1
|
Zheng JJ, Li QZ, Wang Z, Wang X, Zhao Y, Gao X. Computer-aided nanodrug discovery: recent progress and future prospects. Chem Soc Rev 2024. [PMID: 39148378 DOI: 10.1039/d3cs00575e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Nanodrugs, which utilise nanomaterials in disease prevention and therapy, have attracted considerable interest since their initial conceptualisation in the 1990s. Substantial efforts have been made to develop nanodrugs for overcoming the limitations of conventional drugs, such as low targeting efficacy, high dosage and toxicity, and potential drug resistance. Despite the significant progress that has been made in nanodrug discovery, the precise design or screening of nanomaterials with desired biomedical functions prior to experimentation remains a significant challenge. This is particularly the case with regard to personalised precision nanodrugs, which require the simultaneous optimisation of the structures, compositions, and surface functionalities of nanodrugs. The development of powerful computer clusters and algorithms has made it possible to overcome this challenge through in silico methods, which provide a comprehensive understanding of the medical functions of nanodrugs in relation to their physicochemical properties. In addition, machine learning techniques have been widely employed in nanodrug research, significantly accelerating the understanding of bio-nano interactions and the development of nanodrugs. This review will present a summary of the computational advances in nanodrug discovery, focusing on the understanding of how the key interfacial interactions, namely, surface adsorption, supramolecular recognition, surface catalysis, and chemical conversion, affect the therapeutic efficacy of nanodrugs. Furthermore, this review will discuss the challenges and opportunities in computer-aided nanodrug discovery, with particular emphasis on the integrated "computation + machine learning + experimentation" strategy that can potentially accelerate the discovery of precision nanodrugs.
Collapse
Affiliation(s)
- Jia-Jia Zheng
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| | - Qiao-Zhi Li
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| | - Zhenzhen Wang
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| | - Xiaoli Wang
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yuliang Zhao
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| | - Xingfa Gao
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| |
Collapse
|
2
|
Xiang K, Li Y, Cong H, Yu B, Shen Y. Peptide-based non-viral gene delivery: A comprehensive review of the advances and challenges. Int J Biol Macromol 2024; 266:131194. [PMID: 38554914 DOI: 10.1016/j.ijbiomac.2024.131194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Gene therapy is the most effective treatment option for diseases, but its effectiveness is affected by the choice and design of gene carriers. The genes themselves have to pass through multiple barriers in order to enter the cell and therefore require additional vectors to carry them inside the cell. In gene therapy, peptides have unique properties and potential as gene carriers, which can effectively deliver genes into specific cells or tissues, protect genes from degradation, improve gene transfection efficiency, and enhance gene targeting and biological responsiveness. This paper reviews the research progress of peptides and their derivatives in the field of gene delivery recently, describes the obstacles encountered by foreign materials to enter the interior of the cell, and introduces the following classes of functional peptides that can carry materials into the interior of the cell, and assist in transmembrane translocation of carriers, thus breaking through endosomal traps to enable successful entry of genetic materials into the nucleus of the cell. The paper also discusses the combined application of peptide vectors with other vectors to enhance its transfection ability, explores current challenges encountered by peptide vectors, and looks forward to future developments in the field.
Collapse
Affiliation(s)
- Kai Xiang
- College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao 266071, China
| | - Yanan Li
- College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao 266071, China
| | - Hailin Cong
- College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao 266071, China; State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China; School of Materials Science and Engineering, Shandong University of Technology, Zibo 255000, China.
| | - Bing Yu
- College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao 266071, China; State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China.
| | - Youqing Shen
- College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao 266071, China; Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Center for Bio nanoengineering, and Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| |
Collapse
|
3
|
Chen X, Ren X, Gao X. Peptide or
Protein‐Protected
Metal Nanoclusters for Therapeutic Application. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100523] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiaolei Chen
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology Beijing 100124 China
| | - Xiaojun Ren
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology Beijing 100124 China
| | - Xueyun Gao
- Department of Chemistry and Biology, Faculty of Environment and Life Science, Beijing University of Technology Beijing 100124 China
| |
Collapse
|
4
|
Sun M, Wang T, Li L, Li X, Zhai Y, Zhang J, Li W. The Application of Inorganic Nanoparticles in Molecular Targeted Cancer Therapy: EGFR Targeting. Front Pharmacol 2021; 12:702445. [PMID: 34322025 PMCID: PMC8311435 DOI: 10.3389/fphar.2021.702445] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/26/2021] [Indexed: 12/24/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) is an anticancer drug target for a number of cancers, such as non-small cell lung cancer. However, unsatisfying treatment effects, terrible side-effects, and development of drug resistance are current insurmountable challenges of EGFR targeting treatments for cancers. With the advancement of nanotechnology, an increasing number of inorganic nanomaterials are applied in EGFR-mediated therapy to improve those limitations and further potentiate the efficacy of molecular targeted cancer therapy. Given their facile preparation, easy modification, and biosecurity, inorganic nanoparticles (iNPs) have been extensively explored in cancer treatments to date. This review presents an overview of the application of some typical metal nanoparticles and nonmetallic nanoparticles in EGFR-targeted therapy, then discusses and summarizes the relevant advantages. Moreover, we also highlight future perspectives regarding their remaining issues. We hope these discussions inspire future research on EGFR-targeted iNPs.
Collapse
Affiliation(s)
- Meng Sun
- School of Chemistry and Environmental Engineering, Changchun University of Science and Technology, Changchun, China
| | - Ting Wang
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Leijiao Li
- School of Chemistry and Environmental Engineering, Changchun University of Science and Technology, Changchun, China
| | - Xiangyang Li
- School of Chemistry and Environmental Engineering, Changchun University of Science and Technology, Changchun, China
| | - Yutong Zhai
- School of Chemistry and Environmental Engineering, Changchun University of Science and Technology, Changchun, China
| | - Jiantao Zhang
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Wenliang Li
- Jilin Collaborative Innovation Center for Antibody Engineering, Jilin Medical University, Jilin, China
| |
Collapse
|
5
|
Liu LJ, Zhang JW, Asad M, Wang ZY, Zang SQ, Mak TCW. A high-nuclearity Cu I/Cu II nanocluster catalyst for phenol degradation. Chem Commun (Camb) 2021; 57:5586-5589. [PMID: 33970180 DOI: 10.1039/d1cc01319j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Herein, we report a 54-nuclei copper nanocluster, [Cu54S13O6(tBuS)20(tBuSO3)12] (Cu54), which is the largest atom-precise CuI/CuII mix-valent cluster reported. The Cu54 nanoclusters supported by TiO2 exhibit decent photocatalytic activity for phenol degradation under visible light. This work provides a platform to explore the catalytic behaviors of CuI/CuII nanosystems.
Collapse
Affiliation(s)
- Li-Juan Liu
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China.
| | | | | | | | | | | |
Collapse
|
6
|
Liu Y, Zhou Y, Huang K, Fang X, Li Y, Wang F, An L, Chen Q, Zhang Y, Shi A, Yu S, Zhang J. Targeting epidermal growth factor-overexpressing triple-negative breast cancer by natural killer cells expressing a specific chimeric antigen receptor. Cell Prolif 2020; 53:e12858. [PMID: 32592435 PMCID: PMC7445407 DOI: 10.1111/cpr.12858] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Traditional cancer therapy and regular immunotherapy are ineffective for treating triple-negative breast cancer (TNBC) patients. Recently, chimeric antigen receptor-engineered natural killer cells (CAR NK) have been applied to target several hormone receptors on different cancer cells to improve the efficacy of immunotherapy. Furthermore, epidermal growth factor receptor (EGFR) is a potential therapeutic target for TNBC. Here, we demonstrated that EGFR-specific CAR NK cells (EGFR-CAR NK cells) could be potentially used to treat patients with TNBC exhibiting enhanced EGFR expression. MATERIALS AND METHODS We investigated the cytotoxic effects of EGFR-CAR NK cells against TNBC cells in vitro and in vivo. The two types of EGFR-CAR NK cells were generated by transducing lentiviral vectors containing DNA sequences encoding the single-chain variable fragment (scFv) regions of the two anti-EGFR antibodies. The cytotoxic and anti-tumor effects of the two cell types were examined by performing cytokine release and cytotoxicity assays in vitro, and tumor growth assays in breast cancer cell line-derived xenograft (CLDX) and patient-derived xenograft (PDX) mouse models. RESULTS Both EGFR-CAR NK cell types were activated by TNBC cells exhibiting upregulated EGFR expression and specifically triggered the lysis of the TNBC cells in vitro. Furthermore, the two EGFR-CAR NK cell types inhibited CLDX and PDX tumors in mice. CONCLUSIONS This study suggested that treatment with EGFR-CAR NK cells could be a promising strategy for TNBC patients.
Collapse
Affiliation(s)
- Yan Liu
- The Key Laboratory of Bio‐Medical DiagnosticsSuzhou Institute of Biomedical Engineering and Technology (SIBET)Chinese Academy of SciencesSuzhouChina
- Changchun Institute of OpticsFine Mechanics and PhysicsChinese Academy of SciencesChangchunChina
- Zhengzhou Institute of Engineering and Technology Affiliated with SIBETZhengzhouChina
| | | | - Kuo‐Hsiang Huang
- The Key Laboratory of Bio‐Medical DiagnosticsSuzhou Institute of Biomedical Engineering and Technology (SIBET)Chinese Academy of SciencesSuzhouChina
| | - Xujie Fang
- The Key Laboratory of Bio‐Medical DiagnosticsSuzhou Institute of Biomedical Engineering and Technology (SIBET)Chinese Academy of SciencesSuzhouChina
| | - Ying Li
- The Key Laboratory of Bio‐Medical DiagnosticsSuzhou Institute of Biomedical Engineering and Technology (SIBET)Chinese Academy of SciencesSuzhouChina
| | - Feifei Wang
- The Key Laboratory of Bio‐Medical DiagnosticsSuzhou Institute of Biomedical Engineering and Technology (SIBET)Chinese Academy of SciencesSuzhouChina
- Zhengzhou Institute of Engineering and Technology Affiliated with SIBETZhengzhouChina
| | - Li An
- The Key Laboratory of Bio‐Medical DiagnosticsSuzhou Institute of Biomedical Engineering and Technology (SIBET)Chinese Academy of SciencesSuzhouChina
- Zhengzhou Institute of Engineering and Technology Affiliated with SIBETZhengzhouChina
| | - Qingfei Chen
- The Key Laboratory of Bio‐Medical DiagnosticsSuzhou Institute of Biomedical Engineering and Technology (SIBET)Chinese Academy of SciencesSuzhouChina
| | - Yunchao Zhang
- The Key Laboratory of Bio‐Medical DiagnosticsSuzhou Institute of Biomedical Engineering and Technology (SIBET)Chinese Academy of SciencesSuzhouChina
| | - Aihua Shi
- The Key Laboratory of Bio‐Medical DiagnosticsSuzhou Institute of Biomedical Engineering and Technology (SIBET)Chinese Academy of SciencesSuzhouChina
- Zhengzhou Institute of Engineering and Technology Affiliated with SIBETZhengzhouChina
| | - Shuang Yu
- The Key Laboratory of Bio‐Medical DiagnosticsSuzhou Institute of Biomedical Engineering and Technology (SIBET)Chinese Academy of SciencesSuzhouChina
- Xuzhou Medical UniversityXuzhouChina
| | - Jingzhong Zhang
- The Key Laboratory of Bio‐Medical DiagnosticsSuzhou Institute of Biomedical Engineering and Technology (SIBET)Chinese Academy of SciencesSuzhouChina
- Xuzhou Medical UniversityXuzhouChina
- Tianjin Guokeyigong Science and Technology Development Company LimitedTianjinChina
- Zhengzhou Institute of Engineering and Technology Affiliated with SIBETZhengzhouChina
| |
Collapse
|
7
|
Fu X, Lin X, Ren X, Wu R, Liu C, Huang J. The synthesis and structure of the [PdAu 13(PPh 3) 3(SR) 7] + nanocluster. NANOSCALE 2020; 12:11825-11829. [PMID: 32458944 DOI: 10.1039/d0nr01356k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Metal alloy nanoclusters have attracted increasing attention due to the synergistic effect of the foreign atoms. For the first time the synthesis and crystal structure of the [PdAu13(PPh3)3(SR)7]+ nanocluster is reported. The crystal structure of the nanocluster was determined by single crystal X-ray diffraction. The [PdAu13(PPh3)3(SR)7]+ nanocluster has a concave polyhedron Au9Pd kernel, which looks like a girl dancing ballet. The structure shows that [PdAu13(PPh3)3(SR)7]+ has an open shell. Meanwhile, we also carried out ultraviolet-visible (Uv-vis) absorption spectroscopy and fluorescence spectroscopy to study the optical properties of the [PdAu13(PPh3)3(SR)7]+ nanocluster.
Collapse
Affiliation(s)
- Xuemei Fu
- Gold Catalysis Research Center, State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. and Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinzhang Lin
- Gold Catalysis Research Center, State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. and Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuqing Ren
- Gold Catalysis Research Center, State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. and Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Ren'an Wu
- Laboratory of High-Resolution Mass Spectrometry Technologies, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chao Liu
- Gold Catalysis Research Center, State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. and Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jiahui Huang
- Gold Catalysis Research Center, State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China. and Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| |
Collapse
|
8
|
The Accuracy of Determining Cluster Size by Analyzing Ripley’s K Function in Single Molecule Localization Microscopy. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9163271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ripley’s K function was developed to analyze the spatial distribution characteristics in point pattern analysis, including geography, economics and biomedical research. In biomedical applications, it is popularly used to analyze the clusters of proteins on the cell plasma membrane in single molecule localization microscopy (SMLM), such as photo activated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM), universal point accumulation imaging in nanoscale topography (uPAINT), etc. Here, by varying the parameters of the simulated clusters on a modeled SMLM image, the effects of cluster size, cluster separation and protein ratio inside/outside the cluster on the accuracy of cluster analysis by analyzing Ripley’s K function were studied. Although the predicted radius of clusters by analyzing Ripley’s K function did not exactly correspond to the actual radius, we suggest the cluster radius could be estimated within a factor of 1.3. Employing peak analysis methods to analyze the experimental epidermal growth factor receptor (EGFR) clusters at fibroblast-like cell lines derived from monkey kidney tissue - COS7 cell surface observed by uPAINT method, the cluster properties were characterized with errors. Our results present quantification of clusters and can be used to enhance the understanding of clusters in SMLM.
Collapse
|