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Prudinnik DS, Kussanova A, Vorobjev IA, Tikhonov A, Ataullakhanov FI, Barteneva NS. Deformability of Heterogeneous Red Blood Cells in Aging and Related Pathologies. Aging Dis 2025:AD.2024.0526. [PMID: 39012672 DOI: 10.14336/ad.2024.0526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 06/19/2024] [Indexed: 07/17/2024] Open
Abstract
Aging is interrelated with changes in red blood cell parameters and functionality. In this article, we focus on red blood cells (RBCs) and provide a review of the known changes associated with the characterization of RBC deformability in aging and related pathologies. The biophysical parameters complement the commonly used biochemical parameters and may contribute to a better understanding of the aging process. The power of the deformability measurement approach is well established in clinical settings. Measuring RBCs' deformability has the advantage of relative simplicity, and it reflects the complex effects developing in erythrocytes during aging. However, aging and related pathological conditions also promote heterogeneity of RBC features and have a certain impact on the variance in erythrocyte cell properties. The possible applications of deformability as an early biophysical biomarker of pathological states are discussed, and modulating PIEZO1 as a therapeutic target is suggested. The changes in RBCs' shape can serve as a proxy for deformability evaluation, leveraging single-cell analysis with imaging flow cytometry and artificial intelligence algorithms. The characterization of biophysical parameters of RBCs is in progress in humans and will provide a better understanding of the complex dynamics of aging.
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Affiliation(s)
- Dmitry S Prudinnik
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Aigul Kussanova
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Ivan A Vorobjev
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Alexander Tikhonov
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Fazly I Ataullakhanov
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Natasha S Barteneva
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
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2
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Jiao D, Xu L, Gu Z, Yan H, Shen D, Gu X. Pathogenesis, diagnosis, and treatment of epilepsy: electromagnetic stimulation-mediated neuromodulation therapy and new technologies. Neural Regen Res 2025; 20:917-935. [PMID: 38989927 DOI: 10.4103/nrr.nrr-d-23-01444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/18/2024] [Indexed: 07/12/2024] Open
Abstract
Epilepsy is a severe, relapsing, and multifactorial neurological disorder. Studies regarding the accurate diagnosis, prognosis, and in-depth pathogenesis are crucial for the precise and effective treatment of epilepsy. The pathogenesis of epilepsy is complex and involves alterations in variables such as gene expression, protein expression, ion channel activity, energy metabolites, and gut microbiota composition. Satisfactory results are lacking for conventional treatments for epilepsy. Surgical resection of lesions, drug therapy, and non-drug interventions are mainly used in clinical practice to treat pain associated with epilepsy. Non-pharmacological treatments, such as a ketogenic diet, gene therapy for nerve regeneration, and neural regulation, are currently areas of research focus. This review provides a comprehensive overview of the pathogenesis, diagnostic methods, and treatments of epilepsy. It also elaborates on the theoretical basis, treatment modes, and effects of invasive nerve stimulation in neurotherapy, including percutaneous vagus nerve stimulation, deep brain electrical stimulation, repetitive nerve electrical stimulation, in addition to non-invasive transcranial magnetic stimulation and transcranial direct current stimulation. Numerous studies have shown that electromagnetic stimulation-mediated neuromodulation therapy can markedly improve neurological function and reduce the frequency of epileptic seizures. Additionally, many new technologies for the diagnosis and treatment of epilepsy are being explored. However, current research is mainly focused on analyzing patients' clinical manifestations and exploring relevant diagnostic and treatment methods to study the pathogenesis at a molecular level, which has led to a lack of consensus regarding the mechanisms related to the disease.
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Affiliation(s)
- Dian Jiao
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Lai Xu
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Zhen Gu
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Hua Yan
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Dingding Shen
- Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Xiaosong Gu
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
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3
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Wu B, Liu Y, Li H, Zhu L, Zeng L, Zhang Z, Peng W. Liver as a new target organ in Alzheimer's disease: insight from cholesterol metabolism and its role in amyloid-beta clearance. Neural Regen Res 2025; 20:695-714. [PMID: 38886936 DOI: 10.4103/1673-5374.391305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/07/2023] [Indexed: 06/20/2024] Open
Abstract
Alzheimer's disease, the primary cause of dementia, is characterized by neuropathologies, such as amyloid plaques, synaptic and neuronal degeneration, and neurofibrillary tangles. Although amyloid plaques are the primary characteristic of Alzheimer's disease in the central nervous system and peripheral organs, targeting amyloid-beta clearance in the central nervous system has shown limited clinical efficacy in Alzheimer's disease treatment. Metabolic abnormalities are commonly observed in patients with Alzheimer's disease. The liver is the primary peripheral organ involved in amyloid-beta metabolism, playing a crucial role in the pathophysiology of Alzheimer's disease. Notably, impaired cholesterol metabolism in the liver may exacerbate the development of Alzheimer's disease. In this review, we explore the underlying causes of Alzheimer's disease and elucidate the role of the liver in amyloid-beta clearance and cholesterol metabolism. Furthermore, we propose that restoring normal cholesterol metabolism in the liver could represent a promising therapeutic strategy for addressing Alzheimer's disease.
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Affiliation(s)
- Beibei Wu
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Yuqing Liu
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Hongli Li
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Lemei Zhu
- Academician Workstation, Changsha Medical University, Changsha, Hunan Province, China
| | - Lingfeng Zeng
- Academician Workstation, Changsha Medical University, Changsha, Hunan Province, China
| | - Zhen Zhang
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
- Yangsheng College of Traditional Chinese Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou Province, China
- Qinhuangdao Shanhaiguan Pharmaceutical Co., Ltd, Qinhuangdao, Hebei Province, China
| | - Weijun Peng
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
- National Clinical Research Center for Mental Disorder, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
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4
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Pu Z, Wu Y, Zhu Z, Zhao H, Cui D. A new horizon for neuroscience: terahertz biotechnology in brain research. Neural Regen Res 2025; 20:309-325. [PMID: 38819036 DOI: 10.4103/nrr.nrr-d-23-00872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 01/03/2024] [Indexed: 06/01/2024] Open
Abstract
Terahertz biotechnology has been increasingly applied in various biomedical fields and has especially shown great potential for application in brain sciences. In this article, we review the development of terahertz biotechnology and its applications in the field of neuropsychiatry. Available evidence indicates promising prospects for the use of terahertz spectroscopy and terahertz imaging techniques in the diagnosis of amyloid disease, cerebrovascular disease, glioma, psychiatric disease, traumatic brain injury, and myelin deficit. In vitro and animal experiments have also demonstrated the potential therapeutic value of terahertz technology in some neuropsychiatric diseases. Although the precise underlying mechanism of the interactions between terahertz electromagnetic waves and the biosystem is not yet fully understood, the research progress in this field shows great potential for biomedical noninvasive diagnostic and therapeutic applications. However, the biosafety of terahertz radiation requires further exploration regarding its two-sided efficacy in practical applications. This review demonstrates that terahertz biotechnology has the potential to be a promising method in the field of neuropsychiatry based on its unique advantages.
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Affiliation(s)
- Zhengping Pu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Psychiatry, Kangci Hospital of Jiaxing, Tongxiang, Zhejiang Province, China
| | - Yu Wu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai, China
| | - Zhongjie Zhu
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Hongwei Zhao
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Science, Shanghai, China
| | - Donghong Cui
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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5
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Zha X, Zheng G, Skutella T, Kiening K, Unterberg A, Younsi A. Microglia: a promising therapeutic target in spinal cord injury. Neural Regen Res 2025; 20:454-463. [PMID: 38819048 DOI: 10.4103/nrr.nrr-d-23-02044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/22/2024] [Indexed: 06/01/2024] Open
Abstract
Microglia are present throughout the central nervous system and are vital in neural repair, nutrition, phagocytosis, immunological regulation, and maintaining neuronal function. In a healthy spinal cord, microglia are accountable for immune surveillance, however, when a spinal cord injury occurs, the microenvironment drastically changes, leading to glial scars and failed axonal regeneration. In this context, microglia vary their gene and protein expression during activation, and proliferation in reaction to the injury, influencing injury responses both favorably and unfavorably. A dynamic and multifaceted injury response is mediated by microglia, which interact directly with neurons, astrocytes, oligodendrocytes, and neural stem/progenitor cells. Despite a clear understanding of their essential nature and origin, the mechanisms of action and new functions of microglia in spinal cord injury require extensive research. This review summarizes current studies on microglial genesis, physiological function, and pathological state, highlights their crucial roles in spinal cord injury, and proposes microglia as a therapeutic target.
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Affiliation(s)
- Xiaowei Zha
- Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Guoli Zheng
- Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Skutella
- Department of Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Karl Kiening
- Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas Unterberg
- Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Alexander Younsi
- Department of Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
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6
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Miao Y, Wolfe MS. Emerging structures and dynamic mechanisms of γ-secretase for Alzheimer's disease. Neural Regen Res 2025; 20:174-180. [PMID: 38767485 PMCID: PMC11246123 DOI: 10.4103/nrr.nrr-d-23-01781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/19/2023] [Accepted: 01/11/2024] [Indexed: 05/22/2024] Open
Abstract
γ-Secretase, called "the proteasome of the membrane," is a membrane-embedded protease complex that cleaves 150+ peptide substrates with central roles in biology and medicine, including amyloid precursor protein and the Notch family of cell-surface receptors. Mutations in γ-secretase and amyloid precursor protein lead to early-onset familial Alzheimer's disease. γ-Secretase has thus served as a critical drug target for treating familial Alzheimer's disease and the more common late-onset Alzheimer's disease as well. However, critical gaps remain in understanding the mechanisms of processive proteolysis of substrates, the effects of familial Alzheimer's disease mutations, and allosteric modulation of substrate cleavage by γ-secretase. In this review, we focus on recent studies of structural dynamic mechanisms of γ-secretase. Different mechanisms, including the "Fit-Stay-Trim," "Sliding-Unwinding," and "Tilting-Unwinding," have been proposed for substrate proteolysis of amyloid precursor protein by γ-secretase based on all-atom molecular dynamics simulations. While an incorrect registry of the Notch1 substrate was identified in the cryo-electron microscopy structure of Notch1-bound γ-secretase, molecular dynamics simulations on a resolved model of Notch1-bound γ-secretase that was reconstructed using the amyloid precursor protein-bound γ-secretase as a template successfully captured γ-secretase activation for proper cleavages of both wildtype and mutant Notch, being consistent with biochemical experimental findings. The approach could be potentially applied to decipher the processing mechanisms of various substrates by γ-secretase. In addition, controversy over the effects of familial Alzheimer's disease mutations, particularly the issue of whether they stabilize or destabilize γ-secretase-substrate complexes, is discussed. Finally, an outlook is provided for future studies of γ-secretase, including pathways of substrate binding and product release, effects of modulators on familial Alzheimer's disease mutations of the γ-secretase-substrate complexes. Comprehensive understanding of the functional mechanisms of γ-secretase will greatly facilitate the rational design of effective drug molecules for treating familial Alzheimer's disease and perhaps Alzheimer's disease in general.
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Affiliation(s)
- Yinglong Miao
- Computational Medicine Program and Department of Pharmacology, University of North Carolina – Chapel Hill, Chapel Hill, NC, USA
| | - Michael S. Wolfe
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
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He T, Sun J, Deng L, Ming J, Hu C. Recycling Fe and improving organic pollutant removal via in situ forming magnetic core-shell Fe 3O 4@CaFe-LDH in Fe(II)-catalyzed oxidative wastewater treatment. J Environ Sci (China) 2025; 147:523-537. [PMID: 39003068 DOI: 10.1016/j.jes.2023.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/29/2023] [Accepted: 12/18/2023] [Indexed: 07/15/2024]
Abstract
Due to its high efficiency, Fe(II)-based catalytic oxidation has been one of the most popular types of technology for treating growing organic pollutants. A lot of chemical Fe sludge along with various refractory pollutants was concomitantly produced, which may cause secondary environmental problems without proper disposal. We here innovatively proposed an effective method of achieving zero Fe sludge, reusing Fe resources (Fe recovery = 100%) and advancing organics removal (final TOC removal > 70%) simultaneously, based on the in situ formation of magnetic Ca-Fe layered double hydroxide (Fe3O4@CaFe-LDH) nano-material. Cations (Ca2+ and Fe3+) concentration (≥ 30 mmol/L) and their molar ratio (Ca:Fe ≥ 1.75) were crucial to the success of the method. Extrinsic nano Fe3O4 was designed to be involved in the Fe(II)-catalytic wastewater treatment process, and was modified by oxidation intermediates/products (especially those with COO- structure), which promoted the co-precipitation of Ca2+ (originated from Ca(OH)2 added after oxidation process) and by-produced Fe3+ cations on its surface to in situ generate core-shell Fe3O4@CaFe-LDH. The oxidation products were further removed during Fe3O4@CaFe-LDH material formation via intercalation and adsorption. This method was applicable to many kinds of organic wastewater, such as bisphenol A, methyl orange, humics, and biogas slurry. The prepared magnetic and hierarchical CaFe-LDH nanocomposite material showed comparable application performance to the recently reported CaFe-LDHs. This work provides a new strategy for efficiently enhancing the efficiency and economy of Fe(II)-catalyzed oxidative wastewater treatment by producing high value-added LDHs materials.
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Affiliation(s)
- Ting He
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China; Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, China
| | - Jie Sun
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, China; Inner Mongolia Key Laboratory of Fine Organic Synthesis, Inner Mongolia University, Hohhot 010021, China
| | - Liangwei Deng
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, China
| | - Jialin Ming
- Inner Mongolia Key Laboratory of Fine Organic Synthesis, Inner Mongolia University, Hohhot 010021, China.
| | - Changwei Hu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China.
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8
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Peng S, Wang F, Wei D, Wang C, Ma H, Du Y. Application of FTIR two-dimensional correlation spectroscopy (2D-COS) analysis in characterizing environmental behaviors of microplastics: A systematic review. J Environ Sci (China) 2025; 147:200-216. [PMID: 39003040 DOI: 10.1016/j.jes.2023.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/17/2023] [Accepted: 10/06/2023] [Indexed: 07/15/2024]
Abstract
Microplastics (MPs) are ubiquitous in the environment, continuously undergo aging processes and release toxic chemical substances. Understanding the environmental behaviors of MPs is critical to accurately evaluate their long-term ecological risk. Generalized two-dimensional correlation spectroscopy (2D-COS) is a powerful tool for MPs studies, which can dig more comprehensive information hiding in the conventional one-dimensional spectra, such as infrared (IR) and Raman spectra. The recent applications of 2D-COS in analyzing the behaviors and fates of MPs in the environment, including their aging processes, and interactions with natural organic matter (NOM) or other chemical substances, were summarized systematically. The main requirements and limitations of current approaches for exploring these processes are discussed, and the corresponding strategies to address these limitations and drawbacks are proposed as well. Finally, new trends of 2D-COS are prospected for analyzing the properties and behaviors of MPs in both natural and artificial environmental processes.
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Affiliation(s)
- Shuang Peng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feipeng Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongbin Wei
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | | | - Haijun Ma
- North Minzu University, Yinchuan 750001, China
| | - Yuguo Du
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Lin Y, Qiao J, Sun Y, Dong H. The profound review of Fenton process: What's the next step? J Environ Sci (China) 2025; 147:114-130. [PMID: 39003034 DOI: 10.1016/j.jes.2023.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 07/15/2024]
Abstract
Fenton and Fenton-like processes, which could produce highly reactive species to degrade organic contaminants, have been widely used in the field of wastewater treatment. Therein, the chemistry of Fenton process including the nature of active oxidants, the complicated reactions involved, and the behind reason for its strongly pH-dependent performance, is the basis for the application of Fenton and Fenton-like processes in wastewater treatment. Nevertheless, the conflicting views still exist about the mechanism of the Fenton process. For instance, reaching a unanimous consensus on the nature of active oxidants (hydroxyl radical or tetravalent iron) in this process remains challenging. This review comprehensively examined the mechanism of the Fenton process including the debate on the nature of active oxidants, reactions involved in the Fenton process, and the behind reason for the pH-dependent degradation of contaminants in the Fenton process. Then, we summarized several strategies that promote the Fe(II)/Fe(III) cycle, reduce the competitive consumption of active oxidants by side reactions, and replace the Fenton reagent, thus improving the performance of the Fenton process. Furthermore, advances for the future were proposed including the demand for the high-accuracy identification of active oxidants and taking advantages of the characteristic of target contaminants during the degradation of contaminants by the Fenton process.
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Affiliation(s)
- Yimin Lin
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Junlian Qiao
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Yuankui Sun
- Department of Environmental Science, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Hongyu Dong
- Department of Environmental Science, School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China.
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10
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Humayun S, Hayyan M, Alias Y. A review on reactive oxygen species-induced mechanism pathways of pharmaceutical waste degradation: Acetaminophen as a drug waste model. J Environ Sci (China) 2025; 147:688-713. [PMID: 39003083 DOI: 10.1016/j.jes.2023.11.021] [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: 08/04/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 07/15/2024]
Abstract
Innately designed to induce physiological changes, pharmaceuticals are foreknowingly hazardous to the ecosystem. Advanced oxidation processes (AOPs) are recognized as a set of contemporary and highly efficient methods being used as a contrivance for the removal of pharmaceutical residues. Since reactive oxygen species (ROS) are formed in these processes to interact and contribute directly toward the oxidation of target contaminant(s), a profound insight regarding the mechanisms of ROS leading to the degradation of pharmaceuticals is fundamentally significant. The conceptualization of some specific reaction mechanisms allows the design of an effective and safe degradation process that can empirically reduce the environmental impact of the micropollutants. This review mainly deliberates the mechanistic reaction pathways for ROS-mediated degradation of pharmaceuticals often leading to complete mineralization, with a focus on acetaminophen as a drug waste model.
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Affiliation(s)
- Saba Humayun
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; University of Malaya Centre for Ionic Liquids, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Maan Hayyan
- Chemical Engineering Program, Faculty of Engineering and Technology, Muscat University, Muscat P.C.130, Oman.
| | - Yatimah Alias
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia; University of Malaya Centre for Ionic Liquids, University of Malaya, Kuala Lumpur 50603, Malaysia.
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11
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Lindhardt JH, Holm PE, Zhu YG, Lu C, Hansen HCB. Plant-substrate biochar properties critical for mediating reductive debromination of 1,2-dibromoethane. J Environ Sci (China) 2025; 147:1-10. [PMID: 39003031 DOI: 10.1016/j.jes.2023.09.018] [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: 05/25/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 07/15/2024]
Abstract
Dibromoethane is a widespread, persistent organic pollutant. Biochars are known mediators of reductive dehalogenation by layered FeII-FeIII hydroxides (green rust), which can reduce 1,2-dibromoethane to innocuous bromide and ethylene. However, the critical characteristics that determine mediator functionality are lesser known. Fifteen biochar substrates were pyrolyzed at 600 °C and 800 °C, characterized by elemental analysis, X-ray photo spectrometry C and N surface speciation, X-ray powder diffraction, specific surface area analysis, and tested for mediation of reductive debromination of 1,2-dibromoethane by a green rust reductant under anoxic conditions. A statistical analysis was performed to determine the biochar properties, critical for debromination kinetics and total debromination extent. It was shown that selected plant based biochars can mediate debromination of 1,2-dibromoethane, that the highest first order rate constant was 0.082/hr, and the highest debromination extent was 27% in reactivity experiments with 0.1 µmol (20 µmol/L) 1,2-dibromoethane, ≈ 22 mmol/L FeIIGR, and 0.12 g/L soybean meal biochar (7 days). Contents of Ni, Zn, N, and P, and the relative contribution of quinone surface functional groups were significantly (p < 0.05) positively correlated with 1,2-dibromoethane debromination, while adsorption, specific surface area, and the relative contribution of pyridinic N oxide surface groups were significantly negatively correlated with debromination.
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Affiliation(s)
- Jonathan H Lindhardt
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Key lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Sino-Danish Center for education and research, China and Denmark, Dalgas Avenue 4, DK-8000 Aarhus C., Denmark.
| | - Peter E Holm
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Sino-Danish Center for education and research, China and Denmark, Dalgas Avenue 4, DK-8000 Aarhus C., Denmark
| | - Yong-Guan Zhu
- Key lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Sino-Danish Center for education and research, China and Denmark, Dalgas Avenue 4, DK-8000 Aarhus C., Denmark
| | - Changyong Lu
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Hans Christian B Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Sino-Danish Center for education and research, China and Denmark, Dalgas Avenue 4, DK-8000 Aarhus C., Denmark
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12
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Rastegarpanah A, Deng J, Liu Y, Jing L, Pei W, Wang J, Dai H. Bamboo-like MnO 2⋅Co 3O 4: High-performance catalysts for the oxidative removal of toluene. J Environ Sci (China) 2025; 147:617-629. [PMID: 39003076 DOI: 10.1016/j.jes.2023.04.005] [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: 01/19/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 07/15/2024]
Abstract
The manganese-cobalt mixed oxide nanorods were fabricated using a hydrothermal method with different metal precursors (KMnO4 and MnSO4·H2O for MnOx and Co(NO3)2⋅6H2O and CoCl2⋅6H2O for Co3O4). Bamboo-like MnO2⋅Co3O4 (B-MnO2⋅Co3O4 (S)) was derived from repeated hydrothermal treatments with Co3O4@MnO2 and MnSO4⋅H2O, whereas Co3O4@MnO2 nanorods were derived from hydrothermal treatment with Co3O4 nanorods and KMnO4. The study shows that manganese oxide was tetragonal, while the cobalt oxide was found to be cubic in the crystalline arrangement. Mn surface ions were present in multiple oxidation states (e.g., Mn4+ and Mn3+) and surface oxygen deficiencies. The content of adsorbed oxygen species and reducibility at low temperature declined in the sequence of B-MnO2⋅Co3O4 (S) > Co3O4@MnO2 > MnO2 > Co3O4, matching the changing trend in activity. Among all the samples, B-MnO2⋅Co3O4 (S) showed the preeminent catalytic performance for the oxidation of toluene (T10% = 187°C, T50% = 276°C, and T90% = 339°C). In addition, the B-MnO2⋅Co3O4 (S) sample also exhibited good H2O-, CO2-, and SO2-resistant performance. The good catalytic performance of B-MnO2⋅Co3O4 (S) is due to the high concentration of adsorbed oxygen species and good reducibility at low temperature. Toluene oxidation over B-MnO2⋅Co3O4 (S) proceeds through the adsorption of O2 and toluene to form O*, OH*, and H2C(C6H5)* species, which then react to produce benzyl alcohol, benzoic acid, and benzaldehyde, ultimately converting to CO2 and H2O. The findings suggest that B-MnO2⋅Co3O4 (S) has promising potential for use as an effective catalyst in practical applications.
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Affiliation(s)
- Ali Rastegarpanah
- Beijing Key Laboratory for Green Catalysis and Separation, Key Laboratory of Beijing on Regional Air Pollution Control, Key Laboratory of Advanced Functional Materials, Education Ministry of China, Laboratory of Catalysis Chemistry and Nanoscience, Department of Chemical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Jiguang Deng
- Beijing Key Laboratory for Green Catalysis and Separation, Key Laboratory of Beijing on Regional Air Pollution Control, Key Laboratory of Advanced Functional Materials, Education Ministry of China, Laboratory of Catalysis Chemistry and Nanoscience, Department of Chemical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China.
| | - Yuxi Liu
- Beijing Key Laboratory for Green Catalysis and Separation, Key Laboratory of Beijing on Regional Air Pollution Control, Key Laboratory of Advanced Functional Materials, Education Ministry of China, Laboratory of Catalysis Chemistry and Nanoscience, Department of Chemical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Lin Jing
- Beijing Key Laboratory for Green Catalysis and Separation, Key Laboratory of Beijing on Regional Air Pollution Control, Key Laboratory of Advanced Functional Materials, Education Ministry of China, Laboratory of Catalysis Chemistry and Nanoscience, Department of Chemical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Wenbo Pei
- Beijing Key Laboratory for Green Catalysis and Separation, Key Laboratory of Beijing on Regional Air Pollution Control, Key Laboratory of Advanced Functional Materials, Education Ministry of China, Laboratory of Catalysis Chemistry and Nanoscience, Department of Chemical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Jia Wang
- Beijing Key Laboratory for Green Catalysis and Separation, Key Laboratory of Beijing on Regional Air Pollution Control, Key Laboratory of Advanced Functional Materials, Education Ministry of China, Laboratory of Catalysis Chemistry and Nanoscience, Department of Chemical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
| | - Hongxing Dai
- Beijing Key Laboratory for Green Catalysis and Separation, Key Laboratory of Beijing on Regional Air Pollution Control, Key Laboratory of Advanced Functional Materials, Education Ministry of China, Laboratory of Catalysis Chemistry and Nanoscience, Department of Chemical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China.
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13
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Mei Q, Qiu Z, Jiang J, Li M, Wang Q, He M. Ozonolysis of ketoprofen in polluted water: Reaction pathways, kinetics, removal efficiency, and health effects. J Environ Sci (China) 2025; 147:451-461. [PMID: 39003061 DOI: 10.1016/j.jes.2023.10.029] [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: 09/10/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 07/15/2024]
Abstract
Ketoprofen (KET), as a non-steroidal anti-inflammatory drug frequently detected in aqueous environments, is a threat to human health due to its accumulation and low biodegradability, which requires the transformation and degradation of KET in aqueous environments. In this paper, the reaction process of ozone-initiated KET degradation in water was investigated using density functional theory (DFT) method at the M06-2X/6-311++g(3df,2p)//M06-2X/6-31+g(d,p) level. The detailed reaction path of KET ozonation is proposed. The thermodynamic results show that ozone-initiated KET degradation is feasible. Under ultraviolet irradiation, the reaction of ozone with water can also produce OH radicals (HO·) that can react with KET. The degradation reaction of KET caused by HO· was further studied. The kinetic calculation illustrates that the reaction rate (1.99 × 10-1 (mol/L)-1 sec-1) of KET ozonation is relatively slow, but the reaction rate of HO· reaction is relatively high, which can further improve the degradation efficiency. On this basis, the effects of pollutant concentration, ozone concentration, natural organic matter, and pH value on degradation efficiency under UV/O3 process were analyzed. The ozonolysis reaction of KET is not sensitive to pH and is basically unaffected. Finally, the toxicity prediction of oxidation compounds produced by degradation reaction indicates that most of the degradation products are harmless, and a few products containing benzene rings are still toxic and have to be concerned. This study serves as a theoretical basis for analyzing the migration and transformation process of anti-inflammatory compounds in the water environment.
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Affiliation(s)
- Qiong Mei
- School of Land Engineering, Shaanxi Key Laboratory of Land Consolidation, Chang'an University, Xi'an 710064, China; School of Water and Environment, Chang'an University, Xi'an 710054, China
| | - Zhaoxu Qiu
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Jinchan Jiang
- Weihai Water Conservancy Service Center, Weihai 264200, China
| | - Mingxue Li
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Qizhao Wang
- School of Water and Environment, Chang'an University, Xi'an 710054, China.
| | - Maoxia He
- Environment Research Institute, Shandong University, Qingdao 266237, China.
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14
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Park SC, Wiest MJ, Yan V, Wong PT, Schotsaert M. Induction of protective immune responses at respiratory mucosal sites. Hum Vaccin Immunother 2024; 20:2368288. [PMID: 38953250 PMCID: PMC11221474 DOI: 10.1080/21645515.2024.2368288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/11/2024] [Indexed: 07/03/2024] Open
Abstract
Many pathogens enter the host through mucosal sites. Thus, interfering with pathogen entry through local neutralization at mucosal sites therefore is an effective strategy for preventing disease. Mucosally administered vaccines have the potential to induce protective immune responses at mucosal sites. This manuscript delves into some of the latest developments in mucosal vaccination, particularly focusing on advancements in adjuvant technologies and the role of these adjuvants in enhancing vaccine efficacy against respiratory pathogens. It highlights the anatomical and immunological complexities of the respiratory mucosal immune system, emphasizing the significance of mucosal secretory IgA and tissue-resident memory T cells in local immune responses. We further discuss the differences between immune responses induced through traditional parenteral vaccination approaches vs. mucosal administration strategies, and explore the protective advantages offered by immunization through mucosal routes.
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Affiliation(s)
- Seok-Chan Park
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J. Wiest
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Vivian Yan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pamela T. Wong
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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15
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Barbosa-Méndez S, Matus-Ortega M, Hernandez-Miramontes R, Salazar-Juarez A. COT-TT vaccine attenuates cocaine-seeking and cocaine-conditioned place preference in rats. Hum Vaccin Immunother 2024; 20:2299068. [PMID: 38228468 DOI: 10.1080/21645515.2023.2299068] [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: 10/04/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Vaccination active, promising alternative immunological strategy to treat of CUD. Various models of cocaine vaccines have been evaluated in animals and humans with relative success. In this sense, it is necessary to improve or optimize the cocaine vaccines already evaluated. Our laboratory previously reported the efficacy of the tetanus toxoid-conjugated morphine vaccine (M6-TT). The M6-TT vaccine can generate high titers of antibodies and reduce heroin-induced behavioral effects in rodents. So, it would be plausible to assume that if we modify the M6-TT vaccine by changing the hapten and maintaining the rest of the structural elements of the vaccine, we will maintain the properties of the M6-TT vaccine (high antibody titers). The objective of this study was to determine whether the antibodies generated by a tetanus toxoid-conjugated cocaine vaccine (COC-TT) can recognize and capture cocaine and decrease the cocaine-induced reinforcing effects. Male Wistar rats were immunized with the COC-TT. A solid-phase antibody-capture ELISA was used to monitor antibody titer responses after each booster dose in vaccinated animals. The study used cocaine self-administration and place-preference testing to evaluate the cocaine-reinforcing effects. The COC-TT vaccine could generate high levels of anti-cocaine antibodies. The antibodies reduced the cocaine self-administration and cocaine place preference. In addition, they decreased the cocaine-induced Fos protein expression. These findings suggest that the COC-TT vaccine generates a robust immunogenic response capable of reducing the reinforcing effects of cocaine, which supports its possible future use in clinical trials in patients with CUD.
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Affiliation(s)
- Susana Barbosa-Méndez
- Laboratorio de Neurofarmacología Conductual, Microcirugía y Terapéutica Experimental, Subdirección de Investigaciones Clínicas, Instituto Nacional de Psiquiatría, Ciudad de México, México
| | - Maura Matus-Ortega
- Laboratorio de Neurobiología Molecular y Neuroquímica de las Adicciones, Subdirección de Investigaciones Clínicas, Instituto Nacional de Psiquiatría, Ciudad de México, México
| | - Ricardo Hernandez-Miramontes
- Laboratorio de Neurofarmacología Conductual, Microcirugía y Terapéutica Experimental, Subdirección de Investigaciones Clínicas, Instituto Nacional de Psiquiatría, Ciudad de México, México
| | - Alberto Salazar-Juarez
- Laboratorio de Neurofarmacología Conductual, Microcirugía y Terapéutica Experimental, Subdirección de Investigaciones Clínicas, Instituto Nacional de Psiquiatría, Ciudad de México, México
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16
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Dai Z, Cai R, Zeng H, Zhu H, Dou Y, Sun S. Exosome may be the next generation of promising cell-free vaccines. Hum Vaccin Immunother 2024; 20:2345940. [PMID: 38714324 PMCID: PMC11086043 DOI: 10.1080/21645515.2024.2345940] [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: 01/12/2024] [Accepted: 04/18/2024] [Indexed: 05/09/2024] Open
Abstract
Traditional vaccines have limits against some persistent infections and pathogens. The development of novel vaccine technologies is particularly critical for the future. Exosomes play an important role in physiological and pathological processes. Exosomes present many advantages, such as inherent capacity being biocompatible, non-toxic, which make them a more desirable candidate for vaccines. However, research on exosomes are in their infancy and the barriers of low yield, low purity, and weak targeting of exosomes limit their applications in vaccines. Accordingly, further exploration is necessary to improve these problems and subsequently facilitate the functional studies of exosomes. In this study, we reviewed the origin, classification, functions, modifications, separation and purification, and characterization methods of exosomes. Meanwhile, we focused on the role and mechanism of exosomes for cancer and COVID-19 vaccines.
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Affiliation(s)
- Zelan Dai
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital, Kunming Medical University, Kunming, People’s Republic of China
- Department VII of Biological Products, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, People’s Republic of China
| | - Ruiru Cai
- Department VII of Biological Products, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, People’s Republic of China
| | - Hong Zeng
- Department VII of Biological Products, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, People’s Republic of China
| | - Hailian Zhu
- Department VII of Biological Products, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, People’s Republic of China
| | - Youwei Dou
- Department VII of Biological Products, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, People’s Republic of China
| | - Shibo Sun
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital, Kunming Medical University, Kunming, People’s Republic of China
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17
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Shanmugam B, Srinivasan UM. Formulation and characterization of antibiotic drug loaded aquasome for the topical application. Future Sci OA 2024; 10:2367849. [PMID: 38982759 PMCID: PMC11238917 DOI: 10.1080/20565623.2024.2367849] [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: 01/07/2024] [Accepted: 06/04/2024] [Indexed: 07/11/2024] Open
Abstract
Aim: This study aimed to develop a topical antibiotic drug delivery system using aquasomes for enhanced treatment of skin and soft tissue infections (SSTIs). Materials & methods: Cephalothin was loaded into aquasomes using a multi-step process and optimized using design of experiment. The aquasomes were characterized for FT-IR, SEM and zeta potential analysis. Entrapment efficacy, In vitro drug release studies, antibacterial assays and stability study was performed to evaluate the efficacy of the formulated aquasomes. Results & conclusion: The formulated cephalothin-loaded aquasomes exhibited stable properties, controlled drug release and significant antibacterial activity against bacteria. This proves that the developed aquasome-based delivery system has the potential for sustained treatment of SSTIs.
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Affiliation(s)
- Bhuvaneshwari Shanmugam
- Department of Pharmaceutics, SRM College of Pharmacy, SRM Institute of Science & Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Umashankar Marakanam Srinivasan
- Department of Pharmaceutics, SRM College of Pharmacy, SRM Institute of Science & Technology, Kattankulathur, Tamil Nadu, 603203, India
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18
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Portilla Llerena JP, Kiyota E, dos Santos FRC, Garcia JC, de Lima RF, Mayer JLS, dos Santos Brito M, Mazzafera P, Creste S, Nobile PM. ShF5H1 overexpression increases syringyl lignin and improves saccharification in sugarcane leaves. GM CROPS & FOOD 2024; 15:67-84. [PMID: 38507337 PMCID: PMC10956634 DOI: 10.1080/21645698.2024.2325181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
The agricultural sugarcane residues, bagasse and straws, can be used for second-generation ethanol (2GE) production by the cellulose conversion into glucose (saccharification). However, the lignin content negatively impacts the saccharification process. This polymer is mainly composed of guaiacyl (G), hydroxyphenyl (H), and syringyl (S) units, the latter formed in the ferulate 5-hydroxylase (F5H) branch of the lignin biosynthesis pathway. We have generated transgenic lines overexpressing ShF5H1 under the control of the C4H (cinnamate 4-hydroxylase) rice promoter, which led to a significant increase of up to 160% in the S/G ratio and 63% in the saccharification efficiency in leaves. Nevertheless, the content of lignin was unchanged in this organ. In culms, neither the S/G ratio nor sucrose accumulation was altered, suggesting that ShF5H1 overexpression would not affect first-generation ethanol production. Interestingly, the bagasse showed a significantly higher fiber content. Our results indicate that the tissue-specific manipulation of the biosynthetic branch leading to S unit formation is industrially advantageous and has established a foundation for further studies aiming at refining lignin modifications. Thus, the ShF5H1 overexpression in sugarcane emerges as an efficient strategy to improve 2GE production from straw.
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Affiliation(s)
- Juan Pablo Portilla Llerena
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Academic Department of Biology, Professional and Academic School of Biology, Universidad Nacional de San Agustín de Arequipa, Arequipa, Perú
| | - Eduardo Kiyota
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | | | - Julio C. Garcia
- Centro de Cana, Instituto Agronômico (IAC), Ribeirão Preto, Brazil
| | | | | | - Michael dos Santos Brito
- Centro de Cana, Instituto Agronômico (IAC), Ribeirão Preto, Brazil
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Paulo Mazzafera
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Silvana Creste
- Centro de Cana, Instituto Agronômico (IAC), Ribeirão Preto, Brazil
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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19
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Uchiyama H, Kudo T, Yamaguchi T, Obana N, Watanabe K, Abe K, Miyazaki H, Toyofuku M, Nomura N, Akeda Y, Nakao R. Mucosal adjuvanticity and mucosal booster effect of colibactin-depleted probiotic Escherichia coli membrane vesicles. Hum Vaccin Immunother 2024; 20:2337987. [PMID: 38658133 PMCID: PMC11057659 DOI: 10.1080/21645515.2024.2337987] [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: 11/21/2023] [Accepted: 03/29/2024] [Indexed: 04/26/2024] Open
Abstract
There is a growing interest in development of novel vaccines against respiratory tract infections, due to COVID-19 pandemic. Here, we examined mucosal adjuvanticity and the mucosal booster effect of membrane vesicles (MVs) of a novel probiotic E. coli derivative lacking both flagella and potentially carcinogenic colibactin (ΔflhDΔclbP). ΔflhDΔclbP-derived MVs showed rather strong mucosal adjuvanticity as compared to those of a single flagellar mutant strain (ΔflhD-MVs). In addition, glycoengineered ΔflhDΔclbP-MVs displaying serotype-14 pneumococcal capsular polysaccharide (CPS14+MVs) were well-characterized based on biological and physicochemical parameters. Subcutaneous (SC) and intranasal (IN) booster effects of CPS14+MVs on systemic and mucosal immunity were evaluated in mice that have already been subcutaneously prime-immunized with the same MVs. With a two-dose regimen, an IN boost (SC-IN) elicited stronger IgA responses than homologous prime-boost immunization (SC-SC). With a three-dose regimen, serum IgG levels were comparable among all tested regimens. Homologous immunization (SC-SC-SC) elicited the highest IgM responses among all regimens tested, whereas SC-SC-SC failed to elicit IgA responses in blood and saliva. Furthermore, serum IgA and salivary SIgA levels were increased with an increased number of IN doses administrated. Notably, SC-IN-IN induced not only robust IgG response, but also the highest IgA response in both serum and saliva among the groups. The present findings suggest the potential of a heterologous three-dose administration for building both systemic and mucosal immunity, e.g. an SC-IN-IN vaccine regimen could be beneficial. Another important observation was abundant packaging of colibactin in MVs, suggesting increased applicability of ΔflhDΔclbP-MVs in the context of vaccine safety.
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Affiliation(s)
- Hiroki Uchiyama
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
- Department of Vascular Surgery, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Toshifumi Kudo
- Department of Vascular Surgery, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Takehiro Yamaguchi
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Nozomu Obana
- Tsukuba Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kimihiro Abe
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Hidetaka Miyazaki
- Department of Oculoplastic, Orbital and Lacrimal Surgery, Aichi Medical University, Nagakute, Japan
- Department of Oral and Maxillofacial Surgery, Division of Oral Health Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Masanori Toyofuku
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Nobuhiko Nomura
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
| | - Ryoma Nakao
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku-ku, Tokyo, Japan
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20
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Rooney J, Rivera-de-Torre E, Li R, Mclean K, Price DR, Nisbet AJ, Laustsen AH, Jenkins TP, Hofmann A, Bakshi S, Zarkan A, Cantacessi C. Structural and functional analyses of nematode-derived antimicrobial peptides support the occurrence of direct mechanisms of worm-microbiota interactions. Comput Struct Biotechnol J 2024; 23:1522-1533. [PMID: 38633385 PMCID: PMC11021794 DOI: 10.1016/j.csbj.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
The complex relationships between gastrointestinal (GI) nematodes and the host gut microbiota have been implicated in key aspects of helminth disease and infection outcomes. Nevertheless, the direct and indirect mechanisms governing these interactions are, thus far, largely unknown. In this proof-of-concept study, we demonstrate that the excretory-secretory products (ESPs) and extracellular vesicles (EVs) of key GI nematodes contain peptides that, when recombinantly expressed, exert antimicrobial activity in vitro against Bacillus subtilis. In particular, using time-lapse microfluidics microscopy, we demonstrate that exposure of B. subtilis to a recombinant saposin-domain containing peptide from the 'brown stomach worm', Teladorsagia circumcincta, and a metridin-like ShK toxin from the 'barber's pole worm', Haemonchus contortus, results in cell lysis and significantly reduced growth rates. Data from this study support the hypothesis that GI nematodes may modulate the composition of the vertebrate gut microbiota directly via the secretion of antimicrobial peptides, and pave the way for future investigations aimed at deciphering the impact of such changes on the pathophysiology of GI helminth infection and disease.
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Affiliation(s)
- James Rooney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Ruizhe Li
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Kevin Mclean
- Moredun Research Institute, Penicuik Midlothian, United Kingdom
| | | | | | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Andreas Hofmann
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kulmbach, Germany
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Somenath Bakshi
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Ashraf Zarkan
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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21
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Řehulka J, Jurášek M, Dráber P, Ivanová A, Gurská S, Ječmeňová K, Mokshyna O, Hajdúch M, Polishchuk P, Drašar PB, Džubák P. Click estradiol dimers with novel aromatic bridging units: synthesis and anticancer evaluation. J Enzyme Inhib Med Chem 2024; 39:2367139. [PMID: 38904149 PMCID: PMC467089 DOI: 10.1080/14756366.2024.2367139] [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: 11/17/2023] [Accepted: 06/06/2024] [Indexed: 06/22/2024] Open
Abstract
Estradiol dimers (EDs) possess significant anticancer activity by targeting tubulin dynamics. In this study, we synthesised 12 EDs variants via copper-catalysed azide-alkyne cycloaddition (CuAAC) reaction, focusing on structural modifications within the aromatic bridge connecting two estradiol moieties. In vitro testing of these EDs revealed a marked improvement in selectivity towards cancerous cells, particularly for ED1-8. The most active compounds, ED3 (IC50 = 0.38 μM in CCRF-CEM) and ED5 (IC50 = 0.71 μM in CCRF-CEM) demonstrated cytotoxic effects superior to 2-methoxyestradiol (IC50 = 1.61 μM in CCRF-CEM) and exhibited anti-angiogenic properties in an endothelial cell tube-formation model. Cell-based experiments and in vitro assays revealed that EDs interfere with mitotic spindle assembly. Additionally, we proposed an in silico model illustrating the probable binding modes of ED3 and ED5, suggesting that dimers with a simple linker and a single substituent on the aromatic central ring possess enhanced characteristics compared to more complex dimers.
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Affiliation(s)
- Jiří Řehulka
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
| | - Michal Jurášek
- Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague, Praha 6, Czech Republic
| | - Pavel Dráber
- Department of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Praha 4, Czech Republic
| | - Aleksandra Ivanová
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
| | - Soňa Gurská
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
| | - Kateřina Ječmeňová
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
| | - Olena Mokshyna
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha 6, Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
- Laboratory of Experimental Medicine, Institute of Molecular and Translational Medicine, University Hospital Olomouc, Olomouc, Czech Republic
| | - Pavel Polishchuk
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
| | - Pavel B. Drašar
- Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague, Praha 6, Czech Republic
| | - Petr Džubák
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
- Laboratory of Experimental Medicine, Institute of Molecular and Translational Medicine, University Hospital Olomouc, Olomouc, Czech Republic
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22
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He S, Jiang X, Yang J, Wu Y, Shi J, Wu X, Du S, Zhang Y, Gong L, Dong S, Yu J. Nicotinamide mononucleotide alleviates endotoxin-induced acute lung injury by modulating macrophage polarization via the SIRT1/NF-κB pathway. PHARMACEUTICAL BIOLOGY 2024; 62:22-32. [PMID: 38100537 PMCID: PMC10732210 DOI: 10.1080/13880209.2023.2292256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 12/03/2023] [Indexed: 12/17/2023]
Abstract
CONTEXT Sepsis-induced acute lung injury (ALI) is a severe condition with limited effective therapeutics; nicotinamide mononucleotide (NMN) has been reported to exert anti-inflammatory activities. OBJECTIVE This study explores the potential mechanisms by which NMN ameliorates sepsis-induced ALI in vivo and in vitro. MATERIALS AND METHODS Cultured MH-S cells and a murine model were used to evaluate the effect of NMN on sepsis-induced ALI. MH-S cells were stimulated with LPS (1 μg/mL) and NMN (500 μM) for 12 h grouping as control, LPS, and LPS + NMN. Cell viability, apoptotic status, and M1/2 macrophage-related markers were detected. The mice were pretreated intraperitoneally with NMN (500 mg/kg) and/or EX-527 (5 mg/kg) 1 h before LPS injection and randomized into 7 groups (n = 8): control, LPS, LPS + NMN, NMN, LPS + NMN + EX-527 (a SIRT1 inhibitor), LPS + EX-527, and EX-527. After 12 h, lung histopathology, W/D ratio, MPO activity, NAD+ and ATP levels, M1/2 macrophage-related markers, and expression of the SIRT1/NF-κB pathway were detected. RESULTS In MH-S cells, NMN significantly decreased the apoptotic rate from 12.25% to 5.74%. In septic mice, NMN improved the typical pathologic findings in lungs and reduced W/D ratio and MPO activity, but increased NAD+ and ATP levels. Additionally, NMN suppressed M1 but promoted M2 polarization, and upregulated the expression of SIRT1, with inhibition of NF-κB-p65 acetylation and phosphorylation. Furthermore, inhibition of SIRT1 reversed the effects of NMN-induced M2 macrophage polarization. CONCLUSIONS NMN protects against sepsis-induced ALI by promoting M2 macrophage polarization via the SIRT1/NF-κB pathway, it might be an effective strategy for preventing or treating sepsis-induced ALI.
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Affiliation(s)
- Simeng He
- Department of Anesthesiology and Critical Care Medicine, Tianjin Nankai Hospital, Tianjin Medical University, Tianjin, China
| | - Xianhong Jiang
- Department of Anesthesiology and Critical Care Medicine, Tianjin Nankai Hospital, Tianjin Medical University, Tianjin, China
| | - Jing Yang
- Tianjin Key Laboratory of Acute Abdomen Disease Associated Organ Injury and ITCWM Repair, Institute of Acute Abdominal Diseases of Integrated Traditional Chinese and Western Medicine, Tianjin Nankai Hospital, Tianjin, China
| | - Ya Wu
- Department of Anesthesiology and Critical Care Medicine, Tianjin Nankai Hospital, Tianjin Medical University, Tianjin, China
| | - Jia Shi
- Department of Anesthesiology and Critical Care Medicine, Tianjin Nankai Hospital, Tianjin Medical University, Tianjin, China
| | - Xiaoyang Wu
- Department of Anesthesiology and Critical Care Medicine, Tianjin Nankai Hospital, Tianjin Medical University, Tianjin, China
| | - Shihan Du
- Department of Anesthesiology and Critical Care Medicine, Tianjin Nankai Hospital, Tianjin Medical University, Tianjin, China
| | - Yuan Zhang
- Department of Anesthesiology and Critical Care Medicine, Tianjin Nankai Hospital, Tianjin Medical University, Tianjin, China
| | - Lirong Gong
- Department of Anesthesiology and Critical Care Medicine, Tianjin Nankai Hospital, Tianjin Medical University, Tianjin, China
| | - Shuan Dong
- Department of Anesthesiology and Critical Care Medicine, Tianjin Nankai Hospital, Tianjin Medical University, Tianjin, China
| | - Jianbo Yu
- Department of Anesthesiology and Critical Care Medicine, Tianjin Nankai Hospital, Tianjin Medical University, Tianjin, China
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23
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Tsikas D. Acetazolamide and human carbonic anhydrases: retrospect, review and discussion of an intimate relationship. J Enzyme Inhib Med Chem 2024; 39:2291336. [PMID: 38078375 DOI: 10.1080/14756366.2023.2291336] [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: 10/24/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Acetazolamide (AZM) is a strong pharmacological sulphonamide-type (R-SO2-NH2, pKa 7.2) inhibitor of the activity of several carbonic anhydrase (CA) isoforms, notably of renal CA II (Ki, 12 nM) and CA IV (Ki, 74 nM). AZM is clinically used for about eighty years in various diseases including epilepsy and glaucoma. Pharmacological AZM increases temporarily the urinary excretion of bicarbonate (HCO3-) and sodium ions (Na+) and sustainably the urinary pH. AZM is excreted almost unchanged over several hours at high rates in the urine. Closely parallel concentrations of circulating and excretory AZM are observed upon administration of therapeutical doses of AZM. In a proof-of-principle study, we investigated the effects of the ingestion of a 250-mg AZM-containing tablet by a healthy volunteer on the urinary excretion of organic and inorganic substances over 5 h (range, 0, 0.5, 1, 1.5, 2, 3, 4, 5 h). Measured analytes included: AZM, amino acids and their metabolites such as guanidinoacetate, i.e. the precursor of creatine, of asymmetrically (ADMA) and symmetrically (SDMA) dimethylated arginine, nitrite (O = N-O-, pKa 3.4) and nitrate (O2N-O-, pKa -1.37), the major metabolites of nitric oxide (NO), the C-H acidic malondialdehyde (MDA; (CHO)2CH2, pKa 4.5), and creatinine for correction of analytes excretion. All analytes were measured by validated isotopologues using gas chromatography-mass spectrometry (GC-MS) methods. AZM excretion in the urine reached its maximum value after 2 h and was fairly stable for the next 3 h. Time series analysis by the ARIMA method was performed. AZM ingestion increased temporarily the urinary excretion of the amino acids Leu + Ile, nitrite and nitrate, decreased temporarily the urinary excretion of other amino acids. AZM decreased sustainably the urinary excretion of MDA, a biomarker of oxidative stress (i.e. lipid peroxidation). Whether this decrease is due to inhibition of the excretion of MDA or attenuation of oxidative stress by AZM is unknown. The acute and chronic effects of AZM on the urinary excretion of electrolytes and physiological substances reported in the literature are discussed in depth in the light of its extraordinary pharmacokinetics and pharmacodynamics. Tolerance development/drug resistance to AZM in chronic use and potential mechanisms are also addressed.
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Affiliation(s)
- Dimitrios Tsikas
- Core Unit Proteomics, Institute of Toxicology, Hannover Medical School, Hannover, Germany
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24
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Kaweewan I, Mukai K, Rukthanapitak P, Nakagawa H, Hosaka T, Kodani S. Heterologous biosynthesis of myxobacterial lanthipeptides melittapeptins. Appl Microbiol Biotechnol 2024; 108:122. [PMID: 38229328 DOI: 10.1007/s00253-023-12834-4] [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: 03/30/2023] [Revised: 09/28/2023] [Accepted: 10/30/2023] [Indexed: 01/18/2024]
Abstract
The myxobacteria are an attractive bioresource for bioactive compounds since the large size genome contains many biosynthetic gene clusters of secondary metabolites. The genome of the myxobacterium Melittangium boletus contains three biosynthetic gene clusters for lanthipeptide production. One of the gene clusters includes genes coding lanthipeptide precursor (melA), class II lanthipeptide synthetase (melM), and transporter (melT). The amino acid sequence of melA indicated similarity with that of known lanthipeptides mersacidin and lichenicidin A1 by the alignment. To perform heterologous production of new lanthipeptides, the expression vector containing the essential genes (melA and melM) was constructed by utilizing codon-optimized synthetic genes. The co-expression of two genes in the host bacterial cells of Escherichia coli BL21 (DE3) afforded new lanthipeptides named melittapeptins A-C. The structures of melittapeptins A-C including lanthionine/methyllanthionine bridge pattern were proposed based on protease digestion and MS/MS experiments. The native strain of M. boletus did not produce melittapeptins A-C, so heterologous production using the biosynthetic gene cluster was effective in obtaining the lanthipeptides. Melittapeptins A-C showed specific and potent antibacterial activity to the Gram-positive bacterium Micrococcus luteus. To the best of our knowledge, this is the first report of antibacterial lanthipeptides derived from myxobacterial origin. KEY POINTS: • New lanthipeptides melittapeptins were heterologously produced in Escherichia coli. • Melittapeptins showed specific antibacterial activity against Micrococcus luteus. • Melittapeptins were the first antibacterial lanthipeptides of myxobacterial origin.
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Affiliation(s)
- Issara Kaweewan
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
- Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Keiichiro Mukai
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | | | - Hiroyuki Nakagawa
- Research Center for Advanced Analysis, Core Technology Research Headquarters, National Agriculture and Food Research Organization (NARO), Ibaraki, Japan
| | - Takeshi Hosaka
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | - Shinya Kodani
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan.
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan.
- College of Agriculture, Academic Institute, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
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25
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Rocío Hernández A, Bogdanova E, Campos Pacheco JE, Kocherbitov V, Ekström M, Pilkington G, Valetti S. Disordered mesoporous silica particles: an emerging platform to deliver proteins to the lungs. Drug Deliv 2024; 31:2381340. [PMID: 39041383 PMCID: PMC11268259 DOI: 10.1080/10717544.2024.2381340] [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: 12/12/2023] [Accepted: 07/12/2024] [Indexed: 07/24/2024] Open
Abstract
Pulmonary delivery and formulation of biologics are among the more complex and growing scientific topics in drug delivery. We herein developed a dry powder formulation using disordered mesoporous silica particles (MSP) as the sole excipient and lysozyme, the most abundant antimicrobial proteins in the airways, as model protein. The MSP had the optimal size for lung deposition (2.43 ± 0.13 µm). A maximum lysozyme loading capacity (0.35 mg/mg) was achieved in 150 mM PBS, which was seven times greater than that in water. After washing and freeze-drying, we obtained a dry powder consisting of spherical, non-aggregated particles, free from residual buffer, or unabsorbed lysozyme. The presence of lysozyme was confirmed by TGA and FT-IR, while N2 adsorption/desorption and SAXS analysis indicate that the protein is confined within the internal mesoporous structure. The dry powder exhibited excellent aerodynamic performance (fine particle fraction <5 µm of 70.32%). Lysozyme was released in simulated lung fluid in a sustained kinetics and maintaining high enzymatic activity (71-91%), whereas LYS-MSP were shown to degrade into aggregated nanoparticulate microstructures, reaching almost complete dissolution (93%) within 24 h. MSPs were nontoxic to in vitro lung epithelium. The study demonstrates disordered MSP as viable carriers to successfully deliver protein to the lungs, with high deposition and retained activity.
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Affiliation(s)
- Aura Rocío Hernández
- Biofilms – Research Center for Biointerfaces (BRCB), Malmö, Sweden
- Biomedical Science, Faculty of Health and Society, Malmö University, Malmö, Sweden
| | - Ekaterina Bogdanova
- Biofilms – Research Center for Biointerfaces (BRCB), Malmö, Sweden
- Biomedical Science, Faculty of Health and Society, Malmö University, Malmö, Sweden
| | - Jesus E. Campos Pacheco
- Biofilms – Research Center for Biointerfaces (BRCB), Malmö, Sweden
- Biomedical Science, Faculty of Health and Society, Malmö University, Malmö, Sweden
| | - Vitaly Kocherbitov
- Biofilms – Research Center for Biointerfaces (BRCB), Malmö, Sweden
- Biomedical Science, Faculty of Health and Society, Malmö University, Malmö, Sweden
| | | | | | - Sabrina Valetti
- Biofilms – Research Center for Biointerfaces (BRCB), Malmö, Sweden
- Biomedical Science, Faculty of Health and Society, Malmö University, Malmö, Sweden
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26
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Škulj S, Kožić M, Barišić A, Vega A, Biarnés X, Piantanida I, Barisic I, Bertoša B. Comparison of two peroxidases with high potential for biotechnology applications - HRP vs. APEX2. Comput Struct Biotechnol J 2024; 23:742-751. [PMID: 38298178 PMCID: PMC10828542 DOI: 10.1016/j.csbj.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/01/2024] [Accepted: 01/01/2024] [Indexed: 02/02/2024] Open
Abstract
Peroxidases are essential elements in many biotechnological applications. An especially interesting concept involves split enzymes, where the enzyme is separated into two smaller and inactive proteins that can dimerize into a fully active enzyme. Such split forms were developed for the horseradish peroxidase (HRP) and ascorbate peroxidase (APX) already. Both peroxidases have a high potential for biotechnology applications. In the present study, we performed biophysical comparisons of these two peroxidases and their split analogues. The active site availability is similar for all four structures. The split enzymes are comparable in stability with their native analogues, meaning that they can be used for further biotechnology applications. Also, the tertiary structures of the two peroxidases are similar. However, differences that might help in choosing one system over another for biotechnology applications were noticed. The main difference between the two systems is glycosylation which is not present in the case of APX/sAPEX2, while it has a high impact on the HRP/sHRP stability. Further differences are calcium ions and cysteine bridges that are present only in the case of HRP/sHRP. Finally, computational results identified sAPEX2 as the systems with the smallest structural variations during molecular dynamics simulations showing its dominant stability comparing to other simulated proteins. Taken all together, the sAPEX2 system has a high potential for biotechnological applications due to the lack of glycans and cysteines, as well as due to high stability.
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Affiliation(s)
- Sanja Škulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Matej Kožić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
| | - Antun Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
| | - Aitor Vega
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10 000 Zagreb, Croatia
| | - Ivan Barisic
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, Vienna 1210, Austria
- Eko Refugium, Crno Vrelo 2, Slunj 47240, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
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27
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Ma XB, Yue CX, Liu Y, Yang Y, Wang J, Yang XN, Huang LD, Zhu MX, Hattori M, Li CZ, Yu Y, Guo CR. A shared mechanism for TNP-ATP recognition by members of the P2X receptor family. Comput Struct Biotechnol J 2024; 23:295-308. [PMID: 38173879 PMCID: PMC10762375 DOI: 10.1016/j.csbj.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
P2X receptors (P2X1-7) are non-selective cation channels involved in many physiological activities such as synaptic transmission, immunological modulation, and cardiovascular function. These receptors share a conserved mechanism to sense extracellular ATP. TNP-ATP is an ATP derivative acting as a nonselective competitive P2X antagonist. Understanding how it occupies the orthosteric site in the absence of agonism may help reveal the key allostery during P2X gating. However, TNP-ATP/P2X complexes (TNP-ATP/human P2X3 (hP2X3) and TNP-ATP/chicken P2X7 (ckP2X7)) with distinct conformations and different mechanisms of action have been proposed. Whether these represent species and subtype variations or experimental differences remains unclear. Here, we show that a common mechanism of TNP-ATP recognition exists for the P2X family members by combining enhanced conformation sampling, engineered disulfide bond analysis, and covalent occupancy. In this model, the polar triphosphate moiety of TNP-ATP interacts with the orthosteric site, while its TNP-moiety is deeply embedded in the head and dorsal fin (DF) interface, creating a restrictive allostery in these two domains that results in a partly enlarged yet ion-impermeable pore. Similar results were obtained from multiple P2X subtypes of different species, including ckP2X7, hP2X3, rat P2X2 (rP2X2), and human P2X1 (hP2X1). Thus, TNP-ATP uses a common mechanism for P2X recognition and modulation by restricting the movements of the head and DF domains which are essential for P2X activation. This knowledge is applicable to the development of new P2X inhibitors.
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Affiliation(s)
- Xiao-Bo Ma
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chen-Xi Yue
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yan Liu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yang Yang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jin Wang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Na Yang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Li-Dong Huang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Michael X. Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Motoyuki Hattori
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chang-Zhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Ye Yu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Chang-Run Guo
- School of Traditional Chinese Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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28
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Anderson A, Piñeiro Á, García-Fandiño R, O’Connor MS. Cyclodextrins: Establishing building blocks for AI-driven drug design by determining affinity constants in silico. Comput Struct Biotechnol J 2024; 23:1117-1128. [PMID: 38510974 PMCID: PMC10950811 DOI: 10.1016/j.csbj.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/22/2024] Open
Abstract
Cyclodextrins (CDs) are cyclic carbohydrate polymers that hold significant promise for drug delivery and industrial applications. Their effectiveness depends on their ability to encapsulate target molecules with strong affinity and specificity, but quantifying affinities in these systems accurately is challenging for a variety of reasons. Computational methods represent an exceptional complement to in vitro assays because they can be employed for existing and hypothetical molecules, providing high resolution structures in addition to a mechanistic, dynamic, kinetic, and thermodynamic characterization. Here, we employ potential of mean force (PMF) calculations obtained from guided metadynamics simulations to characterize the 1:1 inclusion complexes between four different modified βCDs, with different type, number, and location of substitutions, and two sterol molecules (cholesterol and 7-ketocholesterol). Our methods, validated for reproducibility through four independent repeated simulations per system and different post processing techniques, offer new insights into the formation and stability of CD-sterol inclusion complexes. A systematic distinct orientation preference where the sterol tail projects from the CD's larger face and significant impacts of CD substitutions on binding are observed. Notably, sampling only the CD cavity's wide face during simulations yielded comparable binding energies to full-cavity sampling, but in less time and with reduced statistical uncertainty, suggesting a more efficient approach. Bridging computational methods with complex molecular interactions, our research enables predictive CD designs for diverse applications. Moreover, the high reproducibility, sensitivity, and cost-effectiveness of the studied methods pave the way for extensive studies of massive CD-ligand combinations, enabling AI algorithm training and automated molecular design.
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Affiliation(s)
- Amelia Anderson
- Cyclarity Therapeutics, 8001 Redwood Blvd, Novato, CA 94945, USA
- Department of Organic Chemistry, Center for Research in Biological Chemistry and Molecular Materials, Santiago de Compostela University, CIQUS, Spain
- Soft Matter & Molecular Biophysics Group, Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela, Spain
| | - Ángel Piñeiro
- Soft Matter & Molecular Biophysics Group, Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela, Spain
| | - Rebeca García-Fandiño
- Department of Organic Chemistry, Center for Research in Biological Chemistry and Molecular Materials, Santiago de Compostela University, CIQUS, Spain
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29
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Cabezón A, Suárez-Lestón F, Granja JR, Piñeiro Á, Garcia-Fandino R. CYCLOPEp Builder: Facilitating cyclic peptide and nanotube research through a user-friendly web platform. Comput Struct Biotechnol J 2024; 25:91-94. [PMID: 38966006 PMCID: PMC11222899 DOI: 10.1016/j.csbj.2024.05.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 07/06/2024] Open
Abstract
The study of cyclic peptides (CPs) and self-assembling cyclic peptide nanotubes (SCPNs) is pivotal in advancing applications in diverse fields such as biomedicine, nanoelectronics, and catalysis. Recognizing the limitations in the experimental study of these molecules, this article introduces CYCLOPEp Builder, a comprehensive web-based application designed to facilitate the design, simulation, and visualization of CPs and SCPNs. The tool is engineered to generate molecular topologies, essential for conducting Molecular Dynamics simulations that span All-Atom to Coarse-Grain resolutions. CYCLOPEp Builder's user-friendly interface simplifies the complex process of molecular modeling, providing researchers with the ability to readily construct CPs and SCPNs. The platform is versatile, equipped with various force fields, and capable of producing structures ranging from individual CPs to complex SCPNs with different sequences, offering parallel and antiparallel orientations among them. By enhancing the capacity for detailed visualization of molecular assemblies, CYCLOPEp Builder improves the understanding of CP and SCPN molecular interactions. This tool is a step forward in democratizing access to sophisticated simulations, offering an invaluable resource to the scientific community engaged in the exploration of supramolecular structures. CYCLOPEp is accessible at http://cyclopep.com/.
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Affiliation(s)
- Alfonso Cabezón
- Department of Organic Chemistry, Center for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, CIQUS, Spain
| | - Fabián Suárez-Lestón
- Department of Organic Chemistry, Center for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, CIQUS, Spain
- Soft Matter & Molecular Biophysics Group, Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela, Spain
- MD.USE Innovations S.L., Edificio Emprendia, 15782 Santiago de Compostela, Spain
| | - Juan R. Granja
- Department of Organic Chemistry, Center for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, CIQUS, Spain
| | - Ángel Piñeiro
- Soft Matter & Molecular Biophysics Group, Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela, Spain
| | - Rebeca Garcia-Fandino
- Department of Organic Chemistry, Center for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, CIQUS, Spain
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30
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Schwardmann LS, Benninghaus L, Lindner SN, Wendisch VF. Prospects of formamide as nitrogen source in biotechnological production processes. Appl Microbiol Biotechnol 2024; 108:105. [PMID: 38204134 PMCID: PMC10781810 DOI: 10.1007/s00253-023-12962-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 01/12/2024]
Abstract
This review presents an analysis of formamide, focussing on its occurrence in nature, its functional roles, and its promising applications in the context of the bioeconomy. We discuss the utilization of formamide as an innovative nitrogen source achieved through metabolic engineering. These approaches underscore formamide's potential in supporting growth and production in biotechnological processes. Furthermore, our review illuminates formamide's role as a nitrogen source capable of safeguarding cultivation systems against contamination in non-sterile conditions. This attribute adds an extra layer of practicality to its application, rendering it an attractive candidate for sustainable and resilient industrial practices. Additionally, the article unveils the versatility of formamide as a potential carbon source that could be combined with formate or CO2 assimilation pathways. However, its attributes, i.e., enriched nitrogen content and comparatively limited energy content, led to conclude that formamide is more suitable as a co-substrate and that its use as a sole source of carbon for biomass and bio-production is limited. Through our exploration of formamide's properties and its applications, this review underscores the significance of formamide as valuable resource for a large spectrum of industrial applications. KEY POINTS: • Formidases enable access to formamide as source of nitrogen, carbon, and energy • The formamide/formamidase system supports non-sterile fermentation • The nitrogen source formamide supports production of nitrogenous compounds.
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Affiliation(s)
- Lynn S Schwardmann
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
- , Aminoverse B.V., Daelderweg 9, 6361 HK, Nuth, Beekdaelen, The Netherlands
| | - Leonie Benninghaus
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Steffen N Lindner
- Department of Biochemistry, Charite Universitatsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
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Chen Q, Zheng Y, Jiang X, Wang Y, Chen Z, Wu D. Nature's carriers: leveraging extracellular vesicles for targeted drug delivery. Drug Deliv 2024; 31:2361165. [PMID: 38832506 DOI: 10.1080/10717544.2024.2361165] [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: 08/07/2023] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
With the rapid development of drug delivery systems, extracellular vesicles (EVs) have emerged as promising stars for improving targeting abilities and realizing effective delivery. Numerous studies have shown when compared to conventional strategies in targeted drug delivery (TDD), EVs-based strategies have several distinguished advantages besides targeting, such as participating in cell-to-cell communications and immune response, showing high biocompatibility and stability, penetrating through biological barriers, etc. In this review, we mainly focus on the mass production of EVs including the challenges and strategies for scaling up EVs production in a cost-effective and reproducible manner, the loading and active targeting methods, and examples of EVs as vehicles for TDD in consideration of potential safety and regulatory issues associated. We also conclude and discuss the rigor and reproducibility of EVs production, the current research status of the application of EVs-based strategies to targeted drug delivery, clinical conversion prospects, and existing chances and challenges.
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Affiliation(s)
- Qi Chen
- Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou, P. R. China
| | - Yuyi Zheng
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xuhong Jiang
- Epilepsy Center, Department of Neurology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, PR China
| | - Yi Wang
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- Zhejiang Rehabilitation Medical Center, The Third Affiliated Hospital of Zhejiang, Chinese Medical University, Hangzhou, PR China
| | - Zhong Chen
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- Epilepsy Center, Department of Neurology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, PR China
| | - Di Wu
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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32
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García-Soriano JC, de Lucio H, Elvira-Blázquez D, Alcón-Calderón M, Sanz Del Olmo N, Sánchez-Murcia PA, Ortega P, de la Mata FJ, Jiménez-Ruiz A. The repertoire of iron superoxide dismutases from Leishmania infantum as targets in the search for therapeutic agents against leishmaniasis. J Enzyme Inhib Med Chem 2024; 39:2377586. [PMID: 39037009 DOI: 10.1080/14756366.2024.2377586] [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: 03/21/2024] [Accepted: 07/02/2024] [Indexed: 07/23/2024] Open
Abstract
Species of Leishmania and Trypanosoma genera are the causative agents of relevant parasitic diseases. Survival inside their hosts requires the existence of a potent antioxidant enzymatic machinery. Four iron superoxide dismutases have been described in trypanosomatids (FeSODA, FeSODB1, FeSODB2, and FeSODC) that hold a potential as therapeutic targets. Nonetheless, very few studies have been developed that make use of the purified enzymes. Moreover, FeSODC remains uncharacterised in Leishmania. In this work, for the first time, we describe the purification and enzymatic activity of recombinant versions of the four Leishmania FeSOD isoforms and establish an improved strategy for developing inhibitors. We propose a novel parameter [(V*cyt. c - Vcyt. c)/Vcyt. c] which, in contrast to that used in the classical cytochrome c reduction assay, correlates linearly with enzyme concentration. As a proof of concept, we determine the IC50 values of two ruthenium carbosilane metallodendrimers against these isoforms.
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Affiliation(s)
| | - Héctor de Lucio
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá de Henares, Spain
| | | | | | - Natalia Sanz Del Olmo
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Instituto de Química Andrés Manuel del Río, Alcalá de Henares, Spain
- Instituto de Investigación Sanitaria Ramón y Cajal, IRYCIS, Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, CIBER-BBN, Madrid, Spain
| | - Pedro A Sánchez-Murcia
- Division of Medicinal Chemistry, Laboratory of Computer-Aided Molecular Design, Otto-Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Paula Ortega
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Instituto de Química Andrés Manuel del Río, Alcalá de Henares, Spain
- Instituto de Investigación Sanitaria Ramón y Cajal, IRYCIS, Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, CIBER-BBN, Madrid, Spain
| | - Francisco Javier de la Mata
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, Instituto de Química Andrés Manuel del Río, Alcalá de Henares, Spain
- Instituto de Investigación Sanitaria Ramón y Cajal, IRYCIS, Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, CIBER-BBN, Madrid, Spain
| | - Antonio Jiménez-Ruiz
- Departamento de Biología de Sistemas, Universidad de Alcalá, Alcalá de Henares, Spain
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Li N, Wang Y, Meng Y, Lv Y, Zhang S, Wei S, Ma P, Hu Y, Lin H. Structural and functional characterization of a new thermophilic-like OYE from Aspergillus flavus. Appl Microbiol Biotechnol 2024; 108:134. [PMID: 38229304 DOI: 10.1007/s00253-023-12963-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 01/18/2024]
Abstract
Old yellow enzymes (OYEs) have been proven as powerful biocatalysts for the asymmetric reduction of activated alkenes. Fungi appear to be valuable sources of OYEs, but most of the fungal OYEs are unexplored. To expand the OYEs toolbox, a new thermophilic-like OYE (AfOYE1) was identified from Aspergillus flavus strain NRRL3357. The thermal stability analysis showed that the T1/2 of AfOYE1 was 60 °C, and it had the optimal temperature at 45 °C. Moreover, AfOYE1 exhibited high reduction activity in a wide pH range (pH 5.5-8.0). AfOYE1 could accept cyclic enones, acrylamide, nitroalkenes, and α, β-unsaturated aldehydes as substrates and had excellent enantioselectivity toward prochiral alkenes (> 99% ee). Interestingly, an unexpected (S)-stereoselectivity bioreduction toward 2-methylcyclohexenone was observed. The further crystal structure of AfOYE1 revealed that the "cap" region from Ala132 to Thr182, the loop of Ser316 to Gly325, α short helix of Arg371 to Gln375, and the C-terminal "finger" structure endow the catalytic cavity of AfOYE1 quite deep and narrow, and flavin mononucleotide (FMN) heavily buried at the bottom of the active site tunnel. Furthermore, the catalytic mechanism of AfOYE1 was also investigated, and the results confirmed that the residues His211, His214, and Tyr216 compose its catalytic triad. This newly identified thermophilic-like OYE would thus be valuable for asymmetric alkene hydrogenation in industrial processes. KEY POINTS: A new thermophilic-like OYE AfOYE1 was identified from Aspergillus flavus, and the T1/2 of AfOYE1 was 60 °C AfOYE1 catalyzed the reduction of 2-methylcyclohexenone with (S)-stereoselectivity The crystal structure of AfOYE1 was revealedv.
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Affiliation(s)
- Na Li
- College of Biological Engineering, Henan Unsssiversity of Technology, 100 Lianhua Street, Zhengzhou, 450001, Henan, China
| | - Yuan Wang
- College of Biological Engineering, Henan Unsssiversity of Technology, 100 Lianhua Street, Zhengzhou, 450001, Henan, China
| | - Yinyin Meng
- Henan International Joint Laboratory of Biocatalysis and Bio-Based Products, College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China
| | - Yangyong Lv
- College of Biological Engineering, Henan Unsssiversity of Technology, 100 Lianhua Street, Zhengzhou, 450001, Henan, China
| | - Shuaibing Zhang
- College of Biological Engineering, Henan Unsssiversity of Technology, 100 Lianhua Street, Zhengzhou, 450001, Henan, China
| | - Shan Wei
- College of Biological Engineering, Henan Unsssiversity of Technology, 100 Lianhua Street, Zhengzhou, 450001, Henan, China
| | | | - Yuansen Hu
- College of Biological Engineering, Henan Unsssiversity of Technology, 100 Lianhua Street, Zhengzhou, 450001, Henan, China.
| | - Hui Lin
- Henan International Joint Laboratory of Biocatalysis and Bio-Based Products, College of Life Sciences, Henan Agricultural University, 95 Wenhua Road, Zhengzhou, 450002, China.
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34
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De PS, Theilmann J, Raguin A. A detailed sensitivity analysis identifies the key factors influencing the enzymatic saccharification of lignocellulosic biomass. Comput Struct Biotechnol J 2024; 23:1005-1015. [PMID: 38420218 PMCID: PMC10900831 DOI: 10.1016/j.csbj.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/09/2024] [Accepted: 01/14/2024] [Indexed: 03/02/2024] Open
Abstract
Corn stover is the most abundant form of crop residue that can serve as a source of lignocellulosic biomass in biorefinery approaches, for instance for the production of bioethanol. In such biorefinery processes, the constituent polysaccharide biopolymers are typically broken down into simple monomeric sugars by enzymatic saccharification, for further downstream fermentation into bioethanol. However, the recalcitrance of this material to enzymatic saccharification invokes the need for innovative pre-treatment methods to increase sugar conversion yield. Here, we focus on experimental glucose conversion time-courses for corn stover lignocellulose that has been pre-treated with different acid-catalysed processes and intensities. We identify the key parameters that determine enzymatic saccharification dynamics by performing a Sobol's sensitivity analysis on the comparison between the simulation results from our complex stochastic biophysical model, and the experimental data that we accurately reproduce. We find that the parameters relating to cellulose crystallinity and those associated with the cellobiohydrolase activity are predominantly driving the enzymatic saccharification dynamics. We confirm our computational results using mathematical calculations for a purely cellulosic substrate. On the one hand, having identified that only five parameters drastically influence the saccharification dynamics allows us to reduce the dimensionality of the parameter space (from nineteen to five parameters), which we expect will significantly speed up our fitting algorithm for comparison of experimental and simulated saccharification time-courses. On the other hand, these parameters directly highlight key targets for experimental endeavours in the optimisation of pre-treatment and saccharification conditions. Finally, this systematic and two-fold theoretical study, based on both mathematical and computational approaches, provides experimentalists with key insights that will support them in rationalising their complex experimental results.
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Affiliation(s)
- Partho Sakha De
- Institute for Computational Cell Biology, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, 40225, NRW, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, NRW, Germany
| | - Jasmin Theilmann
- Institute for Computational Cell Biology, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, 40225, NRW, Germany
| | - Adélaïde Raguin
- Institute for Computational Cell Biology, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, 40225, NRW, Germany
- Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich, Jülich, 52425, NRW, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Universitätsstr. 1, Düsseldorf, 40225, NRW, Germany
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35
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Qiao X, Wu X, Chen S, Niu MM, Hua H, Zhang Y. Discovery of novel and potent dual-targeting AXL/HDAC2 inhibitors for colorectal cancer treatment via structure-based pharmacophore modelling, virtual screening, and molecular docking, molecular dynamics simulation studies, and biological evaluation. J Enzyme Inhib Med Chem 2024; 39:2295241. [PMID: 38134358 PMCID: PMC10763849 DOI: 10.1080/14756366.2023.2295241] [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: 08/29/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide. Nowadays, owing to the complex mechanism of tumorigenesis, simultaneous inhibition of multiple targets is an important anticancer strategy. Recent studies have demonstrated receptor tyrosine kinase AXL (AXL) and histone deacetylase 2 (HDAC2) are closely associated with colorectal cancer. Herein, we identified five hit compounds concurrently targeting AXL and HDAC2 using virtual screening. Inhibitory experiments revealed these hit compounds potently inhibited AXL and HDAC2 in the nanomolar range. Among them, Hit-3 showed the strongest inhibitory effects which were better than that of the positive control groups. Additionally, MD assays showed that Hit-3 could bind stably to the AXL and HDAC2 active pockets. Further MTT assays demonstrated that Hit-3 showed potent anti-proliferative activity. Most importantly, Hit-3 exhibited significant in vivo antitumor efficacy in xenograft models. Collectively, this study is the first discovery of dual-targeting AXL/HDAC2 inhibitors for colorectal cancer treatment.
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Affiliation(s)
- Xiao Qiao
- Department of Gastroenterology, The Affiliated Huaian Hospital of Xuzhou Medical University, Huaian, China
| | - Xiangyu Wu
- Department of Gastroenterology, The Affiliated Huaian Hospital of Xuzhou Medical University, Huaian, China
| | - Shutong Chen
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Huilian Hua
- Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Yan Zhang
- Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
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36
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Kim JD, Lee AR, Moon DH, Chung YU, Hong SY, Cho HJ, Kang TH, Jang YH, Sohn MH, Seong BL, Seo SU. Efficacy of genotype-matched vaccine against re-emerging genotype V Japanese encephalitis virus. Emerg Microbes Infect 2024; 13:2343910. [PMID: 38618740 PMCID: PMC11060017 DOI: 10.1080/22221751.2024.2343910] [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: 01/01/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
Japanese encephalitis (JE), caused by the Japanese encephalitis virus (JEV), is a highly threatening disease with no specific treatment. Fortunately, the development of vaccines has enabled effective defense against JE. However, re-emerging genotype V (GV) JEV poses a challenge as current vaccines are genotype III (GIII)-based and provide suboptimal protection. Given the isolation of GV JEVs from Malaysia, China, and the Republic of Korea, there is a concern about the potential for a broader outbreak. Under the hypothesis that a GV-based vaccine is necessary for effective defense against GV JEV, we developed a pentameric recombinant antigen using cholera toxin B as a scaffold and mucosal adjuvant, which was conjugated with the E protein domain III of GV by genetic fusion. This GV-based vaccine antigen induced a more effective immune response in mice against GV JEV isolates compared to GIII-based antigen and efficiently protected animals from lethal challenges. Furthermore, a bivalent vaccine approach, inoculating simultaneously with GIII- and GV-based antigens, showed protective efficacy against both GIII and GV JEVs. This strategy presents a promising avenue for comprehensive protection in regions facing the threat of diverse JEV genotypes, including both prevalent GIII and GI as well as emerging GV strains.
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MESH Headings
- Encephalitis Virus, Japanese/genetics
- Encephalitis Virus, Japanese/immunology
- Encephalitis Virus, Japanese/classification
- Animals
- Genotype
- Encephalitis, Japanese/prevention & control
- Encephalitis, Japanese/immunology
- Encephalitis, Japanese/virology
- Japanese Encephalitis Vaccines/immunology
- Japanese Encephalitis Vaccines/administration & dosage
- Japanese Encephalitis Vaccines/genetics
- Mice
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Humans
- Mice, Inbred BALB C
- Female
- Antigens, Viral/immunology
- Antigens, Viral/genetics
- Vaccine Efficacy
- Cholera Toxin/genetics
- Cholera Toxin/immunology
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Affiliation(s)
- Jae-Deog Kim
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ah-Ra Lee
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dah-Hyun Moon
- The Interdisciplinary Graduate Program in Integrative Biotechnology & Translational Medicine, Yonsei University, Incheon, Republic of Korea
| | - Young-Uk Chung
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Su-Yeon Hong
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyo Je Cho
- Department of Biochemistry, Chungbuk National University, Cheongju, Republic of Korea
| | - Tae Hyun Kang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Yo Han Jang
- Department of Vaccine Biotechnology, Andong National University, Andong, Republic of Korea
| | - Myung Hyun Sohn
- Department of Pediatrics, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Baik-Lin Seong
- Department of Microbiology and Immunology, College of Medicine, Yonsei University, Seoul, Republic of Korea
- Vaccine Innovative Technology ALliance (VITAL)-Korea, Yonsei University, Seoul, Republic of Korea
| | - Sang-Uk Seo
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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37
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Shum MHH, Lee Y, Tam L, Xia H, Chung OLW, Guo Z, Lam TTY. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput Struct Biotechnol J 2024; 23:759-770. [PMID: 38304547 PMCID: PMC10831124 DOI: 10.1016/j.csbj.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.
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Affiliation(s)
- Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Yang Lee
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leighton Tam
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Hui Xia
- Department of Chemistry, South University of Science and Technology of China, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Oscar Lung-Wa Chung
- Department of Chemistry, South University of Science and Technology of China, China
| | - Zhihong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
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Foong YH, Caldwell B, Thorvaldsen JL, Krapp C, Mesaros CA, Zhou W, Kohli RM, Bartolomei MS. TET1 displays catalytic and non-catalytic functions in the adult mouse cortex. Epigenetics 2024; 19:2374979. [PMID: 38970823 PMCID: PMC11229741 DOI: 10.1080/15592294.2024.2374979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024] Open
Abstract
TET1/2/3 dioxygenases iteratively demethylate 5-methylcytosine, beginning with the formation of 5-hydroxymethylcytosine (5hmC). The post-mitotic brain maintains higher levels of 5hmC than most peripheral tissues, and TET1 ablation studies have underscored the critical role of TET1 in brain physiology. However, deletion of Tet1 precludes the disentangling of the catalytic and non-catalytic functions of TET1. Here, we dissect these functions of TET1 by comparing adult cortex of Tet1 wildtype (Tet1 WT), a novel Tet1 catalytically dead mutant (Tet1 HxD), and Tet1 knockout (Tet1 KO) mice. Using DNA methylation array, we uncover that Tet1 HxD and KO mutations perturb the methylation status of distinct subsets of CpG sites. Gene ontology (GO) analysis on specific differential 5hmC regions indicates that TET1's catalytic activity is linked to neuronal-specific functions. RNA-Seq further shows that Tet1 mutations predominantly impact the genes that are associated with alternative splicing. Lastly, we performed High-performance Liquid Chromatography Mass-Spectrometry lipidomics on WT and mutant cortices and uncover accumulation of lysophospholipids lysophosphatidylethanolamine and lysophosphatidylcholine in Tet1 HxD cortex. In summary, we show that Tet1 HxD does not completely phenocopy Tet1 KO, providing evidence that TET1 modulates distinct cortical functions through its catalytic and non-catalytic roles.
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Affiliation(s)
- Yee Hoon Foong
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Blake Caldwell
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Joanne L Thorvaldsen
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Christopher Krapp
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Clementina A Mesaros
- Translational Biomarkers Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wanding Zhou
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Children's Hospital of Philadelphia (CHOP), University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Smilow Center for Translational Rsearch, Philadelphia, PA, USA
| | - Rahul M Kohli
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Smilow Center for Translational Rsearch, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Perelman School of Medicine, Smilow Center for Translational Research, Philadelphia, PA, USA
- Penn Epigenetics Institute, Smilow Center for Translational Rsearch, Philadelphia, PA, USA
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39
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Zheng XJ, Chen Y, Yao L, Li XL, Sun D, Li YQ. Identification of new hub- ferroptosis-related genes in Lupus Nephritis. Autoimmunity 2024; 57:2319204. [PMID: 38409788 DOI: 10.1080/08916934.2024.2319204] [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: 10/26/2023] [Accepted: 02/11/2024] [Indexed: 02/28/2024]
Abstract
Background: Lupus Nephritis (LN) is the primary causation of kidney injury in systemic lupus erythematosus (SLE). Ferroptosis is a programmed cell death. Therefore, understanding the crosstalk between LN and ferroptosis is still a significant challenge. Methods: We obtained the expression profile of LN kidney biopsy samples from the Gene Expression Omnibus database and utilised the R-project software to identify differentially expressed genes (DEGs). Then, we conducted a functional correlation analysis. Ferroptosis-related genes (FRGs) and differentially expressed genes (DEGs) crossover to select FRGs with LN. Afterwards, we used CIBERSORT to assess the infiltration of immune cells in both LN tissues and healthy control samples. Finally, we performed immunohistochemistry on LN human renal tissue. Results: 10619 DEGs screened from the LN biopsy tissue were identified. 22 hub-ferroptosis-related genes with LN (FRGs-LN) were screened out. The CIBERSORT findings revealed that there were significant statistical differences in immune cells between healthy control samples and LN tissues. Immunohistochemistry further demonstrated a significant difference in HRAS, TFRC, ATM, and SRC expression in renal tissue between normal and control groups. Conclusion: We developed a signature that allowed us to identify 22 new biomarkers associated with FRGs-LN. These findings suggest new insights into the pathology and therapeutic potential of LN ferroptosis inhibitors and iron chelators.
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Affiliation(s)
- Xiao-Jie Zheng
- Department of Nephrology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ying Chen
- Department of Nephrology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Li Yao
- Department of Nephrology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiao-Li Li
- Department of Nephrology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Da Sun
- Department of Nephrology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yan-Qiu Li
- Department of Nephrology, The First Affiliated Hospital of China Medical University, Shenyang, China
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Wei Z, Shen H, Wang F, Huang W, Li X, Xu H, Zhu H, Guan J. Melatonin mediates intestinal barrier dysfunction and systemic inflammation in moderate-severe OSA patients. Ann Med 2024; 56:2361825. [PMID: 38973375 PMCID: PMC11232642 DOI: 10.1080/07853890.2024.2361825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/21/2024] [Indexed: 07/09/2024] Open
Abstract
BACKGROUND Intestinal barrier dysfunction and systemic inflammation are common in obstructive sleep apnoea (OSA). We aimed to investigate the role of melatonin, an anti-inflammatory mediator, in mediating the relationships between OSA, intestinal barrier dysfunction and systemic inflammation. METHODS Two hundred and thirty-five male participants who complained with sleep problems and underwent whole night polysomnography at our sleep centre between 2017 and 2018 were enrolled. Polysomnographic data, anthropometric measurements and biochemical indicators were collected. Serum melatonin, intestinal barrier function biomarker zonula occludens-1 (ZO-1) and inflammatory biomarkers C-reactive protein (CRP) with lipopolysaccharide (LPS) were detected. Spearman's correlation analysis assessed the correlations between sleep parameters, melatonin and biomarkers (ZO-1, LPS and CRP). Mediation analysis explored the effect of OSA on intestinal barrier dysfunction and systemic inflammation in moderate-severe OSA patients. RESULTS As OSA severity increased, serum melatonin decreased, whereas ZO-1, LPS and CRP increased. Spearman's correlation analysis showed that serum melatonin was significantly negatively correlated with ZO-1 (r = -0.19, p < .05) and LPS (r = -0.20, p < .05) in the moderate-OSA group; serum melatonin was significantly negatively correlated with ZO-1 (r = -0.46, p < .01), LPS (r = -0.35, p < .01) and CPR (r = -0.30, p < .05) in the severe-OSA group. Mediation analyses showed melatonin explain 36.12% and 35.38% of the effect of apnoea-hypopnea index (AHI) on ZO-1 and LPS in moderate to severe OSA patients. CONCLUSIONS Our study revealed that melatonin may be involved in mediating intestinal barrier dysfunction and systemic inflammation in moderate-to-severe OSA patients.
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Affiliation(s)
- Zhicheng Wei
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
- Otorhinolaryngology Institute of Shanghai Jiao Tong University, Shanghai, China
| | - Hangdong Shen
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
- Otorhinolaryngology Institute of Shanghai Jiao Tong University, Shanghai, China
| | - Fan Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
- Otorhinolaryngology Institute of Shanghai Jiao Tong University, Shanghai, China
| | - Weijun Huang
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
- Otorhinolaryngology Institute of Shanghai Jiao Tong University, Shanghai, China
| | - Xinyi Li
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
- Otorhinolaryngology Institute of Shanghai Jiao Tong University, Shanghai, China
| | - Huajun Xu
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
- Otorhinolaryngology Institute of Shanghai Jiao Tong University, Shanghai, China
| | - Huaming Zhu
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
- Otorhinolaryngology Institute of Shanghai Jiao Tong University, Shanghai, China
| | - Jian Guan
- Department of Otorhinolaryngology Head and Neck Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, China
- Otorhinolaryngology Institute of Shanghai Jiao Tong University, Shanghai, China
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Nguyen LTT, Park AR, Van Le V, Hwang I, Kim JC. Exploration of a multifunctional biocontrol agent Streptomyces sp. JCK-8055 for the management of apple fire blight. Appl Microbiol Biotechnol 2024; 108:49. [PMID: 38183485 DOI: 10.1007/s00253-023-12874-w] [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: 06/14/2023] [Revised: 10/17/2023] [Accepted: 11/05/2023] [Indexed: 01/08/2024]
Abstract
Apple fire blight, caused by the bacterium Erwinia amylovora, is a devastating disease of apple and pear trees. Biological control methods have attracted much attention from researchers to manage plant diseases as they are eco-friendly and viable alternatives to synthetic pesticides. Herein, we isolated Streptomyces sp. JCK-8055 from the root of pepper and investigated its mechanisms of action against E. amylovora. Streptomyces sp. JCK-8055 produced aureothricin and thiolutin, which antagonistically affect E. amylovora. JCK-8055 and its two active metabolites have a broad-spectrum in vitro activity against various phytopathogenic bacteria and fungi. They also effectively suppressed tomato bacterial wilt and apple fire blight in in vivo experiments. Interestingly, JCK-8055 colonizes roots as a tomato seed coating and induces apple leaf shedding at the abscission zone, ultimately halting the growth of pathogenic bacteria. Additionally, JCK-8055 can produce the plant growth regulation hormone indole-3-acetic acid (IAA) and hydrolytic enzymes, including protease, gelatinase, and cellulase. JCK-8055 treatment also triggered the expression of salicylate (SA) and jasmonate (JA) signaling pathway marker genes, such as PR1, PR2, and PR3. Overall, our findings demonstrate that Streptomyces sp. JCK-8055 can control a wide range of plant diseases, particularly apple fire blight, through a combination of mechanisms such as antibiosis and induced resistance, highlighting its excellent potential as a biocontrol agent. KEY POINTS: • JCK-8055 produces the systemic antimicrobial metabolites, aureothricin, and thiolutin. • JCK-8055 treatment upregulates PR gene expression in apple plants against E. amylovora. • JCK-8055 controls plant diseases with antibiotics and induced resistance.
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Affiliation(s)
- Loan Thi Thanh Nguyen
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ae Ran Park
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Ve Van Le
- Cell Factory Research Centre, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Inmin Hwang
- Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, College of Agriculture and Life Sciences, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61186, Republic of Korea.
- JAN153 Biotech Incorporated, Gwangju, 61186, Republic of Korea.
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Ferjancic Z, Bihelovic F, Vulovic B, Matovic R, Trmcic M, Jankovic A, Pavlovic M, Djurkovic F, Prodanovic R, Djurdjevic Djelmas A, Kalicanin N, Zlatovic M, Sladic D, Vallet T, Vignuzzi M, Saicic RN. Development of iminosugar-based glycosidase inhibitors as drug candidates for SARS-CoV-2 virus via molecular modelling and in vitro studies. J Enzyme Inhib Med Chem 2024; 39:2289007. [PMID: 38086763 DOI: 10.1080/14756366.2023.2289007] [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: 07/12/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
We developed new iminosugar-based glycosidase inhibitors against SARS-CoV-2. Known drugs (miglustat, migalastat, miglitol, and swainsonine) were chosen as lead compounds to develop three classes of glycosidase inhibitors (α-glucosidase, α-galactosidase, and mannosidase). Molecular modelling of the lead compounds, synthesis of the compounds with the highest docking scores, enzyme inhibition tests, and in vitro antiviral assays afforded rationally designed inhibitors. Two highly active α-glucosidase inhibitors were discovered, where one of them is the most potent iminosugar-based anti-SARS-CoV-2 agent to date (EC90 = 1.94 µM in A549-ACE2 cells against Omicron BA.1 strain). However, galactosidase inhibitors did not exhibit antiviral activity, whereas mannosidase inhibitors were both active and cytotoxic. As our iminosugar-based drug candidates act by a host-directed mechanism, they should be more resilient to drug resistance. Moreover, this strategy could be extended to identify potential drug candidates for other viral infections.
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Affiliation(s)
| | - Filip Bihelovic
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Bojan Vulovic
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Radomir Matovic
- University of Belgrade-Institute of Chemistry, Technology and Metallurgy, Belgrade, Serbia
| | - Milena Trmcic
- Innovation Centre of the Faculty of Chemistry, Belgrade, Serbia
| | - Aleksandar Jankovic
- University of Belgrade-Institute of Chemistry, Technology and Metallurgy, Belgrade, Serbia
| | - Milos Pavlovic
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Filip Djurkovic
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | | | | | - Nevena Kalicanin
- University of Belgrade-Institute of Chemistry, Technology and Metallurgy, Belgrade, Serbia
| | - Mario Zlatovic
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Dusan Sladic
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Thomas Vallet
- Institut Pasteur, Center for the Viral Populations and Pathogenesis, Paris, France
| | - Marco Vignuzzi
- Institut Pasteur, Center for the Viral Populations and Pathogenesis, Paris, France
- A*STAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Radomir N Saicic
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
- Serbian Academy of Sciences and Arts, Belgrade, Serbia
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Yadav S, Chander S, Gupta A, Kataria N, Khoo KS. Biogenic engineered zinc oxide nanoparticle for sulfur black dye removal from contaminated wastewater: comparative optimization, simulation modeling, and isotherms. Bioengineered 2024; 15:2325721. [PMID: 38465722 PMCID: PMC10936635 DOI: 10.1080/21655979.2024.2325721] [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: 12/09/2023] [Accepted: 02/27/2024] [Indexed: 03/12/2024] Open
Abstract
This research work aimed to isolate and culture the bacterium Bacillus paramycoides for biogenic fabrication of zinc oxide nanoparticles, specifically ZnO and ZnO-ME nanoparticles (nanoparticles fabricated from bacterial extracts only - ZnO, and from bacterial cell mass including extract - ZnO-ME). SEM investigation revealed the spherical-shaped NPs with 22.33 and 39 nm in size for ZnO and ZnO-ME, respectively. The Brunauer, Emmett, and Teller (BET) studies revealed mesoporous structure with pore diameters of 13.839 and 13.88 nm and surface area of 7.617 and 33.635 m2/gm for ZnO and ZnO-ME, respectively. Various parameters for the adsorption of sulfur black dye onto both ZnO and ZnO-ME were screened and optimized using Plackett-Burman Design (PBD), Full Factorial Design (FFD) and Central Composite Design (CCD). The results of the optimization modeling study revealed that FFD yielded the most predictable and best-fitting results among all the models studied, with R2 values of 0.998 for ZnO and 0.993 for ZnO-ME. Notably, ZnO-ME exhibited a greater dye removal efficiency 80% than ZnO i.e., 71%, it may be due to the presence of amorphous carbon on the surface of ZnO-ME. Among the various isothermal models, the Freundlich model displayed the strongest correlation with the dye removal data, confirming the multilayer adsorption of dye on both nanoparticles and supporting physisorption. Therefore, ZnO and ZnO-ME nanoparticles have been proven as potential tools for mitigating environmental impacts associated with dye-containing wastewater.
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Affiliation(s)
- Sangita Yadav
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science & Technology, Hisar, Haryana, India
| | - Subhash Chander
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science & Technology, Hisar, Haryana, India
| | - Asha Gupta
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science & Technology, Hisar, Haryana, India
| | - Navish Kataria
- Department of Environmental Science and Engineering, J. C. Bose University of Science and Technology, YMCA, Faridabad, Haryana, India
| | - Kuan Shiong Khoo
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan, Taiwan
- Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
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De Luca V, Giovannuzzi S, Capasso C, Supuran CT. Cloning, expression, and purification of an α-carbonic anhydrase from Toxoplasma gondii to unveil its kinetic parameters and anion inhibition profile. J Enzyme Inhib Med Chem 2024; 39:2346523. [PMID: 38847581 PMCID: PMC11163988 DOI: 10.1080/14756366.2024.2346523] [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: 02/22/2024] [Accepted: 04/17/2024] [Indexed: 06/12/2024] Open
Abstract
Toxoplasmosis, induced by the intracellular parasite Toxoplasma gondii, holds considerable implications for global health. While treatment options primarily focusing on folate pathway enzymes have notable limitations, current research endeavours concentrate on pinpointing specific metabolic pathways vital for parasite survival. Carbonic anhydrases (CAs, EC 4.2.1.1) have emerged as potential drug targets due to their role in fundamental reactions critical for various protozoan metabolic processes. Within T. gondii, the Carbonic Anhydrase-Related Protein (TgCA_RP) plays a pivotal role in rhoptry biogenesis. Notably, α-CA (TcCA) from another protozoan, Trypanosoma cruzi, exhibited considerable susceptibility to classical CA inhibitors (CAIs) such as anions, sulphonamides, thiols, and hydroxamates. Here, the recombinant DNA technology was employed to synthesise and clone the identified gene in the T. gondii genome, which encodes an α-CA protein (Tg_CA), with the purpose of heterologously overexpressing its corresponding protein. Tg_CA kinetic constants were determined, and its inhibition patterns explored with inorganic metal-complexing compounds, which are relevant for rational compound design. The significance of this study lies in the potential development of innovative therapeutic strategies that disrupt the vital metabolic pathways crucial for T. gondii survival and virulence. This research may lead to the development of targeted treatments, offering new approaches to manage toxoplasmosis.
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Affiliation(s)
- Viviana De Luca
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, Naples, Italy
| | - Simone Giovannuzzi
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, Naples, Italy
| | - Claudiu T. Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
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Nocentini A, Di Porzio A, Bonardi A, Bazzicalupi C, Petreni A, Biver T, Bua S, Marzano S, Amato J, Pagano B, Iaccarino N, De Tito S, Amente S, Supuran CT, Randazzo A, Gratteri P. Development of a multi-targeted chemotherapeutic approach based on G-quadruplex stabilisation and carbonic anhydrase inhibition. J Enzyme Inhib Med Chem 2024; 39:2366236. [PMID: 38905127 PMCID: PMC11195807 DOI: 10.1080/14756366.2024.2366236] [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: 02/23/2024] [Accepted: 06/02/2024] [Indexed: 06/23/2024] Open
Abstract
A novel class of compounds designed to hit two anti-tumour targets, G-quadruplex structures and human carbonic anhydrases (hCAs) IX and XII is proposed. The induction/stabilisation of G-quadruplex structures by small molecules has emerged as an anticancer strategy, disrupting telomere maintenance and reducing oncogene expression. hCAs IX and XII are well-established anti-tumour targets, upregulated in many hypoxic tumours and contributing to metastasis. The ligands reported feature a berberine G-quadruplex stabiliser scaffold connected to a moiety inhibiting hCAs IX and XII. In vitro experiments showed that our compounds selectively stabilise G-quadruplex structures and inhibit hCAs IX and XII. The crystal structure of a telomeric G-quadruplex in complex with one of these ligands was obtained, shedding light on the ligand/target interaction mode. The most promising ligands showed significant cytotoxicity against CA IX-positive HeLa cancer cells in hypoxia, and the ability to stabilise G-quadruplexes within tumour cells.
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Affiliation(s)
- Alessio Nocentini
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Anna Di Porzio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Alessandro Bonardi
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Carla Bazzicalupi
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Andrea Petreni
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Silvia Bua
- Research Institute of the University of Bucharest (ICUB), Bucharest, Romania
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Stefano De Tito
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Claudiu T. Supuran
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Paola Gratteri
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
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McElroy CA, Ihms EC, Kumar Yadav D, Holmquist ML, Wadhwa V, Wysocki VH, Gollnick P, Foster MP. Solution structure, dynamics and tetrahedral assembly of Anti-TRAP, a homo-trimeric triskelion-shaped regulator of tryptophan biosynthesis in Bacillus subtilis. J Struct Biol X 2024; 10:100103. [PMID: 39035014 PMCID: PMC11255114 DOI: 10.1016/j.yjsbx.2024.100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 05/08/2024] [Accepted: 06/10/2024] [Indexed: 07/23/2024] Open
Abstract
Cellular production of tryptophan is metabolically expensive and tightly regulated. The small Bacillus subtilis zinc binding Anti-TRAP protein (AT), which is the product of the yczA/rtpA gene, is upregulated in response to accumulating levels of uncharged tRNATrp through a T-box antitermination mechanism. AT binds to the undecameric axially symmetric ring-shaped protein TRAP (trp RNA Binding Attenuation Protein), thereby preventing it from binding to the trp leader RNA. This reverses the inhibitory effect of TRAP on transcription and translation of the trp operon. AT principally adopts two symmetric oligomeric states, a trimer (AT3) featuring three-fold axial symmetry or a dodecamer (AT12) comprising a tetrahedral assembly of trimers, whereas only the trimeric form binds and inhibits TRAP. We apply native mass spectrometry (nMS) and small-angle x-ray scattering (SAXS), together with analytical ultracentrifugation (AUC) to monitor the pH and concentration-dependent equilibrium between the trimeric and dodecameric structural forms of AT. In addition, we use solution nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of AT3, while heteronuclear 15N relaxation measurements on both oligomeric forms of AT provide insights into the dynamic properties of binding-active AT3 and binding-inactive AT12, with implications for TRAP binding and inhibition.
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Affiliation(s)
- Craig A. McElroy
- Ohio State Biochemistry Program, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Elihu C. Ihms
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, USA
| | - Deepak Kumar Yadav
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Melody L. Holmquist
- Ohio State Biochemistry Program, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vibhuti Wadhwa
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- National Resource for Native MS-Guided Structural Biology, USA
| | - Paul Gollnick
- Department of Biological Sciences, State University of New York, Buffalo, NY 14260, USA
| | - Mark P. Foster
- Ohio State Biochemistry Program, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Program, USA
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Xie H, Su YT, Bu QT, Li YP, Zhao QW, Du YL, Li YQ. Stepwise increase of fidaxomicin in an engineered heterologous host Streptomyces albus through multi-level metabolic engineering. Synth Syst Biotechnol 2024; 9:766-774. [PMID: 39021363 PMCID: PMC11253128 DOI: 10.1016/j.synbio.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/28/2024] [Accepted: 06/12/2024] [Indexed: 07/20/2024] Open
Abstract
The anti-Clostridium difficile infection (CDI) drug fidaxomicin is a natural polyketide metabolite mainly produced by Micromonosporaceae, such as Actinoplanes deccanensis, Dactylosporangium aurantiacum, and Micromonospora echinospora. In the present study, we employed a stepwise strategy by combining heterologous expression, chassis construction, promoter engineering, activator and transporters overexpression, and optimization of fermentation media for high-level production of fidaxomicin. The maximum yield of 384 mg/L fidaxomicin was achieved with engineered Streptomyces albus D7-VHb in 5 L-tank bioreactor, and it was approximately 15-fold higher than the native strain Actinoplanes deccanensis YP-1 with higher strain stability and growth rate. This study developed an enhanced chassis strain, and for the first time, achieved the heterologous synthesis of fidaxomicin through a combinatorial metabolic engineering strategy.
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Affiliation(s)
- Huang Xie
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yi-Ting Su
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qing-Ting Bu
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yue-Ping Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qing-Wei Zhao
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yi-Ling Du
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yong-Quan Li
- First Affiliated Hospital and Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
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Zhang X, Feng Y, Hua Y, Zhang C, Fang B, Long X, Pan Y, Gao B, Zhang JZH, Li L, Ni H, Zhang L. Biosynthesis of eriodictyol in citrus waster by endowing P450BM3 activity of naringenin hydroxylation. Appl Microbiol Biotechnol 2024; 108:84. [PMID: 38189953 PMCID: PMC10787690 DOI: 10.1007/s00253-023-12867-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/20/2023] [Accepted: 10/13/2023] [Indexed: 01/09/2024]
Abstract
The flavonoid naringenin is abundantly present in pomelo peels, and the unprocessed naringenin in wastes is not friendly for the environment once discarded directly. Fortunately, the hydroxylated product of eriodictyol from naringenin exhibits remarkable antioxidant and anticancer properties. The P450s was suggested promising for the bioconversion of the flavonoids, but less naturally existed P450s show hydroxylation activity to C3' of the naringenin. By well analyzing the catalytic mechanism and the conformations of the naringenin in P450, we proposed that the intermediate Cmpd I ((porphyrin)Fe = O) is more reasonable as key conformation for the hydrolyzation, and the distance between C3'/C5' of naringenin to the O atom of CmpdI determines the hydroxylating activity for the naringenin. Thus, the "flying kite model" that gradually drags the C-H bond of the substrate to the O atom of CmpdI was put forward for rational design. With ab initio design, we successfully endowed the self-sufficient P450-BM3 hydroxylic activity to naringenin and obtained mutant M5-5, with kcat, Km, and kcat/Km values of 230.45 min-1, 310.48 µM, and 0.742 min-1 µM-1, respectively. Furthermore, the mutant M4186 was screened with kcat/Km of 4.28-fold highly improved than the reported M13. The M4186 also exhibited 62.57% yield of eriodictyol, more suitable for the industrial application. This study provided a theoretical guide for the rational design of P450s to the nonnative compounds. KEY POINTS: •The compound I is proposed as the starting point for the rational design of the P450BM3 •"Flying kite model" is proposed based on the distance between O of Cmpd I and C3'/C5' of naringenin •Mutant M15-5 with 1.6-fold of activity than M13 was obtained by ab initio modification.
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Affiliation(s)
- Xingyi Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Yinghui Feng
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Yuanzhe Hua
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Chuanxi Zhang
- Department of Micro/Nano Electronics, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bohuan Fang
- Department of Micro/Nano Electronics, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiang Long
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Yue Pan
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Bei Gao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Lijun Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Hui Ni
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China.
| | - Lujia Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China.
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Lima AJF, Hajdu KL, Abdo L, Batista-Silva LR, de Oliveira Andrade C, Correia EM, Aragão EAA, Bonamino MH, Lourenzoni MR. In silico and in vivo analysis reveal impact of c-Myc tag in FMC63 scFv-CD19 protein interface and CAR-T cell efficacy. Comput Struct Biotechnol J 2024; 23:2375-2387. [PMID: 38873646 PMCID: PMC11170440 DOI: 10.1016/j.csbj.2024.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/06/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024] Open
Abstract
Anti-CD19 CAR-T cell therapy represents a breakthrough in the treatment of B-cell malignancies, and it is expected that this therapy modality will soon cover a range of solid tumors as well. Therefore, a universal cheap and sensitive method to detect CAR expression is of foremost importance. One possibility is the use of epitope tags such as c-Myc, HA or FLAG tags attached to the CAR extracellular domain, however, it is important to determine whether these tags can influence binding of the CAR with its target molecule. Here, we conducted in-silico structural modelling of an FMC63-based anti-CD19 single-chain variable fragment (scFv) with and without a c-Myc peptide tag added to the N-terminus portion and performed molecular dynamics simulation of the scFv with the CD19 target. We show that the c-Myc tag presence in the N-terminus portion does not affect the scFv's structural equilibrium and grants more stability to the scFv. However, intermolecular interaction potential (IIP) analysis reveals that the tag can approximate the complementarity-determining regions (CDRs) present in the scFv and cause steric impediment, potentially disturbing interaction with the CD19 protein. We then tested this possibility with CAR-T cells generated from human donors in a Nalm-6 leukemia model, showing that CAR-T cells with the c-Myc tag have overall worse antitumor activity, which was also observed when the tag was added to the C-terminus position. Ultimately, our results suggest that tag addition is an important aspect of CAR design and can influence CAR-T cell function, therefore its use should be carefully considered.
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Affiliation(s)
- Ana Julia Ferreira Lima
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Oswaldo Cruz Foundation Ceará (Fiocruz-CE), São José, Precabura, 61773-270 Eusébio, Ceará, Brazil
- Federal University of Ceará (UFC), Pici campus (Building 873), 60440-970 Fortaleza, Ceará, Brazil
| | - Karina Lobo Hajdu
- Cell and Gene Therapy Program, Research coordination - Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Luiza Abdo
- Cell and Gene Therapy Program, Research coordination - Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | | | - Clara de Oliveira Andrade
- Cell and Gene Therapy Program, Research coordination - Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Eduardo Mannarino Correia
- Cell and Gene Therapy Program, Research coordination - Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | | | - Martín Hernán Bonamino
- Cell and Gene Therapy Program, Research coordination - Brazilian National Cancer Institute, Rio de Janeiro, Brazil
- Vice - Presidency of Research and Biological Collections (VPPCB), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Marcos Roberto Lourenzoni
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Oswaldo Cruz Foundation Ceará (Fiocruz-CE), São José, Precabura, 61773-270 Eusébio, Ceará, Brazil
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50
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Du X, Zhao M, Jiang L, Pang L, Wang J, Lv Y, Yao C, Wu R. A mini-review on gene delivery technique using nanoparticles-mediated photoporation induced by nanosecond pulsed laser. Drug Deliv 2024; 31:2306231. [PMID: 38245895 PMCID: PMC10802807 DOI: 10.1080/10717544.2024.2306231] [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: 04/06/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Nanosecond pulsed laser induced photoporation has gained increasing attention from scholars as an effective method for delivering the membrane-impermeable extracellular materials into living cells. Compared with femtosecond laser, nanosecond laser has the advantage of high throughput and low costs. It also has a higher delivery efficiency than continuous wave laser. Here, we provide an extensive overview of current status of nanosecond pulsed laser induced photoporation, covering the photoporation mechanism as well as various factors that impact the delivery efficiency of photoporation. Additionally, we discuss various techniques for achieving photoporation, such as direct photoporation, nanoparticles-mediated photoporation and plasmonic substrates mediated photoporation. Among these techniques, nanoparticles-mediated photoporation is the most promising approach for potential clinical application. Studies have already been reported to safely destruct the vitreous opacities in vivo by nanosecond laser induced vapor nanobubble. Finally, we discuss the potential of nanosecond laser induced phototoporation for future clinical applications, particularly in the areas of skin and ophthalmic pathologies. We hope this review can inspire scientists to further improve nanosecond laser induced photoporation and facilitate its eventual clinical application.
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Affiliation(s)
- Xiaofan Du
- National Local Joint Engineering Research Center of Precise Surgery & Regenerative Medicine, Shaanxi Pro-vincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
- Center for Regenerative and Reconstructive Medicine, Med-X Institute, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Meng Zhao
- National Local Joint Engineering Research Center of Precise Surgery & Regenerative Medicine, Shaanxi Pro-vincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
- Center for Regenerative and Reconstructive Medicine, Med-X Institute, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Le Jiang
- National Local Joint Engineering Research Center of Precise Surgery & Regenerative Medicine, Shaanxi Pro-vincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
- Center for Regenerative and Reconstructive Medicine, Med-X Institute, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Lihui Pang
- National Local Joint Engineering Research Center of Precise Surgery & Regenerative Medicine, Shaanxi Pro-vincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
- Center for Regenerative and Reconstructive Medicine, Med-X Institute, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Jing Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Institute of Biomedical Photonics and Sensing, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Yi Lv
- National Local Joint Engineering Research Center of Precise Surgery & Regenerative Medicine, Shaanxi Pro-vincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
- Center for Regenerative and Reconstructive Medicine, Med-X Institute, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Cuiping Yao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Institute of Biomedical Photonics and Sensing, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
| | - Rongqian Wu
- National Local Joint Engineering Research Center of Precise Surgery & Regenerative Medicine, Shaanxi Pro-vincial Center for Regenerative Medicine and Surgical Engineering, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
- Center for Regenerative and Reconstructive Medicine, Med-X Institute, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi Province, China
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