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Dorafshan Tabatabai AS, Dehghanian E, Mansouri-Torshizi H. Exploring the Interaction Between the Newly Designed Antitumor Zn(II) Complex and CT-DNA/BSA: Spectroscopic Methods, DFT Computational Analysis, and Docking Simulation. Appl Biochem Biotechnol 2023; 195:6276-6308. [PMID: 36856984 DOI: 10.1007/s12010-023-04394-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2023] [Indexed: 03/02/2023]
Abstract
A new zinc(II) complex formulated as [Zn(pipr-ac)2], where pipr-ac stands for piperidineacetate, was synthesized and structurally identified with the help of experimental and DFT methods. Frontier molecular orbital (FMO) analysis demonstrated that the new complex has higher biological activity compared to the free ligand. Molecular electrostatic potential (MEP) showed the nitrogen atoms and oxygen of carbonyl groups are the active sites of Zn(II) compound. Also, natural bond orbital (NBO) analysis confirmed the charge transfer from the ligating atoms to the metal ion and formation of four coordinated Zn(II) complex. MTT assay illustrated a noticeable cytotoxic activity of the new zinc(II) complex compared to cisplatin on K562 cell line. The CT-DNA and serum albumin (SA) binding of the Zn(II) complex were explored individually. In this regard, UV-Vis spectroscopy and florescence titration revealed the occurrences of fluorescence quenching of CT-DNA/SA by metal compound via static mechanism and creation of hydrogen bonds and van der Waals interactions between them. The binding was further confirmed by viscosity measurement and gel electrophoresis assay for CT-DNA and circular dichroism spectroscopy for SA. Moreover, molecular docking simulation demonstrated that the new compound binds mainly through hydrogen bonds to the groove of DNA and hydrogen bonds and van der Waals interactions to site I of SA.
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Affiliation(s)
| | - Effat Dehghanian
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran.
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2
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Ram Kumar A, Selvaraj S, Azam M, Sheeja Mol G, Kanagathara N, Alam M, Jayaprakash P. Spectroscopic, Biological, and Topological Insights on Lemonol as a Potential Anticancer Agent. ACS OMEGA 2023; 8:31548-31566. [PMID: 37663516 PMCID: PMC10468887 DOI: 10.1021/acsomega.3c04922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/03/2023] [Indexed: 09/05/2023]
Abstract
A monoterpene alcohol known as lemonol was investigated experimentally as well as theoretically in order to gain insights into its geometrical structure, vibrational frequencies, solvent effects on electronic properties, molecular electrostatic potential, Mulliken atomic charge distribution, natural bond orbital, and Nonlinear Optical properties. The frontier molecular orbital energy gap values of 5.9084 eV (gas), 5.9261 eV (ethanol), 5.9185 eV (chloroform), 5.9253 eV (acetone), and 5.9176 eV (diethyl ether) were predicted, and it shows the kinetic stability and chemical reactivity of lemonol. Topological studies were conducted using Multiwfn software to understand the binding sites and weak interactions in lemonol. The antiproliferative effect of lemonol against the breast cancer cell line Michigan Cancer Foundation (MCF-7) was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, while nuclear damage, condensation, and reactive oxygen species generation were identified using acridine orange/ethidium bromide, propidium iodide, and dichlorodihydrofluorescein diacetate staining. The theoretical and experimental findings are highly correlated, confirming the structure, and the results of in vitro studies suggest that lemonol acts as a potent inhibitor against the human breast cancer cell line MCF-7, highlighting its strong antiproliferative activity.
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Affiliation(s)
- A. Ram Kumar
- Department
of Biotechnology, Saveetha School of Engineering,
Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai 602105, Tamil Nadu, India
| | - S. Selvaraj
- Department
of Physics, Saveetha School of Engineering,
Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai 602105, Tamil Nadu, India
| | - Mohammad Azam
- Department
of Chemistry, College of Science, King Saud
University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - G.P. Sheeja Mol
- PG
Department of Physics, St. Joseph’s
College for Women, Alappuzha 688001, Kerala, India
- Affiliated
to University of Kerala, Thiruvananthapuram 695034, Kerala, India
| | - N. Kanagathara
- Department
of Physics, Saveetha School of Engineering,
Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai 602105, Tamil Nadu, India
| | - Mahboob Alam
- Department
of Safety Engineering, Dongguk University, 123 Dongdae-ro, Gyeongju 780714, Gyeongbuk, South Korea
| | - P. Jayaprakash
- Department
of Physics, St. Joseph’s Institute
of Technology, OMR, Chennai 600119, Tamil Nadu, India
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3
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Effect of green solvents physical, chemical, biological and bonding nature on 5-acetyl-thiophene-2-carboxylic acid by DFT and TD-DFT approach – An antiviral agent. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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4
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Rajesh R, Muthu S, Sheela NR. Effect of Amino, Chloro, and Methyl Functional Groups on 4-(4-Hydroxyphenyl) Piperazine by Density Functional Theory and Molecular Docking Studies. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2125992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- R. Rajesh
- Department of Physics, Vel Tech High Tech Dr. Rangarajan Dr. Sakunthala Engineering College (Autonomous), Chennai, India
| | - S. Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, India
| | - N. R. Sheela
- Department of Physics, Sri Venkateswara College of Engineering (Autonomous), Sriperumbudur, India
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Rajesh R, Muthu S, Sheela N. Investigations of 6-Fluoro-4-Oxo-3,4-Dihydro-2H-Chromene-2-Carboxylic Acid by Quantum Computational, Spectroscopic, TD-DFT with Various Solvents and Molecular Docking Studies. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2124284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- R. Rajesh
- Department of Physics, Vel Tech High Tech Dr. Rangarajan Dr. Sakunthala Engineering College (Autonomous), Chennai, India
| | - S. Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, India
| | - N.R. Sheela
- Department of Applied Physics, Sri Venkateswara College of Engineering (Autonomous), Chennai, India
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Spectroscopic and molecular electronic property investigation of 2-phenylpyrimidine-4, 6-diamine via 1H NMR, UV–vis, FT-Raman, FT-IR, and DFT approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133195] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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7
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Govindammal M, Kannan S, Srinivasan P, Prasath M. Quantum chemical calculations, spectroscopic studies and molecular docking investigations of the anti-cancer drug quercitrin with B-RAF inhibitor. Heliyon 2022; 8:e09539. [PMID: 35663763 PMCID: PMC9160043 DOI: 10.1016/j.heliyon.2022.e09539] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/23/2021] [Accepted: 05/19/2022] [Indexed: 11/27/2022] Open
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8
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Ahamed JI, Ramkumaar G, Kamalarajan P, Narendran K, Valan M, Sundareswaran T, Sundaravadivel T, Venkatadri B, Bharathi S. Novel quinoxaline derivatives of 2, 3-diphenylquinoxaline-6-carbaldehyde and 4, 4′-(6-methylquinoxaline-2,3-diyl)bis(N,N-diphenylaniline): Synthesis, structural, DFT-computational, molecular docking, antibacterial, antioxidant, and anticancer studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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9
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Spectroscopic (FT-IR, FT-Raman) investigations, quantum chemical calculations, ADMET and molecular docking studies of phloretin with B-RAF inhibitor. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01576-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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FT-IR and FT-Raman investigation, quantum chemical studies, molecular docking study and antimicrobial activity studies on novel bioactive drug of 1-(2,4-Dichlorobenzyl)-3-[2-(3-(4-chlorophenyl)-5-(4-(propan-2-yl)phenyl-4,5-dihydro-1H-pyrazol-1-yl]-4-oxo-4,5-dihydro-1,3-thiazol-5(4H)-ylidence]-2,3-dihydro-1H-indol-2-one. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128244] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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11
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Govindammal M, Prasath M. Vibrational spectra, Hirshfeld surface analysis, molecular docking studies of (RS)-N,N-bis(2-chloroethyl)-1,3,2-oxazaphosphinan-2-amine 2-oxide by DFT approach. Heliyon 2020; 6:e04641. [PMID: 32904270 PMCID: PMC7452535 DOI: 10.1016/j.heliyon.2020.e04641] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/11/2020] [Accepted: 08/03/2020] [Indexed: 01/06/2023] Open
Abstract
The Cyclophosphamide (CYC) is used as an anti cancer agent. It is chemically known as (RS)-N,N-bis(2-chloroethyl)-1,3,2-oxazaphosphinan-2-amine 2-oxide. The vibrational assignments survey of the CYC was implemented by employing FT-IR and FT-Raman spectroscopic investigation and the results are compared with theoretical features. The optimized geometrical parameters, IR intensity and Raman Activity of the vibrational bands of CYC were determined from the B3LYP functional with 6-311++G (d, p) level of theory. In the current work, quantum chemical calculations were adopted to contemplate the vibrational assignments of CYC and the outcomes are compared with experimental findings. Molecular Electrostatic Potential (MEP) and HOMO-LUMO energies are very effective in the examination of charge transfer and distribution of the molecular structure. The molecular orbital contributions were evaluated by using the Total Density of States (TDOS). The analysis of Natural Bond Orbital (NBO), Mulliken population and Fukui function studies were done. Intermolecular interaction of the title compound was examined through Hirshfeld surface analysis. The evaluation of drug-likeness was accomplished in accordance with Lipinski's Rule of Five and molecular descriptors were utilized to predict the ADMET profiles of the CYC molecule. The recent research studies reports that the structural and bio-activity of the CYC was affirmed by the docking analysis of CYC with protein PI3K/AKT inhibitor, it acts as anti-lung cancer agent.
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Affiliation(s)
- M. Govindammal
- Department of Physics, Periyar University PG Extension Centre, Dharmapuri, 636701, India
| | - M. Prasath
- Department of Physics, Periyar University PG Extension Centre, Dharmapuri, 636701, India
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Sathya B, Karthi S, Ajaijawahar K, Prasath M. Probing the vibrational spectroscopic properties and binding mechanism of anti-influenza agent Liquiritin using experimental and computational studies. RESEARCH ON CHEMICAL INTERMEDIATES 2020. [DOI: 10.1007/s11164-020-04216-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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13
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Quantum chemical calculations, spectroscopic investigation and molecular docking analysis of 4-chloro-N-methylpyridine-2-carboxamide. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Viji A, Balachandran V, Babiyana S, Narayana B, Saliyan VV. Molecular docking and quantum chemical calculations of 4-methoxy-{2-[3-(4-chlorophenyl)-5-(4-(propane-2-yl) PHENYL)-4, 5-dihydro-1H-pyrazol-1-yl]- 1, 3-thiazol-4-yl}phenol. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127452] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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15
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Saji RS, Prasana JC, Muthu S, George J, Kuruvilla TK, Raajaraman BR. Spectroscopic and quantum computational study on naproxen sodium. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 226:117614. [PMID: 31606674 DOI: 10.1016/j.saa.2019.117614] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/05/2019] [Accepted: 10/06/2019] [Indexed: 06/10/2023]
Abstract
The spectroscopic (FT-IR, FT-Raman, NMR), electronic (UV--Vis.), structural and thermodynamical properties of an anti-inflammatory analgesic called Naproxen Sodium, (s)-6-methoxy-α-methyl-2-naphthaleneacetic acid sodium salt are submitted by using both experimental techniques and theoretical methods as quantum chemical calculations in this work. The equilibrium geometry and vibrational spectra are calculated by using DFT (B3LYP) with 6-311++G (d,p) basis set using GAUSSIAN 09. The vibrational wavenumbers are also corrected with scale factor to take better results for the calculated data. The HOMO-LUMO calculations are carried out on the title compound. The theoretical and experimental NMR peaks were found to be in good agreement. In addition, the detailed study on the Non-Bonding Orbitals, the excitation energies, AIM charges, condensed fukui calculations, thermodynamical properties, Localized Orbital Locator (LOL) and Electron Localization Function (ELF) are also performed. Furthermore, the study is extended to calculate the first order hyperpolarizability and to predict its NLO properties. The docking studies details helped on predicting the binding with different proteins.
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Affiliation(s)
- Rinnu Sara Saji
- Department of Physics, Madras Christian College, East Tambaram, 600059, Tamil Nadu, India; University of Madras, Chennai, 600005, Tamilnadu, India
| | | | - S Muthu
- Department of Physics, Arignar Anna Government Arts College, Cheyyar, 604407, Tamil Nadu, India.
| | - Jacob George
- Department of Physics, Madras Christian College, East Tambaram, 600059, Tamil Nadu, India
| | - Tintu K Kuruvilla
- Department of Physics, Madras Christian College, East Tambaram, 600059, Tamil Nadu, India
| | - B R Raajaraman
- Department of Physics, Sri Venkateswara College of Engineering, Sriperumbudur, 602 117, Tamil Nadu, India
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Basha SJ, Chamundeeswari SV, Muthu S, Raajaraman BR. Quantum computational, spectroscopic investigations on 6-aminobenzimidazole by DFT/TD-DFT with different solvents and molecular docking studies. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111787] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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17
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Raajaraman BR, Sheela NR, Muthu S. Spectroscopic, quantum computational and molecular docking studies on 1-phenylcyclopentane carboxylic acid. Comput Biol Chem 2019; 82:44-56. [PMID: 31260880 DOI: 10.1016/j.compbiolchem.2019.05.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/18/2019] [Accepted: 05/27/2019] [Indexed: 12/20/2022]
Abstract
The vibrational wavenumbers of optimized molecular structure of 1-phenylcyclopentane carboxylic acid (1PCPCA) molecule have been calculated by quantum chemical theory and compared with experimental results. The density functional theory (DFT) approach is followed using the method B3LYP and 6-311++G(d,p) basis set. Using potential energy distribution, all the assignments of the basic vibrational modes were calculated. Natural bond orbital (NBO) and atoms in molecules (AIM) topological studies applied to get the intermolecular interactions of the compound. 1H and 13C chemical shift of NMR was estimated on the molecule and also compared with the experimental spectra. In order to find the band gap, the time-dependent (TD-DFT) method is used to get the higher order energy levels properties and also compared with experimental data of UV-vis spectrum. From the analysis of various spectroscopic studies, there is a good relationship between the experimental and theoretical values obtained. Quantum characters, bio-active nature and reactive areas of the molecule are revealed by Fukui function, molecular electrostatic potential (MEP) and Hirshfeld surface studies. The human enzyme steroidogenic types and their protein targets were tested with this molecule by molecular docking.
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Affiliation(s)
- B R Raajaraman
- Department of Applied Physics, Sri Venkateswara College of Engineering, Sriperumbudur, 602 117, Tamil Nadu, India
| | - N R Sheela
- Department of Applied Physics, Sri Venkateswara College of Engineering, Sriperumbudur, 602 117, Tamil Nadu, India
| | - S Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, 604 407, Tamil Nadu, India.
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Influence of acetyl, hydroxy and methyl functional groups on 2-phenylbutanoic acid by quantum computational, spectroscopic and ligand-protein docking studies. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.03.093] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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19
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Aayisha S, Renuga Devi T, Janani S, Muthu S, Raja M, Sevvanthi S. DFT, molecular docking and experimental FT-IR, FT-Raman, NMR inquisitions on “4-chloro-N-(4,5-dihydro-1H-imidazol-2-yl)-6-methoxy-2-methylpyrimidin-5-amine”: Alpha-2-imidazoline receptor agonist antihypertensive agent. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.03.056] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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20
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Zhang M, Zeng G, Liao X, Wang Y. An antibacterial and biocompatible piperazine polymer. RSC Adv 2019; 9:10135-10147. [PMID: 35520902 PMCID: PMC9062374 DOI: 10.1039/c9ra02219h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 12/20/2022] Open
Abstract
Bacterial repellence by biomedical materials is a desirable property that can potentially improve the healing process. In this study, we described a simple and green method to prepare a novel piperazine polymer (PE), which was based on the raw materials piperazine (PA) and ethylenediaminetetraacetic dianhydride (EDTAD). The structure and thermal stability of the obtained material were characterized using Fourier transform infrared spectrometry (FTIR), nuclear magnetic resonance spectroscopy (NMR), elementary analysis, differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). To evaluate the antibacterial properties of PE, a strain of Gram-negative Escherichia coli (E. coli) bacteria and a strain of Gram-positive Staphylococcus aureus (S. aureus) bacteria were used. The results indicated that PE exhibited good antibacterial activity against both strains of bacteria in a short time frame. The initial cytotoxicity test of the obtained material was based on the changes in the morphology and proliferation of osteoblasts, and the results demonstrated that the cytotoxicity of PE was concentration-dependent. Combining the experimental results of these two parts, it was shown that bacteria could be inhibited by a certain concentration of PE, while its toxicity toward osteoblasts was very low. In summary, these results revealed the potential usefulness of PE in biomedical applications.
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Affiliation(s)
- Maolan Zhang
- Chongqing University of Science and Technology Chongqing 401331 China +86 17830862118 +86 17830862118
| | - Guoming Zeng
- Chongqing University of Science and Technology Chongqing 401331 China +86 17830862118 +86 17830862118
| | - Xiaoling Liao
- Chongqing University of Science and Technology Chongqing 401331 China +86 17830862118 +86 17830862118
| | - Yuanliang Wang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education Chongqing 400044 China
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