1
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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] [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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2
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Yue C, Yuan Z, Xu G, Guan XN, Wei B, Yao H, Yang CG, Zhang T. Structure-Guided Design, Synthesis, and Antivirulence Assessment of Covalent Staphylococcus aureus Sortase A Inhibitors. J Med Chem 2024; 67:1127-1146. [PMID: 38170998 DOI: 10.1021/acs.jmedchem.3c01615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Sortase A (SrtA) is a membrane-associated cysteine transpeptidase required for bacterial virulence regulation and anchors surface proteins to cell wall, thereby assisting biofilm formation. SrtA is targeted in antivirulence treatments against Gram-positive bacterial infections. However, the development of potent small-molecule SrtA inhibitors is constrained owing to the limited understanding of the mode of action of inhibitors in the SrtA binding pocket. Herein, we designed and synthesized a novel class of covalent SrtA inhibitors based on the binding mode detailed in the X-ray crystal structure of the ML346/Streptococcus pyogenes SrtA complex. ML346 analog Y40 exhibited 2-fold increased inhibitory activity on Staphylococcus aureus SrtA and showed superior inhibitory effects on biofilm formation in vitro. Y40 protected Galleria mellonella larvae fromS. aureusinfections in vivo while minimally attenuating staphylococcal growth in vitro. Our study indicates that the covalent SrtA inhibitor Y40 is an antivirulence agent that is effective againstS. aureusinfections.
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Affiliation(s)
- Chuan Yue
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ziqi Yuan
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guobin Xu
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiang-Na Guan
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingyan Wei
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Hequan Yao
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Cai-Guang Yang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Tao Zhang
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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3
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Zhang R, Wang P, Wei B, Chen L, Song X, Pan Y, Li J, Gan J, Zhang T, Yang CG. Assessment of the structure-activity relationship and antileukemic activity of diacylpyramide compounds as human ClpP agonists. Eur J Med Chem 2023; 258:115577. [PMID: 37352796 DOI: 10.1016/j.ejmech.2023.115577] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023]
Abstract
Human caseinolytic protease P (ClpP) is required for the regulatory hydrolysis of mitochondrial proteins. Allosteric ClpP agonists dysfunctionally activate mitochondrial ClpP in antileukemic therapies. We previously developed ZG111, a potent ClpP agonist derived from ICG-001, inhibits the proliferation of pancreatic ductal adenocarcinoma cell lines in vitro and in vivo by degrading respiratory chain complex proteins. Herein, we studied the structure-activity relationships of ICG-001 analogs as antileukemia agents. Compound ZG36 exhibited improved stabilization effects on the thermal stability of ClpP in acute myeloid leukemia (AML) cell lines compared with the stabilization effects of ZG111, indicating a direct binding between ZG36 and ClpP. Indeed, the resolved ZG36/ClpP structural complex reveals the mode of action of ZG36 during ClpP binding. Compound ZG36 nonselectively degrades respiratory chain complexes and decreases the mitochondrial DNA, eventually leading to the collapse of mitochondrial function and leukemic cell death. Finally, ZG36 treatment inhibited 3-D cell growth in vitro and suppressed the tumorigenesis of AML cells in xenografted mice models. Collectively, we developed a new class of human ClpP agonists that can be used as potential antileukemic therapies.
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Affiliation(s)
- Ranran Zhang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Pengyu Wang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Bingyan Wei
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Chen
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaomin Song
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yihui Pan
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiahui Li
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianhua Gan
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Tao Zhang
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Cai-Guang Yang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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Wei B, Zhang T, Wang P, Pan Y, Li J, Chen W, Zhang M, Ji Q, Wu W, Lan L, Gan J, Yang CG. Anti-infective therapy using species-specific activators of Staphylococcus aureus ClpP. Nat Commun 2022; 13:6909. [PMID: 36376309 PMCID: PMC9663597 DOI: 10.1038/s41467-022-34753-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
The emergence of methicillin-resistant Staphylococcus aureus isolates highlights the urgent need to develop more antibiotics. ClpP is a highly conserved protease regulated by ATPases in bacteria and in mitochondria. Aberrant activation of bacterial ClpP is an alternative method of discovering antibiotics, while it remains difficult to develop selective Staphylococcus aureus ClpP activators that can avoid disturbing Homo sapiens ClpP functions. Here, we use a structure-based design to identify (R)- and (S)-ZG197 as highly selective Staphylococcus aureus ClpP activators. The key structural elements in Homo sapiens ClpP, particularly W146 and its joint action with the C-terminal motif, significantly contribute to the discrimination of the activators. Our selective activators display wide antibiotic properties towards an array of multidrug-resistant staphylococcal strains in vitro, and demonstrate promising antibiotic efficacy in zebrafish and murine skin infection models. Our findings indicate that the species-specific activators of Staphylococcus aureus ClpP are exciting therapeutic agents to treat staphylococcal infections.
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Affiliation(s)
- Bingyan Wei
- grid.410726.60000 0004 1797 8419School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024 China ,grid.9227.e0000000119573309State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Tao Zhang
- grid.9227.e0000000119573309State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China
| | - Pengyu Wang
- grid.410726.60000 0004 1797 8419School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024 China ,grid.9227.e0000000119573309State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yihui Pan
- grid.410726.60000 0004 1797 8419School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024 China ,grid.9227.e0000000119573309State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jiahui Li
- grid.9227.e0000000119573309State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Weizhong Chen
- grid.440637.20000 0004 4657 8879School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210 China
| | - Min Zhang
- grid.24516.340000000123704535Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123 China
| | - Quanjiang Ji
- grid.440637.20000 0004 4657 8879School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210 China
| | - Wenjuan Wu
- grid.24516.340000000123704535Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123 China
| | - Lefu Lan
- grid.410726.60000 0004 1797 8419School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024 China ,grid.9227.e0000000119573309State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jianhua Gan
- grid.8547.e0000 0001 0125 2443School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Cai-Guang Yang
- grid.410726.60000 0004 1797 8419School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024 China ,grid.9227.e0000000119573309State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
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5
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The Development of the Bengamides as New Antibiotics against Drug-Resistant Bacteria. Mar Drugs 2022; 20:md20060373. [PMID: 35736176 PMCID: PMC9228497 DOI: 10.3390/md20060373] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 02/04/2023] Open
Abstract
The bengamides comprise an interesting family of natural products isolated from sponges belonging to the prolific Jaspidae family. Their outstanding antitumor properties, coupled with their unique mechanism of action and unprecedented molecular structures, have prompted an intense research activity directed towards their total syntheses, analogue design, and biological evaluations for their development as new anticancer agents. Together with these biological studies in cancer research, in recent years, the bengamides have been identified as potential antibiotics by their impressive biological activities against various drug-resistant bacteria such as Mycobacterium tuberculosis and Staphylococcus aureus. This review reports on the new advances in the chemistry and biology of the bengamides during the last years, paying special attention to their development as promising new antibiotics. Thus, the evolution of the bengamides from their initial exploration as antitumor agents up to their current status as antibiotics is described in detail, highlighting the manifold value of these marine natural products as valid hits in medicinal chemistry.
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6
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Hao Z, Wang W, Yu B, Qi X, Lv Y, Liu X, Chen H, Kalinina TA, Glukhareva TV, Fan Z. Design, Synthesis, and Evaluation of Fungicidal Activity of Novel
Pyrazole‐Containing
Strobilurin Derivatives
†. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zesheng Hao
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Weibo Wang
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Bin Yu
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Xin Qi
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - You Lv
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Xiaoyu Liu
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Haoyin Chen
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
| | - Tatiana A. Kalinina
- The Ural Federal University Named after the First President of Russia B. N. Yeltsin Yeltsin UrFU 620002 Ekaterinburg Russia
| | - Tatiana V. Glukhareva
- The Ural Federal University Named after the First President of Russia B. N. Yeltsin Yeltsin UrFU 620002 Ekaterinburg Russia
| | - Zhijin Fan
- State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University Tianjin 300071 China
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7
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Yu C, Wei B, Kong X, Yang C, Nan F. Synthesis and
Structure‐Activity
Relationships of
Ring‐Opened
Bengamide Analogues against
Methicillin‐Resistant
Staphylococcus aureus
†. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202000502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Chen‐Xi Yu
- State Key Laboratory of Drug Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences No.19A Yuquan Road Beijing 100049 China
| | - Bing‐Yan Wei
- State Key Laboratory of Drug Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS Hangzhou Zhejiang 310024 China
| | - Xue‐Qing Kong
- State Key Laboratory of Drug Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences No.19A Yuquan Road Beijing 100049 China
| | - Cai‐Guang Yang
- State Key Laboratory of Drug Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences No.19A Yuquan Road Beijing 100049 China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS Hangzhou Zhejiang 310024 China
| | - Fa‐Jun Nan
- State Key Laboratory of Drug Research, the National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences No.19A Yuquan Road Beijing 100049 China
- Yantai Key Laboratory of Nanomedicine & Advanced Preparations, Yantai Institute of Materia Medica Yantai Shandong 264000 China
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