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Tu B, Cao N, Zhang B, Zheng W, Li J, Tang X, Su K, Li J, Zhang Z, Yan Z, Li D, Zheng X, Zhang K, Hong WD, Wu P. Synthesis and Biological Evaluation of Novel Fusidic Acid Derivatives as Two-in-One Agent with Potent Antibacterial and Anti-Inflammatory Activity. Antibiotics (Basel) 2022; 11:antibiotics11081026. [PMID: 36009895 PMCID: PMC9405029 DOI: 10.3390/antibiotics11081026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/24/2022] [Accepted: 07/28/2022] [Indexed: 12/10/2022] Open
Abstract
Fusidic acid (FA), a narrow-spectrum antibiotics, is highly sensitive to various Gram-positive cocci associated with skin infections. It has outstanding antibacterial effects against certain Gram-positive bacteria whilst no cross-resistance with other antibiotics. Two series of FA derivatives were synthesized and their antibacterial activities were tested. A new aromatic side-chain analog, FA-15 exhibited good antibacterial activity with MIC values in the range of 0.781–1.563 µM against three strains of Staphylococcus spp. Furthermore, through the assessment by the kinetic assay, similar characteristics of bacteriostasis by FA and its aromatic derivatives were observed. In addition, anti-inflammatory activities of FA and its aromatic derivatives were evaluated by using a 12-O-tetradecanoylphorbol-13-acetate (TPA) induced mouse ear edema model. The results also indicated that FA and its aromatic derivatives effectively reduced TPA-induced ear edema in a dose-dependent manner. Following, multiform computerized simulation, including homology modeling, molecular docking, molecular dynamic simulation and QSAR was conducted to clarify the mechanism and regularity of activities. Overall, the present work gave vital clues about structural modifications and has profound significance in deeply scouting for bioactive potentials of FA and its derivatives.
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Affiliation(s)
- Borong Tu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
| | - Nana Cao
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
| | - Bingjie Zhang
- School of Biomedicine and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China;
| | - Wende Zheng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
| | - Jiahao Li
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
| | - Xiaowen Tang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
| | - Kaize Su
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
| | - Jinxuan Li
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
| | - Zhen Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
| | - Zhenping Yan
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
| | - Dongli Li
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
| | - Xi Zheng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
| | - Kun Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
- School of Biomedicine and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China;
- Correspondence: (K.Z.); (W.D.H.); (P.W.); Tel.: +86-13822330019 (K.Z.); +44-7863354263 (W.D.H.); +86-18825179347 (P.W.)
| | - Weiqian David Hong
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, UK
- Correspondence: (K.Z.); (W.D.H.); (P.W.); Tel.: +86-13822330019 (K.Z.); +44-7863354263 (W.D.H.); +86-18825179347 (P.W.)
| | - Panpan Wu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (B.T.); (N.C.); (W.Z.); (J.L.); (X.T.); (K.S.); (J.L.); (Z.Z.); (Z.Y.); (D.L.); (X.Z.)
- International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, China
- School of Biomedicine and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China;
- Correspondence: (K.Z.); (W.D.H.); (P.W.); Tel.: +86-13822330019 (K.Z.); +44-7863354263 (W.D.H.); +86-18825179347 (P.W.)
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Yuanyuan Z, Hongrui C, Qingrong S, Hongli C, Weiqing Y, Menglin M. Theoretical and experimental studies on the fluorescence properties of aluminum(III), cadmium(II), zinc(II), and copper(II) complexes of substituted 8-hydroxyquinoline. JOURNAL OF CHEMICAL RESEARCH 2020. [DOI: 10.1177/1747519820973601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Fifty-five 8-hydroxyquinoline (8-HQ) derivatives are synthesized and the corresponding aluminum(III), cadmium(II), copper(II), and zinc(II) metal complexes are prepared and their fluorescent activities are evaluated. The results indicate that the aluminum complexes have the best fluorescence properties, followed by zinc and cadmium complexes, while almost no fluorescence is observed with the copper complexes. The relationship between the fluorescence properties and complex structure is summarized and a predictive three-dimensional quantitative structure–property relationship model is established using the multifit molecular alignment rule of Sybyl program. With the introduction of groups at the C-2 position or electron-withdrawing groups to the 8-hydroxyquinoline framework, fluorescence wavelength blue shifts are observed with the zinc, aluminum, and cadmium complexes. At the same time, a red shift of the fluorescence emission wavelength is detected for the aluminum and zinc complexes when C-5 of 8-hydroxyquinoline was substituted with halogens or a methyl group. Moreover, the zinc, cadmium, and aluminum complexes with 2,4-dimethyl substituents on the 8-hydroxyquinoline all show good fluorescence properties. The highest occupied molecular orbital and lowest unoccupied molecular orbital energies of the complexes are also calculated and the fluorescence properties of the metal complexes are analyzed from the viewpoint of molecular orbitals.
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Affiliation(s)
- Zhang Yuanyuan
- School of Science, Xihua University, Chengdu, P.R. China
- College of Chemical Engineering, Sichuan University, Chengdu, P.R. China
| | - Cheng Hongrui
- School of Science, Xihua University, Chengdu, P.R. China
| | - Sun Qingrong
- School of Science, Xihua University, Chengdu, P.R. China
| | - Chen Hongli
- School of Science, Xihua University, Chengdu, P.R. China
| | - Yang Weiqing
- School of Science, Xihua University, Chengdu, P.R. China
| | - Ma Menglin
- School of Science, Xihua University, Chengdu, P.R. China
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Ahmad M, Dwivedy A, Mariadasse R, Tiwari S, Kar D, Jeyakanthan J, Biswal BK. Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase. ACS OMEGA 2020; 5:18356-18366. [PMID: 32743211 PMCID: PMC7391942 DOI: 10.1021/acsomega.0c02096] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/30/2020] [Indexed: 05/08/2023]
Abstract
The current COVID-19 outbreak warrants the design and development of novel anti-COVID therapeutics. Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. GTP is crucial for the formation of the initiation complex during RNA replication. This site was computationally targeted using a number of small molecule inhibitors of the hepatitis C RNA polymerase reported previously. Further optimizations suggested a lead molecule that may prove fruitful in the development of potent inhibitors against the RdRp of SARS-CoV2.
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Affiliation(s)
- Mohammed Ahmad
- National
Institute of Immunology, New Delhi 110067, India
| | | | - Richard Mariadasse
- Department
of Bioinformatics, Alagappa University, karaikudi 630004, Tamil Nadu, India
| | - Satish Tiwari
- National
Institute of Immunology, New Delhi 110067, India
| | - Deepsikha Kar
- National
Institute of Immunology, New Delhi 110067, India
| | - Jeyaraman Jeyakanthan
- Department
of Bioinformatics, Alagappa University, karaikudi 630004, Tamil Nadu, India
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Liu YY, Feng XY, Jia WQ, Jing Z, Xu WR, Cheng XC. Virtual identification of novel PPARα/γ dual agonists by 3D-QSAR, molecule docking and molecular dynamics studies. J Biomol Struct Dyn 2019; 38:2672-2685. [DOI: 10.1080/07391102.2019.1656110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ya-Ya Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiao-Yan Feng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wen-Qing Jia
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Zhi Jing
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ren Xu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Xian-Chao Cheng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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Vásquez-Domínguez E, Armijos-Jaramillo VD, Tejera E, González-Díaz H. Multioutput Perturbation-Theory Machine Learning (PTML) Model of ChEMBL Data for Antiretroviral Compounds. Mol Pharm 2019; 16:4200-4212. [PMID: 31426639 DOI: 10.1021/acs.molpharmaceut.9b00538] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Retroviral infections, such as HIV, are, until now, diseases with no cure. Medicine and pharmaceutical chemistry need and consider it a huge goal to define target proteins of new antiretroviral compounds. ChEMBL manages Big Data features with a complex data set, which is hard to organize. This makes information difficult to analyze due to a big number of characteristics described in order to predict new drug candidates for retroviral infections. For this reason, we propose to develop a new predictive model combining perturbation theory (PT) bases and machine learning (ML) modeling to create a new tool that can take advantage of all the available information. The PTML model proposed in this work for the ChEMBL data set preclinical experimental assays for antiretroviral compounds consists of a linear equation with four variables. The PT operators used are founded on multicondition moving averages, combining different features and simplifying the difficulty to manage all data. More than 140 000 preclinical assays for 56 105 compounds with different characteristics or experimental conditions have been carried out and can be found in ChEMBL database, covering combinations with 359 biological activity parameters (c0), 55 protein accessions (c1), 83 cell lines (c2), 64 organisms of assay (c3), and 773 subtypes or strains. We have included 150 148 preclinical experimental assays for HIV virus, 1188 for HTLV virus, 84 for simian immunodeficiency virus, 370 for murine leukemia virus, 119 for Rous sarcoma virus, 1581 for MMTV, etc. We also included 5277 assays for hepatitis B virus. The developed PTML model reached considerable values in sensibility (73.05% for training and 73.10% for validation), specificity (86.61% for training and 87.17% for validation), and accuracy (75.84% for training and 75.98% for validation). We also compared alternative PTML models with different PT operators such as covariance, moments, and exponential terms. Finally, we made a comparison between literature ML models with our PTML model and also artificial neural network (ANN) nonlinear models. We conclude that this PTML model is the first one to consider multiple characteristics of preclinical experimental antiretroviral assays combined, generating a simple, useful, and adaptable instrument, which could reduce time and costs in antiretroviral drugs research.
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Affiliation(s)
- Emilia Vásquez-Domínguez
- Department of Organic Chemistry II , University of Basque Country UPV/EHU , 48940 Leioa , Spain.,Faculty of Engineering and Applied Sciences-Biotechnology , Universidad de Las Américas (UDLA) , 170125 Quito , Ecuador
| | - Vinicio Danilo Armijos-Jaramillo
- Faculty of Engineering and Applied Sciences-Biotechnology , Universidad de Las Américas (UDLA) , 170125 Quito , Ecuador.,Bio-chemioinformatics group , Universidad de Las Américas (UDLA) , 170125 Quito , Ecuador
| | - Eduardo Tejera
- Faculty of Engineering and Applied Sciences-Biotechnology , Universidad de Las Américas (UDLA) , 170125 Quito , Ecuador.,Bio-chemioinformatics group , Universidad de Las Américas (UDLA) , 170125 Quito , Ecuador
| | - Humbert González-Díaz
- Department of Organic Chemistry II , University of Basque Country UPV/EHU , 48940 Leioa , Spain.,IKERBASQUE, Basque Foundation for Science , 48011 Bilbao , Spain
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Molecular mechanisms of tetrahydropyrrolo[1,2-c]pyrimidines as HBV capsid assembly inhibitors. Arch Biochem Biophys 2019; 663:1-10. [DOI: 10.1016/j.abb.2018.12.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/20/2018] [Accepted: 12/23/2018] [Indexed: 12/22/2022]
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Wang X, Xu Y, Yang L, Lu X, Zou H, Yang W, Zhang Y, Li Z, Ma M. Synthesis, Spectra, and Theoretical Investigations of 1,3,5-Triazines Compounds as Ultraviolet Rays Absorber Based on Time-Dependent Density Functional Calculations and three-Dimensional Quantitative Structure-Property Relationship. J Fluoresc 2018; 28:707-723. [PMID: 29717399 DOI: 10.1007/s10895-018-2235-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/23/2018] [Indexed: 11/26/2022]
Abstract
A series of 1,3,5-triazines were synthesized and their UV absorption properties were tested. The computational chemistry methods were used to construct quantitative structure-property relationship (QSPR), which was used to computer aided design of new 1,3,5-triazines ultraviolet rays absorber compounds. The experimental UV absorption data are in good agreement with those predicted data using the Time-dependent density functional theory (TD-DFT) [B3LYP/6-311 + G(d,p)]. A suitable forecasting model (R > 0.8, P < 0.0001) was revealed. Predictive three-dimensional quantitative structure-property relationship (3D-QSPR) model was established using multifit molecular alignment rule of Sybyl program, which conclusion is consistent with the TD-DFT calculation. The exceptional photostability mechanism of such ultraviolet rays absorber compounds was studied and confirmed as principally banked upon their ability to undergo excited-state deactivation via an ultrafast excited-state proton transfer (ESIPT). The intramolecular hydrogen bond (IMHB) of 1,3,5-triazines compounds is the basis for the excited state proton transfer, which was explored by IR spectroscopy, UV spectra, structural and energetic aspects of different conformers and frontier molecular orbitals analysis.
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Affiliation(s)
- Xueding Wang
- Key Lab of Advanced Scientific Computation of Sichuan Province, School of Science, Xihua University, Chengdu, 610039, China
| | - Yilian Xu
- Key Lab of Advanced Scientific Computation of Sichuan Province, School of Science, Xihua University, Chengdu, 610039, China
| | - Lu Yang
- Key Lab of Advanced Scientific Computation of Sichuan Province, School of Science, Xihua University, Chengdu, 610039, China
| | - Xiang Lu
- Key Lab of Advanced Scientific Computation of Sichuan Province, School of Science, Xihua University, Chengdu, 610039, China
| | - Hao Zou
- Key Lab of Advanced Scientific Computation of Sichuan Province, School of Science, Xihua University, Chengdu, 610039, China
| | - Weiqing Yang
- Key Lab of Advanced Scientific Computation of Sichuan Province, School of Science, Xihua University, Chengdu, 610039, China
| | - Yuanyuan Zhang
- Key Lab of Advanced Scientific Computation of Sichuan Province, School of Science, Xihua University, Chengdu, 610039, China
- Key lab of Green Chemistry and Technology of Ministry of Education. Faculty of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Zicheng Li
- College of Chemical Engineering, Sichuan University, Chengdu, 610065, China
| | - Menglin Ma
- Key Lab of Advanced Scientific Computation of Sichuan Province, School of Science, Xihua University, Chengdu, 610039, China.
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Tu J, Li JJ, Shan ZJ, Zhai HL. Exploring the binding mechanism of Heteroaryldihydropyrimidines and Hepatitis B Virus capsid combined 3D-QSAR and molecular dynamics. Antiviral Res 2017; 137:151-164. [DOI: 10.1016/j.antiviral.2016.11.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 11/23/2016] [Accepted: 11/27/2016] [Indexed: 02/08/2023]
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