Bioscience Method 2024, Vol.15 http://bioscipublisher.com/index.php/bm © 2024 BioSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved.
Bioscience Method 2024, Vol.15 http://bioscipublisher.com/index.php/bm © 2024 BioSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. BioSci Publisher is an international Open Access publisher specializing in bioscience methods, including technology, lab tool, statistical software and relative fields registered at the publishing platform that is operated by Sophia Publishing Group (SPG), founded in British Columbia of Canada. Publisher BioSci Publisher Editedby Editorial Team of Bioscience Methods Email: edit@bm.bioscipublisher.com Website: http://bioscipublisher.com/index.php/bm Address: 11388 Stevenston Hwy, PO Box 96016, Richmond, V7A 5J5, British Columbia Canada Bioscience Methods (ISSN 1925-1920) is an open access, peer reviewed journal published online by BioSciPublisher. The journal publishes all the latest and outstanding research articles, letters and reviews in all areas of bioscience, the range of topics including (but are not limited to) technology review, technique know-how, lab tool, statistical software and known technology modification. Case studies on technologies for gene discovery and function validation as well as genetic transformation. All the articles published in Bioscience Methods are Open Access, and are distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. BioSci Publisher uses CrossCheck service to identify academic plagiarism through the world’s leading plagiarism prevention tool, iParadigms, and to protect the original authors’ copyrights.
Bioscience Methods (online), 2024, Vol.15, No.2 ISSN 1925-1920 https://bioscipublisher.com/index.php/bm © 2024 BioSci Publisher, registered at the publishing platform that is operated by Sophia Publishing Group, founded in British Columbia of Canada. All Rights Reserved. Latest Content Structural Analysis of Drugs by Cryo-electron Microscopy Reveals Their Mechanisms of Action Jiayao Zhou Bioscience Methods, 2024, Vol.15, No.2, 50-57 Technological Innovation in Disease Detection and Management in Sugarcane Planting AmengLi Bioscience Methods, 2024, Vol.15, No.2, 58-65 Innovative Breeding Techniques for Cassava: The Role of Doubled Haploids and Genetic Engineering JiongFu Bioscience Methods, 2024, Vol.15, No.2, 66-75 Decoding Microbial Interactions: Mechanistic Insights into Engineered SynComs at the Microscopic Level Xiaoqinq Tang Bioscience Methods, 2024, Vol.15, No.2, 76-88 Breakthrough in Biomolecular Interaction Prediction with AlphaFold 3 Jessi Zhang Bioscience Methods, 2024, Vol.15, No.2, 89-90
Bioscience Method 2024, Vol.15, No.2, 50-57 http://bioscipublisher.com/index.php/bm 50 Review and Progress Open Access Structural Analysis of Drugs by Cryo-electron Microscopy Reveals Their Mechanisms of Action Jiayao Zhou Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, China Corresponding email: 2013478397@qq.com Bioscience Method, 2024, Vol.15, No.2 doi: 10.5376/bm.2024.15.0006 Received: 02 Jan., 2024 Accepted: 13 Feb., 2024 Published: 01 Mar., 2024 Copyright © 2024 Zhou, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhou J.Y., 2024, Structural analysis of drugs by cryo-electron microscopy reveals their mechanisms of action, Bioscience Method, 15(2): 50-57 (doi: 10.5376/bm.2024.15.0006) Abstract Cryo-electron microscopy is a crucial tool for studying the mechanisms of drug action, as it provides high-resolution structural analysis of biological macromolecules, revealing the interactions between drugs and these macromolecules. This study delves into the importance of drug action mechanisms and the challenges they pose. It begins by introducing the principles, workflow, and widespread applications of cryo-electron microscopy in biological macromolecule structure analysis, particularly its unique advantages in drug mechanism studies. Through several successful cases, the study illustrates the practical applications of cryo-electron microscopy in drug mechanism analysis, explores its use in drug screening and optimization, and how it can accelerate the discovery and development of new drugs. The paper concludes by summarizing the significant role of cryo-electron microscopy in drug mechanism analysis and looking ahead to its future potential and applications in drug research and development. This research aims to provide new perspectives and methods for studying drug action mechanisms through cryo-electron microscopy, contributing to the advancement of drug discovery and development. Keywords Cryo-electron microscopy; Drug mechanism of action; Biological macromolecule structure; Drug discovery; Interaction mechanism The mechanism of drug action is a core issue in drug development, determining how drugs interact with biological systems to produce therapeutic effects and possible side effects. Drug interactions in the body usually involve multiple biomolecules, such as proteins and nucleic acids, which are structurally complex and functionally diverse, making these interactions highly intricate. Traditional research methods, such as biochemical analysis and genetic techniques, although informative, often fail to fully reveal the detailed mechanisms of drug interactions with biomolecules (Radostin et al., 2019). In this context, cryo-electron microscopy (cryo-EM) has emerged as a prominent technique due to its unique advantages. Cryo-EM can capture the structures of biomolecules under near-physiological conditions and provide near-atomic resolution images, allowing researchers to directly observe the details of drug interactions with biomolecules. Moreover, cryo-EM can capture the dynamic changes of biomolecules, offering insights into the dynamic mechanisms of drug action (Cheng, 2018; Nannenga and Gonen, 2018). This review aims to explore the application of cryo-EM in studying the mechanisms of drug action, revealing its potential and advantages in elucidating drug interactions with biomolecules. The manuscript introduces the basic principles and workflow of cryo-EM and discusses its widespread use in structural analysis of biomolecules. Through case studies, it demonstrates how cryo-EM provides robust support in deciphering drug action mechanisms, including drug binding modes and drug-induced conformational changes. The discussion extends to the application of cryo-EM in drug screening and optimization, and its role in advancing new drug discovery and development. This review seeks to provide a new perspective and approach to the research on drug action mechanisms, aiming to advance the field of drug development. It also hopes to draw more researchers' attention to and interest in cryo-EM, encouraging the exploration of its broader applications in drug research. With ongoing technological advancements, cryo-EM is expected to play an increasingly significant role in studying drug action mechanisms, contributing greatly to human health endeavors.
Bioscience Method 2024, Vol.15, No.2, 50-57 http://bioscipublisher.com/index.php/bm 51 1 Fundamentals of Cryo-Electron Microscopy 1.1 Principle and workflow of cryo-electron microscopy Cryo-electron microscopy, also known as cryo-transmission electron microscopy, is a high-resolution imaging technique used for structural analysis of biological macromolecules under near-physiological conditions. Its principles and workflow are closely linked, ensuring high-quality and accurate imaging of biological samples (Angel and Marta, 2019). The core of cryo-electron microscopy lies in its "freezing" step. In a low-temperature environment (typically around -180 °C), biological samples are rapidly frozen to stabilize their bioactivity and structure. This freezing process minimizes radiation damage and ice crystal formation in the sample, thereby preserving its original state. The frozen samples are then placed under an electron microscope. Instead of visible light used in conventional optical microscopes, an electron microscope uses a high-energy electron beam to observe the sample. As the electron beam passes through the sample, it interacts with atoms within, causing scattering and absorption effects. These effects are captured by an electron detector and converted into visible images. Clare et al. (2017) noted that during the image formation process, the electron microscope adjusts parameters such as the electron beam focus, exposure time, and detector sensitivity to capture the fine structure of the sample. Further processing and analysis of the electron images provide three-dimensional information about the structure of biological macromolecules. The workflow of cryo-electron microscopy requires highly precise instruments and strict operating procedures, as well as accurate sample preparation and in-depth data analysis. The advantage of this technique is its ability to perform high-resolution imaging of biological macromolecules under conditions close to physiological, thereby revealing details of the interactions between drugs and biological macromolecules, and providing important insights into the mechanisms of drug action. 1.2 Application of cryo-electron microscopy in the structural analysis of biological macromolecules Cryo-electron microscopy plays a crucial role in the structural analysis of biological macromolecules. Because it can image biological samples at low temperatures close to physiological conditions, it has become a powerful tool for studying the structures of biological macromolecules, especially those samples that are difficult to crystallize. In the structural analysis of biological macromolecules, cryo-electron microscopy provides high-resolution three-dimensional images, allowing for the direct observation of the fine structures and dynamic changes of biological macromolecules (Figure 1). This includes not only the structures of individual biological macromolecules such as proteins and nucleic acids but also their interactions and the formation of complexes. Figure 1 CryoEM technique for imaging (Adopted from Sara et al., 2021) Image caption: a: lower distribution of biomolecules; b: higher magnification reveals their relationship with the surface of nanoparticles (Adopted from Sara et al., 2021)
Bioscience Method 2024, Vol.15, No.2, 50-57 http://bioscipublisher.com/index.php/bm 52 For example, in the study of drug action mechanisms, cryo-electron microscopy can reveal the binding patterns of drug molecules to biological macromolecular targets and the conformational changes in biological macromolecules caused by drugs. This information is crucial for understanding the mechanisms of drug action, optimizing drug design, and discovering new drugs. The application of cryo-electron microscopy in the structural analysis of biological macromolecules not only broadens our understanding of the structure and function of biological macromolecules but also provides significant support for the development of the pharmaceutical research field. 1.3 Applicability of cryo-EM technology in elucidating mechanisms of drug action Cryo-electron microscopy (Cryo-EM) technology has broad applicability in elucidating the mechanisms of drug action. Whether dealing with small molecule drugs or biological macromolecules, this technology can provide key structural and dynamic information, helping to deeply understand the mechanisms of drug action. It allows for imaging of biological macromolecules under near-physiological conditions, meaning it can observe the interactions between drugs and biological macromolecules in a state close to their natural state. The structures of biological macromolecules under these conditions are usually more authentic, hence making the drug mechanism information obtained more reliable (Nannenga and Gonen, 2018). The high-resolution images provided by Cryo-EM technology enable the capture of fine details of the interactions between drugs and biological macromolecules. These details may involve the precise binding sites of the drug molecules, modes of binding, and the consequent conformational changes in the biological macromolecules. This information is crucial for understanding the mechanisms of drug action as they reveal how drugs interact with biological macromolecules to produce therapeutic effects or side effects (Hutchings et al., 2018). Cryo-EM technology also captures the dynamic changes of biological macromolecules under the influence of drugs. This dynamic observation provides important information about how drugs affect the functions of biological macromolecules, including drug-induced signaling pathways and conformational transitions of the macromolecules. This information is essential for understanding the comprehensive mechanisms of drug action as they reveal the complex processes of drug actions within biological systems. 2 Practical Applications of Cryo-EM in the Analysis of Drug Mechanisms of Action 2.1 Cases of successful resolution of drug mechanisms using cryo-EM 2.1.1 Analysis of the drug mechanism of G protein-coupled receptors (GPCRs) GPCRs are a significant class of drug targets involved in various physiological and pathological processes. Using cryo-electron microscopy, Daniel and José (2020) successfully resolved the three-dimensional structures of multiple GPCRs bound with drugs, revealing how drugs bind to and either activate or inhibit their activity. These studies not only help understand the drug mechanisms of GPCRs but also provide essential guidance for the design and optimization of drugs targeting these receptors. 2.1.2 Analysis of antiviral drug mechanisms Cryo-EM has also been widely used in the study of antiviral drug mechanisms. For example, Zhu et al. (2021) utilized this technique to analyze the binding mechanism of the influenza virus neuraminidase with the antiviral drug oseltamivir and the structure of the N501Y spike protein of the novel coronavirus complexed with ACE2 and two effective neutralizing antibodies. This analysis provided a detailed glimpse into the cryo-EM structure of the complex formed between the extracellular domain of the N501Y spike protein and the extracellular domain of the ACE2 receptor, revealing how the drug inhibits the viral replication process (Figure 2). This offers new insights and approaches for the design and development of antiviral drugs. 2.1.3 Analysis of protein degradation drug mechanisms Protein degradation plays a crucial role within the cell, and drug development targeting protein degradation processes has always been a hot area. Cryo-EM has successfully resolved the binding patterns of various protein degradation-related complexes with drugs, such as the interactions between key proteins in the ubiquitin-proteasome system and the autophagy pathway with drugs. These studies not only aid in understanding
Bioscience Method 2024, Vol.15, No.2, 50-57 http://bioscipublisher.com/index.php/bm 53 the drug mechanisms of protein degradation but also provide a significant basis for the design and development of drugs targeting this pathway (Kondylis et al., 2019). Figure 2 Structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to the ACE2 ectodomain (Adopted from Zhu et al., 2021) 2.2 Key findings and significance in the case study GPCR Drug Mechanism Elucidation: Utilizing cryo-electron microscopy, Liu et al. (2019) not only observed the precise binding sites of drug molecules to GPCRs but also captured the conformational changes following the drug-receptor interactions. These changes involve multiple structural domains and key amino acid residues of the receptor, thereby revealing the complete pathway of drug-induced activation or inhibition of GPCR signaling. These discoveries provide a novel perspective on understanding the complex physiological functions of GPCRs and bring significant value to drug development. By simulating and optimizing the binding patterns of drugs to GPCRs, drugs that are more selective and have fewer side effects can be designed, thus more effectively treating various diseases related to GPCRs, such as heart disease, neurological disorders, and cancer. Antiviral Drug Mechanism Elucidation: Cryo-electron microscopy has revealed the precise binding modes of antiviral drugs to viral proteins and deeply explored how drugs interfere with the viral life cycle. These findings include the binding kinetics of drugs to viral proteins, drug-induced conformational changes in viral proteins, and
Bioscience Method 2024, Vol.15, No.2, 50-57 http://bioscipublisher.com/index.php/bm 54 how these changes affect the virus's replication and release processes. These insights are crucial for the development and optimization of antiviral drugs. They not only provide a structural basis for drug design but also offer important evidence for assessing drug efficacy and predicting drug resistance. Protein Degradation Drug Mechanism Elucidation: Through cryo-electron microscopy, Valle (2018) meticulously observed how drugs interact with key complexes in the protein degradation pathway and how they regulate the activity of these complexes. These findings involve the interaction patterns between drugs and complexes, drug-induced conformational changes, and how these changes affect the rate and selectivity of protein degradation. These discoveries are vital for understanding the regulatory mechanisms of protein homeostasis and provide new directions for developing drugs targeted at specific diseases. For example, in neurodegenerative diseases, regulating protein degradation processes can help clear harmful protein aggregates; in cancer therapy, inhibiting the degradation of specific proteins can enhance the efficacy of anticancer drugs. 2.3 How cryo-EM provides insights into drug interactions with biomolecules Cryo-electron microscopy (Cryo-EM) offers a powerful tool for revealing detailed information about the interactions between drugs and biomolecules through its unique imaging capabilities. Its working principle is based on rapidly freezing the sample under near-physiological conditions, thereby preserving the natural state and activity of biomolecules. Subsequently, under an electron microscope, these frozen samples are penetrated by a high-energy electron beam, which interacts with the atoms in the sample to produce scattering and absorption effects. These effects are then captured by an electron detector and converted into visible images. These images not only possess extremely high resolution but also capture the static and dynamic details of interactions between biomolecules and drug molecules. Through in-depth analysis of these images, the binding sites of drug molecules on biomolecules can be precisely determined, providing insights into how drugs interact with specific amino acid residues on biomolecules. Cryo-EM can also reveal conformational changes in biomolecules after drug binding, which may involve protein folding, domain rearrangement, or adjustments in overall structure, further elucidating how drugs affect the function of biomolecules (Twarock et al., 2018). In addition to providing static structural information, Cryo-EM can also capture the dynamic processes of drug interactions with biomolecules. This includes how drug molecules gradually approach and ultimately bind to biomolecules, and how binding triggers a series of biological effects. This dynamic observation provides key clues for understanding the comprehensive mechanisms of drug action, helping to more fully comprehend how drugs function at the cellular level. 3 Impact of Cryo-Electron Microscopy on Drug Discovery and Design 3.1 Application of cryo-electron microscopy in drug screening and optimization Cryo-electron microscopy (cryo-EM) has broad applications in the drug screening and optimization process. During the drug screening phase, cryo-EM can provide high-resolution images of the interaction between candidate drugs and biological macromolecular targets. This helps researchers quickly identify potential drugs. By observing and comparing the binding modes and affinities of different drugs to the targets, it can be preliminarily determined which drugs are worth further in-depth study (Twarock and Stockley, 2019). In the drug optimization phase, cryo-EM can reveal detailed mechanisms of interaction between drugs and biomolecules. This includes how drugs affect the conformation, function, and signaling pathways of the targets. By studying these interaction details extensively, the structure of drugs can be optimized, their efficacy improved, and potential side effects reduced. The data provided by cryo-EM offers significant theoretical support and experimental evidence for drug improvements (Michael et al., 2021). Cryo-EM can also be used to evaluate drug resistance. The emergence of resistance is a common challenge in drug development. By using cryo-EM to observe the interactions between drugs and resistant mutants, a deeper understanding of resistance mechanisms can be gained. This knowledge allows for the design of new drug strategies to overcome resistance, providing new ideas and methods for drug development and clinical treatment.
Bioscience Method 2024, Vol.15, No.2, 50-57 http://bioscipublisher.com/index.php/bm 55 3.2 How cryo-EM accelerates the discovery and development of new drugs Cryo-electron microscopy (cryo-EM) significantly accelerates the process of new drug discovery and development through its unique capabilities. In the early stages of drug discovery, cryo-EM provides high-resolution structural information of biological macromolecular targets, enabling research teams to more precisely understand the three-dimensional structure and characteristics of these targets. This precise structural information is crucial for drug screening and design, as it helps identify drug candidates that can effectively bind to the target. Cryo-EM reveals the intricate details of the interactions between drugs and biological macromolecules. By observing how drug molecules bind to targets and how this binding affects the target’s function and activity, a deeper understanding of the drug’s mechanism of action can be achieved. This understanding not only aids in predicting the drug’s efficacy and side effects but also guides further drug optimization and improvement efforts (Sara et al., 2021). Furthermore, cryo-EM accelerates the iterative process of drug development. In traditional drug development workflows, screening and optimizing drug candidates typically require multiple rounds of experiments and testing. However, using the high-resolution structural and interaction information provided by cryo-EM, potential drug candidates can be identified early on, and structural optimization can be rapidly conducted. This significantly reduces the time and cost of drug development, enhancing research and development efficiency. 3.3 Future trends of cryo-electron microscopy in drug discovery and design The future trends of cryo-electron microscopy in drug discovery and design suggest that it will continue to play a significant role and will be combined with other advanced technologies to drive greater breakthroughs in the field of drug research and development. With technological advancements, the resolution and imaging speed of cryo-electron microscopy will further improve, allowing for more detailed observation of the interactions between drugs and biomolecules. This will contribute to a deeper understanding of the mechanisms of drugs, providing more precise and comprehensive information for drug discovery and design. The integration of cryo-electron microscopy with other technologies will foster innovation in the drug development process. Twarock and Stockley (2019) found that combining it with artificial intelligence and machine learning algorithms can facilitate rapid screening and optimization of a large number of drug candidates. By integrating with multi-omics data such as genomics, proteomics, and metabolomics, cryo-electron microscopy will be able to provide more comprehensive and holistic information about the structure and function of biomolecules, offering a broader perspective for drug discovery and design. Additionally, cryo-electron microscopy will also play an important role in other aspects of new drug development. For example, in the optimization of drug crystal forms, cryo-electron microscopy can reveal the structure and stability of different crystal forms of drug molecules, providing guidance for the development of drug formulations. In studies of drug interactions with cell membranes, cryo-electron microscopy will be able to reveal how drugs penetrate cell membranes and interact with them, providing crucial insights for the development of drugs with better bioavailability. 4 Summary and Outlook Cryo-electron microscopy has played a crucial role in elucidating the mechanisms of drug action. It not only provides high-resolution images of the interactions between drugs and biomolecules, but also reveals in detail the dynamic processes of these interactions. Through cryo-electron microscopy, it is possible to precisely identify the binding sites of drug molecules on biomolecules, and understand how drugs exert their therapeutic effects by interfering with or regulating the functions of biomolecules (Zhu et al., 2021). This deep understanding not only enhances our knowledge of drug mechanisms but also provides important theoretical support and experimental evidence for drug research and optimization.
Bioscience Method 2024, Vol.15, No.2, 50-57 http://bioscipublisher.com/index.php/bm 56 In the field of drug research and development, the potential of cryo-electron microscopy is enormous. With continuous advancements in technology, the resolution and imaging speed of cryo-electron microscopy will improve, allowing for more detailed observations of the interactions between drugs and biomolecules. Additionally, with the integration of multi-omics data and the application of advanced technologies such as artificial intelligence, cryo-electron microscopy will be able to provide more comprehensive and accurate information, offering more efficient and reliable tools for drug discovery and design. More importantly, the application of cryo-electron microscopy in the field of drug research is gradually expanding. It is used not only for analyzing drug mechanisms but also plays a significant role in drug screening, optimization, and quality control. With cryo-electron microscopy, potential drug candidates can be quickly screened, their interactions with biomolecules assessed, and directions for subsequent research provided. Cryo-electron microscopy can also be used to study the distribution and metabolism of drugs within cells, providing important data for the evaluation of drug efficacy and safety. In the future, cryo-electron microscopy is expected to continue playing a significant role in the field of drug research. On one hand, with ongoing innovations and upgrades, cryo-electron microscopy will continually enhance its imaging quality and resolution, providing more in-depth and detailed information about drug mechanisms. On the other hand, as the needs and complexities of drug development increase, cryo-electron microscopy will be integrated with other technologies to form a more complete and efficient drug development system. It is believed that in the near future, cryo-electron microscopy will bring more breakthroughs and innovations to the field of drug research and development, making a more significant contribution to human health. Reference Angel R.C., and Marta C., 2019, Editorial: Technical advances in cryo-electron microscopy, Front. Mol. Biosci., 6: 22. https://doi.org/10.3389/fmolb.2019.00072 Cheng Y., 2018, Single-particle cryo-EM - How did it get here and where will it go., Science, 361: 876. https://doi.org/10.1126/science.aat4346 Clare D.K., Siebert C.A., Hecksel C., Hagen C., Mordhorst V., and Grange M., 2017, Zhang electron bio-imaging centre (eBIC): the UK national research facility for biological electron microscopy, P. Acta Crystallogr. D Struct. Biol., 73(6): 488-495. https://doi.org/10.1107/S2059798317007756 Daniel L., and José R.C., 2020, Cryo-electron microscopy for the study of virus assembly, Nature Chemical Biology, 16: 231-239. https://doi.org/10.1038/s41589-020-0477-1 Hutchings J., Stancheva V., Miller E.A., and Zanetti G., 2018, Subtomogram averaging of COPII assemblies reveals how coat organization dictates membrane shape, Nat. Commun., 9: 4154. https://doi.org/10.1038/s41467-018-06577-4 Kondylis P., Schlicksup C.J., Zlotnick A., and Jacobson S.C., 2019, Analytical techniques to characterize the structure, properties, and assembly of virus capsids, Anal. Chem., 91: 622-636. https://doi.org/10.1021/acs.analchem.8b04824 LiuY.,HuynhD.T.andYeatesT.O.A.,2019, Åresolutioncryo-EMstructureofasmallproteinboundtoanimagingscaffold,Nat.Commun.,10:1864. https://doi.org/10.1038/s41467-019-09836-0 Michael J.R., Justin G.M., and Georgios S., 2021, Drug discovery in the era of cryo-electron microscopy, Treeds in Biochemical Sciences, 47(2): 124-135. https://doi.org/10.1016/j.tibs.2021.06.008 Nannenga B.L., and Gonen T., 2018, MicroED: a versatile cryoEM method for structure determination, Emerg. Top. Life Sci., 2: 1-8. https://doi.org/10.1042/ETLS20170082 Radostin D., Haruaki Y., and Masahide K., 2019, Cryo-electron microscopy methodology: current aspects and future directions, Treeds in Biochemical Sciences, 44(10): 837-848. https://doi.org/10.1016/j.tibs.2019.04.008 Sara S., Kaustuv B., Ali F., Aliakbar A., Muneyoshi I., John F.P., Khanh H.B., Mohammad R.E., Hojatollah V., and Morteza M., 2021, Nanoscale characterization of the biomolecular corona by cryo-electron microscopy, cryo-electron tomography, and image simulation, Nature Communications, 12: 573. https://doi.org/10.1038/s41467-020-20884-9 Twarock R., and Stockley P.G., 2019, RNA-mediated virus assembly: Mechanisms and consequences for viral evolution and therapy, Annu. Rev. Biophys., 48: 495-514. https://doi.org/10.1146/annurev-biophys-052118-115611
Bioscience Method 2024, Vol.15, No.2, 50-57 http://bioscipublisher.com/index.php/bm 57 Twarock R., Bingham R.J., Dykeman E.C. and Stockley P.G., 2018, A modelling paradigm for RNA virus assembly, Curr. Opin. Virol., 31: 74-81. https://doi.org/10.1016/j.coviro.2018.07.003 Valle M., 2018, Structural homology between nucleoproteins of ssRNA Viruses, Subcell. Biochem., 88: 129-145. https://doi.org/10.1007/978-981-10-8456-0_6 Zhu X., Dhiraj M., Shanti S.S., Alison M.B., Jean-Philippe D., James W.S., Karoline L., Wei L., Dimiter S.D., Katharine S.T., Steven Z., Sagar C., and Sriram S., 2021, Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies, PLoS Biol., 19(4): e3001237. https://doi.org/10.1371/journal.pbio.3001237
Bioscience Method 2024, Vol.15, No.2, 58-65 http://bioscipublisher.com/index.php/bm 58 Research Report Open Access Technological Innovation in Disease Detection and Management in Sugarcane Planting Ameng Li CRO Service Station, Sanya Tihitar SciTech Breeding Service Inc., Sanya, 572025, Hainan, China Corresponding email: ameng.li@hitar.org Bioscience Method, 2024, Vol.15, No.2 doi: 10.5376/bm.2024.15.0007 Received: 15 Jan., 2024 Accepted: 25 Feb., 2024 Published: 15 Mar., 2024 Copyright © 2024 Li, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Li A.M., 2024, Technological innovation in disease detection and management in sugarcane planting, Bioscience Method, 15(2): 58-65 (doi: 10.5376/bm.2024.15.0007) Abstract The objective of this study is to systematically examine recent technological innovations in disease detection and management within sugarcane cultivation. It seeks to identify key advancements in digital imaging, molecular diagnostics, and genetic engineering that have significantly improved the detection, monitoring, and control of sugarcane diseases, aiming to enhance overall crop health and productivity. This study identifies several crucial technologies that have reshaped disease management strategies in sugarcane cultivation. It highlights the effectiveness of machine learning algorithms and remote sensing technology in detecting and diagnosing plant diseases at early stages. Developments in molecular diagnostics have allowed for rapid and precise pathogen identification. Additionally, genetic engineering has contributed to the creation of disease-resistant sugarcane varieties, thereby reducing dependency on chemical treatments. Integration of these technologies has led to improved disease surveillance and management, resulting in healthier crops and increased yields. The convergence of machine learning, remote sensing, molecular diagnostics, and genetic engineering represents a transformative shift in managing sugarcane diseases. These technologies not only enhance the ability to detect and manage diseases more efficiently but also contribute to sustainable agriculture practices by reducing chemical use and improving crop resilience. Continued innovation and integration of these technologies hold the promise of further gains in productivity and sustainability in sugarcane agriculture. Keywords Sugarcane cultivation; Disease detection; Machine learning; Remote sensing; Molecular diagnostics; Genetic engineering; Sustainable agriculture Sugarcane is a critical agricultural commodity with a significant role in the global economy, providing raw material for sugar production and biofuels, among other products. The cultivation of sugarcane is not without challenges, particularly in the form of diseases that can severely impact yield and quality. Common diseases affecting sugarcane include those caused by fungi, bacteria, viruses, and phytoplasmas, which can lead to substantial economic losses. The traditional methods for disease detection, which often rely on visual inspection, are labor-intensive and can be inaccurate. Moreover, the asymptomatic nature of some diseases makes early detection difficult, necessitating more advanced and reliable methods. Technological innovations in disease detection and management are therefore essential to sustain and improve sugarcane production. Recent advancements in machine learning and image processing techniques have shown promise in addressing these challenges. Support vector machines (SVM) and machine vision technology have been utilized to detect sugarcane borer diseases with high accuracy, demonstrating the potential of these methods to replace laborious manual selection processes. Similarly, machine learning classifiers applied to multispectral images from unmanned aerial vehicles (UAVs) have been effective in detecting white leaf disease in sugarcane, even at early stages (Narmilan et al., 2022). Deep learning frameworks have also been explored for their ability to identify diseased sugarcane plants by analyzing leaf and stem characteristics, with some models achieving high levels of accuracy (Srivastava et al., 2020). The Internet of Things (IoT) has been integrated into agricultural practices, enabling targeted disease management and reducing the environmental impact of excessive pesticide use (Thangadurai et al.,
Bioscience Method 2024, Vol.15, No.2, 58-65 http://bioscipublisher.com/index.php/bm 59 2020). Transfer learning approaches using deep learning models like VGG-16 and ResNet have been applied to sugarcane disease classification, further illustrating the potential of these technologies to revolutionize disease detection in agriculture (Daphal and Koli, 2021). Moreover, the development of mobile applications using deep learning architectures like Faster Region-based Convolutional Neural Network (Faster RCNN) has made it possible for farmers to detect diseases in sugarcane crops quickly and efficiently (Murugeswari et al., 2022). These technological innovations represent a significant step towards more sustainable and effective disease management in sugarcane cultivation, which is crucial for maintaining the crop's global economic importance. In summary, the need for technological innovation in the detection and management of sugarcane diseases is clear. The integration of advanced machine learning techniques, remote sensing, and IoT into agricultural practices offers promising solutions to improve disease management and ensure the sustainability of sugarcane production worldwide. 1 Innovations in Disease Detection 1.1 Machine vision and image processing Recent advancements in machine vision and image processing have significantly improved the detection of diseases in sugarcane crops. Support vector machines (SVM) have been utilized to detect sugarcane borer diseases with a high accuracy rate, demonstrating the effectiveness of machine vision technology when combined with threshold segmentation and image processing techniques. Similarly, image processing based disease detection for sugarcane leaves has been implemented, focusing on major diseases such as red rot, mosaic, and leaf scald. The use of computer vision techniques has shown promise in changing the agricultural landscape by enabling automatic disease detection. Furthermore, deep learning frameworks have been proposed to detect diseased sugarcane plants by analyzing leaves, stems, and color, with models like Inception v3, VGG-16, and VGG-19 showing high accuracy in disease identification (Srivastava et al., 2020). The application of transfer learning approaches, such as VGG-16 net and ResNet, has also been explored for sugarcane foliar disease classification, yielding promising results even with limited datasets (Daphal and Koli, 2021). Additionally, the use of Convolutional Neural Networks (CNNs) has been proposed for the automated recognition of sugarcane diseases, further illustrating the potential of machine vision and deep learning in disease detection (Kotekan et al., 2023). 1.2 Molecular diagnostics Molecular diagnostics have emerged as a powerful tool for the management of major diseases in sugarcane. The development of specific and sensitive diagnostic tools using PCR-based detection methods has facilitated the timely detection of pathogens, which is crucial for disease management. These molecular techniques have been applied to a range of sugarcane diseases, including red rot, smut, yellow leaf syndrome, and others, highlighting the need for highly sensitive, specific, and cost-effective detection tools for large-scale applications. 1.3 Remote sensing and UAV technologies Remote sensing and UAV (Unmanned Aerial Vehicle) technologies have been recognized as innovative approaches for plant disease detection. These techniques, coupled with spectroscopy-based methods, allow for the rapid preliminary identification of primary infections and high spatialization of diagnostic results. Novel sensors based on the analysis of host responses, such as differential mobility spectrometers and lateral flow devices, can deliver instantaneous results and effectively detect early infections directly in the field. Biosensors based on phage display and biophotonics have also been developed to provide instantaneous infection detection, which can be integrated with other systems for enhanced disease management. Additionally, the integration of IoT (Internet of Things) in agriculture has led to the development of automated systems that can identify diseases in sugarcane leaves with high accuracy, demonstrating the potential of technology-driven solutions to improve agricultural production and minimize risks (Thangadurai et al., 2020).
Bioscience Method 2024, Vol.15, No.2, 58-65 http://bioscipublisher.com/index.php/bm 60 2 Innovations in Disease Management 2.1 Genetic engineering and breeding Recent advancements in sugarcane genomics have played a pivotal role in enhancing agronomic traits and crop yield, addressing the increasing global demand for sugar and biofuel amidst climate change challenges. Conventional breeding methods face difficulties due to the complex, polygenic nature of agronomic traits and the highly heterozygous autopolyploid nature of the sugarcane genome. However, the identification of superior agronomic traits/genes for higher cane yield, sugar production, and disease/pest resistance has been facilitated through quantitative trait loci mapping, genome-wide association studies, and transcriptome approaches (Meena et al., 2022). Genetic engineering approaches have also been employed to enhance insect pest resistance in sugarcane by overexpressing cry proteins, vegetative insecticidal proteins (vip), lectins, and proteinase inhibitors (PI). Additionally, cutting-edge biotechnological tools such as host-induced gene silencing (HIGS) and CRISPR/Cas9 offer sustainable control of insect pests (Iqbal et al., 2021). 2.2 Agronomic practices In Tucumán, Argentina, an integrated management approach incorporating biotechnological tools has significantly improved sugarcane productivity. The use of molecular markers to identify the Bru1 gene for brown rust resistance and SNP alleles linked to novel sources of resistance has been instrumental in developing resistant varieties. Furthermore, seed cane sanitation projects employing hydrothermal therapy, in vitro culture techniques, molecular diagnosis, and bionanoparticles have reduced the incidence of systemic diseases (Racedo et al., 2023). In India, agronomic approaches and physical methods like heat therapy, along with the propagation of disease-resistant varieties, have been effective in managing sugarcane diseases. The multiplication of sugarcane through tissue culture is advocated to produce disease-free planting materials. 2.3 Advanced biological and chemical treatments The application of biotechnology in sugarcane agriculture and industry has evolved significantly, with advances in genomics, proteomics, and metabolomics enhancing our understanding of genetic material and its expression. These advancements have facilitated the development of transgenic or GMO crops, the identification and utilization of molecular markers for traits, and the improvement of value-added products such as biofuel. Transgene-free genome editing techniques, such as the delivery of ribonucleoprotein (RNP) complexes, virus-induced genome editing (VIGE), and transient expression of CRISPR/Cas reagents, have emerged as promising methods for creating new cultivars with improved resistance to biotic and abiotic stresses (Krishna et al., 2023). Biotechnological developments have also focused on in vitro culture systems, radiation/chemical-induced mutagenesis for mutant isolation, and the application of genomics tools for a detailed understanding of stress responses, which are crucial for sugarcane improvement. 3 Case Studies and Success Stories 3.1 Detailed analysis of technological adoption in Brazil, the world’s largest sugarcane producer Brazil's sugarcane industry has significantly benefited from the adoption of precision agriculture (PA) technologies, particularly in São Paulo state, which accounts for 60% of the country's sugarcane production. The use of PA technologies has led to managerial improvements, higher yields, lower costs, and minimized environmental impacts. Moreover, the quality of sugarcane has improved due to these technological advancements. A study investigating the extent of PA technology adoption in the sugar-ethanol industry revealed that companies utilizing these technologies have experienced substantial benefits. The research also highlighted the importance of primary data obtained from questionnaires sent to companies in the region, which provided insights into the adoption and impact of PA technologies (Meena et al., 2022). The Brazilian sugarcane innovation system has played a crucial role in the success of the industry, which is not solely due to natural comparative advantages but also as a result of technological learning and incremental innovations. The innovation system around the sugarcane industry is based on the interaction of
Bioscience Method 2024, Vol.15, No.2, 58-65 http://bioscipublisher.com/index.php/bm 61 various institutional actors, including sugar and ethanol mills, industrial goods suppliers, public and private research institutions, and governmental agencies. This system has been instrumental in developing a trajectory of technological advancements that have led to the production of low-cost bioethanol with low greenhouse gas emissions, positioning Brazil as a global leader in sugarcane bioethanol production (Iqbal et al., 2021). 3.2 Impact of technology on sugarcane yield and disease management in India In India, integrated disease management (IDM) practices have shown a positive impact on sugarcane yield and quality. Field experiments conducted at the Sugarcane Research Station in Nayagarh, Orissa, demonstrated that IDM practices resulted in significant improvements in yield, germination, millable cane per hectare, average cane weight, and sucrose content. Additionally, there was a notable reduction in Grassy Shoot Disease incidence. These findings underscore the economic viability and practical feasibility of IDM practices in enhancing sugarcane production in India (Racedo et al., 2023). Another study conducted at the IISR institute farm in Lucknow focused on IDM strategies for red rot disease in sugarcane. The study revealed that IDM practices not only reduced red rot incidence but also enhanced growth parameters and quality attributes of sugarcane compared to non-integrated disease management practices. The use of IDM practices led to improvements in various yield and quality parameters in both plant and ratoon crops, highlighting the benefits of IDM in controlling red rot and improving the overall health and productivity of sugarcane. 3.3 Case study of integrated disease management approaches in Australia The Australian sugarcane industry has faced challenges with diseases such as smut and orange rust. However, the industry has responded with the development of disease-resistant varieties and the incorporation of new technologies in disease control strategies. The adoption of green technologies, such as in vitro propagation, has provided opportunities for the development of novel varieties with disease resistance and improved potential for cane yield and sugar recovery. These advancements have been crucial in managing existing diseases and combating emerging threats to the industry (Hoarau et al., 2021). In addition to breeding and variety selection programs, the Australian sugarcane industry has also benefited from the use of image processing techniques for disease detection. Research on the effectiveness of image processing and computer vision techniques for detecting diseases in sugarcane plants has shown promise in improving disease management practices (Figure 1). These technologies enable rapid and early detection of diseases, which is essential for implementing timely and effective control measures. Overall, the case studies from Brazil, India, and Australia demonstrate the significant impact of technological innovation on disease detection and management in sugarcane planting. The adoption of precision agriculture, integrated disease management practices, and advanced imaging techniques has led to improvements in yield, quality, and sustainability of sugarcane production in these countries. 4 Integration of Technology and Farmer Practices 4.1 Education and training for farmers The integration of technology in disease detection and management in sugarcane planting necessitates the education and training of farmers. As advanced methods of plant disease detection evolve, including DNA-based and serological methods, farmers must be trained to understand and utilize these tools effectively. The use of machine learning techniques over UAV multispectral images for the detection of white leaf disease in sugarcane is a prime example of technological advancement that requires a certain level of technical knowledge for operation and interpretation (Narmilan et al., 2022). Furthermore, the application of image processing techniques for disease detection in sugarcane leaves indicates a shift towards more sophisticated agricultural practices that farmers need to be acquainted with.
Bioscience Method 2024, Vol.15, No.2, 58-65 http://bioscipublisher.com/index.php/bm 62 4.2 Technological accessibility and affordability While the development of novel sensors and remote sensing techniques offers instantaneous and effective disease detection, the accessibility and affordability of such technologies are critical for widespread adoption by farmers. The use of support vector machines (SVM) for detecting sugarcane borer diseases demonstrates the potential for technology to reduce labor and misjudgment in disease detection. However, the cost and complexity of these technologies must be considered to ensure they are accessible and affordable for farmers, particularly in less developed agricultural settings. 4.3 Data management and decision support systems The implementation of machine learning algorithms and deep learning frameworks for sugarcane disease detection generates a significant amount of data that must be managed efficiently (Srivastava et al., 2020). The use of IoT for disease detection in sugarcane leaf further emphasizes the need for robust data management systems that can handle the information collected from sensor nodes. Decision support systems that can process this data and provide actionable insights are essential for farmers to make informed decisions regarding disease management. Transfer learning approaches to sugarcane foliar disease classification and the development of mobile applications for disease detection are examples of how technology can aid in data management and decision-making processes (Daphal and Koli, 2021). Figure 1 Optical sensing technologies for plant viral disease detection can be classified by their platform and associated spatial resolution and extent (Adopted from Wang et al., 2022) Image caption: Sensors also vary by band position, the spectral range within the whole electromagnetic spectrum (Adopted from Wang et al., 2022) In conclusion, the integration of technology in sugarcane disease detection and management involves a multifaceted approach that includes educating farmers, ensuring the accessibility and affordability of technologies, and implementing effective data management and decision support systems. These components
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