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Folate-Targeted Curcumin-Loaded Niosomes for Site-Specific Delivery in Breast Cancer Treatment: In Silico and In Vitro Study. Molecules 2022; 27:molecules27144634. [PMID: 35889513 PMCID: PMC9322601 DOI: 10.3390/molecules27144634] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 12/21/2022] Open
Abstract
As the most common cancer in women, efforts have been made to develop novel nanomedicine-based therapeutics for breast cancer. In the present study, the in silico curcumin (Cur) properties were investigated, and we found some important drawbacks of Cur. To enhance cancer therapeutics of Cur, three different nonionic surfactants (span 20, 60, and 80) were used to prepare various Cur-loaded niosomes (Nio-Cur). Then, fabricated Nio-Cur were decorated with folic acid (FA) and polyethylene glycol (PEG) for breast cancer suppression. For PEG-FA@Nio-Cur, the gene expression levels of Bax and p53 were higher compared to free drug and Nio-Cur. With PEG-FA-decorated Nio-Cur, levels of Bcl2 were lower than the free drug and Nio-Cur. When MCF7 and 4T1 cell uptake tests of PEG-FA@Nio-Cur and Nio-Cur were investigated, the results showed that the PEG-FA-modified niosomes exhibited the most preponderant endocytosis. In vitro experiments demonstrate that PEG-FA@Nio-Cur is a promising strategy for the delivery of Cur in breast cancer therapy. Breast cancer cells absorbed the prepared nanoformulations and exhibited sustained drug release characteristics.
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Virtual screening of potential inhibitors from TCM for the CPSF30 binding site on the NS1A protein of influenza A virus. J Mol Model 2014; 20:2142. [PMID: 24562912 DOI: 10.1007/s00894-014-2142-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
Abstract
Inhibition of CPSF30 function by the effector domain of influenza A virus of non-structural protein 1 (NS1A) protein plays a critical role in the suppression of host key antiviral response. The CPSF30-binding site of NS1A appears to be a very attractive target for the development of new drugs against influenza A virus. In this study, structure-based molecular docking was utilized to screen more than 30,000 compounds from a Traditional Chinese Medicine (TCM) database. Four drug-like compounds were selected as potential inhibitors for the CPSF30-binding site of NS1A. Docking conformation analysis results showed that these potential inhibitors could bind to the CPSF30-binding site with strong hydrophobic interactions and weak hydrogen bonds. Molecular dynamics simulations and MM-PBSA calculations suggested that two of the inhibitors, compounds 32056 and 31674, could stably bind to the CPSF30-binding site with high binding free energy. These two compounds could be modified to achieve higher binding affinity, so that they may be used as potential leads in the development of new anti-influenza drugs.
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Zhou ZL, Liu HL, Wu JW, Tsao CW, Chen WH, Liu KT, Ho Y. Combining Structure-Based Pharmacophore andIn SilicoApproaches to Discover Novel Selective Serotonin Reuptake Inhibitors. Chem Biol Drug Des 2013; 82:705-17. [DOI: 10.1111/cbdd.12192] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 06/20/2013] [Accepted: 07/09/2013] [Indexed: 01/04/2023]
Affiliation(s)
- Zheng-Li Zhou
- Institute of Biochemical and Biomedical Engineering; National Taipei University of Technology; 1 Sec. 3 ZhongXiao E. Road Taipei 10608 Taiwan
| | - Hsuan-Liang Liu
- Institute of Biochemical and Biomedical Engineering; National Taipei University of Technology; 1 Sec. 3 ZhongXiao E. Road Taipei 10608 Taiwan
- Department of Chemical Engineering and Biotechnology; National Taipei University of Technology; 1 Sec. 3 ZhongXiao E. Road Taipei 10608 Taiwan
| | - Josephine W. Wu
- Department of Optometry; Central Taiwan University of Science and Technology; 666 Buzih Road Taichung 40601 Taiwan
| | - Cheng-Wen Tsao
- Department of Applied Cosmetology; Taoyuan Innovation Institute of Technology; 414 Sec. 3, Jhongshan E. Road Jhongli City Taoyuan County 32091 Taiwan
| | - Wei-Hsi Chen
- Chemistry Division; Institute of Nuclear Energy Research; 1000 Wunhua Road Longtan Township Taoyuan County 32546 Taiwan
| | - Kung-Tien Liu
- Everlight Chemical Industrial Corporation; 6th Fl, 77, Tun Hua South Road, Sec.2 Taipei 106 Taiwan
| | - Yih Ho
- School of Pharmacy; Taipei Medical University; 250 Wu-Hsing Street Taipei 110 Taiwan
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Chen KC, Chang SS, Tsai FJ, Chen CYC. Han ethnicity-specific type 2 diabetic treatment from traditional Chinese medicine? J Biomol Struct Dyn 2012; 31:1219-35. [PMID: 23146021 DOI: 10.1080/07391102.2012.732340] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Insulin-degrading enzyme (IDE) gene is one of the type 2 diabetes mellitus susceptibility genes specific to the Han Chinese population. IDE, a zinc-metalloendopeptidase, is a potential target for controlling insulin degradation. Potential lead compounds for IDE inhibition were identified from traditional Chinese medicine (TCM) through virtual screening and evaluation of their pharmacokinetic properties of absorption, distribution, metabolism, excretion, and toxicity. Molecular dynamics (MD) simulation was performed to validate the stability of complexes from docking simulation. The top three TCM compounds, dihydrocaffeic acid, isopraeroside IV, and scopolin, formed stable H-bond interactions with key residue Asn139, and were linked to active pocket residues His108, His112, and Glu189 through zinc. Torsion angle trajectories also indicated some stable interactions for each ligand with IDE. Molecular level analysis revealed that the TCM candidates might affect IDE through competitive binding to the active site and steric hindrance. Structural feature analysis reveals that high amounts of hydroxyl groups and carboxylic moieties contribute to anchor the ligand within the complex. Hence, we suggest the top three TCM compounds as potential inhibitor leads against IDE protein to control insulin degradation for type 2 diabetes mellitus. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:29.
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Affiliation(s)
- Kuan-Chung Chen
- a Graduate Institute of Pharmaceutical Chemistry, China Medical University , Taichung , 40402 , Taiwan
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Chen KC, Jian YR, Sun MF, Chang TT, Lee CC, Chen CYC. Investigation of silent information regulator 1 (Sirt1) agonists from Traditional Chinese Medicine. J Biomol Struct Dyn 2012; 31:1207-18. [PMID: 23075283 DOI: 10.1080/07391102.2012.726191] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Silent information regulator 1 (Sirt1), a class III nicotinamide adenine dinucleotide dependent histone deacetylases, is important in cardioprotection, neuroprotection, metabolic disease, calorie restriction, and diseases associated with aging. Traditional Chinese Medicine (TCM) compounds from TCM Database@Taiwan ( http://tcm.cmu.edu.tw/ ) were employed for screening potent Sirt1 agonists, and molecular dynamics (MD) simulation was implemented to simulate ligand optimum docking poses and protein structure under dynamic conditions. TCM compounds such as (S)-tryptophan-betaxanthin, 5-O-feruloylquinic acid, and RosA exhibited good binding affinity across different computational methods, and their drug-like potential were validated by MD simulation. Docking poses indicate that the carboxylic group of the three candidates generated H-bonds with residues in the protein chain from Ser441 to Lys444 and formed H-bond, π-cation interactions, or hydrophobic contacts with Phe297 and key active residue, His363. During MD, stable π-cation interactions with residues Phe273 or Arg274 were formed by (S)-tryptophan-betaxanthin and RosA. All candidates were anchored to His363 by stable π- or H-bonds. Hence, we propose (S)-tryptophan-betaxanthin, 5-O-feruloylquinic acid, and RosA as potential lead compounds that can be further tested in drug development process for diseases associated with aging An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:28.
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Affiliation(s)
- Kuan-Chung Chen
- a Graduate Institute of Pharmaceutical Chemistry, China Medical University , Taichung , 40402 , Taiwan
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Chen KC, Chang SS, Huang HJ, Lin TL, Wu YJ, Chen CYC. Three-in-one agonists for PPAR-α, PPAR-γ, and PPAR-δ from traditional Chinese medicine. J Biomol Struct Dyn 2012; 30:662-83. [DOI: 10.1080/07391102.2012.689699] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Chang SS, Huang HJ, Chen CYC. Two birds with one stone? Possible dual-targeting H1N1 inhibitors from traditional Chinese medicine. PLoS Comput Biol 2011; 7:e1002315. [PMID: 22215997 PMCID: PMC3245300 DOI: 10.1371/journal.pcbi.1002315] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 11/03/2011] [Indexed: 12/20/2022] Open
Abstract
The H1N1 influenza pandemic of 2009 has claimed over 18,000 lives. During this pandemic, development of drug resistance further complicated efforts to control and treat the widespread illness. This research utilizes traditional Chinese medicine Database@Taiwan (TCM Database@Taiwan) to screen for compounds that simultaneously target H1 and N1 to overcome current difficulties with virus mutations. The top three candidates were de novo derivatives of xylopine and rosmaricine. Bioactivity of the de novo derivatives against N1 were validated by multiple machine learning prediction models. Ability of the de novo compounds to maintain CoMFA/CoMSIA contour and form key interactions implied bioactivity within H1 as well. Addition of a pyridinium fragment was critical to form stable interactions in H1 and N1 as supported by molecular dynamics (MD) simulation. Results from MD, hydrophobic interactions, and torsion angles are consistent and support the findings of docking. Multiple anchors and lack of binding to residues prone to mutation suggest that the TCM de novo derivatives may be resistant to drug resistance and are advantageous over conventional H1N1 treatments such as oseltamivir. These results suggest that the TCM de novo derivatives may be suitable candidates of dual-targeting drugs for influenza.
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Affiliation(s)
- Su-Sen Chang
- Laboratory of Computational and Systems Biology, China Medical University, Taichung, Taiwan
| | - Hung-Jin Huang
- Sciences and Chinese Medicine Resources, China Medical University, Taichung, Taiwan
| | - Calvin Yu-Chian Chen
- Laboratory of Computational and Systems Biology, China Medical University, Taichung, Taiwan
- Department of Bioinformatics, Asia University, Taichung, Taiwan
- China Medical University Beigang Hospital, Yunlin, Taiwan
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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Chang TT, Sun MF, Chen HY, Tsai FJ, Fisher M, Lin JG, Chen CYC. Screening from the world's largest TCM database against H1N1 virus. J Biomol Struct Dyn 2011; 28:773-86. [PMID: 21294588 DOI: 10.1080/07391102.2011.10508605] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The swine influenza virus (H1N1) 2009 pandemic highlights the importance of having effective anti-viral strategies. Recently, oseltamivir (Tamiflu) resistant influenza viruses are identified; which further emphasizes the urgency in developing new antiviral agents. In influenza virus replication cycle, viral surface glycoprotein, hemagglutinin, is responsible for viral entry into host cells. Hence, a potentially effective antiviral strategy is to inhibit viral entry mechanism. To develop novel antiviral agent that inhibits viral entry, we analyzed 20,000 traditional Chinese medicine (TCM) ingredients in hemagglutinin subtype H1 sialic acid binding site found on H1N1 virus. We then performed molecular dynamics simulations to investigate receptor-ligand interaction of the candidates obtained from docking. Here, we report three TCM derivatives that have high binding affinities to H1 sialic acid binding site residues based on structure-based calculations. The top three derivatives, xylopine_2, rosmaricine_14 and rosmaricine_15, all have an amine group that interact with Glu83 and a pyridinium group that interact with Asp103. Molecular dynamics simulations show that these derivatives form strong hydrogen bonding with Glu83 but interact transiently with Asp103. We therefore suggest that an enhanced hemagglutinin inhibitor, based on our scaffold, should be designed to bind both Glu83 and Asp103 with high affinity.
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Affiliation(s)
- Tung-Ti Chang
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
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Sun MF, Yang SC, Chang KW, Tsai TY, Chen HY, Tsai FJ, Lin JG, Chen CYC. Screening from TCM Database@Taiwan and QSAR model for identifying HER2 inhibitors. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.569550] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Combined ligand based pharmacophore modeling, virtual screening methods to identify critical chemical features of novel potential inhibitors for phosphodiesterase-5. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2011.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Drug design for mPGES-1 from traditional Chinese medicine database: A screening, docking, QSAR, molecular dynamics, and pharmacophore mapping study. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2010.11.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Chang TT, Sun MF, Chen HY, Tsai FJ, Chen CYC. Drug design for hemagglutinin: Screening and molecular dynamics from traditional Chinese medicine database. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2010.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tsai TY, Chang KW, Chen CYC. iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan. J Comput Aided Mol Des 2011; 25:525-31. [PMID: 21647737 DOI: 10.1007/s10822-011-9438-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 05/16/2011] [Indexed: 11/26/2022]
Abstract
The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.
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Affiliation(s)
- Tsung-Ying Tsai
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
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Chang TT, Sun MF, Chang KW, Chen HY, Tsai FJ, Fisher M, Lin JG, Chen CYC. Screening from the world's largest TCM database for inhibiting DNA repair protein XRCC4. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.554550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Lin CH, Chang TT, Sun MF, Chen HY, Tsai FJ, Chang KL, Fisher M, Chen CYC. Potent inhibitor design against H1N1 swine influenza: structure-based and molecular dynamics analysis for M2 inhibitors from traditional Chinese medicine database. J Biomol Struct Dyn 2011; 28:471-82. [PMID: 21142218 DOI: 10.1080/07391102.2011.10508589] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The rapid spread of influenza virus subtype H1N1 poses a great threat to million lives worldwide. To search for new anti-influenza compounds, we performed molecular docking and molecular dynamics simulation to identify potential traditional Chinese medicine (TCM) constituents that could block influenza M2 channel activity. Quinic acid, genipin, syringic acid, cucurbitine, fagarine, and methyl isoferulate all have extremely well docking results as compared to control amantadine. Further de novo drug design suggests that derivatives of genipin and methyl isoferulate could have enhanced binding affinity towards M2 channel. Selected molecular dynamics simulations of M2-derivative complexes show stable hydrogen bond interactions between the derivatives and M2 residues, Ser10 and Ala9. To our best knowledge, this is the first study on the anti-viral activity of the above listed TCM compounds.
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Affiliation(s)
- Chia-Hui Lin
- Department of Chinese Medicine, China Medical University Hospital, Taiwan
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Du QS, Wei H, Huang RB, Chou KC. Progress in structure-based drug design against influenza A virus. Expert Opin Drug Discov 2011; 6:619-31. [PMID: 22646152 DOI: 10.1517/17460441.2011.571671] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The 2009-H1N1 influenza pandemic has prompted new global efforts to develop new drugs and drug design techniques to combat influenza viruses. While there have been a number of attempts to provide drugs to treat influenza, drug resistance has been a major problem with only four drugs currently approved by the FDA for its treatment. AREAS COVERED In this review, the drug-resistant problem of influenza A viruses is discussed and summarized. The article also introduces the experimental and computational structures of drug targeting proteins, neuraminidases, and of the M2 proton channel. Furthermore, the article illustrates the latest drug candidates and techniques of computer-aided drug design with examples of their application, including virtual in silico screening and scoring, AutoDock and evolutionary technique AutoGrow. EXPERT OPINION Structure-based drug design is the inventive process for finding new drugs based on the structural knowledge of the biological target. Computer-aided drug design strategies and techniques will make drug discovery more effective and economical. It is anticipated that the recent advances in structure-based drug design techniques will greatly help scientists to develop more powerful and specific drugs to fight the next generation of influenza viruses.
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Affiliation(s)
- Qi-Shi Du
- Guangxi University, Life Science and Biotechnology College, Nanning, Guangxi, 530004 , China
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Lai CY, Chang TT, Sun MF, Chen HY, Tsai FJ, Lin JG, Chen CYC. Molecular dynamics analysis of potent inhibitors of M2 proton channel against H1N1 swine influenza virus. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2010.543972] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Huang HJ, Chen CY, Chen HY, Tsai FJ, Chen CYC. Computational screening and QSAR analysis for design of AMP-activated protein kinase agonist. J Taiwan Inst Chem Eng 2010. [DOI: 10.1016/j.jtice.2009.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Chen CYC. Computational screening and design of traditional Chinese medicine (TCM) to block phosphodiesterase-5. J Mol Graph Model 2009; 28:261-9. [PMID: 19747866 DOI: 10.1016/j.jmgm.2009.08.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 07/31/2009] [Accepted: 08/03/2009] [Indexed: 01/25/2023]
Abstract
The traditional Chinese medicines (TCM), Epimedium sagittatum (ESs), Cnidium monnieri (CMs), and Semen cuscutae (SCs), were used for treating erectile dysfunction since the ancient Han dynasty (202 BC-AD 220). Phosphodiesterase-5 (PDE-5) is deemed the target protein for inhibition to treat erectile dysfunction. In this study, a reliable multiple linear regression (MLR) model (r value=0.8484) was used to predict the activities of new candidates which were designed from ES, CM, and SC. From docking and pharmacophore analysis, the potent candidates among ES, CM, and SC were screened. SC01, SC03, and ES03b were predicted to have high potencies based on MLR analysis and high docking scores. Additionally, from our analysis, we make the follow conclusion (1) Hydrophobic compounds tend to be more potent PDE-5 inhibitors; (2) Because of the big binding site, inhibitors with molecular weights over 500 remain potent; (3) From the pharmacophore analysis, the features of hydrogen bond acceptors are the basis for designing novel inhibitors of PDE-5 and (4) According to MLR analysis, the number of ring groups could be up to 6, but the number of aromatic rings was limited to 4 to be potent. This study offers an alternative way to screen PDE-5 inhibitors from TCM and provides a scientific basis for confirming pharmacological actions of TCM.
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Affiliation(s)
- Calvin Yu-Chian Chen
- Laboratory of Pharmacoinformatics and Nanotechnology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan, ROC.
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