Literature (Narrative) Review

Deep Learning in Drug Design—Progress, Methods, and Challenges

Abstract

Purpose: Artificial Intelligence (AI), which mimics the human brain structure and operation, simulates intelligence. The aim of Machine Learning (ML), which is a branch of artificial intelligence, is to create models by analyzing data. Another type of artificial intelligence, Deep Learning (DL), depicts geometric changes using several layers of model representations. Since DL broke the computational analysis record, AI has advanced in many areas.

Materials and Methods: Contrary to the widespread use of conventional ML methodologies, there is still a need to promote the use and popularity of DL for pharmaceutical research and development. Drug discovery and design have been enhanced by ML and DL in major research projects. To fully realize its potential, drug design must overcome many challenges and issues. Various aspects of medication design must be considered to successfully address these concerns and challenges. This review article explains DL's significance both in technological breakthroughs and in effective medications.

Results: There are numerous barriers and substantial challenges associated with drug design associated with DL architectures and key application domains. The article discusses several elements of medication development that have been influenced by existing research. Two widely used and efficient Neural Network (NN) designs are discussed in this article: Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs).

Conclusion: It is described how these tools can be utilized to design and discover small molecules for drug discovery. They are also given an overview of the history of DL approaches, as well as a discussion of some of their drawbacks.

1- J. W. Scannell, A. Blanckley, H. Boldon, and B. Warrington, "Diagnosing the decline in pharmaceutical R&D efficiency." Nat Rev Drug Discov, Vol. 11 (No. 3), pp. 191-200, Mar 1 (2012).
2- D. Krentzel, S. L. Shorte, and C. Zimmer, "Deep learning in image-based phenotypic drug discovery." Trends Cell Biol, Jan 7 (2023).
3- S. Kim et al., "PubChem Substance and Compound databases." Nucleic Acids Res, Vol. 44 (No. D1), pp. D1202-13, Jan 4 (2016).
4- E. J. Topol, "High-performance medicine: the convergence of human and artificial intelligence." Nat Med, Vol. 25 (No. 1), pp. 44-56, Jan (2019).
5- B. B. Hansen et al., "Deep Eutectic Solvents: A Review of Fundamentals and Applications." Chem Rev, Vol. 121 (No. 3), pp. 1232-85, Feb 10 (2021).
6- E. J. Pérez-Pérez, F. R. López-Estrada, G. Valencia-Palomo, L. Torres, V. Puig, and J. D. Mina-Antonio, "Leak diagnosis in pipelines using a combined artificial neural network approach." Control Engineering Practice, Vol. 107(2021).
7- Connor Shorten and Taghi M. Khoshgoftaar, "A survey on Image Data Augmentation for Deep Learning." Journal of Big Data, Vol. 6 (No. 1), (2019).
8- C. Ma, L. Wang, and X. Q. Xie, "GPU accelerated chemical similarity calculation for compound library comparison." J Chem Inf Model, Vol. 51 (No. 7), pp. 1521-7, Jul 25 (2011).
9- Adam P. Piotrowski, Jaroslaw J. Napiorkowski, and Agnieszka E. Piotrowska, "Impact of deep learning-based dropout on shallow neural networks applied to stream temperature modelling." Earth-Science Reviews, Vol. 201(2020).
10- Qifeng Bai et al., "Application advances of deep learning methods for de novo drug design and molecular dynamics simulation." WIREs Computational Molecular Science, Vol. 12 (No. 3), (2021).
11- G. E. Hinton, S. Osindero, and Y. W. Teh, "A fast learning algorithm for deep belief nets." Neural Comput, Vol. 18 (No. 7), pp. 1527-54, Jul (2006).
12- K. G. Liakos, P. Busato, D. Moshou, S. Pearson, and D. Bochtis, "Machine Learning in Agriculture: A Review." Sensors (Basel), Vol. 18 (No. 8), Aug 14 (2018).
13- X. Yang, Y. Wang, R. Byrne, G. Schneider, and S. Yang, "Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery." Chem Rev, Vol. 119 (No. 18), pp. 10520-94, Sep 25 (2019).
14- Yaguo Lei, Bin Yang, Xinwei Jiang, Feng Jia, Naipeng Li, and Asoke K. Nandi, "Applications of machine learning to machine fault diagnosis: A review and roadmap." Mechanical Systems and Signal Processing, Vol. 138(2020).
15- H. Bennett-Lenane, B. T. Griffin, and J. P. O'Shea, "Machine learning methods for prediction of food effects on bioavailability: A comparison of support vector machines and artificial neural networks." Eur J Pharm Sci, Vol. 168p. 106018, Jan 1 (2022).
16- G. B. Goh, N. O. Hodas, and A. Vishnu, "Deep learning for computational chemistry." J Comput Chem, Vol. 38 (No. 16), pp. 1291-307, Jun 15 (2017).
17- C. Angermueller, T. Parnamaa, L. Parts, and O. Stegle, "Deep learning for computational biology." Mol Syst Biol, Vol. 12 (No. 7), p. 878, Jul 29 (2016).
18- T. Zhang, J. Leng, and Y. Liu, "Deep learning for drug-drug interaction extraction from the literature: a review." Brief Bioinform, Vol. 21 (No. 5), pp. 1609-27, Sep 25 (2020).
19- A. Lavecchia, "Deep learning in drug discovery: opportunities, challenges and future prospects." Drug Discov Today, Vol. 24 (No. 10), pp. 2017-32, Oct (2019).
20- G. E. Dahl, Yu Dong, Deng Li, and A. Acero, "Context-Dependent Pre-Trained Deep Neural Networks for Large-Vocabulary Speech Recognition." IEEE Transactions on Audio, Speech, and Language Processing, Vol. 20 (No. 1), pp. 30-42, (2012).
21- Y. Yu et al., "A Novel Scalarized Scaffold Hopping Algorithm with Graph-Based Variational Autoencoder for Discovery of JAK1 Inhibitors." ACS Omega, Vol. 6 (No. 35), pp. 22945-54, Sep 7 (2021).
22- J. Schmidhuber, "Deep learning in neural networks: an overview." Neural Netw, Vol. 61pp. 85-117, Jan (2015).
23- T. Ching et al., "Opportunities and obstacles for deep learning in biology and medicine." J R Soc Interface, Vol. 15 (No. 141), Apr (2018).
24- Liuying Wang et al., "Advances of Artificial Intelligence in Anti-Cancer Drug Design: A Review of the Past Decade." Pharmaceuticals, Vol. 16 (No. 2), (2023).
25- D. M. Walden, Y. Bundey, A. Jagarapu, V. Antontsev, K. Chakravarty, and J. Varshney, "Molecular Simulation and Statistical Learning Methods toward Predicting Drug-Polymer Amorphous Solid Dispersion Miscibility, Stability, and Formulation Design." Molecules, Vol. 26 (No. 1), Jan 1 (2021).
26- R. Gupta et al., "OdoriFy: A conglomerate of artificial intelligence-driven prediction engines for olfactory decoding." J Biol Chem, Vol. 297 (No. 2), p. 100956, Aug (2021).
27- O. T. Jones et al., "Artificial Intelligence Techniques That May Be Applied to Primary Care Data to Facilitate Earlier Diagnosis of Cancer: Systematic Review." J Med Internet Res, Vol. 23 (No. 3), p. e23483, Mar 3 (2021).
28- L. Chen, X. Pan, Y. H. Zhang, M. Liu, T. Huang, and Y. D. Cai, "Classification of Widely and Rarely Expressed Genes with Recurrent Neural Network." Comput Struct Biotechnol J, Vol. 17pp. 49-60, (2019).
29- N. Hampe et al., "Deep learning-based detection of functionally significant stenosis in coronary CT angiography." Front Cardiovasc Med, Vol. 9p. 964355, (2022).
30- V. B. Mathema, P. Sen, S. Lamichhane, M. Oresic, and S. Khoomrung, "Deep learning facilitates multi-data type analysis and predictive biomarker discovery in cancer precision medicine." Comput Struct Biotechnol J, Vol. 21pp. 1372-82, (2023).
31- S. Luukkonen, H. W. van den Maagdenberg, M. T. M. Emmerich, and G. J. P. van Westen, "Artificial intelligence in multi-objective drug design." Curr Opin Struct Biol, Vol. 79p. 102537, Apr (2023).
32- S. Shukar et al., "Drug Shortage: Causes, Impact, and Mitigation Strategies." Front Pharmacol, Vol. 12p. 693426, (2021).
33- G. Latif, S. E. Abdelhamid, R. E. Mallouhy, J. Alghazo, and Z. A. Kazimi, "Deep Learning Utilization in Agriculture: Detection of Rice Plant Diseases Using an Improved CNN Model." Plants (Basel), Vol. 11 (No. 17), Aug 28 (2022).
34- A. Churcher et al., "An Experimental Analysis of Attack Classification Using Machine Learning in IoT Networks." Sensors (Basel), Vol. 21 (No. 2), Jan 10 (2021).
35- M. Yang et al., "Prediction of biomarker-disease associations based on graph attention network and text representation." Brief Bioinform, Vol. 23 (No. 5), Sep 20 (2022).
36- T. W. Laetsch, S. G. DuBois, J. G. Bender, M. E. Macy, and L. Moreno, "Opportunities and Challenges in Drug Development for Pediatric Cancers." Cancer Discov, Vol. 11 (No. 3), pp. 545-59, Mar (2021).
37- A. A. Kalinin et al., "Deep learning in pharmacogenomics: from gene regulation to patient stratification." Pharmacogenomics, Vol. 19 (No. 7), pp. 629-50, May (2018).
38- M. M. A. Monshi, J. Poon, and V. Chung, "Deep learning in generating radiology reports: A survey." Artif Intell Med, Vol. 106p. 101878, Jun (2020).
39- Y. Chen, Z. Lin, X. Zhao, G. Wang and Y. Gu, "Deep learning-based classification of hyperspectral data.", IEEE J. Sel. Topics Appl. Earth Observ. Remote Sens., Vol. 7 (No. 6), pp. 2094-2107, Jun (2014).
40- C. Qu, B. I. Schneider, A. J. Kearsley, W. Keyrouz, and T. C. Allison, "Predicting Kovats Retention Indices Using Graph Neural Networks." J Chromatogr A, Vol. 1646p. 462100, Jun 7 (2021).
41- T. B. Hughes, G. P. Miller, and S. J. Swamidass, "Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network." ACS Cent Sci, Vol. 1 (No. 4), pp. 168-80, Jul 22 (2015).
42- D. Paul, G. Sanap, S. Shenoy, D. Kalyane, K. Kalia, and R. K. Tekade, "Artificial intelligence in drug discovery and development." Drug Discov Today, Vol. 26 (No. 1), pp. 80-93, Jan (2021).
43- D. Baptista, J. Correia, B. Pereira, and M. Rocha, "Evaluating molecular representations in machine learning models for drug response prediction and interpretability." J Integr Bioinform, Vol. 19 (No. 3), Sep 1 (2022).
44- Z. Qriouet, Z. Qmichou, N. Bouchoutrouch, H. Mahi, Y. Cherrah, and H. Sefrioui, "Analytical Methods Used for the Detection and Quantification of Benzodiazepines." J Anal Methods Chem, Vol. 2019, p. 2035492, (2019).
45- R. J. Tyson et al., "Precision Dosing Priority Criteria: Drug, Disease, and Patient Population Variables." Front Pharmacol, Vol. 11, p. 420, (2020).
46- W. Chen, X. Liu, S. Zhang, and S. Chen, "Artificial intelligence for drug discovery: Resources, methods, and applications." Mol Ther Nucleic Acids, Vol. 31pp. 691-702, Mar 14 (2023).
47- M. Batool, B. Ahmad, and S. Choi, "A Structure-Based Drug Discovery Paradigm." Int J Mol Sci, Vol. 20 (No. 11), Jun 6 (2019).
48- Junxiong Wu, Xiaochuan Chen, Wei Fan, Xiaoyan Li, Yiu-Wing Mai, and Yuming Chen, "Rationally designed alloy phases for highly reversible alkali metal batteries." Energy Storage Materials, Vol. 48, pp. 223-43, (2022).
49- Md Zahangir Alom et al., "A State-of-the-Art Survey on Deep Learning Theory and Architectures." Electronics, Vol. 8 (No. 3), (2019).
50- Caiming Zhang and Yang Lu, "Study on artificial intelligence: The state of the art and future prospects." Journal of Industrial Information Integration, Vol. 23(2021).
51- R. Miotto, F. Wang, S. Wang, X. Jiang, and J. T. Dudley, "Deep learning for healthcare: review, opportunities and challenges." Brief Bioinform, Vol. 19 (No. 6), pp. 1236-46, Nov 27 (2018).
52- L. Maziarka, A. Pocha, J. Kaczmarczyk, K. Rataj, T. Danel, and M. Warchol, "Mol-CycleGAN: a generative model for molecular optimization." J Cheminform, Vol. 12 (No. 1), p. 2, Jan 8 (2020).
53- J. Meyers, B. Fabian, and N. Brown, "De novo molecular design and generative models." Drug Discov Today, Vol. 26 (No. 11), pp. 2707-15, Nov (2021).
54- G. Q. Sun et al., "Impacts of climate change on vegetation pattern: Mathematical modeling and data analysis." Phys Life Rev, Vol. 43, pp. 239-70, Dec (2022).
55- D. Singh, V. Kumar, Vaishali, and M. Kaur, "Classification of COVID-19 patients from chest CT images using multi-objective differential evolution-based convolutional neural networks." Eur J Clin Microbiol Infect Dis, Vol. 39 (No. 7), pp. 1379-89, Jul (2020).
56- L. Alzubaidi et al., "Review of deep learning: concepts, CNN architectures, challenges, applications, future directions." J Big Data, Vol. 8 (No. 1), p. 53, (2021).
57- Luning Sun, Han Gao, Shaowu Pan, and Jian-Xun Wang, "Surrogate modeling for fluid flows based on physics-constrained deep learning without simulation data." Computer Methods in Applied Mechanics and Engineering, Vol. 361(2020).
58- I. Castiglioni et al., "AI applications to medical images: From machine learning to deep learning." Phys Med, Vol. 83pp. 9-24, Mar (2021).
59- A. C. Turkmen, T. Januschowski, Y. Wang, and A. T. Cemgil, "Forecasting intermittent and sparse time series: A unified probabilistic framework via deep renewal processes." PLoS One, Vol. 16 (No. 11), p. e0259764, (2021).
60- Xuan Cao, Yanwei Zhang, Song Lang, and Yan Gong, "Swin-Transformer-Based YOLOv5 for Small-Object Detection in Remote Sensing Images." Sensors, Vol. 23 (No. 7), (2023).
61- Y. LeCun, Y. Bengio, and G. Hinton, "Deep learning." Nature, Vol. 521 (No. 7553), pp. 436-44, May 28 (2015).
62- R. Thirunavukarasu, G. P. D. C, G. R, M. Gopikrishnan, and V. Palanisamy, "Towards computational solutions for precision medicine based big data healthcare system using deep learning models: A review." Comput Biol Med, Vol. 149, p. 106020, Oct (2022).
63- Chenguang Song, Kai Shu, and Bin Wu, "Temporally evolving graph neural network for fake news detection." Information Processing & Management, Vol. 58 (No. 6), (2021).
64- A. Fotiadis, S. Polyzos, and T. T. C. Huan, "The good, the bad and the ugly on COVID-19 tourism recovery." Ann Tour Res, Vol. 87, p. 103117, Mar (2021).
65- Ha Nguyen, "Role design considerations of conversational agents to facilitate discussion and systems thinking." Computers & Education, Vol. 192(2023).
66- Z. Sun, Q. Ke, H. Rahmani, M. Bennamoun, G. Wang, and J. Liu, "Human Action Recognition From Various Data Modalities: A Review." IEEE Trans Pattern Anal Mach Intell, Vol. PPJun 14 (2022).
67- T. Ozturk, M. Talo, E. A. Yildirim, U. B. Baloglu, O. Yildirim, and U. Rajendra Acharya, "Automated detection of COVID-19 cases using deep neural networks with X-ray images." Comput Biol Med, Vol. 121, p. 103792, Jun (2020).
68- K. Ahmad, A. Rizzi, R. Capelli, D. Mandelli, W. Lyu, and P. Carloni, "Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective." Front Mol Biosci, Vol. 9, p. 899805, (2022).
69- P. Yao et al., "Fully hardware-implemented memristor convolutional neural network." Nature, Vol. 577 (No. 7792), pp. 641-46, Jan (2020).
70- Qian Lv, Xiaoling Yu, Haihui Ma, Junchao Ye, Weifeng Wu, and Xiaolin Wang, "Applications of Machine Learning to Reciprocating Compressor Fault Diagnosis: A Review." Processes, Vol. 9 (No. 6), (2021).
71- Abid Haleem, Mohd Javaid, and Ibrahim Haleem Khan, "Current status and applications of Artificial Intelligence (AI) in medical field: An overview." Current Medicine Research and Practice, Vol. 9 (No. 6), pp. 231-37, (2019).
72- Soo Young Lee, Seokyeong Byeon, Hyoung Seop Kim, Hyungyu Jin, and Seungchul Lee, "Deep learning-based phase prediction of high-entropy alloys: Optimization, generation, and explanation." Materials & Design, Vol. 197(2021).
73- O. I. Abiodun, A. Jantan, A. E. Omolara, K. V. Dada, N. A. Mohamed, and H. Arshad, "State-of-the-art in artificial neural network applications: A survey." Heliyon, Vol. 4 (No. 11), p. e00938, Nov (2018).
74- Shota Harada, Hideaki Hayashi, and Seiichi Uchida, "Biosignal Generation and Latent Variable Analysis With Recurrent Generative Adversarial Networks." IEEE Access, Vol. 7, pp. 144292-302, (2019).
75- Guillermo Iglesias, Edgar Talavera, and Alberto Díaz-Álvarez, "A survey on GANs for computer vision: Recent research, analysis and taxonomy." Computer Science Review, Vol. 48(2023).
76- A. E. Blanchard, C. Stanley, and D. Bhowmik, "Using GANs with adaptive training data to search for new molecules." J Cheminform, Vol. 13 (No. 1), p. 14, Feb 23 (2021).
77- V. Thambawita et al., "SinGAN-Seg: Synthetic training data generation for medical image segmentation." PLoS One, Vol. 17 (No. 5), p. e0267976, (2022).
78- S. Bond-Taylor, A. Leach, Y. Long, and C. G. Willcocks, "Deep Generative Modelling: A Comparative Review of VAEs, GANs, Normalizing Flows, Energy-Based and Autoregressive Models." IEEE Trans Pattern Anal Mach Intell, Vol. 44 (No. 11), pp. 7327-47, Nov (2022).
79- Z. Zhou, V. Sodha, J. Pang, M. B. Gotway, and J. Liang, "Models Genesis." Med Image Anal, Vol. 67, p. 101840, Jan (2021).
80- Junyi Chai, Hao Zeng, Anming Li, and Eric W. T. Ngai, "Deep learning in computer vision: A critical review of emerging techniques and application scenarios." Machine Learning with Applications, Vol. 6(2021).
81- T. Song et al., "DNMG: Deep molecular generative model by fusion of 3D information for de novo drug design." Methods, Vol. 211, pp. 10-22, Mar (2023).
82- Ruben Tolosana, Ruben Vera-Rodriguez, Julian Fierrez, Aythami Morales, and Javier Ortega-Garcia, "Deepfakes and beyond: A Survey of face manipulation and fake detection." Information Fusion, Vol. 64, pp. 131-48, (2020).
83- Carlo Abate, Sergio Decherchi, and Andrea Cavalli, "Graph neural networks for conditional de novo drug design." WIREs Computational Molecular Science, (2023).
84- R. Shi et al., "Generative adversarial network constrained multiple loss autoencoder: A deep learning-based individual atrophy detection for Alzheimer's disease and mild cognitive impairment." Hum Brain Mapp, Vol. 44 (No. 3), pp. 1129-46, Feb 15 (2023).
85- E. Lin, S. Mukherjee, and S. Kannan, "A deep adversarial variational autoencoder model for dimensionality reduction in single-cell RNA sequencing analysis." BMC Bioinformatics, Vol. 21 (No. 1), p. 64, Feb 21 (2020).
86- Kamran Javed, Nizam Ud Din, Ghulam Hussain, and Tahir Farooq, "Throwaway Shadows Using Parallel Encoders Generative Adversarial Network." Applied Sciences, Vol. 12 (No. 2), (2022).
87- Siyu Shao, Pu Wang, and Ruqiang Yan, "Generative adversarial networks for data augmentation in machine fault diagnosis." Computers in Industry, Vol. 106, pp. 85-93, (2019).
88- Yushi Chen, Zhouhan Lin, Xing Zhao, Gang Wang, and Yanfeng Gu, "Deep Learning-Based Classification of Hyperspectral Data." IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing, Vol. 7 (No. 6), pp. 2094-107, (2014).
89- I. E. Agbehadji, B. O. Awuzie, A. B. Ngowi, and R. C. Millham, "Review of Big Data Analytics, Artificial Intelligence and Nature-Inspired Computing Models towards Accurate Detection of COVID-19 Pandemic Cases and Contact Tracing." Int J Environ Res Public Health, Vol. 17 (No. 15), Jul 24 (2020).
90- Z. Wu et al., "Do we need different machine learning algorithms for QSAR modeling? A comprehensive assessment of 16 machine learning algorithms on 14 QSAR data sets." Brief Bioinform, Vol. 22 (No. 4), Jul 20 (2021).
91- Günter Klambauer, Thomas Unterthiner, Andreas Mayr, and Sepp Hochreiter, "DeepTox: Toxicity prediction using deep learning." Toxicology Letters, Vol. 280(2017).
92- G. Palla, D. S. Fischer, A. Regev, and F. J. Theis, "Spatial components of molecular tissue biology." Nat Biotechnol, Vol. 40 (No. 3), pp. 308-18, Mar (2022).
93- K. V. Chuang, L. M. Gunsalus, and M. J. Keiser, "Learning Molecular Representations for Medicinal Chemistry." J Med Chem, Vol. 63 (No. 16), pp. 8705-22, Aug 27 (2020).
94- B. Ramsundar et al., "Is Multitask Deep Learning Practical for Pharma?" J Chem Inf Model, Vol. 57 (No. 8), pp. 2068-76, Aug 28 (2017).
95- E. B. Lenselink et al., "Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set." J Cheminform, Vol. 9 (No. 1), p. 45, Aug 14 (2017).
96- A. Aliper, S. Plis, A. Artemov, A. Ulloa, P. Mamoshina, and A. Zhavoronkov, "Deep Learning Applications for Predicting Pharmacological Properties of Drugs and Drug Repurposing Using Transcriptomic Data." Mol Pharm, Vol. 13 (No. 7), pp. 2524-30, Jul 5 (2016).
97- A. Lusci, G. Pollastri, and P. Baldi, "Deep architectures and deep learning in chemoinformatics: the prediction of aqueous solubility for drug-like molecules." J Chem Inf Model, Vol. 53 (No. 7), pp. 1563-75, Jul 22 (2013).
98- Y. Xu, Z. Dai, F. Chen, S. Gao, J. Pei, and L. Lai, "Deep Learning for Drug-Induced Liver Injury." J Chem Inf Model, Vol. 55 (No. 10), pp. 2085-93, Oct 26 (2015).
99- M. H. S. Segler, T. Kogej, C. Tyrchan, and M. P. Waller, "Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks." ACS Cent Sci, Vol. 4 (No. 1), pp. 120-31, Jan 24 (2018).
100- C. W. Coley, R. Barzilay, W. H. Green, T. S. Jaakkola, and K. F. Jensen, "Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction." J Chem Inf Model, Vol. 57 (No. 8), pp. 1757-72, Aug 28 (2017).
101- E. J. Bjerrum and B. Sattarov, "Improving Chemical Autoencoder Latent Space and Molecular De Novo Generation Diversity with Heteroencoders." Biomolecules, Vol. 8 (No. 4), Oct 30 (2018).
102- Abdulelah S. Alshehri, Rafiqul Gani, and Fengqi You, "Deep learning and knowledge-based methods for computer-aided molecular design—toward a unified approach: State-of-the-art and future directions." Computers & Chemical Engineering, Vol. 141(2020).
103- S. D'Souza, K. V. Prema, and S. Balaji, "Machine learning models for drug-target interactions: current knowledge and future directions." Drug Discov Today, Vol. 25 (No. 4), pp. 748-56, Apr (2020).
104- Y. C. Lo, S. E. Rensi, W. Torng, and R. B. Altman, "Machine learning in chemoinformatics and drug discovery." Drug Discov Today, Vol. 23 (No. 8), pp. 1538-46, Aug (2018).
105- X. Zeng et al., "Deep generative molecular design reshapes drug discovery." Cell Rep Med, Vol. 3 (No. 12), p. 100794, Dec 20 (2022).
106- Z. Zhou, S. Kearnes, L. Li, R. N. Zare, and P. Riley, "Optimization of Molecules via Deep Reinforcement Learning." Sci Rep, Vol. 9 (No. 1), p. 10752, Jul 24 (2019).
107- A. Kadurin et al., "The cornucopia of meaningful leads: Applying deep adversarial autoencoders for new molecule development in oncology." Oncotarget, Vol. 8 (No. 7), pp. 10883-90, Feb 14 (2017).
108- A. Kadurin, S. Nikolenko, K. Khrabrov, A. Aliper, and A. Zhavoronkov, "druGAN: An Advanced Generative Adversarial Autoencoder Model for de Novo Generation of New Molecules with Desired Molecular Properties in Silico." Mol Pharm, Vol. 14 (No. 9), pp. 3098-104, Sep 5 (2017).
109- T. Blaschke, M. Olivecrona, O. Engkvist, J. Bajorath, and H. Chen, "Application of Generative Autoencoder in De Novo Molecular Design." Mol Inform, Vol. 37 (No. 1-2), Jan (2018).
110- K. Seeliger, U. Guclu, L. Ambrogioni, Y. Gucluturk, and M. A. J. van Gerven, "Generative adversarial networks for reconstructing natural images from brain activity." Neuroimage, Vol. 181, pp. 775-85, Nov 1 (2018).
111- Ian Goodfellow et al., "Generative adversarial networks." Communications of the ACM, Vol. 63 (No. 11), pp. 139-44, (2020).
112- N. Suresh, N. Chinnakonda Ashok Kumar, S. Subramanian, and G. Srinivasa, "Memory augmented recurrent neural networks for de-novo drug design." PLoS One, Vol. 17 (No. 6), p. e0269461, (2022).
113- F. Noe, A. Tkatchenko, K. R. Muller, and C. Clementi, "Machine Learning for Molecular Simulation." Annu Rev Phys Chem, Vol. 71, pp. 361-90, Apr 20 (2020).
114- A. Gupta, A. T. Muller, B. J. H. Huisman, J. A. Fuchs, P. Schneider, and G. Schneider, "Generative Recurrent Networks for De Novo Drug Design." Mol Inform, Vol. 37 (No. 1-2), Jan (2018).
115- V. Gallego, R. Naveiro, C. Roca, D. Rios Insua, and N. E. Campillo, "AI in drug development: a multidisciplinary perspective." Mol Divers, Vol. 25 (No. 3), pp. 1461-79, Aug (2021).
116- B. Tang et al., "AI-Aided Design of Novel Targeted Covalent Inhibitors against SARS-CoV-2." Biomolecules, Vol. 12 (No. 6), May 25 (2022).
117- Martha M. Flores-Leonar et al., "Materials Acceleration Platforms: On the way to autonomous experimentation." Current Opinion in Green and Sustainable Chemistry, Vol. 25(2020).
118- P. Szymanski, M. Markowicz, and E. Mikiciuk-Olasik, "Adaptation of high-throughput screening in drug discovery-toxicological screening tests." Int J Mol Sci, Vol. 13 (No. 1), pp. 427-52, (2012).
119- Khalid Albulayhi, Qasem Abu Al-Haija, Suliman A. Alsuhibany, Ananth A. Jillepalli, Mohammad Ashrafuzzaman, and Frederick T. Sheldon, "IoT Intrusion Detection Using Machine Learning with a Novel High Performing Feature Selection Method." Applied Sciences, Vol. 12 (No. 10), (2022).
120- M. Bagherian, E. Sabeti, K. Wang, M. A. Sartor, Z. Nikolovska-Coleska, and K. Najarian, "Machine learning approaches and databases for prediction of drug-target interaction: a survey paper." Brief Bioinform, Vol. 22 (No. 1), pp. 247-69, Jan 18 (2021).
121- Y. Zeng, X. Chen, Y. Luo, X. Li, and D. Peng, "Deep drug-target binding affinity prediction with multiple attention blocks." Brief Bioinform, Vol. 22 (No. 5), Sep 2 (2021).
122- B. Han, X. H. He, Y. Q. Liu, G. He, C. Peng, and J. L. Li, "Asymmetric organocatalysis: an enabling technology for medicinal chemistry." Chem Soc Rev, Vol. 50 (No. 3), pp. 1522-86, Feb 15 (2021).
123- S. Dara, S. Dhamercherla, S. S. Jadav, C. M. Babu, and M. J. Ahsan, "Machine Learning in Drug Discovery: A Review." Artif Intell Rev, Vol. 55 (No. 3), pp. 1947-99, (2022).
124- J. Jimenez, S. Doerr, G. Martinez-Rosell, A. S. Rose, and G. De Fabritiis, "DeepSite: protein-binding site predictor using 3D-convolutional neural networks." Bioinformatics, Vol. 33 (No. 19), pp. 3036-42, Oct 1 (2017).
125- J. Jimenez, M. Skalic, G. Martinez-Rosell, and G. De Fabritiis, "K(DEEP): Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks." J Chem Inf Model, Vol. 58 (No. 2), pp. 287-96, Feb 26 (2018).
126- Betsabeh Tanoori, Mansoor Zolghadri Jahromi, and Eghbal G. Mansoori, "Drug-target continuous binding affinity prediction using multiple sources of information." Expert Systems with Applications, Vol. 186(2021).
127- Edna Chebet Too, Li Yujian, Sam Njuki, and Liu Yingchun, "A comparative study of fine-tuning deep learning models for plant disease identification." Computers and Electronics in Agriculture, Vol. 161, pp. 272-79, (2019).
128- M. H. S. Segler and M. P. Waller, "Modelling Chemical Reasoning to Predict and Invent Reactions." Chemistry, Vol. 23 (No. 25), pp. 6118-28, May 2 (2017).
129- D. T. Ahneman, J. G. Estrada, S. Lin, S. D. Dreher, and A. G. Doyle, "Predicting reaction performance in C-N cross-coupling using machine learning." Science, Vol. 360 (No. 6385), pp. 186-90, Apr 13 (2018).
130- P. Schwaller, B. Hoover, J. L. Reymond, H. Strobelt, and T. Laino, "Extraction of organic chemistry grammar from unsupervised learning of chemical reactions." Sci Adv, Vol. 7 (No. 15), Apr (2021).
131- Tfgg Cova and Aacc Pais, "Deep Learning for Deep Chemistry: Optimizing the Prediction of Chemical Patterns." Front Chem, Vol. 7, p. 809, (2019).
132- A. C. Mater and M. L. Coote, "Deep Learning in Chemistry." J Chem Inf Model, Vol. 59 (No. 6), pp. 2545-59, Jun 24 (2019).
133- M. H. S. Segler, M. Preuss, and M. P. Waller, "Planning chemical syntheses with deep neural networks and symbolic AI." Nature, Vol. 555 (No. 7698), pp. 604-10, Mar 28 (2018).
134- L. Tao, G. Chen, and Y. Li, "Machine learning discovery of high-temperature polymers." Patterns (N Y), Vol. 2 (No. 4), p. 100225, Apr 9 (2021).
135- B. Liu et al., "Retrosynthetic Reaction Prediction Using Neural Sequence-to-Sequence Models." ACS Cent Sci, Vol. 3 (No. 10), pp. 1103-13, Oct 25 (2017).
136- Y. Li, K. Li, C. Zhang, J. Montoya, and G. H. Chen, "Learning to Reconstruct Computed Tomography Images Directly From Sinogram Data Under A Variety of Data Acquisition Conditions." IEEE Trans Med Imaging, Vol. 38 (No. 10), pp. 2469-81, Oct (2019).
137- C. W. Coley, R. Barzilay, T. S. Jaakkola, W. H. Green, and K. F. Jensen, "Prediction of Organic Reaction Outcomes Using Machine Learning." ACS Cent Sci, Vol. 3 (No. 5), pp. 434-43, May 24 (2017).
138- Z. Zhou, X. Li, and R. N. Zare, "Optimizing Chemical Reactions with Deep Reinforcement Learning." ACS Cent Sci, Vol. 3 (No. 12), pp. 1337-44, Dec 27 (2017).
139- L. B. Ayres, F. J. V. Gomez, J. R. Linton, M. F. Silva, and C. D. Garcia, "Taking the leap between analytical chemistry and artificial intelligence: A tutorial review." Anal Chim Acta, Vol. 1161, p. 338403, May 29 (2021).
140- M. Reichstein et al., "Deep learning and process understanding for data-driven Earth system science." Nature, Vol. 566 (No. 7743), pp. 195-204, Feb (2019).
141- Y. Jing, Y. Bian, Z. Hu, L. Wang, and X. Q. Xie, "Deep Learning for Drug Design: an Artificial Intelligence Paradigm for Drug Discovery in the Big Data Era." AAPS J, Vol. 20 (No. 3), p. 58, Mar 30 (2018).
142- D. Rogers and M. Hahn, "Extended-connectivity fingerprints." J Chem Inf Model, Vol. 50 (No. 5), pp. 742-54, May 24 (2010).
143- K. Gao, D. D. Nguyen, V. Sresht, A. M. Mathiowetz, M. Tu, and G. W. Wei, "Are 2D fingerprints still valuable for drug discovery?" Phys Chem Chem Phys, Vol. 22 (No. 16), pp. 8373-90, Apr 29 (2020).
144- Y. Bian and X. Q. Xie, "Generative chemistry: drug discovery with deep learning generative models." J Mol Model, Vol. 27 (No. 3), p. 71, Feb 4 (2021).
145- J. Jimenez-Luna, M. Skalic, N. Weskamp, and G. Schneider, "Coloring Molecules with Explainable Artificial Intelligence for Preclinical Relevance Assessment." J Chem Inf Model, Vol. 61 (No. 3), pp. 1083-94, Mar 22 (2021).
146- S. Kearnes, K. McCloskey, M. Berndl, V. Pande, and P. Riley, "Molecular graph convolutions: moving beyond fingerprints." J Comput Aided Mol Des, Vol. 30 (No. 8), pp. 595-608, Aug (2016).
147- P. Reiser et al., "Graph neural networks for materials science and chemistry." Commun Mater, Vol. 3 (No. 1), p. 93, (2022).
148- A. Gaulton et al., "ChEMBL: a large-scale bioactivity database for drug discovery." Nucleic Acids Res, Vol. 40 (No. Database issue), pp. D1100-7, Jan (2012).
149- E. H. B. Maia, L. C. Assis, T. A. de Oliveira, A. M. da Silva, and A. G. Taranto, "Structure-Based Virtual Screening: From Classical to Artificial Intelligence." Front Chem, Vol. 8, p. 343, (2020).
150- W. P. Walters and R. Barzilay, "Applications of Deep Learning in Molecule Generation and Molecular Property Prediction." Acc Chem Res, Vol. 54 (No. 2), pp. 263-70, Jan 19 (2021).
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IssueVol 11 No 3 (2024) QRcode
SectionLiterature (Narrative) Review(s)
DOI https://doi.org/10.18502/fbt.v11i3.15893
Keywords
Machine Learning Deep Learning Drug Design Drug Discovery Neural Network

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Masoomkhah SS, Rezaee K, Ansari M, Eslami H. Deep Learning in Drug Design—Progress, Methods, and Challenges. Frontiers Biomed Technol. 2024;11(3):492-508.