A, Dey S, Zhang P. Interpretable drug target prediction using deep neural representation. In. IJCAI; 2018. 2018. 3371-3377
  • 71 Filella-Merce I, Molina A, Orzechowski M, Díaz L, Zhu YM, Mor JV, Guallar V. Optimizing Drug Design by Merging Generative AI With Active Learning Frameworks. arXiv preprint arXiv. 2305.06334 2023
  • 72 Chen C, Shi H, Jiang Z, Salhi A, Chen R, Cui X, Yu B. DNN-DTIs: Improved drug-target interactions prediction using XGBoost feature selection and deep neural network. Comput Biol Med 2021; 136: 104676
  • 73 You J, McLeod RD, Hu P. Predicting drug-target interaction network using deep learning model. Comput Biol Chem 2019; 80: 90-101
  • 74 Rayhan F, Ahmed S, Shatabda S, Farid DM, Mousavian Z, Dehzangi A, Rahman MS. iDTI-ESBoost: identification of drug target interaction using evolutionary and structural features with boosting. Sci Rep 2017; 7: 17731
  • 75 Mahmud SH, Chen W, Meng H, Jahan H, Liu Y, Hasan SM. Prediction of drug-target interaction based on protein features using undersampling and feature selection techniques with boosting. Anal Biochem 2020; 589: 113507
  • 76 Mahmud SH, Chen W, Jahan H, Liu Y, Sujan NI, Ahmed S. iDTi-CSsmoteB: identification of drug–target interaction based on drug chemical structure and protein sequence using XGBoost with over-sampling technique SMOTE. IEEE Access 2019; 7: 48699-48714
  • 77 Jung YS, Kim Y, Cho YR. Comparative analysis of network-based approaches and machine learning algorithms for predicting drug-target interactions. Methods 2022; 198: 19-31
  • 78 Lin X, Xu M, Yu H. Prediction of Drug-Target Interactions with CNNs and Random Forest. In: Intell Comput Theories Appl 16th Int Conf ICIC 2020. Springer Int Publ; 2020: 361-370
  • 79 Rayhan F, Ahmed S, Shatabda S, Farid DM. CFSBoost: cumulative feature subspace boosting for drug-target interaction prediction. J Theor Biol 2019; 464: 1-8
  • 80 Chen C, Shi H, Jiang Z, Salhi A, Chen R, Cui X, Yu B. DNN-DTIs: Improved drug-target interactions prediction using XGBoost feature selection and deep neural network. Comput Biol Med 2021; 136: 104676
  • 81 Mahmud SH, Chen W, Liu Y, Awal MA, Ahmed K, Rahman MH, Moni MA. PreDTIs: prediction of drug–target interactions based on multiple feature information using gradient boosting framework with data balancing and feature selection techniques. Brief Bioinform 2021; 22: bbab046
  • 82 Chu Y, Kaushik AC, Wang X, Wang W, Zhang Y, Shan X, Wei DQ. DTI-CDF: a cascade deep forest model towards the prediction of drug-target interactions based on hybrid features. Brief Bioinform 2021; 22: 451-462
  • 83 Thafar MA, Albaradie S, Olayan RS, Ashoor H, Essack M, Bajic VB. Computational drug-target interaction prediction based on graph embedding and graph mining. In: Proc 2020 10th Int Conf Biosci Biochem Bioinforma. 2020: 14-21
  • 84 Zhang YF, Wang X, Kaushik AC, Chu Y, Shan X, Zhao MZ, Wei DQ. SPVec: a Word2vec-inspired feature representation method for drug-target interaction prediction. Front Chem 2020; 7: 895
  • 85 Tanoori B, Zolghadri Jahromi M, Mansoori EG. Binding affinity prediction for binary drug–target interactions using semi-supervised transfer learning. J Comput-Aided Mol Des 2021; 35: 883-900
  • 86 Zhang Y, Jiang Z, Chen C, Wei Q, Gu H, Yu B. DeepStack-DTIs: Predicting drug–target interactions using LightGBM feature selection and deep-stacked ensemble classifier. Interdiscip Sci 2022; 311-330
  • 87 Hu L, Fu C, Ren Z, Cai Y, Yang J, Xu S, Tang D. SSELM-neg: spherical search-based extreme learning machine for drug–target interaction prediction. BMC Bioinf 2023; 24: 38
  • 88 Chu Y, Shan X, Chen T, Jiang M, Wang Y, Wang Q, Wei DQ. DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method. Brief Bioinform 2021; 22: bbaa205
  • 89 Tayebi A, Yousefi N, Yazdani-Jahromi M, Kolanthai E, Neal CJ, Seal S, Garibay OO. UnbiasedDTI: Mitigating real-world bias of drug-target interaction prediction by using deep ensemble-balanced learning. Molecules 2022; 27: 2980
  • 90 Puri A, Gupta MK, Sachdev K. An ensemble-based approach using structural feature extraction method with class imbalance handling technique for drug-target interaction prediction. Multimedia Tools Appl 2022; 81: 37499-37517
  • 91 Thafar MA, Olayan RS, Ashoor H, Albaradei S, Bajic VB, Gao X, Essack M. DTiGEMS+: drug–target interaction prediction using graph embedding, graph mining, and similarity-based techniques. J Cheminform 2020; 12: 1-17
  • 92 Song J, Xu Z, Cao L, Wang M, Hou Y, Li K. The discovery of new drug-target interactions for breast cancer treatment. Molecules 2021; 26: 7474
  • 93 Liu Y, Zhang X, Lin X. Incorporating FPConv-DTI deep learning network and borderline-SMOTE algorithm for predicting drug-target interactions. In: 2021 11th International Conference on Bioscience, Biochemistry, Bioinformatics. 2021: 22-32
  • 94 Lian M, Wang X, Du W. Drug-target interactions prediction based on network topology feature representation embedded deep forest. Neurocomputing 2023; 551: 126509
  • 95 Li J, Wang Y, Li Z, Lin H, Wu B. LM-DTI: a tool of predicting drug-target interactions using the node2vec and network path score methods. Front Genet 2023; 14: 1181592
  • 96 Bahi M, Batouche M. Convolutional neural network with stacked autoencoders for predicting drug-target interaction and binding affinity. Int J Data Min Modell Manage 2022; 13: 81-113
  • 97 Zheng Y, Wu Z. Cascade Deep Forest With Heterogeneous Similarity Measures for Drug–Target Interaction Prediction. Front Genet 2021; 12: 702259
  • 98 Orellana MC, Ñanculef R, Valle C. Boosting Collaborative Filters for Drug-Target Interaction Prediction. In: Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications: 23rd Iberoamerican Congress, CIARP 2018. Springer International Publishing; 2019: 212-220