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Fu W, Shentu C, Chen D, Qiu J, Zong C, Yu H, Zhang Y, Chen Y, Liu X, Xu T. Network pharmacology combined with affinity ultrafiltration to elucidate the potential compounds of Shaoyao Gancao Fuzi Decoction for the treatment of rheumatoid arthritis. J Ethnopharmacol 2024; 330:118268. [PMID: 38677569 DOI: 10.1016/j.jep.2024.118268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/13/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Shaoyao Gancao Fuzi Decoction (SGFD), has been employed for thousands of years in the treatment of rheumatoid arthritis (RA) with remarkable clinical efficacy. However, the material basis underlying the effectiveness of SGFD still remains unclear. AIM OF THE REVIEW This study aims to elucidate the material basis of SGFD through the application of network pharmacology and biological affinity ultrafiltration. RESULTS UPLC-Q-TOF-MS/MS was employed to characterize the components in SGFD, the identified 145 chemical components were mainly categorized into alkaloids, flavonoids, triterpenoids, and monoterpenoids according to the structures. Network pharmacology method was utilized to identify potential targets and signaling pathways of SGFD in the RA treatment, and the anti-inflammatory and anti-RA effects of SGFD were validated through in vivo and in vitro experiments. Moreover, as the significant node in the pharmacology network, TNF-α, a classical therapeutic target in RA, was subsequent employed to screen the interacting compounds in SGFD via affinity ultrafiltration screening method, 6 active molecules (i.e.,glycyrrhizic acid, paeoniflorin, formononetin, isoliquiritigenin, benzoyl mesaconitine, and glycyrrhetinic acid) were exhibited significant interactions. Finally, the significant anti-inflammatory and anti-TNF-α effects of these compounds were validated at the cellular level. CONCLUSIONS In conclusion, this study comprehensively elucidates the pharmacodynamic material basis of SGFD, offering a practical reference model for the systematic investigation of traditional Chinese medicine formulas.
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Affiliation(s)
- Weiliang Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Chengyu Shentu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Dan Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Junjie Qiu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, No. 366, Xingke Road, Lingxi Town, Cangnan County, Wenzhou, Zhejiang Province, 325899, China
| | - Chuhong Zong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Hengyuan Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Yiwei Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China
| | - Yong Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, No. 366, Xingke Road, Lingxi Town, Cangnan County, Wenzhou, Zhejiang Province, 325899, China
| | - Xuesong Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, No. 366, Xingke Road, Lingxi Town, Cangnan County, Wenzhou, Zhejiang Province, 325899, China.
| | - Tengfei Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou, Zhejiang Province, 310058, China; Cangnan County Qiushi Innovation Research Institute of Traditional Chinese Medicine, No. 366, Xingke Road, Lingxi Town, Cangnan County, Wenzhou, Zhejiang Province, 325899, China.
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2
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Fralish Z, Chen A, Khan S, Zhou P, Reker D. The landscape of small-molecule prodrugs. Nat Rev Drug Discov 2024; 23:365-380. [PMID: 38565913 DOI: 10.1038/s41573-024-00914-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2024] [Indexed: 04/04/2024]
Abstract
Prodrugs are derivatives with superior properties compared with the parent active pharmaceutical ingredient (API), which undergo biotransformation after administration to generate the API in situ. Although sharing this general characteristic, prodrugs encompass a wide range of different chemical structures, therapeutic indications and properties. Here we provide the first holistic analysis of the current landscape of approved prodrugs using cheminformatics and data science approaches to reveal trends in prodrug development. We highlight rationales that underlie prodrug design, their indications, mechanisms of API release, the chemistry of promoieties added to APIs to form prodrugs and the market impact of prodrugs. On the basis of this analysis, we discuss strengths and limitations of current prodrug approaches and suggest areas for future development.
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Affiliation(s)
- Zachary Fralish
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Ashley Chen
- Department of Computer Science, Duke University, Durham, NC, USA
| | | | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Daniel Reker
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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3
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Kuznetsova V, Coogan Á, Botov D, Gromova Y, Ushakova EV, Gun'ko YK. Expanding the Horizons of Machine Learning in Nanomaterials to Chiral Nanostructures. Adv Mater 2024; 36:e2308912. [PMID: 38241607 DOI: 10.1002/adma.202308912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/10/2024] [Indexed: 01/21/2024]
Abstract
Machine learning holds significant research potential in the field of nanotechnology, enabling nanomaterial structure and property predictions, facilitating materials design and discovery, and reducing the need for time-consuming and labor-intensive experiments and simulations. In contrast to their achiral counterparts, the application of machine learning for chiral nanomaterials is still in its infancy, with a limited number of publications to date. This is despite the great potential of machine learning to advance the development of new sustainable chiral materials with high values of optical activity, circularly polarized luminescence, and enantioselectivity, as well as for the analysis of structural chirality by electron microscopy. In this review, an analysis of machine learning methods used for studying achiral nanomaterials is provided, subsequently offering guidance on adapting and extending this work to chiral nanomaterials. An overview of chiral nanomaterials within the framework of synthesis-structure-property-application relationships is presented and insights on how to leverage machine learning for the study of these highly complex relationships are provided. Some key recent publications are reviewed and discussed on the application of machine learning for chiral nanomaterials. Finally, the review captures the key achievements, ongoing challenges, and the prospective outlook for this very important research field.
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Affiliation(s)
- Vera Kuznetsova
- School of Chemistry, CRANN and AMBER Research Centres, Trinity College Dublin, College Green, Dublin, D02 PN40, Ireland
| | - Áine Coogan
- School of Chemistry, CRANN and AMBER Research Centres, Trinity College Dublin, College Green, Dublin, D02 PN40, Ireland
| | - Dmitry Botov
- Everypixel Media Innovation Group, 021 Fillmore St., PMB 15, San Francisco, CA, 94115, USA
- Neapolis University Pafos, 2 Danais Avenue, Pafos, 8042, Cyprus
| | - Yulia Gromova
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St., Cambridge, MA, 02138, USA
| | - Elena V Ushakova
- Department of Materials Science and Engineering, and Centre for Functional Photonics (CFP), City University of Hong Kong, Hong Kong SAR, 999077, P. R. China
| | - Yurii K Gun'ko
- School of Chemistry, CRANN and AMBER Research Centres, Trinity College Dublin, College Green, Dublin, D02 PN40, Ireland
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4
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Wang C, Wu Y, Xue Y, Zou L, Huang Y, Zhang P, Ji J. Combinatorial discovery of antibacterials via a feature-fusion based machine learning workflow. Chem Sci 2024; 15:6044-6052. [PMID: 38665528 PMCID: PMC11041243 DOI: 10.1039/d3sc06441g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/08/2024] [Indexed: 04/28/2024] Open
Abstract
The discovery of new antibacterials within the vast chemical space is crucial in combating drug-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA). However, the traditional approach of screening the entire chemical library in an ergodic manner can be laborious and time-consuming. Machine learning-assisted screening of antibacterials alleviates the exploration effort but suffers from the lack of reliable and related datasets. To address these challenges, we devised a combinatorial library comprising over 110 000 candidates based on the Ugi reaction. A focused library was subsequently generated through uniform sampling of the entire library to narrow down the preliminary screening scale. A novel feature-fusion architecture called the latent space constraint neural network was developed which incorporated both fingerprint and physicochemical molecular descriptors to predict the antibacterial properties. This integration allowed the model to leverage the complementary information provided by these descriptors and improve the accuracy of predictions. Three lead compounds that demonstrated excellent efficacy against MRSA while alleviating drug resistance were identified. This workflow highlights the integration of machine learning with the combinatorial chemical library to expedite high-quality data collection and extensive data mining for antibacterial screening.
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Affiliation(s)
- Cong Wang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
- International Research Center for X Polymers, International Campus, Zhejiang University Haining Zhejiang 314400 PR China
| | - Yuhui Wu
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
- International Research Center for X Polymers, International Campus, Zhejiang University Haining Zhejiang 314400 PR China
| | - Yunfan Xue
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
| | - Lingyun Zou
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
| | - Yue Huang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
| | - Peng Zhang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
- International Research Center for X Polymers, International Campus, Zhejiang University Haining Zhejiang 314400 PR China
- State Key Laboratory of Transvascular Implantation Devices, Zhejiang University Hangzhou Zhejiang 311202 P. R. China
| | - Jian Ji
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Hangzhou Zhejiang 310027 PR China
- International Research Center for X Polymers, International Campus, Zhejiang University Haining Zhejiang 314400 PR China
- State Key Laboratory of Transvascular Implantation Devices, Zhejiang University Hangzhou Zhejiang 311202 P. R. China
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5
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Capponi S, Wang S. AI in cellular engineering and reprogramming. Biophys J 2024:S0006-3495(24)00245-5. [PMID: 38576162 DOI: 10.1016/j.bpj.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/19/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024] Open
Abstract
During the last decade, artificial intelligence (AI) has increasingly been applied in biophysics and related fields, including cellular engineering and reprogramming, offering novel approaches to understand, manipulate, and control cellular function. The potential of AI lies in its ability to analyze complex datasets and generate predictive models. AI algorithms can process large amounts of data from single-cell genomics and multiomic technologies, allowing researchers to gain mechanistic insights into the control of cell identity and function. By integrating and interpreting these complex datasets, AI can help identify key molecular events and regulatory pathways involved in cellular reprogramming. This knowledge can inform the design of precision engineering strategies, such as the development of new transcription factor and signaling molecule cocktails, to manipulate cell identity and drive authentic cell fate across lineage boundaries. Furthermore, when used in combination with computational methods, AI can accelerate and improve the analysis and understanding of the intricate relationships between genes, proteins, and cellular processes. In this review article, we explore the current state of AI applications in biophysics with a specific focus on cellular engineering and reprogramming. Then, we showcase a couple of recent applications where we combined machine learning with experimental and computational techniques. Finally, we briefly discuss the challenges and prospects of AI in cellular engineering and reprogramming, emphasizing the potential of these technologies to revolutionize our ability to engineer cells for a variety of applications, from disease modeling and drug discovery to regenerative medicine and biomanufacturing.
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Affiliation(s)
- Sara Capponi
- IBM Almaden Research Center, San Jose, California; Center for Cellular Construction, San Francisco, California.
| | - Shangying Wang
- Bay Area Institute of Science, Altos Labs, Redwood City, California.
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Li Z, Song P, Li G, Han Y, Ren X, Bai L, Su J. AI energized hydrogel design, optimization and application in biomedicine. Mater Today Bio 2024; 25:101014. [PMID: 38464497 PMCID: PMC10924066 DOI: 10.1016/j.mtbio.2024.101014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/12/2024] Open
Abstract
Traditional hydrogel design and optimization methods usually rely on repeated experiments, which is time-consuming and expensive, resulting in a slow-moving of advanced hydrogel development. With the rapid development of artificial intelligence (AI) technology and increasing material data, AI-energized design and optimization of hydrogels for biomedical applications has emerged as a revolutionary breakthrough in materials science. This review begins by outlining the history of AI and the potential advantages of using AI in the design and optimization of hydrogels, such as prediction and optimization of properties, multi-attribute optimization, high-throughput screening, automated material discovery, optimizing experimental design, and etc. Then, we focus on the various applications of hydrogels supported by AI technology in biomedicine, including drug delivery, bio-inks for advanced manufacturing, tissue repair, and biosensors, so as to provide a clear and comprehensive understanding of researchers in this field. Finally, we discuss the future directions and prospects, and provide a new perspective for the research and development of novel hydrogel materials for biomedical applications.
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Affiliation(s)
- Zuhao Li
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Peiran Song
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Guangfeng Li
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Yafei Han
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Xiaoxiang Ren
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Long Bai
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Jiacan Su
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
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7
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Kim J, Eygeris Y, Ryals RC, Jozić A, Sahay G. Strategies for non-viral vectors targeting organs beyond the liver. Nat Nanotechnol 2024; 19:428-447. [PMID: 38151642 DOI: 10.1038/s41565-023-01563-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 11/01/2023] [Indexed: 12/29/2023]
Abstract
In recent years, nanoparticles have evolved to a clinical modality to deliver diverse nucleic acids. Rising interest in nanomedicines comes from proven safety and efficacy profiles established by continuous efforts to optimize physicochemical properties and endosomal escape. However, despite their transformative impact on the pharmaceutical industry, the clinical use of non-viral nucleic acid delivery is limited to hepatic diseases and vaccines due to liver accumulation. Overcoming liver tropism of nanoparticles is vital to meet clinical needs in other organs. Understanding the anatomical structure and physiological features of various organs would help to identify potential strategies for fine-tuning nanoparticle characteristics. In this Review, we discuss the source of liver tropism of non-viral vectors, present a brief overview of biological structure, processes and barriers in select organs, highlight approaches available to reach non-liver targets, and discuss techniques to accelerate the discovery of non-hepatic therapies.
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Affiliation(s)
- Jeonghwan Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR, USA
- College of Pharmacy, Yeungnam University, Gyeongsan, South Korea
| | - Yulia Eygeris
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR, USA
| | - Renee C Ryals
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, OR, USA
| | - Antony Jozić
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR, USA
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR, USA.
- Department of Ophthalmology, Casey Eye Institute, Oregon Health and Science University, Portland, OR, USA.
- Department of Biomedical Engineering, Robertson Life Sciences Building, Oregon Health and Science University, Portland, OR, USA.
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8
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Zheng J, Wang R, Wang Y. New concepts drive the development of delivery tools for sustainable treatment of diabetic complications. Biomed Pharmacother 2024; 171:116206. [PMID: 38278022 DOI: 10.1016/j.biopha.2024.116206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024] Open
Abstract
Diabetic complications, especially diabetic retinopathy, diabetic nephropathy and painful diabetic neuropathy, account for a large portion of patients with diabetes and display rising global prevalence. They are the leading causes of blindness, kidney failure and hypersensitivity to pain caused by diabetes. Current approved therapeutics against the diabetic complications are few and exhibit limited efficacy. The enhanced cell-specificity, stability, biocompatibility, and loading capacity of drugs are essential for the mitigation of diabetic complications. In the article, we have critically discussed the recent studies over the past two years in material sciences and biochemistry. The insightful concepts in these studies drive the development of novel nanoparticles and mesenchymal stem cells-derived extracellular vesicles to meet the need for treatment of diabetic complications. Their underlying biochemical principles, advantages and limitations have been in-depth analyzed. The nanoparticles discussed in the article include double-headed nanodelivery system, nanozyme, ESC-HCM-B system, soft polymer nanostars, tetrahedral DNA nanostructures and hydrogels. They ameliorate the diabetic complication through attenuation of inflammation, apoptosis and restoration of metabolic homeostasis. Moreover, mesenchymal stem cell-derived extracellular vesicles efficiently deliver therapeutic proteins to the retinal cells to suppress the angiogenesis, inflammation, apoptosis and oxidative stress to reverse diabetic retinopathy. Collectively, we provide a critical discussion on the concept, mechanism and therapeutic applicability of new delivery tools to treat these three devastating diabetic complications.
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Affiliation(s)
- Jianan Zheng
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Ru Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, China.
| | - Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, China.
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9
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Hamilton S, Kingston BR. Applying artificial intelligence and computational modeling to nanomedicine. Curr Opin Biotechnol 2024; 85:103043. [PMID: 38091874 DOI: 10.1016/j.copbio.2023.103043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Achieving specific and targeted delivery of nanomedicines to diseased tissues is a major challenge. This is because the process of designing, formulating, testing, and selecting a nanoparticle delivery vehicle for a specific disease target is governed by complex multivariate interactions. Computational modeling and artificial intelligence are well-suited for analyzing and modeling large multivariate datasets in short periods of time. Computational approaches can be applied to help design nanomedicine formulations, interpret nanoparticle-biological interactions, and create models from high-throughput screening techniques to improve the selection of the ideal nanoparticle carrier. In the future, many steps in the nanomedicine development process will be done computationally, reducing the number of experiments and time needed to select the ideal nanomedicine formulation.
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Affiliation(s)
- Sean Hamilton
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S. Moody Avenue, Portland, OR 97201, United States
| | - Benjamin R Kingston
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S. Moody Avenue, Portland, OR 97201, United States.
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Castillo Henríquez L, Bahloul B, Alhareth K, Oyoun F, Frejková M, Kostka L, Etrych T, Kalshoven L, Guillaume A, Mignet N, Corvis Y. Step-By-Step Standardization of the Bottom-Up Semi-Automated Nanocrystallization of Pharmaceuticals: A Quality By Design and Design of Experiments Joint Approach. Small 2024:e2306054. [PMID: 38299478 DOI: 10.1002/smll.202306054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/10/2023] [Indexed: 02/02/2024]
Abstract
Nanosized drug crystals have been reported with enhanced apparent solubility, bioavailability, and therapeutic efficacy compared to microcrystal materials, which are not suitable for parenteral administration. However, nanocrystal design and development by bottom-up approaches are challenging, especially considering the non-standardized process parameters in the injection step. This work aims to present a systematic step-by-step approach through Quality-by-Design (QbD) and Design of Experiments (DoE) for synthesizing drug nanocrystals by a semi-automated nanoprecipitation method. Curcumin is used as a drug model due to its well-known poor water solubility (0.6 µg mL-1 , 25 °C). Formal and informal risk assessment tools allow identifying the critical factors. A fractional factorial 24-1 screening design evaluates their impact on the average size and polydispersity of nanocrystals. The optimization of significant factors is done by a Central Composite Design. This response surface methodology supports the rational design of the nanocrystals, identifying and exploring the design space. The proposed joint approach leads to a reproducible, robust, and stable nanocrystalline preparation of 316 nm with a PdI of 0.217 in compliance with the quality profile. An orthogonal approach for particle size and polydispersity characterization allows discarding the formation of aggregates. Overall, the synergy between advanced data analysis and semi-automated standardized nanocrystallization of drugs is highlighted.
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Affiliation(s)
- Luis Castillo Henríquez
- CNRS, INSERM, Chemical and Biological Technologies for Health Group (UTCBS), Université Paris Cité, Paris, F-75006, France
| | - Badr Bahloul
- Drug Development Laboratory LR12ES09, Faculty of Pharmacy, University of Monastir, Monastir, 5060, Tunisia
| | - Khair Alhareth
- CNRS, INSERM, Chemical and Biological Technologies for Health Group (UTCBS), Université Paris Cité, Paris, F-75006, France
| | - Feras Oyoun
- CNRS, INSERM, Chemical and Biological Technologies for Health Group (UTCBS), Université Paris Cité, Paris, F-75006, France
| | - Markéta Frejková
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského náměstí 2, Prague, CZ-162 06, Czech Republic
| | - Libor Kostka
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského náměstí 2, Prague, CZ-162 06, Czech Republic
| | - Tomáš Etrych
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského náměstí 2, Prague, CZ-162 06, Czech Republic
| | - Luc Kalshoven
- EuroAPI France, Particle Engineering and Sizing Department, Vertolaye, F-63480, France
| | - Alain Guillaume
- EuroAPI France, Particle Engineering and Sizing Department, Vertolaye, F-63480, France
| | - Nathalie Mignet
- CNRS, INSERM, Chemical and Biological Technologies for Health Group (UTCBS), Université Paris Cité, Paris, F-75006, France
| | - Yohann Corvis
- CNRS, INSERM, Chemical and Biological Technologies for Health Group (UTCBS), Université Paris Cité, Paris, F-75006, France
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Tao J, Guo F, Sun Y, Sun X, Hu Y. Self-Assembled Nanotubes Based on Chiral H 8-BINOL Modified with 1,2,3-Triazole to Recognize Bi 3+ Efficiently by ICT Mechanism. Micromachines (Basel) 2024; 15:163. [PMID: 38276862 PMCID: PMC10821062 DOI: 10.3390/mi15010163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 01/27/2024]
Abstract
A novel fluorescent "off" probe R-β-D-1 containing a 1,2,3-triazole moiety was obtained by the Click reaction with azidoglucose using H8-BINOL as a substrate, and the structure was characterized by 1H NMR and 13C NMR and ESI-MS analysis. The fluorescence properties of R-β-D-1 in methanol were investigated, and it was found that R-β-D-1 could be selectively fluorescently quenched by Bi3+ in the recognition of 19 metal ions and basic cations. The recognition process of Bi3+ by R-β-D-1 was also investigated by fluorescence spectroscopy, SEM, AFM, etc. The complex pattern of R-β-D-1 with Bi3+ was determined by Job's curve as 1 + 1, and the binding constant Ka of R-β-D-1 and Bi3+ was valued by the Benesi-Hildebrand equation as 1.01 × 104 M-1, indicating that the binding force of R-β-D-1 and Bi3+ was medium. The lowest detection limit (LOD) of the self-assembled H8-BINOL derivative for Bi3+ was up to 0.065 µM. The mechanism for the recognition of Bi3+ by the sensor R-β-D-1 may be the intramolecular charge transfer effect (ICT), which was attributed to the fact that the N-3 of the triazole readily serves as an electron acceptor while the incorporation of Bi3+ serves as an electron donor, and the two readily undergo coordination leading to the quenching of fluorescence. The recognition mechanism and recognition site could be verified by DFT calculation and CDD (Charge Density Difference).
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Affiliation(s)
- Jisheng Tao
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, Nanchang 330013, China; (J.T.); (F.G.)
| | - Fang Guo
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, Nanchang 330013, China; (J.T.); (F.G.)
| | - Yue Sun
- State Key Laboratory of Molecular Engineering of Polymers, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials iChEM, Department of Chemistry, Fudan University, Shanghai 200433, China;
| | - Xiaoxia Sun
- Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, Nanchang 330013, China; (J.T.); (F.G.)
| | - Yu Hu
- College of Chemistry, Nanchang University, Nanchang 330031, China
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12
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Matharoo N, Mohd H, Michniak-Kohn B. Transferosomes as a transdermal drug delivery system: Dermal kinetics and recent developments. Wiley Interdiscip Rev Nanomed Nanobiotechnol 2024; 16:e1918. [PMID: 37527953 DOI: 10.1002/wnan.1918] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 08/03/2023]
Abstract
The development of innovative approaches to deliver medications has been growing now for the last few decades and generates a growing interest in the dermatopharmaceutical field. Transdermal drug delivery in particular, remains an attractive alternative route for many therapeutics. However, due to the limitations posed by the barrier properties of the stratum corneum, the delivery of many pharmaceutical dosage forms remains a challenge. Most successful therapies using the transdermal route have been ones containing smaller lipophilic molecules with molecular weights of a few hundred Daltons. To overcome these limitations of size and lipophilicity of the drugs, transferosomes have emerged as a successful tool for transdermal delivery of a variety of therapeutics including hydrophilic actives, larger molecules, peptides, proteins, and nucleic acids. Transferosomes exhibit a flexible structure and higher surface hydrophilicity which both play a critical role in the transport of drugs and other solutes using hydration gradients as a driving force to deliver the molecules into and across the skin. This results in enhanced overall permeation as well as controlled release of the drug in the skin layers. Additionally, the physical-chemical properties of the transferosomes provide increased stability by preventing degradation of the actives by oxidation, light, and temperature. Here, we present the history of transferosomes from solid lipid nanoparticles and liposomes, their physical-chemical properties, dermal kinetics, and their recent advances as marketed dosage forms. This article is categorized under: Biology-Inspired Nanomaterials > Lipid-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Namrata Matharoo
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Center for Dermal Research, Life Sciences Building, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Hana Mohd
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Center for Dermal Research, Life Sciences Building, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Bozena Michniak-Kohn
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
- Center for Dermal Research, Life Sciences Building, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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13
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Lasota M, Jankowski D, Wiśniewska A, Sarna M, Kaczor-Kamińska M, Misterka A, Szczepaniak M, Dulińska-Litewka J, Górecki A. The Potential of Congo Red Supplied Aggregates of Multitargeted Tyrosine Kinase Inhibitor (Sorafenib, BAY-43-9006) in Enhancing Therapeutic Impact on Bladder Cancer. Int J Mol Sci 2023; 25:269. [PMID: 38203437 PMCID: PMC10779242 DOI: 10.3390/ijms25010269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Bladder cancer is a common malignancy associated with high recurrence rates and potential progression to invasive forms. Sorafenib, a multi-targeted tyrosine kinase inhibitor, has shown promise in anti-cancer therapy, but its cytotoxicity to normal cells and aggregation in solution limits its clinical application. To address these challenges, we investigated the formation of supramolecular aggregates of sorafenib with Congo red (CR), a bis-azo dye known for its supramolecular interaction. We analyzed different mole ratios of CR-sorafenib aggregates and evaluated their effects on bladder cancer cells of varying levels of malignancy. In addition, we also evaluated the effect of the test compounds on normal uroepithelial cells. Our results demonstrated that sorafenib inhibits the proliferation of bladder cancer cells and induces apoptosis in a dose-dependent manner. However, high concentrations of sorafenib also showed cytotoxicity to normal uroepithelial cells. In contrast, the CR-BAY aggregates exhibited reduced cytotoxicity to normal cells while maintaining anti-cancer activity. The aggregates inhibited cancer cell migration and invasion, suggesting their potential for metastasis prevention. Dynamic light scattering and UV-VIS measurements confirmed the formation of stable co-aggregates with distinctive spectral properties. These CR-sorafenib aggregates may provide a promising approach to targeted therapy with reduced cytotoxicity and improved stability for drug delivery in bladder cancer treatment. This work shows that the drug-excipient aggregates proposed and described so far, as Congo red-sorafenib, can be a real step forward in anti-cancer therapies.
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Affiliation(s)
- Małgorzata Lasota
- Chair of Medical Biochemistry, Jagiellonian University Medical College, Kopernika 7, 31-034 Krakow, Poland; (M.K.-K.); (A.M.); (J.D.-L.)
- SSG of Targeted Therapy and Supramolecular Systems, Jagiellonian University Medical College, Kopernika 7, 31-034 Krakow, Poland; (D.J.); (M.S.)
| | - Daniel Jankowski
- SSG of Targeted Therapy and Supramolecular Systems, Jagiellonian University Medical College, Kopernika 7, 31-034 Krakow, Poland; (D.J.); (M.S.)
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland;
| | - Anna Wiśniewska
- Chair of Pharmacology, Faculty of Medicine, Jagiellonian University Medical College, Grzegórzecka 16, 31-531 Krakow, Poland;
| | - Michał Sarna
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland;
| | - Marta Kaczor-Kamińska
- Chair of Medical Biochemistry, Jagiellonian University Medical College, Kopernika 7, 31-034 Krakow, Poland; (M.K.-K.); (A.M.); (J.D.-L.)
| | - Anna Misterka
- Chair of Medical Biochemistry, Jagiellonian University Medical College, Kopernika 7, 31-034 Krakow, Poland; (M.K.-K.); (A.M.); (J.D.-L.)
- SSG of Targeted Therapy and Supramolecular Systems, Jagiellonian University Medical College, Kopernika 7, 31-034 Krakow, Poland; (D.J.); (M.S.)
| | - Mateusz Szczepaniak
- SSG of Targeted Therapy and Supramolecular Systems, Jagiellonian University Medical College, Kopernika 7, 31-034 Krakow, Poland; (D.J.); (M.S.)
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland;
| | - Joanna Dulińska-Litewka
- Chair of Medical Biochemistry, Jagiellonian University Medical College, Kopernika 7, 31-034 Krakow, Poland; (M.K.-K.); (A.M.); (J.D.-L.)
| | - Andrzej Górecki
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland;
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14
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Chen C, Wu Y, Wang ST, Berisha N, Manzari MT, Vogt K, Gang O, Heller DA. Fragment-based drug nanoaggregation reveals drivers of self-assembly. Nat Commun 2023; 14:8340. [PMID: 38097573 PMCID: PMC10721832 DOI: 10.1038/s41467-023-43560-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
Drug nanoaggregates are particles that can deleteriously cause false positive results during drug screening efforts, but alternatively, they may be used to improve pharmacokinetics when developed for drug delivery purposes. The structural features of molecules that drive nanoaggregate formation remain elusive, however, and the prediction of intracellular aggregation and rational design of nanoaggregate-based carriers are still challenging. We investigate nanoaggregate self-assembly mechanisms using small molecule fragments to identify the critical molecular forces that contribute to self-assembly. We find that aromatic groups and hydrogen bond acceptors/donors are essential for nanoaggregate formation, suggesting that both π-π stacking and hydrogen bonding are drivers of nanoaggregation. We apply structure-assembly-relationship analysis to the drug sorafenib and discover that nanoaggregate formation can be predicted entirely using drug fragment substructures. We also find that drug nanoaggregates are stabilized in an amorphous core-shell structure. These findings demonstrate that rational design can address intracellular aggregation and pharmacologic/delivery challenges in conventional and fragment-based drug development processes.
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Affiliation(s)
- Chen Chen
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - You Wu
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Shih-Ting Wang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Naxhije Berisha
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- The Graduate Center of the City University of New York, New York, NY, 10016, USA
- Department of Chemistry, Hunter College, City University of New York, New York, 10065, USA
| | - Mandana T Manzari
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Kaleidoscope Technologies, Inc., New York, NY, 10003, USA
| | - Kristen Vogt
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Oleg Gang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027, USA
| | - Daniel A Heller
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, 10065, USA.
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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15
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Hoseini B, Jaafari MR, Golabpour A, Momtazi-Borojeni AA, Karimi M, Eslami S. Application of ensemble machine learning approach to assess the factors affecting size and polydispersity index of liposomal nanoparticles. Sci Rep 2023; 13:18012. [PMID: 37865639 PMCID: PMC10590434 DOI: 10.1038/s41598-023-43689-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/27/2023] [Indexed: 10/23/2023] Open
Abstract
Liposome nanoparticles have emerged as promising drug delivery systems due to their unique properties. Assessing particle size and polydispersity index (PDI) is critical for evaluating the quality of these liposomal nanoparticles. However, optimizing these parameters in a laboratory setting is both costly and time-consuming. This study aimed to apply a machine learning technique to assess the impact of specific factors, including sonication time, extrusion temperature, and compositions, on the size and PDI of liposomal nanoparticles. Liposomal solutions were prepared and subjected to sonication with varying values for these parameters. Two compositions: (A) HSPC:DPPG:Chol:DSPE-mPEG2000 at 55:5:35:5 molar ratio and (B) HSPC:Chol:DSPE-mPEG2000 at 55:40:5 molar ratio, were made using remote loading method. Ensemble learning (EL), a machine learning technique, was employed using the Least-squares boosting (LSBoost) algorithm to accurately model the data. The dataset was randomly split into training and testing sets, with 70% allocated for training. The LSBoost algorithm achieved mean absolute errors of 1.652 and 0.0105 for modeling the size and PDI, respectively. Under conditions where the temperature was set at approximately 60 °C, our EL model predicted a minimum particle size of 116.53 nm for composition (A) with a sonication time of approximately 30 min. Similarly, for composition (B), the model predicted a minimum particle size of 129.97 nm with sonication times of approximately 30 or 55 min. In most instances, a PDI of less than 0.2 was achieved. These results highlight the significant impact of optimizing independent factors on the characteristics of liposomal nanoparticles and demonstrate the potential of EL as a decision support system for identifying the best liposomal formulation. We recommend further studies to explore the effects of other independent factors, such as lipid composition and surfactants, on liposomal nanoparticle characteristics.
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Affiliation(s)
- Benyamin Hoseini
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahmoud Reza Jaafari
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amin Golabpour
- Department of Health Information Technology, School of Allied Medical Sciences, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Amir Abbas Momtazi-Borojeni
- Department of Medical Biotechnology, School of Medicine, Neyshabur University of Medical Sciences, Neyshabur, Iran
- Healthy Ageing Research Centre, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Maryam Karimi
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, USA
| | - Saeid Eslami
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Informatics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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16
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Zhou L, Yi W, Zhang Z, Shan X, Zhao Z, Sun X, Wang J, Wang H, Jiang H, Zheng M, Wang D, Li Y. STING agonist-boosted mRNA immunization via intelligent design of nanovaccines for enhancing cancer immunotherapy. Natl Sci Rev 2023; 10:nwad214. [PMID: 37693123 PMCID: PMC10484175 DOI: 10.1093/nsr/nwad214] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 07/03/2023] [Accepted: 07/24/2023] [Indexed: 09/12/2023] Open
Abstract
Messenger RNA (mRNA) vaccine is revolutionizing the methodology of immunization in cancer. However, mRNA immunization is drastically limited by multistage biological barriers including poor lymphatic transport, rapid clearance, catalytic hydrolysis, insufficient cellular entry and endosome entrapment. Herein, we design a mRNA nanovaccine based on intelligent design to overcome these obstacles. Highly efficient nanovaccines are carried out with machine learning techniques from datasets of various nanocarriers, ensuring successful delivery of mRNA antigen and cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) to targets. It activates stimulator of interferon genes (STING), promotes mRNA-encoded antigen presentation and boosts antitumour immunity in vivo, thus inhibiting tumour growth and ensuring long-term survival of tumour-bearing mice. This work provides a feasible and safe strategy to facilitate STING agonist-synergized mRNA immunization, with great translational potential for enhancing cancer immunotherapy.
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Affiliation(s)
- Lei Zhou
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Wenzhe Yi
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Univerisity of Chinese Academy of Sciences, Beijing 100049, China
| | - Zehong Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Univerisity of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoting Shan
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Univerisity of Chinese Academy of Sciences, Beijing 100049, China
| | - Zitong Zhao
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiangshi Sun
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jue Wang
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Univerisity of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Wang
- China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Univerisity of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Univerisity of Chinese Academy of Sciences, Beijing 100049, China
| | - Dangge Wang
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Yaping Li
- State Key Laboratory of Drug Research & Center of Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Univerisity of Chinese Academy of Sciences, Beijing 100049, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai 264000, China
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17
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Xiang Y, Tang YH, Lin G, Reker D. Interpretable Molecular Property Predictions Using Marginalized Graph Kernels. J Chem Inf Model 2023; 63:4633-4640. [PMID: 37504964 DOI: 10.1021/acs.jcim.3c00396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Marginalized graph kernels have shown competitive performance in molecular machine learning tasks but currently lack measures of interpretability, which are important to improve trust in the models, detect biases, and inform molecular optimization campaigns. We here conceive and implement two interpretability measures for Gaussian process regression using a marginalized graph kernel (GPR-MGK) to quantify (1) the contribution of specific training data to the prediction and (2) the contribution of specific nodes of the graph to the prediction. We demonstrate the applicability of these interpretability measures for molecular property prediction. We compare GPR-MGK to graph neural networks on four logic and two real-world toxicology data sets and find that the atomic attribution of GPR-MGK generally outperforms the atomic attribution of graph neural networks. We also perform a detailed molecular attribution analysis using the FreeSolv data set, showing how molecules in the training set influence machine learning predictions and why Morgan fingerprints perform poorly on this data set. This is the first systematic examination of the interpretability of GPR-MGK and thereby is an important step in the further maturation of marginalized graph kernel methods for interpretable molecular predictions.
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Affiliation(s)
- Yan Xiang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27705, United States
| | - Yu-Hang Tang
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Guang Lin
- Department of Mathematics & School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Daniel Reker
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27705, United States
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18
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Azagury DM, Gluck BF, Harris Y, Avrutin Y, Niezni D, Sason H, Shamay Y. Prediction of cancer nanomedicines self-assembled from meta-synergistic drug pairs. J Control Release 2023; 360:418-432. [PMID: 37406821 DOI: 10.1016/j.jconrel.2023.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 06/07/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
Combination therapy is widely used in cancer medicine due to the benefits of drug synergy and the reduction of acquired resistance. To minimize emergent toxicities, nanomedicines containing drug combinations are being developed, and they have shown encouraging results. However, developing multi-drug loaded nanoparticles is highly complex and lacks predictability. Previously, it was shown that single drugs can self-assemble with near-infrared dye, IR783, to form cancer-targeted nanoparticles. A structure-based predictive model showed that only 4% of the drug space self-assembles with IR783. Here, we mapped the self-assembly outcomes of 77 small molecule drugs and drug pairs with IR783. We found that the small molecule drug space can be divided into five types, and type-1 drugs self-assemble with three out of four possible drug types that do not form stable nanoparticles. To predict the self-assembly outcome of any drug pair, we developed a machine learning model based on decision trees, which was trained and tested with F1-scores of 89.3% and 87.2%, respectively. We used literature text mining to capture drug pairs with biological synergy together with synergistic chemical self-assembly and generated a database with 1985 drug pairs for 70 cancers. We developed an online search tool to identify cancer-specific, meta-synergistic drug pairs (both chemical and biological synergism) and validated three different pairs in vitro. Lastly, we discovered a novel meta-synergistic pair, bortezomib-cabozantinib, which formed stable nanoparticles with improved biodistribution, efficacy, and reduced toxicity, even over single drugs, in an in vivo model of head and neck cancer.
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Affiliation(s)
- Dana Meron Azagury
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Ben Friedmann Gluck
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel; Faculty of Electrical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yuval Harris
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yulia Avrutin
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Danna Niezni
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Hagit Sason
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yosi Shamay
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
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19
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Yi Y, An HW, Wang H. Intelligent Biomaterialomics: Molecular Design, Manufacturing, and Biomedical Applications. Adv Mater 2023:e2305099. [PMID: 37490938 DOI: 10.1002/adma.202305099] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/14/2023] [Indexed: 07/27/2023]
Abstract
Materialomics integrates experiment, theory, and computation in a high-throughput manner, and has changed the paradigm for the research and development of new functional materials. Recently, with the rapid development of high-throughput characterization and machine-learning technologies, the establishment of biomaterialomics that tackles complex physiological behaviors has become accessible. Breakthroughs in the clinical translation of nanoparticle-based therapeutics and vaccines have been observed. Herein, recent advances in biomaterials, including polymers, lipid-like materials, and peptides/proteins, discovered through high-throughput screening or machine learning-assisted methods, are summarized. The molecular design of structure-diversified libraries; high-throughput characterization, screening, and preparation; and, their applications in drug delivery and clinical translation are discussed in detail. Furthermore, the prospects and main challenges in future biomaterialomics and high-throughput screening development are highlighted.
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Affiliation(s)
- Yu Yi
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Haidian District, Beijing, 100190, China
| | - Hong-Wei An
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Haidian District, Beijing, 100190, China
| | - Hao Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Haidian District, Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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20
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Greenberg ZF, Graim KS, He M. Towards artificial intelligence-enabled extracellular vesicle precision drug delivery. Adv Drug Deliv Rev 2023:114974. [PMID: 37356623 DOI: 10.1016/j.addr.2023.114974] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Extracellular Vesicles (EVs), particularly exosomes, recently exploded into nanomedicine as an emerging drug delivery approach due to their superior biocompatibility, circulating stability, and bioavailability in vivo. However, EV heterogeneity makes molecular targeting precision a critical challenge. Deciphering key molecular drivers for controlling EV tissue targeting specificity is in great need. Artificial intelligence (AI) brings powerful prediction ability for guiding the rational design of engineered EVs in precision control for drug delivery. This review focuses on cutting-edge nano-delivery via integrating large-scale EV data with AI to develop AI-directed EV therapies and illuminate the clinical translation potential. We briefly review the current status of EVs in drug delivery, including the current frontier, limitations, and considerations to advance the field. Subsequently, we detail the future of AI in drug delivery and its impact on precision EV delivery. Our review discusses the current universal challenge of standardization and critical considerations when using AI combined with EVs for precision drug delivery. Finally, we will conclude this review with a perspective on future clinical translation led by a combined effort of AI and EV research.
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Affiliation(s)
- Zachary F Greenberg
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, 32610, USA
| | - Kiley S Graim
- Department of Computer & Information Science & Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, Florida, 32610, USA
| | - Mei He
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, 32610, USA.
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21
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Chen L, Wang Y. Interdisciplinary advances reshape the delivery tools for effective NASH treatment. Mol Metab 2023; 73:101730. [PMID: 37142161 DOI: 10.1016/j.molmet.2023.101730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Nonalcoholic steatohepatitis (NASH), a severe systemic and inflammatory subtype of nonalcoholic fatty liver disease, eventually develops into cirrhosis and hepatocellular carcinoma with few options for effective treatment. Currently potent small molecules identified in preclinical studies are confronted with adverse effects and long-term ineffectiveness in clinical trials. Nevertheless, highly specific delivery tools designed from interdisciplinary concepts may address the significant challenges by either effectively increasing the concentrations of drugs in target cell types, or selectively manipulating the gene expression in liver to resolve NASH. SCOPE OF REVIEW We focus on dissecting the detailed principles of the latest interdisciplinary advances and concepts that direct the design of future delivery tools to enhance the efficacy. Recent advances have indicated that cell and organelle-specific vehicles, non-coding RNA research (e.g. saRNA, hybrid miRNA) improve the specificity, while small extracellular vesicles and coacervates increase the cellular uptake of therapeutics. Moreover, strategies based on interdisciplinary advances drastically elevate drug loading capacity and delivery efficiency and ameliorate NASH and other liver diseases. MAJOR CONCLUSIONS The latest concepts and advances in chemistry, biochemistry and machine learning technology provide the framework and strategies for the design of more effective tools to treat NASH, other pivotal liver diseases and metabolic disorders.
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Affiliation(s)
- Linshan Chen
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health.
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22
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Donders EN, Slaughter KV, Dank C, Ganesh AN, Shoichet BK, Lautens M, Shoichet MS. Synthetic Ionizable Colloidal Drug Aggregates Enable Endosomal Disruption. Adv Sci (Weinh) 2023; 10:e2300311. [PMID: 36905240 PMCID: PMC10161099 DOI: 10.1002/advs.202300311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 05/06/2023]
Abstract
Colloidal drug aggregates enable the design of drug-rich nanoparticles; however, the efficacy of stabilized colloidal drug aggregates is limited by entrapment in the endo-lysosomal pathway. Although ionizable drugs are used to elicit lysosomal escape, this approach is hindered by toxicity associated with phospholipidosis. It is hypothesized that tuning the pKa of the drug would enable endosomal disruption while avoiding phospholipidosis and minimizing toxicity. To test this idea, 12 analogs of the nonionizable colloidal drug fulvestrant are synthesized with ionizable groups to enable pH-dependent endosomal disruption while maintaining bioactivity. Lipid-stabilized fulvestrant analog colloids are endocytosed by cancer cells, and the pKa of these ionizable colloids influenced the mechanism of endosomal and lysosomal disruption. Four fulvestrant analogs-those with pKa values between 5.1 and 5.7-disrupted endo-lysosomes without measurable phospholipidosis. Thus, by manipulating the pKa of colloid-forming drugs, a tunable and generalizable strategy for endosomal disruption is established.
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Affiliation(s)
- Eric N Donders
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON, M5S3E1, Canada
| | - Kai V Slaughter
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON, M5S3E1, Canada
| | - Christian Dank
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Ahil N Ganesh
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON, M5S3E1, Canada
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 Fourth Street, Mail Box 2550, San Francisco, CA, 94143, USA
| | - Mark Lautens
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Molly S Shoichet
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON, M5S3E1, Canada
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23
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Zhang Z, Wei X. Artificial intelligence-assisted selection and efficacy prediction of antineoplastic strategies for precision cancer therapy. Semin Cancer Biol 2023; 90:57-72. [PMID: 36796530 DOI: 10.1016/j.semcancer.2023.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/12/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023]
Abstract
The rapid development of artificial intelligence (AI) technologies in the context of the vast amount of collectable data obtained from high-throughput sequencing has led to an unprecedented understanding of cancer and accelerated the advent of a new era of clinical oncology with a tone of precision treatment and personalized medicine. However, the gains achieved by a variety of AI models in clinical oncology practice are far from what one would expect, and in particular, there are still many uncertainties in the selection of clinical treatment options that pose significant challenges to the application of AI in clinical oncology. In this review, we summarize emerging approaches, relevant datasets and open-source software of AI and show how to integrate them to address problems from clinical oncology and cancer research. We focus on the principles and procedures for identifying different antitumor strategies with the assistance of AI, including targeted cancer therapy, conventional cancer therapy, and cancer immunotherapy. In addition, we also highlight the current challenges and directions of AI in clinical oncology translation. Overall, we hope this article will provide researchers and clinicians with a deeper understanding of the role and implications of AI in precision cancer therapy, and help AI move more quickly into accepted cancer guidelines.
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Affiliation(s)
- Zhe Zhang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, PR China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, PR China.
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24
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Qu H, Chen H, Cheng W, Wang Y, Xia Y, Zhang L, Ma B, Hu R, Xue X. A Supramolecular Assembly Strategy for Hydrophilic Drug Delivery towards Synergistic Cancer Treatment. Acta Biomater 2023; 164:407-421. [PMID: 37088157 DOI: 10.1016/j.actbio.2023.04.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/24/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
To improve the drug loading, tumor targeting, and delivery simplicity of hydrophilic drugs, we propose a supramolecular assembly strategy that potentially benefits a wide range of hydrophilic drug delivery. Firstly, we choose a hydrophilic drug (tirapazamine) as a model drug to directly co-assemble with chlorin e6 (Ce6) at different molar ratios, and systematically evaluate the resultant Ce6-tirapazamine nanoparticles (CT NPs) in aspects of size distribution, polydispersity, morphology, optical properties and molecular dynamics simulation. Based on the assembling facts between Ce6 and tirapazamine, we summarize a plausible rule of the supramolecular assembly for hydrophilic drugs. To validate our findings, more drugs with increasing hydrophilicity, such as temozolomide, gemcitabine hydrochloride and 5-azacytidine, successfully co-assemble with Ce6 into nanostructures by following similar assembling behaviors, demonstrating that our assembling rule may guide a wide range of hydrophilic drug delivery. Next, the combination of Ce6 and tirapazamine was chosen as the representative to investigate the anti-tumor activities of the supramolecular assemblies. CT NPs showed synergistic anti-tumor efficacy, increased tumor accumulation and significant tumor progression and metastasis inhibition in tumor-bearing mice. We anticipate that the supramolecular assembly mechanism will provide broad guidance for developing easy-to-make but functional nanomedicines. STATEMENT OF SIGNIFICANCE: Although thousands of nanomedicines have been developed, only a few have been approved for clinical use. The manufacturing complexity significantly hinders the "bench-to-bed" translation of nanomedicines. Hence, we need to rethink how to conduct research on translational nanomedicines by avoiding more and more complex chemistry and complicated nanostructures. Here, we summarize a plausible rule according to multiple supramolecular assembly pairs and propose a supramolecular assembly strategy that can improve the drug loading, tumor targeting, and manufacturing simplicity of nanomedicine for hydrophilic drugs. The supramolecular assembly strategy would guide a broader range of drug delivery to provide a new paradigm for developing easy-to-make but multifunctional nanoformulations for synergistic cancer treatment.
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Affiliation(s)
- Haijing Qu
- School of Pharmacy, Shanghai Frontiers Science Center for Drug Target Identification and Drug Delivery, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Han Chen
- School of Pharmacy, Shanghai Frontiers Science Center for Drug Target Identification and Drug Delivery, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Cheng
- School of Pharmacy, Shanghai Frontiers Science Center for Drug Target Identification and Drug Delivery, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yanjun Wang
- School of Pharmacy, Shanghai Frontiers Science Center for Drug Target Identification and Drug Delivery, Shanghai Jiao Tong University, Shanghai, 200240, China; Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Centre for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai 200011, China
| | - Yangyang Xia
- School of Pharmacy, Shanghai Frontiers Science Center for Drug Target Identification and Drug Delivery, Shanghai Jiao Tong University, Shanghai, 200240, China; Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Centre for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai 200011, China
| | - Linghao Zhang
- School of Pharmacy, Shanghai Frontiers Science Center for Drug Target Identification and Drug Delivery, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Buyong Ma
- School of Pharmacy, Shanghai Frontiers Science Center for Drug Target Identification and Drug Delivery, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rong Hu
- Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Centre for Specialty Strategy Research of Shanghai Jiao Tong University China Hospital Development Institute, Shanghai 200011, China.
| | - Xiangdong Xue
- School of Pharmacy, Shanghai Frontiers Science Center for Drug Target Identification and Drug Delivery, Shanghai Jiao Tong University, Shanghai, 200240, China.
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25
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Trac N, Ashraf A, Giblin J, Prakash S, Mitragotri S, Chung EJ. Spotlight on Genetic Kidney Diseases: A Call for Drug Delivery and Nanomedicine Solutions. ACS Nano 2023; 17:6165-6177. [PMID: 36988207 PMCID: PMC10145694 DOI: 10.1021/acsnano.2c12140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Nanoparticles as drug delivery carriers have benefited diseases, including cancer, since the 1990s, and more recently, their promise to quickly and efficiently be mobilized to fight against global diseases such as in the COVID-19 pandemic have been proven. Despite these success stories, there are limited nanomedicine efforts for chronic kidney diseases (CKDs), which affect 844 million people worldwide and can be linked to a variety of genetic kidney diseases. In this Perspective, we provide a brief overview of the clinical status of genetic kidney diseases, background on kidney physiology and a summary of nanoparticle design that enable kidney access and targeting, and emerging technological strategies that can be applied for genetic kidney diseases, including rare and congenital kidney diseases. Finally, we conclude by discussing gaps in knowledge remaining in both genetic kidney diseases and kidney nanomedicine and collective efforts that are needed to bring together stakeholders from diverse expertise and industries to enable the development of the most relevant drug delivery strategies that can make an impact in the clinic.
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Affiliation(s)
- Noah Trac
- Department
of Biomedical Engineering, University of
Southern California, Los Angeles, California 90089, United States
| | - Anisa Ashraf
- Department
of Biomedical Engineering, University of
Southern California, Los Angeles, California 90089, United States
| | - Joshua Giblin
- Department
of Biomedical Engineering, University of
Southern California, Los Angeles, California 90089, United States
| | - Supriya Prakash
- John
A. Paulson School of Engineering & Applied Sciences, Harvard University, Allston, Massachusetts 02134, United States
- Wyss
Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Samir Mitragotri
- John
A. Paulson School of Engineering & Applied Sciences, Harvard University, Allston, Massachusetts 02134, United States
- Wyss
Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, United States
| | - Eun Ji Chung
- Department
of Biomedical Engineering, University of
Southern California, Los Angeles, California 90089, United States
- Division
of Nephrology and Hypertension, Department of Medicine, Keck School
of Medicine, University of Southern California, Los Angeles, California 90033, United States
- Norris
Comprehensive Cancer Center, University
of Southern California, Los Angeles, California 90033, United States
- Eli and Edythe
Broad Center for Regenerative Medicine and Stem Cell Research, Keck
School of Medicine, University of Southern
California, Los Angeles, California 90033, United States
- Division
of Vascular Surgery and Endovascular Therapy, Department of Surgery,
Keck School of Medicine, University of Southern
California, Los Angeles, California 90033, United States
- Mork
Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, United States
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26
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Owh C, Ho D, Loh XJ, Xue K. Towards machine learning for hydrogel drug delivery systems. Trends Biotechnol 2023; 41:476-479. [PMID: 36376126 DOI: 10.1016/j.tibtech.2022.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/15/2022]
Abstract
Hydrogel drug delivery system development is complex and laborious, and machine learning (ML) techniques hold great promise in accelerating the process. We highlight recent advances and strategies for data collection and ML, and we discuss the potential for and barriers to the broader use of ML for hydrogel drug delivery systems.
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Affiliation(s)
- Cally Owh
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, #08-03 Innovis, Singapore 138634, Singapore; Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Engineering Block 4, Singapore 117583, Singapore
| | - Dean Ho
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Engineering Block 4, Singapore 117583, Singapore; The N.1 Institute for Health (N.1), 28 Medical Drive, National University of Singapore (NUS), 116456, Singapore; The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, 28 Medical Drive, National University of Singapore (NUS), 116456, Singapore; The Department of Pharmacology, Yong Loo Lin School of Medicine, 16 Medical Drive, National University of Singapore (NUS), 117600, Singapore.
| | - Xian Jun Loh
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, #08-03 Innovis, Singapore 138634, Singapore; Department of Materials Science and Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117575, Singapore; School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, #01-30 General Office, Block N4.1, 639798, Singapore.
| | - Kun Xue
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, #08-03 Innovis, Singapore 138634, Singapore.
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27
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Xu K, Li S, Zhou Y, Gao X, Mei J, Liu Y. Application of Computing as a High-Practicability and -Efficiency Auxiliary Tool in Nanodrugs Discovery. Pharmaceutics 2023; 15:pharmaceutics15041064. [PMID: 37111551 PMCID: PMC10144056 DOI: 10.3390/pharmaceutics15041064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 03/28/2023] Open
Abstract
Research and development (R&D) of nanodrugs is a long, complex and uncertain process. Since the 1960s, computing has been used as an auxiliary tool in the field of drug discovery. Many cases have proven the practicability and efficiency of computing in drug discovery. Over the past decade, computing, especially model prediction and molecular simulation, has been gradually applied to nanodrug R&D, providing substantive solutions to many problems. Computing has made important contributions to promoting data-driven decision-making and reducing failure rates and time costs in discovery and development of nanodrugs. However, there are still a few articles to examine, and it is necessary to summarize the development of the research direction. In the review, we summarize application of computing in various stages of nanodrug R&D, including physicochemical properties and biological activities prediction, pharmacokinetics analysis, toxicological assessment and other related applications. Moreover, current challenges and future perspectives of the computing methods are also discussed, with a view to help computing become a high-practicability and -efficiency auxiliary tool in nanodrugs discovery and development.
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Affiliation(s)
- Ke Xu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilin Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangkai Zhou
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinglong Gao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Mei
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
- Correspondence: ; Tel.: +86-1082-545-526
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28
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Abstract
Biomimetic science has attracted great interest in the fields of chemistry, biology, materials science, and energy. Biomimetic mineralization is the process of synthesizing inorganic minerals under the control of organic molecules or biomolecules under mild conditions. Peptides are the motifs that constitute proteins, and can self-assemble into various hierarchical structures and show a high affinity for inorganic substances. Therefore, peptides can be used as building blocks for the synthesis of functional biomimetic materials. With the participation of peptides, the morphology, size, and composition of mineralized materials can be controlled precisely. Peptides not only provide well-defined templates for the nucleation and growth of inorganic nanomaterials but also have the potential to confer inorganic nanomaterials with high catalytic efficiency, selectivity, and biotherapeutic functions. In this review, we systematically summarize research progress in the formation mechanism, nanostructural manipulation, and applications of peptide-templated mineralized materials. These can further inspire researchers to design structurally complex and functionalized biomimetic materials with great promising applications.
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Affiliation(s)
- Qing Li
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Gong Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou Industrial Park, Suzhou 215123, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
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29
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Wang Y. Multidisciplinary Advances Address the Challenges in Developing Drugs against Transient Receptor Potential Channels to Treat Metabolic Disorders. ChemMedChem 2023; 18:e202200562. [PMID: 36530131 DOI: 10.1002/cmdc.202200562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/01/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
Transient receptor potential (TRP) channels are cation channels that regulate key physiological and pathological processes in response to a broad range of stimuli. Moreover, they systemically regulate the release of hormones, metabolic homeostasis, and complications of diabetes, which positions them as promising therapeutic targets to combat metabolic disorders. Nevertheless, there are significant challenges in the design of TRP ligands with high potency and durability. Herein we summarize the four challenges as hydrophobicity, selectivity, mono-target therapy, and interspecies discrepancy. We present 1134 TRP ligands with diversified modes of TRP-ligand interaction and provide a detailed discussion of the latest strategies, especially cryogenic electron microscopy (cryo-EM) and computational methods. We propose solutions to address the challenges with a critical analysis of advances in membrane partitioning, polypharmacology, biased agonism, and biochemical screening of transcriptional modulators. They are fueled by the breakthrough from cryo-EM, chemoinformatics and bioinformatics. The discussion is aimed to shed new light on designing next-generation drugs to treat obesity, diabetes and its complications, with optimal hydrophobicity, higher mode selectivity, multi-targeting and consistent activities between human and rodents.
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Affiliation(s)
- Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai, 200438, P. R. China.,Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, Shanghai, 200438, P. R. China
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30
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Tan P, Chen X, Zhang H, Wei Q, Luo K. Artificial intelligence aids in development of nanomedicines for cancer management. Semin Cancer Biol 2023; 89:61-75. [PMID: 36682438 DOI: 10.1016/j.semcancer.2023.01.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/28/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023]
Abstract
Over the last decade, the nanomedicine has experienced unprecedented development in diagnosis and management of diseases. A number of nanomedicines have been approved in clinical use, which has demonstrated the potential value of clinical transition of nanotechnology-modified medicines from bench to bedside. The application of artificial intelligence (AI) in development of nanotechnology-based products could transform the healthcare sector by realizing acquisition and analysis of large datasets, and tailoring precision nanomedicines for cancer management. AI-enabled nanotechnology could improve the accuracy of molecular profiling and early diagnosis of patients, and optimize the design pipeline of nanomedicines by tuning the properties of nanomedicines, achieving effective drug synergy, and decreasing the nanotoxicity, thereby, enhancing the targetability, personalized dosing and treatment potency of nanomedicines. Herein, the advances in AI-enabled nanomedicines in cancer management are elaborated and their application in diagnosis, monitoring and therapy as well in precision medicine development is discussed.
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Affiliation(s)
- Ping Tan
- Department of Urology, and Department of Radiology, Institute of Urology, and Huaxi MR Research Center (HMRRC), Animal Experimental Center, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaoting Chen
- Department of Urology, and Department of Radiology, Institute of Urology, and Huaxi MR Research Center (HMRRC), Animal Experimental Center, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hu Zhang
- Amgen Bioprocessing Centre, Keck Graduate Institute, Claremont, CA 91711, USA
| | - Qiang Wei
- Department of Urology, and Department of Radiology, Institute of Urology, and Huaxi MR Research Center (HMRRC), Animal Experimental Center, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Kui Luo
- Department of Urology, and Department of Radiology, Institute of Urology, and Huaxi MR Research Center (HMRRC), Animal Experimental Center, National Clinical Research Center for Geriatrics, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
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31
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Asmat-Campos D, de Oca-Vásquez GM, Rojas-Jaimes J, Delfín-Narciso D, Juárez-Cortijo L, Nazario-Naveda R, Batista Menezes D, Pereira R, de la Cruz MS. Cu 2O nanoparticles synthesized by green and chemical routes, and evaluation of their antibacterial and antifungal effect on functionalized textiles. Biotechnol Rep (Amst) 2023; 37:e00785. [PMID: 36785536 PMCID: PMC9918746 DOI: 10.1016/j.btre.2023.e00785] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
The potential for the application of metal-containing nanomaterials at the nanoscale promotes the opportunity to search for new methods for their elaboration, with special attention to those sustainable methods. In response to these challenges, we have investigated a new method for green synthesis of cuprous oxide nanoparticles (Cu2O NPs) using Myrciaria dubia juice as an organic reductant and, comparing it with chemical synthesis, evaluating in both cases the influence of the volume of the organic (juice) and chemical (ascorbic acid) reductants, for which a large number of techniques such as spectrophotometry, EDX spectrometry, TEM, SEM, DLS, FTIR spectroscopy have been used. Likewise, the nanomaterial with better morphological characteristics, stability, and size homogeneity has been applied in the functionalization of textiles by means of in situ and post-synthesis impregnation methods. The success of the synthesis process has been demonstrated by the antimicrobial activity (bacteria and fungi) of textiles impregnated with Cu2O NPs.
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Affiliation(s)
- David Asmat-Campos
- Universidad Privada del Norte, Dirección de Investigación, Innovación & Responsabilidad Social, Trujillo, Perú,Grupo de Investigación en Ciencias Aplicadas y Nuevas Tecnologías, Universidad Privada del Norte, Trujillo, Perú,Corresponding author.
| | | | - Jesús Rojas-Jaimes
- Universidad Privada del Norte, Dirección de Investigación, Innovación & Responsabilidad Social, Trujillo, Perú,Facultad de Ciencias de la Salud, Universidad Privada del Norte, Av. El Sol 461, San Juan de Lurigancho, Lima, 15434, Perú
| | - Daniel Delfín-Narciso
- Grupo de Investigación en Ciencias Aplicadas y Nuevas Tecnologías, Universidad Privada del Norte, Trujillo, Perú
| | - Luisa Juárez-Cortijo
- Grupo de Investigación en Ciencias Aplicadas y Nuevas Tecnologías, Universidad Privada del Norte, Trujillo, Perú
| | - Renny Nazario-Naveda
- Grupo de Investigación en Ciencias Aplicadas y Nuevas Tecnologías, Universidad Privada del Norte, Trujillo, Perú,Universidad Autónoma del Perú, Lima, Perú
| | - Diego Batista Menezes
- Laboratorio Nacional de Nanotecnología, Centro Nacional de Alta Tecnología, 10109 Pavas, San José, Costa Rica
| | - Reinaldo Pereira
- Laboratorio Nacional de Nanotecnología, Centro Nacional de Alta Tecnología, 10109 Pavas, San José, Costa Rica
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Huang J, Xu Y, Xue Y, Huang Y, Li X, Chen X, Xu Y, Zhang D, Zhang P, Zhao J, Ji J. Identification of potent antimicrobial peptides via a machine-learning pipeline that mines the entire space of peptide sequences. Nat Biomed Eng 2023:10.1038/s41551-022-00991-2. [PMID: 36635418 DOI: 10.1038/s41551-022-00991-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 11/29/2022] [Indexed: 01/14/2023]
Abstract
Systematically identifying functional peptides is difficult owing to the vast combinatorial space of peptide sequences. Here we report a machine-learning pipeline that mines the hundreds of billions of sequences in the entire virtual library of peptides made of 6-9 amino acids to identify potent antimicrobial peptides. The pipeline consists of trainable machine-learning modules (for performing empirical selection, classification, ranking and regression tasks) assembled sequentially following a coarse-to-fine design principle to gradually narrow down the search space. The leading three antimicrobial hexapeptides identified by the pipeline showed strong activities against a wide range of clinical isolates of multidrug-resistant pathogens. In mice with bacterial pneumonia, aerosolized formulations of the identified peptides showed therapeutic efficacy comparable to penicillin, negligible toxicity and a low propensity to induce drug resistance. The machine-learning pipeline may accelerate the discovery of new functional peptides.
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Affiliation(s)
- Junjie Huang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China.,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China
| | - Yanchao Xu
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Yunfan Xue
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China.,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China
| | - Yue Huang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xu Li
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xiaohui Chen
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Yao Xu
- R&D Department of AtaGenix Laboratories Co., Ltd. (Wuhan), Wuhan, China
| | - Dongxiang Zhang
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Peng Zhang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China. .,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China.
| | - Junbo Zhao
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China.
| | - Jian Ji
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China. .,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China.
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33
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McCoubrey LE, Favaron A, Awad A, Orlu M, Gaisford S, Basit AW. Colonic drug delivery: Formulating the next generation of colon-targeted therapeutics. J Control Release 2023; 353:1107-1126. [PMID: 36528195 DOI: 10.1016/j.jconrel.2022.12.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/26/2022]
Abstract
Colonic drug delivery can facilitate access to unique therapeutic targets and has the potential to enhance drug bioavailability whilst reducing off-target effects. Delivering drugs to the colon requires considered formulation development, as both oral and rectal dosage forms can encounter challenges if the colon's distinct physiological environment is not appreciated. As the therapeutic opportunities surrounding colonic drug delivery multiply, the success of novel pharmaceuticals lies in their design. This review provides a modern insight into the key parameters determining the effective design and development of colon-targeted medicines. Influential physiological features governing the release, dissolution, stability, and absorption of drugs in the colon are first discussed, followed by an overview of the most reliable colon-targeted formulation strategies. Finally, the most appropriate in vitro, in vivo, and in silico preclinical investigations are presented, with the goal of inspiring strategic development of new colon-targeted therapeutics.
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Affiliation(s)
- Laura E McCoubrey
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Alessia Favaron
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Atheer Awad
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Mine Orlu
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Simon Gaisford
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Abdul W Basit
- 29 - 39 Brunswick Square, UCL School of Pharmacy, University College London, London, WC1N 1AX, UK.
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34
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Pereira GC. Nanotechnology-Driven Delivery Systems in Inoculation Therapies. Methods Mol Biol 2023; 2575:39-57. [PMID: 36301470 DOI: 10.1007/978-1-0716-2716-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nanotechnology and genomics are the newest allies of inoculation design. In recent years, nucleic acids have been targeted as sources of therapeutics to stimulate immune responses, to both fight disease and create memory to trigger further responses to threat. A myriad of promising findings in cancer research and virology has been reported in the current literature. Nanosystems are demonstrating their capabilities as efficient carriers, improving the efficacy of drug delivery, including nucleic acids as therapeutics, at focal sites, in living systems. This chapter approaches major elements involved in the successful use of nanotechnology as delivery platforms to optimise the efficacy of nucleic acids-driven therapeutics, particularly mRNA vectors as coding engines for targeted viral proteins. Latest findings in nanotechnological design are highlighted, key discoveries associated with the success of nanodelivery platforms are presented, and key characteristics of nanodelivery systems in nucleic acids-based vaccine technology are discussed, to illustrate their distinct advantages and disadvantages.
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35
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Zheng K, Hou Y, Zhang Y, Wang F, Sun A, Yang D. Molecular features and predictive models identify the most lethal subtype and a therapeutic target for osteosarcoma. Front Oncol 2023; 13:1111570. [PMID: 36874110 PMCID: PMC9980341 DOI: 10.3389/fonc.2023.1111570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/23/2023] [Indexed: 02/18/2023] Open
Abstract
Background Osteosarcoma is the most common primary malignant bone tumor. The existing treatment regimens remained essentially unchanged over the past 30 years; hence the prognosis has plateaued at a poor level. Precise and personalized therapy is yet to be exploited. Methods One discovery cohort (n=98) and two validation cohorts (n=53 & n=48) were collected from public data sources. We performed a non-negative matrix factorization (NMF) method on the discovery cohort to stratify osteosarcoma. Survival analysis and transcriptomic profiling characterized each subtype. Then, a drug target was screened based on subtypes' features and hazard ratios. We also used specific siRNAs and added a cholesterol pathway inhibitor to osteosarcoma cell lines (U2OS and Saos-2) to verify the target. Moreover, PermFIT and ProMS, two support vector machine (SVM) tools, and the least absolute shrinkage and selection operator (LASSO) method, were employed to establish predictive models. Results We herein divided osteosarcoma patients into four subtypes (S-I ~ S-IV). Patients of S- I were found probable to live longer. S-II was characterized by the highest immune infiltration. Cancer cells proliferated most in S-III. Notably, S-IV held the most unfavorable outcome and active cholesterol metabolism. SQLE, a rate-limiting enzyme for cholesterol biosynthesis, was identified as a potential drug target for S-IV patients. This finding was further validated in two external independent osteosarcoma cohorts. The function of SQLE to promote proliferation and migration was confirmed by cell phenotypic assays after the specific gene knockdown or addition of terbinafine, an inhibitor of SQLE. We further employed two machine learning tools based on SVM algorithms to develop a subtype diagnostic model and used the LASSO method to establish a 4-gene model for predicting prognosis. These two models were also verified in a validation cohort. Conclusion The molecular classification enhanced our understanding of osteosarcoma; the novel predicting models served as robust prognostic biomarkers; the therapeutic target SQLE opened a new way for treatment. Our results served as valuable hints for future biological studies and clinical trials of osteosarcoma.
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Affiliation(s)
- Kun Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.,Department of Orthopedics, General Hospital of Southern Theater Command, Guangzhou, China
| | - Yushan Hou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yiming Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Wang
- Department of Orthopedics, General Hospital of Southern Theater Command, Guangzhou, China
| | - Aihua Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.,Research Unit of Proteomics Driven Cancer Precision Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
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36
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DeRidder L, Rubinson DA, Langer R, Traverso G. The past, present, and future of chemotherapy with a focus on individualization of drug dosing. J Control Release 2022; 352:840-60. [PMID: 36334860 DOI: 10.1016/j.jconrel.2022.10.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 10/14/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022]
Abstract
While there have been rapid advances in developing new and more targeted drugs to treat cancer, much less progress has been made in individualizing dosing. Even though the introduction of immunotherapies such as CAR T-cells and checkpoint inhibitors, as well as personalized therapies that target specific mutations, have transformed clinical treatment of cancers, chemotherapy remains a mainstay in oncology. Chemotherapies are typically dosed on either a body surface area (BSA) or weight basis, which fails to account for pharmacokinetic differences between patients. Drug absorption, distribution, metabolism, and excretion rates can vary between patients, resulting in considerable differences in exposure to the active drugs. These differences result in suboptimal dosing, which can reduce efficacy and increase side-effects. Therapeutic drug monitoring (TDM), genotype guided dosing, and chronomodulation have been developed to address this challenge; however, despite improving clinical outcomes, they are rarely implemented in clinical practice for chemotherapies. Thus, there is a need to develop interventions that allow for individualized drug dosing of chemotherapies, which can help maximize the number of patients that reach the most efficacious level of drug in the blood while mitigating the risks of underdosing or overdosing. In this review, we discuss the history of the development of chemotherapies, their mechanisms of action and how they are dosed. We discuss substantial intraindividual and interindividual variability in chemotherapy pharmacokinetics. We then propose potential engineering solutions that could enable individualized dosing of chemotherapies, such as closed-loop drug delivery systems and bioresponsive biomaterials.
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37
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Harris Y, Sason H, Niezni D, Shamay Y. Automated discovery of nanomaterials via drug aggregation induced emission. Biomaterials 2022; 289:121800. [PMID: 36166893 DOI: 10.1016/j.biomaterials.2022.121800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 12/19/2022]
Abstract
Nanoformulations of small molecule drugs are essential to effectively deliver them and treat a wide range of diseases. They are normally complex to develop, lack predictability, and exhibit low drug loading. Recently, nanoparticles made via co-assembly of hydrophobic drugs and organic dyes, exhibited drug-loading of up to 90% with high predictability from the drug structure. However, these particles have relatively short stability and can formulate only a small fraction of the drug space. Here, we developed an automated workflow to synthesize and select novel dye stabilizers, based on their ability to inhibit drug aggregation-induced emission (AIE). We first screened and identified 10 drugs with previously unknown strong AIE activity and exploited this trait to automatically synthesize and select a new ultra-stabilizer named R595. Interestingly, it shares several synthetic similarities and advantages with polydopamine. We found that R595 is superior to myriad types of excipients and solubilizers such as cyclodextrins, poloxamers, albumin, and previously published organic dyes, in both long-term stability and drug compatibility. We investigated the biodistribution, pharmacokinetics, safety and efficacy of the AIEgenic MEK inhibitor trametinib-R595 nanoparticles in vitro and in vivo and demonstrated that they are non-toxic and effective in KRAS driven colon and lung cancer models.
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Affiliation(s)
- Yuval Harris
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Hagit Sason
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Danna Niezni
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yosi Shamay
- Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
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38
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Abstract
Nanoparticles (NPs) have attracted tremendous interest in drug delivery in the past decades. Microfluidics offers a promising strategy for making NPs for drug delivery due to its capability in precisely controlling NP properties. The recent success of mRNA vaccines using microfluidics represents a big milestone for microfluidic NPs for pharmaceutical applications, and its rapid scaling up demonstrates the feasibility of using microfluidics for industrial-scale manufacturing. This article provides a critical review of recent progress in microfluidic NPs for drug delivery. First, the synthesis of organic NPs using microfluidics focusing on typical microfluidic methods and their applications in making popular and clinically relevant NPs, such as liposomes, lipid NPs, and polymer NPs, as well as their synthesis mechanisms are summarized. Then, the microfluidic synthesis of several representative inorganic NPs (e.g., silica, metal, metal oxide, and quantum dots), and hybrid NPs is discussed. Lastly, the applications of microfluidic NPs for various drug delivery applications are presented.
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Affiliation(s)
- Yun Liu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Guangze Yang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yue Hui
- Institute of Advanced Technology, Westlake University, Hangzhou, Zhejiang, 310024, China
| | - Supun Ranaweera
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Chun-Xia Zhao
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Chemical Engineering and Advanced Materials, Faculty of Engineering, Computer and Mathematical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
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39
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Wang X, Jiang S, Hu W, Ye S, Wang T, Wu F, Yang L, Li X, Zhang G, Chen X, Jiang J, Luo Y. Quantitatively Determining Surface-Adsorbate Properties from Vibrational Spectroscopy with Interpretable Machine Learning. J Am Chem Soc 2022; 144:16069-16076. [PMID: 36001497 DOI: 10.1021/jacs.2c06288] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Learning microscopic properties of a material from its macroscopic measurables is a grand and challenging goal in physical science. Conventional wisdom is to first identify material structures exploiting characterization tools, such as spectroscopy, and then to infer properties of interest, often with assistance of theory and simulations. This indirect approach has limitations due to the accumulation of errors from retrieving structures from spectral signals and the lack of quantitative structure-property relationship. A new pathway directly from spectral signals to microscopic properties is highly desirable, as it would offer valuable guidance toward materials evaluation and design via spectroscopic measurements. Herein, we exploit machine-learned vibrational spectroscopy to establish quantitative spectrum-property relationships. Key interaction properties of substrate-adsorbate systems, including adsorption energy and charge transfer, are quantitatively determined directly from Infrared and Raman spectroscopic signals of the adsorbates. The machine-learned spectrum-property relationships are presented as mathematical formulas, which are physically interpretable and therefore transferrable to a series of metal/alloy surfaces. The demonstrated ability of quantitative determination of hard-to-measure microscopic properties using machine-learned spectroscopy will significantly broaden the applicability of conventional spectroscopic techniques for materials design and high throughput screening under operando conditions.
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Affiliation(s)
- Xijun Wang
- Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Shuang Jiang
- Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Wei Hu
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Science), Jinan 250353, China
| | - Sheng Ye
- Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China.,School of Artificial Intelligence, Anhui University, Hefei 230601, China
| | - Tairan Wang
- Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Fan Wu
- Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Li Yang
- Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Xiyu Li
- Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Guozhen Zhang
- Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Xin Chen
- GuSu Laboratory of Materials, Suzhou 215123, China
| | - Jun Jiang
- Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China.,Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China
| | - Yi Luo
- Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China.,Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China
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Rickert CA, Lieleg O. Machine learning approaches for biomolecular, biophysical, and biomaterials research. Biophys Rev (Melville) 2022; 3:021306. [PMID: 38505413 PMCID: PMC10914139 DOI: 10.1063/5.0082179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/12/2022] [Indexed: 03/21/2024]
Abstract
A fluent conversation with a virtual assistant, person-tailored news feeds, and deep-fake images created within seconds-all those things that have been unthinkable for a long time are now a part of our everyday lives. What these examples have in common is that they are realized by different means of machine learning (ML), a technology that has fundamentally changed many aspects of the modern world. The possibility to process enormous amount of data in multi-hierarchical, digital constructs has paved the way not only for creating intelligent systems but also for obtaining surprising new insight into many scientific problems. However, in the different areas of biosciences, which typically rely heavily on the collection of time-consuming experimental data, applying ML methods is a bit more challenging: Here, difficulties can arise from small datasets and the inherent, broad variability, and complexity associated with studying biological objects and phenomena. In this Review, we give an overview of commonly used ML algorithms (which are often referred to as "machines") and learning strategies as well as their applications in different bio-disciplines such as molecular biology, drug development, biophysics, and biomaterials science. We highlight how selected research questions from those fields were successfully translated into machine readable formats, discuss typical problems that can arise in this context, and provide an overview of how to resolve those encountered difficulties.
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41
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Bender A, Schneider N, Segler M, Patrick Walters W, Engkvist O, Rodrigues T. Evaluation guidelines for machine learning tools in the chemical sciences. Nat Rev Chem 2022; 6:428-442. [PMID: 37117429 DOI: 10.1038/s41570-022-00391-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2022] [Indexed: 02/07/2023]
Abstract
Machine learning (ML) promises to tackle the grand challenges in chemistry and speed up the generation, improvement and/or ordering of research hypotheses. Despite the overarching applicability of ML workflows, one usually finds diverse evaluation study designs. The current heterogeneity in evaluation techniques and metrics leads to difficulty in (or the impossibility of) comparing and assessing the relevance of new algorithms. Ultimately, this may delay the digitalization of chemistry at scale and confuse method developers, experimentalists, reviewers and journal editors. In this Perspective, we critically discuss a set of method development and evaluation guidelines for different types of ML-based publications, emphasizing supervised learning. We provide a diverse collection of examples from various authors and disciplines in chemistry. While taking into account varying accessibility across research groups, our recommendations focus on reporting completeness and standardizing comparisons between tools. We aim to further contribute to improved ML transparency and credibility by suggesting a checklist of retro-/prospective tests and dissecting their importance. We envisage that the wide adoption and continuous update of best practices will encourage an informed use of ML on real-world problems related to the chemical sciences.
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Abstract
The technology of drug delivery systems (DDSs) has demonstrated an outstanding performance and effectiveness in production of pharmaceuticals, as it is proved by many FDA-approved nanomedicines that have an enhanced selectivity, manageable drug release kinetics and synergistic therapeutic actions. Nonetheless, to date, the rational design and high-throughput development of nanomaterial-based DDSs for specific purposes is far from a routine practice and is still in its infancy, mainly due to the limitations in scientists' capabilities to effectively acquire, analyze, manage, and comprehend complex and ever-growing sets of experimental data, which is vital to develop DDSs with a set of desired functionalities. At the same time, this task is feasible for the data-driven approaches, high throughput experimentation techniques, process automatization, artificial intelligence (AI) technology, and machine learning (ML) approaches, which is referred to as The Fourth Paradigm of scientific research. Therefore, an integration of these approaches with nanomedicine and nanotechnology can potentially accelerate the rational design and high-throughput development of highly efficient nanoformulated drugs and smart materials with pre-defined functionalities. In this Review, we survey the important results and milestones achieved to date in the application of data science, high throughput, as well as automatization approaches, combined with AI and ML to design and optimize DDSs and related nanomaterials. This manuscript mission is not only to reflect the state-of-art in data-driven nanomedicine, but also show how recent findings in the related fields can transform the nanomedicine's image. We discuss how all these results can be used to boost nanomedicine translation to the clinic, as well as highlight the future directions for the development, data-driven, high throughput experimentation-, and AI-assisted design, as well as the production of nanoformulated drugs and smart materials with pre-defined properties and behavior. This Review will be of high interest to the chemists involved in materials science, nanotechnology, and DDSs development for biomedical applications, although the general nature of the presented approaches enables knowledge translation to many other fields of science.
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Affiliation(s)
- Nikita Serov
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, Saint-Petersburg 191002, Russian Federation
| | - Vladimir Vinogradov
- International Institute "Solution Chemistry of Advanced Materials and Technologies", ITMO University, Saint-Petersburg 191002, Russian Federation.
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43
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Chen C, Yaari Z, Apfelbaum E, Grodzinski P, Shamay Y, Heller DA. Merging data curation and machine learning to improve nanomedicines. Adv Drug Deliv Rev 2022; 183:114172. [PMID: 35189266 DOI: 10.1016/j.addr.2022.114172] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/28/2022] [Accepted: 02/16/2022] [Indexed: 12/12/2022]
Abstract
Nanomedicine design is often a trial-and-error process, and the optimization of formulations and in vivo properties requires tremendous benchwork. To expedite the nanomedicine research progress, data science is steadily gaining importance in the field of nanomedicine. Recently, efforts have explored the potential to predict nanomaterials synthesis and biological behaviors via advanced data analytics. Machine learning algorithms process large datasets to understand and predict various material properties in nanomedicine synthesis, pharmacologic parameters, and efficacy. "Big data" approaches may enable even larger advances, especially if researchers capitalize on data curation methods. However, the concomitant use of data curation processes needed to facilitate the acquisition and standardization of large, heterogeneous data sets, to support advanced data analytics methods such as machine learning has yet to be leveraged. Currently, data curation and data analytics areas of nanotechnology-focused data science, or 'nanoinformatics', have been proceeding largely independently. This review highlights the current efforts in both areas and the potential opportunities for coordination to advance the capabilities of data analytics in nanomedicine.
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Khedri M, Beheshtizadeh N, Rostami M, Sufali A, Rezvantalab S, Dahri M, Maleki R, Santos HA, Shahbazi MA. Artificial Intelligence Deep Exploration of Influential Parameters on Physicochemical Properties of Curcumin‐Loaded Electrospun Nanofibers. Advanced NanoBiomed Research 2022. [DOI: 10.1002/anbr.202100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Mohammad Khedri
- Computational Biology and Chemistry Group (CBCG) Universal Scientific Education and Research Network (USERN) Tehran Iran
| | - Nima Beheshtizadeh
- Department of Tissue Engineering School of Advanced Technologies in Medicine Tehran University of Medical Sciences 14177-55469 Tehran Iran
- Regenerative Medicine group (REMED) Universal Scientific Education and Research Network (USERN) Tehran Iran
| | - Mohammadreza Rostami
- Division of Food Safety and Hygiene Department of Environmental Health Engineering School of Public Health Tehran University of Medical Sciences Tehran Iran
- Food Science and Nutrition group (FSAN) Universal Scientific Education and Research Network (USERN) Tehran Iran
| | - Ali Sufali
- Computational Biology and Chemistry Group (CBCG) Universal Scientific Education and Research Network (USERN) Tehran Iran
| | - Sima Rezvantalab
- Renewable Energies Department Faculty of Chemical Engineering Urmia University of Technology 57166-419 Urmia Iran
| | - Mohammad Dahri
- Computational Biology and Chemistry Group (CBCG) Universal Scientific Education and Research Network (USERN) Tehran Iran
| | - Reza Maleki
- Computational Biology and Chemistry Group (CBCG) Universal Scientific Education and Research Network (USERN) Tehran Iran
| | - Hélder A. Santos
- Department of Biomedical Engineering University Medical Center Groningen University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
- Drug Research Program Division of Pharmaceutical Chemistry and Technology Faculty of Pharmacy University of Helsinki 00014 Helsinki Finland
- Helsinki Institute of Life Science (HiLIFE) University of Helsinki 00014 Helsinki Finland
| | - Mohammad-Ali Shahbazi
- Department of Biomedical Engineering University Medical Center Groningen University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
- Zanjan Pharmaceutical Nanotechnology Research Center (ZPNRC) Zanjan University of Medical Sciences 45139-56184 Zanjan Iran
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45
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Xue YF, He Y, Wang J, Ren KF, Tian P, Ji J. Label-Free and In Situ Identification of Cells via Combinational Machine Learning Models. Small Methods 2022; 6:e2101405. [PMID: 34954897 DOI: 10.1002/smtd.202101405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Indexed: 06/14/2023]
Abstract
Cell identification and counting in living and coculture systems are crucial in cell interaction studies, but current methods primarily rely on complicated and time-consuming staining techniques. Here, a label-free method to precisely recognize, identify, and instantly count cells in situ in coculture systems via combinational machine learning models s presented. A convolutional neural network (CNN) model is first used to generate virtual images of cell nuclei based on unlabeled phase-contrast images. Coordinates of all the cells are then returned according to the virtual nucleus images using two clustering algorithms. Finally, phase-contrast images of single cells are cropped based on the coordinates and sent into another CNN model for cell-type identification. This combinational approach is highly automatic and efficient, which requires few to no manual annotations of images in the training phase. It shows practical performance in different cell culture conditions including cell ratios, densities, and substrate materials, having great potential in real-time cell tracking and analyzing.
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Affiliation(s)
- Yun-Fan Xue
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Yang He
- School of Life Sciences, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| | - Jing Wang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Ke-Feng Ren
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Pu Tian
- School of Life Sciences, School of Artificial Intelligence, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| | - Jian Ji
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, P. R. China
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46
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Abstract
In recent years, nanodrug delivery systems have attracted increasing attention due to their advantages, such as the high drug loading, low toxicity and side effects, improved bioavailability, long half-life, well...
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47
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Smith CW, Hizir MS, Nandu N, Yigit MV. Algorithmically Guided Optical Nanosensor Selector (AGONS): Guiding Data Acquisition, Processing, and Discrimination for Biological Sampling. Anal Chem 2021; 94:1195-1202. [PMID: 34964601 DOI: 10.1021/acs.analchem.1c04379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Here, we report a biomarker-free detection of various biological targets through a programmed machine learning algorithm and an automated computational selection process termed algorithmically guided optical nanosensor selector (AGONS). The optical data processed/used by algorithms are obtained through a nanosensor array selected from a library of nanosensors through AGONS. The nanosensors are assembled using two-dimensional nanoparticles (2D-nps) and fluorescently labeled single-stranded DNAs (F-ssDNAs) with random sequences. Both 2D-np and F-ssDNA components are cost-efficient and easy to synthesize, allowing for scaled-up data collection essential for machine learning modeling. The nanosensor library was subjected to various target groups, including proteins, breast cancer cells, and lethal-7 (let-7) miRNA mimics. We have demonstrated that AGONS could select the most essential nanosensors while achieving 100% predictive accuracy in all cases. With this approach, we demonstrate that machine learning can guide the design of nanosensor arrays with greater predictive accuracy while minimizing manpower, material cost, computational resources, instrumentation usage, and time. The biomarker-free detection attribute makes this approach readily available for biological targets without any detectable biomarker. We believe that AGONS can guide optical nanosensor array setups, opening broader opportunities through a biomarker-free detection approach for most challenging biological targets.
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Affiliation(s)
- Christopher W Smith
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States.,The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Mustafa Salih Hizir
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Nidhi Nandu
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Mehmet V Yigit
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States.,The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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48
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Awad A, Trenfield SJ, Pollard TD, Ong JJ, Elbadawi M, McCoubrey LE, Goyanes A, Gaisford S, Basit AW. Connected healthcare: Improving patient care using digital health technologies. Adv Drug Deliv Rev 2021; 178:113958. [PMID: 34478781 DOI: 10.1016/j.addr.2021.113958] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/12/2021] [Accepted: 08/29/2021] [Indexed: 12/22/2022]
Abstract
Now more than ever, traditional healthcare models are being overhauled with digital technologies of Healthcare 4.0 increasingly adopted. Worldwide, digital devices are improving every stage of the patient care pathway. For one, sensors are being used to monitor patient metrics 24/7, permitting swift diagnosis and interventions. At the treatment stage, 3D printers are under investigation for the concept of personalised medicine by allowing patients access to on-demand, customisable therapeutics. Robots are also being explored for treatment, by empowering precision surgery, rehabilitation, or targeted drug delivery. Within medical logistics, drones are being leveraged to deliver critical treatments to remote areas, collect samples, and even provide emergency aid. To enable seamless integration within healthcare, the Internet of Things technology is being exploited to form closed-loop systems that remotely communicate with one another. This review outlines the most promising healthcare technologies and devices, their strengths, drawbacks, and opportunities for clinical adoption.
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Affiliation(s)
- Atheer Awad
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Sarah J Trenfield
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Thomas D Pollard
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Jun Jie Ong
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Moe Elbadawi
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Laura E McCoubrey
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Alvaro Goyanes
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; FabRx Ltd., Henwood House, Henwood, Ashford, Kent TN24 8DH, UK; Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma (GI-1645), Facultad de Farmacia, Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, 15782, Spain
| | - Simon Gaisford
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; FabRx Ltd., Henwood House, Henwood, Ashford, Kent TN24 8DH, UK
| | - Abdul W Basit
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; FabRx Ltd., Henwood House, Henwood, Ashford, Kent TN24 8DH, UK.
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49
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Tomé I, Francisco V, Fernandes H, Ferreira L. High-throughput screening of nanoparticles in drug delivery. APL Bioeng 2021; 5:031511. [PMID: 34476328 PMCID: PMC8397474 DOI: 10.1063/5.0057204] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/30/2021] [Indexed: 12/19/2022] Open
Abstract
The use of pharmacologically active compounds to manage and treat diseases is of utmost relevance in clinical practice. It is well recognized that spatial-temporal control over the delivery of these biomolecules will greatly impact their pharmacokinetic profile and ultimately their therapeutic effect. Nanoparticles (NPs) prepared from different materials have been tested successfully in the clinic for the delivery of several biomolecules including non-coding RNAs (siRNA and miRNA) and mRNAs. Indeed, the recent success of mRNA vaccines is in part due to progress in the delivery systems (NP based) that have been developed for many years. In most cases, the identification of the best formulation was done by testing a small number of novel formulations or by modification of pre-existing ones. Unfortunately, this is a low throughput and time-consuming process that hinders the identification of formulations with the highest potential. Alternatively, high-throughput combinatorial design of NP libraries may allow the rapid identification of formulations with the required release and cell/tissue targeting profile for a given application. Combinatorial approaches offer several advantages over conventional methods since they allow the incorporation of multiple components with varied chemical properties into materials, such as polymers or lipid-like materials, that will subsequently form NPs by self-assembly or chemical conjugation processes. The current review highlights the impact of high-throughput in the development of more efficient drug delivery systems with enhanced targeting and release kinetics. It also describes the current challenges in this research area as well as future directions.
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Affiliation(s)
| | - Vitor Francisco
- Biomaterials and Stem-Cell Based Therapeutics Group, Centre of Neuroscience and Cell Biology, University of Coimbra, 3060-197 Cantanhede, Portugal
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50
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Xue K, Wang F, Suwardi A, Han MY, Teo P, Wang P, Wang S, Ye E, Li Z, Loh XJ. Biomaterials by design: Harnessing data for future development. Mater Today Bio 2021; 12:100165. [PMID: 34877520 PMCID: PMC8628044 DOI: 10.1016/j.mtbio.2021.100165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 01/18/2023] Open
Abstract
Biomaterials is an interdisciplinary field of research to achieve desired biological responses from new materials, regardless of material type. There have been many exciting innovations in this discipline, but commercialization suffers from a lengthy discovery to product pipeline, with many failures along the way. Success can be greatly accelerated by harnessing machine learning techniques to comb through large amounts of data. There are many potential benefits of moving from an unstructured empirical approach to a development strategy that is entrenched in data. Here, we discuss the recent work on the use of machine learning in the discovery and design of biomaterials, including new polymeric, metallic, ceramics, and nanomaterials, and how machine learning can interface with emerging use cases of 3D printing. We discuss the steps for closer integration of machine learning to make this exciting possibility a reality.
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Affiliation(s)
| | | | | | | | | | | | | | - Enyi Ye
- Institute of Materials Research and Engineering, A∗STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634, Singapore
| | - Zibiao Li
- Institute of Materials Research and Engineering, A∗STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634, Singapore
| | - Xian Jun Loh
- Institute of Materials Research and Engineering, A∗STAR (Agency for Science, Technology and Research), 2 Fusionopolis Way, Innovis, #08-03, Singapore, 138634, Singapore
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