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Razlivina J, Dmitrenko A, Vinogradov V. AI-Powered Knowledge Base Enables Transparent Prediction of Nanozyme Multiple Catalytic Activity. J Phys Chem Lett 2024; 15:5804-5813. [PMID: 38781458 DOI: 10.1021/acs.jpclett.4c00959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Nanozymes are unique materials with many valuable properties for applications in biomedicine, biosensing, environmental monitoring, and beyond. In this work, we developed a machine learning (ML) approach to search for new nanozymes and deployed a web platform, DiZyme, featuring a state-of-the-art database of nanozymes containing 1210 experimental samples, catalytic activity prediction, and DiZyme Assistant interface powered by a large language model (LLM). For the first time, we enable the prediction of multiple catalytic activities of nanozymes by training an ensemble learning algorithm achieving R2 = 0.75 for the Michaelis-Menten constant and R2 = 0.77 for the maximum velocity on unseen test data. We envision an accurate prediction of multiple catalytic activities (peroxidase, oxidase, and catalase) promoting novel applications for a wide range of surface-modified inorganic nanozymes. The DiZyme Assistant based on the ChatGPT model provides users with supporting information on experimental samples, such as synthesis procedures, measurement protocols, etc. DiZyme (dizyme.aicidlab.itmo.ru) is now openly available worldwide.
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Affiliation(s)
- Julia Razlivina
- Center for AI in Chemistry, SCAMT institute, ITMO University, Saint-Petersburg 191002, Russian Federation
| | - Andrei Dmitrenko
- Center for AI in Chemistry, SCAMT institute, ITMO University, Saint-Petersburg 191002, Russian Federation
| | - Vladimir Vinogradov
- Center for AI in Chemistry, SCAMT institute, ITMO University, Saint-Petersburg 191002, Russian Federation
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2
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Sun L, Hu J, Yang Y, Wang Y, Wang Z, Gao Y, Nie Y, Liu C, Kan H. ChatGPT Combining Machine Learning for the Prediction of Nanozyme Catalytic Types and Activities. J Chem Inf Model 2024. [PMID: 38829968 DOI: 10.1021/acs.jcim.4c00600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
The design of nanozymes with superior catalytic activities is a prerequisite for broadening their biomedical applications. Previous studies have exerted significant effort in theoretical calculation and experimental trials for enhancing the catalytic activity of nanozyme. Machine learning (ML) provides a forward-looking aid in predicting nanozyme catalytic activity. However, this requires a significant amount of human effort for data collection. In addition, the prediction accuracy urgently needs to be improved. Herein, we demonstrate that ChatGPT can collaborate with humans to efficiently collect data. We establish four qualitative models (random forest (RF), decision tree (DT), adaboost random forest (adaboost-RF), and adaboost decision tree (adaboost-DT)) for predicting nanozyme catalytic types, such as peroxidase, oxidase, catalase, superoxide dismutase, and glutathione peroxidase. Furthermore, we use five quantitative models (random forest (RF), decision tree (DT), Support Vector Regression (SVR), gradient boosting regression (GBR), and fully connected deep neuron network (DNN)) to predict nanozyme catalytic activities. We find that GBR model demonstrates superior prediction performance for nanozyme catalytic activities (R2 = 0.6476 for Km and R2 = 0.95 for Kcat). Moreover, an open-access web resource, AI-ZYMES, with a ChatGPT-based nanozyme copilot is developed for predicting nanozyme catalytic types and activities and guiding the synthesis of nanozyme. The accuracy of the nanozyme copilot's responses reaches more than 90% through the retrieval augmented generation. This study provides a new potential application for ChatGPT in the field of nanozymes.
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Affiliation(s)
- Liping Sun
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
| | - Jili Hu
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
| | - Yinfeng Yang
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
| | - Yongkang Wang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Zijian Wang
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
| | - Yong Gao
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
| | - Yiqi Nie
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
| | - Can Liu
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
| | - Hongxing Kan
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, Anhui 230012, China
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3
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Qiao C, Wang X, Gao Y, Li J, Zhao J, Luo H, Zhang S, Huo D, Hou C. A novel colorimetric and fluorometric dual-signal identification of organics and Baijiu based on nanozymes with peroxidase-like activity. Food Chem 2024; 439:138157. [PMID: 38081097 DOI: 10.1016/j.foodchem.2023.138157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/10/2024]
Abstract
Nanozymes were nanomaterials with enzymatic properties. They had diverse functions, adjustable catalytic activity, high stability, and easy large-scale production, attracting interest in biosensing. However, nanozymes were scarcely applied in Baijiu identification. Herein, a colorimetric and fluorometric dual-signal determination mediated by a nanozyme-H2O2-TMB system was developed for the first time to identify organics and Baijiu. Since the diverse peroxidase-like activity of nanozymes, resulted in different degrees of oxidized TMB. Based on this, 21 organics were identified qualitatively and quantitatively by colorimetric method with a rapid response (<12 min), broad linearity (0.0005-35 mM), and low detection limits (a minimum of 30 nM for glutaric acids). Furthermore, the fluorometric method exhibited excellent potential for accurate determination of organics, with detection ranges of 2-200 µmol/L (LOD: 0.22 µmol/L) for l-ascorbic acid and 2-300 µmol/L (LOD: 0.59 µmol/L) for guaiacol. Finally, the sensor was successfully applied to identify fake Baijiu and Baijiu from 16 different brands.
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Affiliation(s)
- Cailin Qiao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Xinrou Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Yuwei Gao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Jiawei Li
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Jinsong Zhao
- Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, 188 University Town, Yi bin 644000, PR China; Sichuan Liquor Group Co., Ltd., Chengdu 610000, PR China
| | - Huibo Luo
- Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, 188 University Town, Yi bin 644000, PR China
| | - Suyi Zhang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China; National Engineering Research Center of Solid-State Brewing, Luzhou Laojiao Group Co., Ltd., Luzhou 646000, PR China.
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China; Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, 188 University Town, Yi bin 644000, PR China.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China; Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, 188 University Town, Yi bin 644000, PR China.
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4
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Gao Y, Zhu Z, Chen Z, Guo M, Zhang Y, Wang L, Zhu Z. Machine learning in nanozymes: from design to application. Biomater Sci 2024; 12:2229-2243. [PMID: 38497247 DOI: 10.1039/d4bm00169a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Nanozymes, a distinctive class of nanomaterials endowed with enzyme-like activity and kinetics akin to enzyme-catalysed reactions, present several advantages over natural enzymes, including cost-effectiveness, heightened stability, and adjustable activity. However, the conventional trial-and-error methodology for developing novel nanozymes encounters growing challenges as research progresses. The advent of artificial intelligence (AI), particularly machine learning (ML), has ushered in innovative design approaches for researchers in this domain. This review delves into the burgeoning role of ML in nanozyme research, elucidating the advancements achieved through ML applications. The review explores successful instances of ML in nanozyme design and implementation, providing a comprehensive overview of the evolving landscape. A roadmap for ML-assisted nanozyme research is outlined, offering a universal guideline for research in this field. In the end, the review concludes with an analysis of challenges encountered and anticipates future directions for ML in nanozyme research. The synthesis of knowledge in this review aims to foster a cross-disciplinary study, propelling the revolutionary field forward.
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Affiliation(s)
- Yubo Gao
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Zhicheng Zhu
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Zhen Chen
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Meng Guo
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Yiqing Zhang
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Lina Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
| | - Zhiling Zhu
- College of Materials Science and Engineering, Qingdao University of Science and Technology, Qingdao, Shandong 266042, China.
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Peng C, Pang R, Li J, Wang E. Current Advances on the Single-Atom Nanozyme and Its Bioapplications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2211724. [PMID: 36773312 DOI: 10.1002/adma.202211724] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Nanozymes, a class of nanomaterials mimicking the function of enzymes, have aroused much attention as the candidate in diverse fields with the arbitrarily tunable features owing to the diversity of crystalline nanostructures, composition, and surface configurations. However, the uncertainty of their active sites and the lower intrinsic deficiencies of nanomaterial-initiated catalysis compared with the natural enzymes promote the pursuing of alternatives by imitating the biological active centers. Single-atom nanozymes (SAzymes) maximize the atom utilization with the well-defined structure, providing an important bridge to investigate mechanism and the relationship between structure and catalytic activity. They have risen as the new burgeoning alternative to the natural enzyme from in vitro bioanalytical tool to in vivo therapy owing to the flexible atomic engineering structure. Here, focus is mainly on the three parts. First, a detailed overview of single-atom catalyst synthesis strategies including bottom-up and top-down approaches is given. Then, according to the structural feature of single-atom nanocatalysts, the influence factors such as central metal atom, coordination number, heteroatom doping, and the metal-support interaction are discussed and the representative biological applications (including antibacterial/antiviral performance, cancer therapy, and biosensing) are highlighted. In the end, the future perspective and challenge facing are demonstrated.
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Affiliation(s)
- Chao Peng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Ruoyu Pang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Jing Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, P. R. China
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6
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Shen X, Wang Z, Gao XJ, Gao X. Reaction Mechanisms and Kinetics of Nanozymes: Insights from Theory and Computation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2211151. [PMID: 36641629 DOI: 10.1002/adma.202211151] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/28/2022] [Indexed: 06/17/2023]
Abstract
"Nanozymes" usually refers to inorganic nanomaterials with enzyme-like catalytic activities. The research into nanozymes is one of the hot topics on the horizon of interdisciplinary science involving materials, chemistry, and biology. Although great progress has been made in the design, synthesis, characterization, and application of nanozymes, the study of the underlying microscopic mechanisms and kinetics is still not straightforward. Density functional theory (DFT) calculations compute the potential energy surfaces along the reaction coordinates for chemical reactions, which can give atomistic-level insights into the micro-mechanisms and kinetics for nanozymes. Therefore, DFT calculations have been playing an increasingly important role in exploring the mechanisms and kinetics for nanozymes in the past years. The calculations either predict the microscopic details for the catalytic processes to complement the experiments or further develop theoretical models to depict the physicochemical rules. In this review, the corresponding research progress is summarized. Particularly, the review focuses on the computational studies that closely interplay with the experiments. The relevant experimental results without DFT calculations will be also briefly discussed to offer a historic overview of how the computations promote the understanding of the microscopic mechanisms and kinetics of nanozymes.
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Affiliation(s)
- Xiaomei Shen
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, China
| | - Zhenzhen Wang
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xuejiao J Gao
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, China
| | - Xingfa Gao
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
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7
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Sheng J, Wu Y, Ding H, Feng K, Shen Y, Zhang Y, Gu N. Multienzyme-Like Nanozymes: Regulation, Rational Design, and Application. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2211210. [PMID: 36840985 DOI: 10.1002/adma.202211210] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Nanomaterials with more than one enzyme-like activity are termed multienzymic nanozymes, and they have received increasing attention in recent years and hold huge potential to be applied in diverse fields, especially for biosensing and therapeutics. Compared to single enzyme-like nanozymes, multienzymic nanozymes offer various unique advantages, including synergistic effects, cascaded reactions, and environmentally responsive selectivity. Nevertheless, along with these merits, the catalytic mechanism and rational design of multienzymic nanozymes are more complicated and elusive as compared to single-enzymic nanozymes. In this review, the multienzymic nanozymes classification scheme based on the numbers/types of activities, the internal and external factors regulating the multienzymatic activities, the rational design based on chemical, biomimetic, and computer-aided strategies, and recent progress in applications attributed to the advantages of multicatalytic activities are systematically discussed. Finally, current challenges and future perspectives regarding the development and application of multienzymatic nanozymes are suggested. This review aims to deepen the understanding and inspire the research in multienzymic nanozymes to a greater extent.
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Affiliation(s)
- Jingyi Sheng
- Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210009, P. R. China
| | - Yuehuang Wu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu, 210009, P. R. China
| | - He Ding
- Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210009, P. R. China
| | - Kaizheng Feng
- Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210009, P. R. China
| | - Yan Shen
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, P. R. China
| | - Yu Zhang
- Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210009, P. R. China
| | - Ning Gu
- Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210009, P. R. China
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, P. R. China
- Medical School, Nanjing University, Nanjing, 210093, P. R. China
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8
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Zhuang J, Midgley AC, Wei Y, Liu Q, Kong D, Huang X. Machine-Learning-Assisted Nanozyme Design: Lessons from Materials and Engineered Enzymes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2210848. [PMID: 36701424 DOI: 10.1002/adma.202210848] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/03/2023] [Indexed: 05/11/2023]
Abstract
Nanozymes are nanomaterials that exhibit enzyme-like biomimicry. In combination with intrinsic characteristics of nanomaterials, nanozymes have broad applicability in materials science, chemical engineering, bioengineering, biochemistry, and disease theranostics. Recently, the heterogeneity of published results has highlighted the complexity and diversity of nanozymes in terms of consistency of catalytic capacity. Machine learning (ML) shows promising potential for discovering new materials, yet it remains challenging for the design of new nanozymes based on ML approaches. Alternatively, ML is employed to promote optimization of intelligent design and application of catalytic materials and engineered enzymes. Incorporation of the successful ML algorithms used in the intelligent design of catalytic materials and engineered enzymes can concomitantly facilitate the guided development of next-generation nanozymes with desirable properties. Here, recent progress in ML, its utilization in the design of catalytic materials and enzymes, and how emergent ML applications serve as promising strategies to circumvent challenges associated with time-expensive and laborious testing in nanozyme research and development are summarized. The potential applications of successful examples of ML-aided catalytic materials and engineered enzymes in nanozyme design are also highlighted, with special focus on the unified aims in enhancing design and recapitulation of substrate selectivity and catalytic activity.
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Affiliation(s)
- Jie Zhuang
- School of Medicine, and State, Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, China
| | - Adam C Midgley
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, and Frontiers, Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Yonghua Wei
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, and Frontiers, Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Qiqi Liu
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, and Frontiers, Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Deling Kong
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, and Frontiers, Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
| | - Xinglu Huang
- Key Laboratory of Bioactive Materials for the Ministry of Education, College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, and Frontiers, Science Center for Cell Responses, Nankai University, Tianjin, 300071, China
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9
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Jyakhwo S, Serov N, Dmitrenko A, Vinogradov VV. Machine Learning Reinforced Genetic Algorithm for Massive Targeted Discovery of Selectively Cytotoxic Inorganic Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2305375. [PMID: 37771186 DOI: 10.1002/smll.202305375] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/11/2023] [Indexed: 09/30/2023]
Abstract
Nanoparticles (NPs) have been employed as drug delivery systems (DDSs) for several decades, primarily as passive carriers, with limited selectivity. However, recent publications have shed light on the emerging phenomenon of NPs exhibiting selective cytotoxicity against cancer cell lines, attributable to distinct metabolic disparities between healthy and pathological cells. This study revisits the concept of NPs selective cytotoxicity, and for the first time proposes a high-throughput in silico screening approach to massive targeted discovery of selectively cytotoxic inorganic NPs. In the first step, this work trains a gradient boosting regression model to predict viability of NP-treated cell lines. The model achieves mean cross-validation (CV) Q2 = 0.80 and root mean square error (RMSE) of 13.6. In the second step, this work develops a machine learning (ML) reinforced genetic algorithm (GA), capable of screening >14 900 candidates/min, to identify the best-performing selectively cytotoxic NPs. As proof-of-concept, DDS candidates for the treatment of liver cancer are screened on HepG2 and hepatocytes cell lines resulting in Ag NPs with selective toxicity score of 42%. This approach opens the door for clinical translation of NPs, expanding their therapeutic application to a wider range of chemical space of NPs and living organisms such as bacteria and fungi.
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Affiliation(s)
- Susan Jyakhwo
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, Saint-Petersburg, 191002, Russian Federation
| | - Nikita Serov
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, Saint-Petersburg, 191002, Russian Federation
| | - Andrei Dmitrenko
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, Saint-Petersburg, 191002, Russian Federation
| | - Vladimir V Vinogradov
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, Saint-Petersburg, 191002, Russian Federation
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Yang L, Dong S, Gai S, Yang D, Ding H, Feng L, Yang G, Rehman Z, Yang P. Deep Insight of Design, Mechanism, and Cancer Theranostic Strategy of Nanozymes. NANO-MICRO LETTERS 2023; 16:28. [PMID: 37989794 PMCID: PMC10663430 DOI: 10.1007/s40820-023-01224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/23/2023] [Indexed: 11/23/2023]
Abstract
Since the discovery of enzyme-like activity of Fe3O4 nanoparticles in 2007, nanozymes are becoming the promising substitutes for natural enzymes due to their advantages of high catalytic activity, low cost, mild reaction conditions, good stability, and suitable for large-scale production. Recently, with the cross fusion of nanomedicine and nanocatalysis, nanozyme-based theranostic strategies attract great attention, since the enzymatic reactions can be triggered in the tumor microenvironment to achieve good curative effect with substrate specificity and low side effects. Thus, various nanozymes have been developed and used for tumor therapy. In this review, more than 270 research articles are discussed systematically to present progress in the past five years. First, the discovery and development of nanozymes are summarized. Second, classification and catalytic mechanism of nanozymes are discussed. Third, activity prediction and rational design of nanozymes are focused by highlighting the methods of density functional theory, machine learning, biomimetic and chemical design. Then, synergistic theranostic strategy of nanozymes are introduced. Finally, current challenges and future prospects of nanozymes used for tumor theranostic are outlined, including selectivity, biosafety, repeatability and stability, in-depth catalytic mechanism, predicting and evaluating activities.
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Affiliation(s)
- Lu Yang
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China
| | - Shuming Dong
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China
| | - Shili Gai
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China.
- Yantai Research Institute, Harbin Engineering University, Yantai, 264000, People's Republic of China.
| | - Dan Yang
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China
| | - He Ding
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China
| | - Lili Feng
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China
| | - Guixin Yang
- Key Laboratory of Green Chemical Engineering and Technology of Heilongjiang Province, College of Material Science and Chemical Engineering, Harbin University of Science and Technology, Harbin, 150040, People's Republic of China
| | - Ziaur Rehman
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Piaoping Yang
- Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education, College of Materials Science and Chemical Engineering, Harbin Engineering University, Harbin, 150001, People's Republic of China.
- Yantai Research Institute, Harbin Engineering University, Yantai, 264000, People's Republic of China.
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11
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Kim P, Serov N, Falchevskaya A, Shabalkin I, Dmitrenko A, Kladko D, Vinogradov V. Quantifying the Efficacy of Magnetic Nanoparticles for MRI and Hyperthermia Applications via Machine Learning Methods. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303522. [PMID: 37563807 DOI: 10.1002/smll.202303522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/16/2023] [Indexed: 08/12/2023]
Abstract
Magnetic nanoparticles are a prospective class of materials for use in biomedicine as agents for magnetic resonance imagining (MRI) and hyperthermia treatment. However, synthesis of nanoparticles with high efficacy is resource-intensive experimental work. In turn, the use of machine learning (ML) methods is becoming useful in materials design and serves as a great approach to designing nanomagnets for biomedicine. In this work, for the first time, an ML-based approach is developed for the prediction of main parameters of material efficacy, i.e., specific absorption rate (SAR) for hyperthermia and r1 /r2 relaxivities in MRI, with parameters of nanoparticles as well as experimental conditions as descriptors. For that, a unique database with more than 980 magnetic nanoparticles collected from scientific articles is assembled. Using this data, several tree-based ensemble models are trained to predict SAR, r1 and r2 relaxivity. After hyperparameter optimization, models reach performances of R2 = 0.86, R2 = 0.78, and R2 = 0.75, respectively. Testing the models on samples unseen during the training shows no performance drops. Finally, DiMag, an open access resource created to guide synthesis of novel nanosized magnets for MRI and hyperthermia treatment with machine learning and boost development of new biomedical agents, is developed.
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Affiliation(s)
- Pavel Kim
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, St. Petersburg, 191002, Russian Federation
| | - Nikita Serov
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, St. Petersburg, 191002, Russian Federation
| | - Aleksandra Falchevskaya
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, St. Petersburg, 191002, Russian Federation
| | - Ilia Shabalkin
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, St. Petersburg, 191002, Russian Federation
| | - Andrei Dmitrenko
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, St. Petersburg, 191002, Russian Federation
| | - Daniil Kladko
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, St. Petersburg, 191002, Russian Federation
| | - Vladimir Vinogradov
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, St. Petersburg, 191002, Russian Federation
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12
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Wang Q, Liu X, Tao S, Wang H, Lu S, Xiang Y, Zhang J. Machine Learning Study on Microwave-Assisted Batch Preparation and Oxygen Reduction Performance of Fe-N-C Catalysts. J Phys Chem Lett 2023; 14:9082-9089. [PMID: 37788256 DOI: 10.1021/acs.jpclett.3c02308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The Fe-N-C catalyst represents one of the most promising candidates for replacing platinum-based catalysts toward the oxygen reduction reaction. The pivotal factor in the successful integration of Fe-N-C catalysts within applications is the attainment of a large-scale production capability. Microwave-assisted pyrolysis offers various advantages, including enhanced energy and time efficiency, uniform heating, and high yield in single-batch processes. These characteristics render it exceptionally suitable for the mass production of catalysts. Through a synergistic approach involving machine learning techniques and microscopic characterization, we discerned performance trends and underlying mechanisms within batch-synthesized Fe-N-C catalysts under microwave-assisted preparation conditions. Machine learning analysis revealed that the precursor mass exerts the most substantial influence on product performance. Furthermore, microscopic characterization unveiled that these influencing factors impact catalyst performance by modulating the degree of agglomeration. Our research introduces an efficacious machine learning model for prognosticating performance and dissecting the influencing factors pertinent to Fe-N-C catalyst synthesis within a microwave system.
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Affiliation(s)
- Qingxin Wang
- Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, School of Energy and Power Engineering, Beihang University, Beijing 100191, People's Republic of China
| | - Xinrui Liu
- Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, School of Energy and Power Engineering, Beihang University, Beijing 100191, People's Republic of China
| | - Siying Tao
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, People's Republic of China
| | - Haining Wang
- Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, School of Energy and Power Engineering, Beihang University, Beijing 100191, People's Republic of China
| | - Shanfu Lu
- Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, School of Energy and Power Engineering, Beihang University, Beijing 100191, People's Republic of China
| | - Yan Xiang
- Beijing Key Laboratory of Bio-inspired Energy Materials and Devices, School of Energy and Power Engineering, Beihang University, Beijing 100191, People's Republic of China
| | - Jing Zhang
- School of Optoelectronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, People's Republic of China
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13
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Jin K, Wang W, Qi G, Peng X, Gao H, Zhu H, He X, Zou H, Yang L, Yuan J, Zhang L, Chen H, Qu X. An explainable machine-learning approach for revealing the complex synthesis path-property relationships of nanomaterials. NANOSCALE 2023; 15:15358-15367. [PMID: 37698588 DOI: 10.1039/d3nr02273k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Machine learning (ML) models have recently shown important advantages in predicting nanomaterial properties, which avoids many trial-and-error explorations. However, complex variables that control the formation of nanomaterials exhibiting the desired properties still need to be better understood owing to the low interpretability of ML models and the lack of detailed mechanism information on nanomaterial properties. In this study, we developed a methodology for accurately predicting multiple synthesis parameter-property relationships of nanomaterials to improve the interpretability of the nanomaterial property mechanism. As a proof-of-concept, we designed glutathione-gold nanoclusters (GSH-AuNCs) exhibiting an appropriate fluorescence quantum yield (QY). First, we conducted 189 experiments and synthesized different GSH-AuNCs by varying the thiol-to-metal molar ratio and reaction temperature and time in reasonable ranges. The fluorescence QY of GSH-AuNCs could be systematically and independently programmed using different experimental parameters. We used limited GSH-AuNC synthesis parameter data to train an extreme gradient boosting regressor model. Moreover, we improved the interpretability of the ML model by combining individual conditional expectation, double-variable partial dependence, and feature interaction network analyses. The interpretability analyses established the relationship between multiple synthesis parameters and fluorescence QYs of GSH-AuNCs. The results represent an essential step towards revealing the complex fluorescence mechanism of thiolated AuNCs. Finally, we constructed a synthesis phase diagram exceeding 6.0 × 104 prediction variables for accurately predicting the fluorescence QY of GSH-AuNCs. A multidimensional synthesis phase diagram was obtained for the fluorescence QY of GSH-AuNCs by searching the synthesis parameter space in the trained ML model. Our methodology is a general and powerful complementary strategy for application in material informatics.
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Affiliation(s)
- Kun Jin
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China.
| | - Wentao Wang
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China.
| | - Guangpei Qi
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China.
| | | | - Haonan Gao
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China.
| | - Hongjiang Zhu
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China.
| | - Xin He
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China.
| | - Haixia Zou
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China.
| | - Lin Yang
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China.
| | - Junjie Yuan
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China.
| | - Liyuan Zhang
- School of Petroleum Engineering, State Key Laboratory of Heavy Oil Processing China University of Petroleum (East China), Qingdao, 266580, China
| | - Hong Chen
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, Fujian 361005, China
| | - Xiangmeng Qu
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China.
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14
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Liang S, Chen T, Zhao Y, Ren Y, Li M, Lu D, Wang J, Dai Y, Guo Y. Revealing the intrinsic peroxidase-like catalytic mechanism of O-doped CoS 2 nanoparticles. NANOSCALE 2023; 15:13666-13674. [PMID: 37551931 DOI: 10.1039/d3nr02496b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
CoS2 nanoparticles (NPs) have shown promise as potential peroxidase (POD)-like catalysts, but the catalytic molecular mechanisms are largely unknown. Moreover, no study has adequately explored the influence of O-doping induced by the inevitable oxidation of CoS2 on their POD-like activity. Here, O-doped CoS2 NPs were prepared by a one-step method, and their intrinsic POD-like catalytic mechanism was investigated with a combined experimental and theoretical approach. The hydroxyl radical (˙OH) and the superoxide radical (O2˙-) have been found to play significant roles in the POD-like activity, and ˙OH is the major radical. The O-doping could reduce the transition-state energy barrier of H2O2 dissociation, thus promoting the decomposition of H2O2 to ˙OH and inducing the formation of O2˙-. Therefore, O-doping is an effective method for enhancing the catalytic activity of CoS2 NPs. Furthermore, due to the excellent oxidation property of ˙OH and O2˙-, this nanozyme exhibited efficient catalytic activity towards the degradation of organic dyes with H2O2. This manuscript provides a new inspiration for designing more promising anion-defective transition-metal sulfide nanozymes for different applications.
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Affiliation(s)
- Shufeng Liang
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, China.
- Department of Clinical Laboratory, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, China
| | - Tingyu Chen
- School of Environment and Energy, Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, South China University of Technology, Guangzhou 510000, China
| | - Yun Zhao
- School of Environment and Energy, Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, South China University of Technology, Guangzhou 510000, China
| | - Yali Ren
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, China.
| | - Miaomiao Li
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, China.
| | - Dongtao Lu
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, China.
| | - Junhao Wang
- Institute of Crystalline Materials, Shanxi University, Taiyuan 030006, China
| | - Yan Dai
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, China.
| | - Yujing Guo
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, China.
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15
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Abstract
Nanozymes constitute an emerging class of nanomaterials with enzyme-like characteristics. Over the past 15 years, more than 1200 nanozymes have been developed, and they have demonstrated promising potentials in broad applications. With the diversification and complexity of its applications, traditional empirical and trial-and-error design strategies no longer meet the requirements for efficient nanozyme design. Thanks to the rapid development of computational chemistry and artificial intelligence technologies, first-principles methods and machine-learning algorithms are gradually being adopted as a more efficient and easier means to assist nanozyme design. This review focuses on the potential elementary reaction mechanisms in the rational design of nanozymes, including peroxidase (POD)-, oxidase (OXD)-, catalase (CAT)-, superoxide dismutase (SOD)-, and hydrolase (HYL)-like nanozymes. The activity descriptors are introduced, with the aim of providing further guidelines for nanozyme active material screening. The computing- and data-driven approaches are thoroughly reviewed to give a proposal on how to proceed with the next-generation paradigm rational design. At the end of this review, personal perspectives on the prospects and challenges of the rational design of nanozymes are put forward, hoping to promote the further development of nanozymes toward superior application performance in the future.
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Affiliation(s)
- Zhen Chen
- College of Materials Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong 266042, People's Republic of China
| | - Yixin Yu
- College of Materials Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong 266042, People's Republic of China
| | - Yonghui Gao
- College of Materials Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong 266042, People's Republic of China
| | - Zhiling Zhu
- College of Materials Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong 266042, People's Republic of China
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16
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Li Y, Zhang R, Yan X, Fan K. Machine learning facilitating the rational design of nanozymes. J Mater Chem B 2023. [PMID: 37325942 DOI: 10.1039/d3tb00842h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
As a component substitute for natural enzymes, nanozymes have the advantages of easy synthesis, convenient modification, low cost, and high stability, and are widely used in many fields. However, their application is seriously restricted by the difficulty of rapidly creating high-performance nanozymes. The use of machine learning techniques to guide the rational design of nanozymes holds great promise to overcome this difficulty. In this review, we introduce the recent progress of machine learning in assisting the design of nanozymes. Particular attention is given to the successful strategies of machine learning in predicting the activity, selectivity, catalytic mechanisms, optimal structures and other features of nanozymes. The typical procedures and approaches for conducting machine learning in the study of nanozymes are also highlighted. Moreover, we discuss in detail the difficulties of machine learning methods in dealing with the redundant and chaotic nanozyme data and provide an outlook on the future application of machine learning in the nanozyme field. We hope that this review will serve as a useful handbook for researchers in related fields and promote the utilization of machine learning in nanozyme rational design and related topics.
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Affiliation(s)
- Yucong Li
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100408, China
| | - Ruofei Zhang
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiyun Yan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100408, China
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Kelong Fan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Protein and Peptide Pharmaceutical, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100408, China
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
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17
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Shirokii N, Din Y, Petrov I, Seregin Y, Sirotenko S, Razlivina J, Serov N, Vinogradov V. Quantitative Prediction of Inorganic Nanomaterial Cellular Toxicity via Machine Learning. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207106. [PMID: 36772908 DOI: 10.1002/smll.202207106] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/09/2023] [Indexed: 05/11/2023]
Abstract
Organic chemistry has seen colossal progress due to machine learning (ML). However, the translation of artificial intelligence (AI) into materials science is challenging, where biological behavior prediction becomes even more complicated. Nanotoxicity is a critical parameter that describes their interaction with the living organisms screened in every bio-related research. To prevent excessive experiments, such properties have to be pre-evaluated. Several existing ML models partially fulfill the gap by predicting whether a nanomaterial is toxic or not. Yet, this binary categorization neglects the concentration dependencies crucial for experimental scientists. Here, an ML-based approach is proposed to the quantitative prediction of inorganic nanomaterial cytotoxicity achieving the precision expressed by 10-fold cross-validation (CV) Q2 = 0.86 with the root mean squared error (RMSE) of 12.2% obtained by the correlation-based feature selection and grid search-based model hyperparameters optimization. To provide further model flexibility, quantitative atom property-based nanomaterial descriptors are introduced allowing the model to extrapolate on unseen samples. Feature importance is calculated to find an interpretable model with optimal decision-making. These findings allow experimental scientists to perform primary in silico candidate screening and minimize the number of excessive, labor-intensive experiments enabling the rapid development of nanomaterials for medicinal purposes.
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Affiliation(s)
- Nikolai Shirokii
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, 191002, Saint-Petersburg, Russian Federation
| | - Yevgeniya Din
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, 191002, Saint-Petersburg, Russian Federation
| | - Ilya Petrov
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, 191002, Saint-Petersburg, Russian Federation
| | - Yurii Seregin
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, 191002, Saint-Petersburg, Russian Federation
| | - Sofia Sirotenko
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, 191002, Saint-Petersburg, Russian Federation
| | - Julia Razlivina
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, 191002, Saint-Petersburg, Russian Federation
| | - Nikita Serov
- Advanced Engineering School, Almetyevsk State Oil Institute, Almetyevsk, Russia
| | - Vladimir Vinogradov
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, 191002, Saint-Petersburg, Russian Federation
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18
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Gao XJ, Yan J, Zheng JJ, Zhong S, Gao X. Clear-Box Machine Learning for Virtual Screening of 2D Nanozymes to Target Tumor Hydrogen Peroxide. Adv Healthc Mater 2022; 12:e2202925. [PMID: 36565096 DOI: 10.1002/adhm.202202925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/10/2022] [Indexed: 12/25/2022]
Abstract
Targeting tumor hydrogen peroxide (H2 O2 ) with catalytic materials has provided a novel chemotherapy strategy against solid tumors. Because numerous materials have been fabricated so far, there is an urgent need for an efficient in silico method, which can automatically screen out appropriate candidates from materials libraries for further therapeutic evaluation. In this work, adsorption-energy-based descriptors and criteria are developed for the catalase-like activities of materials surfaces. The result enables a comprehensive prediction of H2 O2 -targeted catalytic activities of materials by density functional theory (DFT) calculations. To expedite the prediction, machine learning models, which efficiently calculate the adsorption energies for 2D materials without DFT, are further developed. The finally obtained method takes advantage of both interpretability of physics model and high efficiency of machine learning. It provides an efficient approach for in silico screening of 2D materials toward tumor catalytic therapy, and it will greatly promote the development of catalytic nanomaterials for medical applications.
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Affiliation(s)
- Xuejiao J Gao
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, P. R. China.,Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, P. R. China
| | - Jun Yan
- State Key Laboratory of Information Security, Institute of Information Engineering, Chinese Academy of Sciences, Beijing, 100195, P. R. China.,School of Cyber Security, University of Chinese Academy of Sciences, Beijing, 100195, P. R. China
| | - Jia-Jia Zheng
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, P. R. China
| | - Shengliang Zhong
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, P. R. China
| | - Xingfa Gao
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, P. R. China
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19
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Zhang C, Yu Y, Shi S, Liang M, Yang D, Sui N, Yu WW, Wang L, Zhu Z. Machine Learning Guided Discovery of Superoxide Dismutase Nanozymes for Androgenetic Alopecia. NANO LETTERS 2022; 22:8592-8600. [PMID: 36264822 DOI: 10.1021/acs.nanolett.2c03119] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Androgenetic alopecia (AGA) is a common form of hair loss, which is mainly caused by oxidative stress induced dysregulation of hair follicles (HF). Herein, a highly efficient manganese thiophosphite (MnPS3) based superoxide dismutase (SOD) mimic was discovered using machine learning (ML) tools. Remarkably, the IC50 of MnPS3 is 3.61 μg·mL-1, up to 12-fold lower than most reported SOD-like nanozymes. Moreover, a MnPS3 microneedle patch (MnMNP) was constructed to treat AGA that could diffuse into the deep skin where HFs exist and remove excess reactive oxygen species. Compared with the widely used minoxidil, MnMNP exhibits higher ability on hair regeneration, even at a reduced frequency of application. This study not only provides a general guideline for the accelerated discovery of SOD-like nanozymes by ML techniques, but also shows a great potential as a next generation approach for rational design of nanozymes.
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Affiliation(s)
- Chaohui Zhang
- College of Materials Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong266042, China
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong266042, China
| | - Yixin Yu
- College of Materials Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong266042, China
| | - Shugao Shi
- College of Materials Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong266042, China
| | - Manman Liang
- College of Materials Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong266042, China
| | - Dongqin Yang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, 12 Middle Urumqi Road, Shanghai200040, China
| | - Ning Sui
- College of Materials Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong266042, China
| | - William W Yu
- School of Chemistry and Chemical Engineering, Shandong University, 27 South Shanda Road, Jinan, Shandong250100, China
| | - Lina Wang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong266042, China
| | - Zhiling Zhu
- College of Materials Science and Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, Shandong266042, China
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20
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Serov N, Vinogradov V. Artificial intelligence to bring nanomedicine to life. Adv Drug Deliv Rev 2022; 184:114194. [PMID: 35283223 DOI: 10.1016/j.addr.2022.114194] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 12/13/2022]
Abstract
The technology of drug delivery systems (DDSs) has demonstrated an outstanding performance and effectiveness in production of pharmaceuticals, as it is proved by many FDA-approved nanomedicines that have an enhanced selectivity, manageable drug release kinetics and synergistic therapeutic actions. Nonetheless, to date, the rational design and high-throughput development of nanomaterial-based DDSs for specific purposes is far from a routine practice and is still in its infancy, mainly due to the limitations in scientists' capabilities to effectively acquire, analyze, manage, and comprehend complex and ever-growing sets of experimental data, which is vital to develop DDSs with a set of desired functionalities. At the same time, this task is feasible for the data-driven approaches, high throughput experimentation techniques, process automatization, artificial intelligence (AI) technology, and machine learning (ML) approaches, which is referred to as The Fourth Paradigm of scientific research. Therefore, an integration of these approaches with nanomedicine and nanotechnology can potentially accelerate the rational design and high-throughput development of highly efficient nanoformulated drugs and smart materials with pre-defined functionalities. In this Review, we survey the important results and milestones achieved to date in the application of data science, high throughput, as well as automatization approaches, combined with AI and ML to design and optimize DDSs and related nanomaterials. This manuscript mission is not only to reflect the state-of-art in data-driven nanomedicine, but also show how recent findings in the related fields can transform the nanomedicine's image. We discuss how all these results can be used to boost nanomedicine translation to the clinic, as well as highlight the future directions for the development, data-driven, high throughput experimentation-, and AI-assisted design, as well as the production of nanoformulated drugs and smart materials with pre-defined properties and behavior. This Review will be of high interest to the chemists involved in materials science, nanotechnology, and DDSs development for biomedical applications, although the general nature of the presented approaches enables knowledge translation to many other fields of science.
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Affiliation(s)
- Nikita Serov
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, Saint-Petersburg 191002, Russian Federation
| | - Vladimir Vinogradov
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, Saint-Petersburg 191002, Russian Federation.
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