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Pantelic L, Skaro Bogojevic S, Andrejević TP, Pantović BV, Marković VR, Ašanin DP, Milanović Ž, Ilic-Tomic T, Nikodinovic-Runic J, Glišić BĐ, Lazic J. Copper(II) and Zinc(II) Complexes with Bacterial Prodigiosin Are Targeting Site III of Bovine Serum Albumin and Acting as DNA Minor Groove Binders. Int J Mol Sci 2024; 25:8395. [PMID: 39125963 PMCID: PMC11313072 DOI: 10.3390/ijms25158395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
The negative environmental and social impacts of food waste accumulation can be mitigated by utilizing bio-refineries' approach where food waste is revalorized into high-value products, such as prodigiosin (PG), using microbial bioprocesses. The diverse biological activities of PG position it as a promising compound, but its high production cost and promiscuous bioactivity hinder its wide application. Metal ions can modulate the electronic properties of organic molecules, leading to novel mechanisms of action and increased target potency, while metal complex formation can improve the stability, solubility and bioavailability of the parent compound. The objectives of this study were optimizing PG production through bacterial fermentation using food waste, allowing good quantities of the pure natural product for further synthesizing and evaluating copper(II) and zinc(II) complexes with it. Their antimicrobial and anticancer activities were assessed, and their binding affinity toward biologically important molecules, bovine serum albumin (BSA) and DNA was investigated by fluorescence emission spectroscopy and molecular docking. The yield of 83.1 mg/L of pure PG was obtained when processed meat waste at 18 g/L was utilized as the sole fermentation substrate. The obtained complexes CuPG and ZnPG showed high binding affinity towards target site III of BSA, and molecular docking simulations highlighted the affinity of the compounds for DNA minor grooves.
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Affiliation(s)
- Lena Pantelic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia; (L.P.); (S.S.B.); (T.I.-T.); (J.N.-R.)
| | - Sanja Skaro Bogojevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia; (L.P.); (S.S.B.); (T.I.-T.); (J.N.-R.)
| | - Tina P. Andrejević
- Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia; (T.P.A.); (B.V.P.); (V.R.M.)
| | - Bojana V. Pantović
- Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia; (T.P.A.); (B.V.P.); (V.R.M.)
| | - Violeta R. Marković
- Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia; (T.P.A.); (B.V.P.); (V.R.M.)
| | - Darko P. Ašanin
- Department of Science, Institute for Information Technologies Kragujevac, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia; (D.P.A.); (Ž.M.)
| | - Žiko Milanović
- Department of Science, Institute for Information Technologies Kragujevac, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia; (D.P.A.); (Ž.M.)
| | - Tatjana Ilic-Tomic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia; (L.P.); (S.S.B.); (T.I.-T.); (J.N.-R.)
| | - Jasmina Nikodinovic-Runic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia; (L.P.); (S.S.B.); (T.I.-T.); (J.N.-R.)
| | - Biljana Đ. Glišić
- Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia; (T.P.A.); (B.V.P.); (V.R.M.)
| | - Jelena Lazic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11000 Belgrade, Serbia; (L.P.); (S.S.B.); (T.I.-T.); (J.N.-R.)
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Structures, biosynthesis, and bioactivities of prodiginine natural products. Appl Microbiol Biotechnol 2022; 106:7721-7735. [DOI: 10.1007/s00253-022-12245-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/06/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022]
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Huang X, Zhan J, Huang Y, Chen H, Liang Z, Gan C. Studies on the interaction between 3-biotinylate-6-benzimidazole B-nor-cholesterol analogs and ct-DNA. NEW J CHEM 2022. [DOI: 10.1039/d2nj00896c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction mechanism between 3-biotinylate-6-benzimidazole B-nor-cholesterol analogs and ct-DNA was studied under conditions similar to physiological. The interaction mechanism between ct-DNA and three different types of compounds was studied by spectroscopic...
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Kettenmann SD, White M, Colard-Thomas J, Kraft M, Feßler AT, Danz K, Wieland G, Wagner S, Schwarz S, Wiehe A, Kulak N. Investigating Alkylated Prodigiosenes and Their Cu(II)-Dependent Biological Activity: Interactions with DNA, Antimicrobial and Photoinduced Anticancer Activity. ChemMedChem 2021; 17:e202100702. [PMID: 34779147 PMCID: PMC9306646 DOI: 10.1002/cmdc.202100702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Indexed: 11/23/2022]
Abstract
Prodigiosenes are a family of red pigments with versatile biological activity. Their tripyrrolic core structure has been modified many times in order to manipulate the spectrum of activity. We have been looking systematically at prodigiosenes substituted at the C ring with alkyl chains of different lengths, in order to assess the relevance of this substituent in a context that has not been investigated before for these derivatives: Cu(II) complexation, DNA binding, self‐activated DNA cleavage, photoinduced cytotoxicity and antimicrobial activity. Our results indicate that the hydrophobic substituent has a clear influence on the different aspects of their biological activity. The cytotoxicity study of the Cu(II) complexes of these prodigiosenes shows that they exhibit a strong cytotoxic effect towards the tested tumor cell lines. The Cu(II) complex of a prodigiosene lacking any alkyl chain excelled in its photoinduced anticancer activity, thus demonstrating the potential of prodigiosenes and their metal complexes for an application in photodynamic therapy (PDT). Two derivatives along with their Cu(II) complexes showed also antimicrobial activity against Staphylococcus aureus strains.
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Affiliation(s)
| | - Matthew White
- Imperial College London, Department of Chemistry, UNITED KINGDOM
| | - Julien Colard-Thomas
- Ecole Nationale Superieur de Chimie de Paris: Ecole nationale superieure de chimie de Paris, Chimie, FRANCE
| | - Matilda Kraft
- Freie Universität Berlin: Freie Universitat Berlin, Institut für Chemie und Biochemie, GERMANY
| | - Andrea T Feßler
- Freie Universität Berlin: Freie Universitat Berlin, Institute for Microbiology, GERMANY
| | - Karin Danz
- Fraunhofer-Institut fur Biomedizinische Technik IBMT, Zellmodelle und Toxikologie, GERMANY
| | | | - Sylvia Wagner
- Fraunhofer-Institut fur Biomedizinische Technik IBMT, Zellmodelle und Toxikologie, GERMANY
| | - Stefan Schwarz
- Freie Universität Berlin: Freie Universitat Berlin, Institut für Mikrobiologie, GERMANY
| | | | - Nora Kulak
- Otto von Guericke Universitat Magdeburg, Institut für Chemie, Universitätsplatz 2, 39106, Magdeburg, GERMANY
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Zare-Feizabadi N, Amiri-Tehranizadeh Z, Sharifi-Rad A, Mokaberi P, Nosrati N, Hashemzadeh F, Rahimi HR, Saberi MR, Chamani J. Determining the Interaction Behavior of Calf Thymus DNA with Anastrozole in the Presence of Histone H1: Spectroscopies and Cell Viability of MCF-7 Cell Line Investigations. DNA Cell Biol 2021; 40:1039-1051. [PMID: 34165362 DOI: 10.1089/dna.2021.0052] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The interaction of calf thymus DNA (ct DNA) with anastrozole, which is acknowledged as an antineoplastic drug, has been enquired into in the absence and presence of histone H1, through the means of absorbance, fluorescence, circular dichroism spectroscopy, viscosity, thermal melting, and molecular modeling techniques. In addition, the effects of anastrozole on MCF 7 cell line have been thoroughly investigated. Fluorescence spectroscopy results have indicated that quenching mechanism of ct DNA-anastrozole are known as static quenching procedures, since the Stern-Volmer quenching constant (KSV) seems to face a decrease as the temperature is enhanced; this is a significant evidence for intercalative binding mode of anastrozole with ct DNA. Regarding the ternary system in the presence of H1, the constant of Stern-Volmer quenching was increased as the temperature was heightened. The thermodynamic parameters suggested that the binding could be characterized as exothermic by negative and positive enthalpy and entropy changes in both binary and ternary systems, respectively. It is vital to mention that hydrogen bonds and hydrophobic contributions play significant roles in anastrozole association to ct DNA in the absence and presence of H1. In accordance to the absorption spectroscopy and melting temperature curve outcomes, the binding mode of anastrozole with ct DNA in absence and presence of H1 was indicative of intercalative and nonintercalative bindings, respectively. The viscosity results as binary and ternary systems, which have been elucidated from a sensitive viscometer, have confirmed the fluorescence spectroscopy determinations. The intercalation of anastrozole to ct DNA seemed to be significantly related to an induced reduction in MCF-7 cell proliferation. The molecular modeling results have suggested that anastrozole could bind to H1 in ct DNA-H1 complex in ternary systems, which supports the conclusions that have been obtained from experimental data.
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Affiliation(s)
- Najmeh Zare-Feizabadi
- Department of Biology, Faculty of Sciences, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Zeinab Amiri-Tehranizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atena Sharifi-Rad
- Department of Chemistry, Faculty of Sciences, Islamic Azad University, Neyshabur Branch, Neyshabur, Iran
| | - Parisa Mokaberi
- Department of Biology, Faculty of Sciences, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Niknaz Nosrati
- Department of Biology, Faculty of Sciences, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Fatemeh Hashemzadeh
- Department of Biology, Faculty of Sciences, Islamic Azad University, Mashhad Branch, Mashhad, Iran
| | - Hamid Reza Rahimi
- Department of Modern Sciences and Technologies, Faculty of Medicine, Mashhad University of Medical Sciences. Mashhad, Iran
| | - Mohammad Reza Saberi
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Islamic Azad University, Mashhad Branch, Mashhad, Iran
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Ambrose AJ, Pham NT, Sivinski J, Guimarães L, Mollasalehi N, Jimenez P, Abad MA, Jeyaprakash AA, Shave S, Costa-Lotufo LV, La Clair JJ, Auer M, Chapman E. A two-step resin based approach to reveal survivin-selective fluorescent probes. RSC Chem Biol 2021; 2:181-186. [PMID: 34458780 PMCID: PMC8342005 DOI: 10.1039/d0cb00122h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/07/2020] [Indexed: 01/24/2023] Open
Abstract
The identification of modulators for proteins without assayable biochemical activity remains a challenge in chemical biology. The presented approach adapts a high-throughput fluorescence binding assay and functional chromatography, two protein-resin technologies, enabling the discovery and isolation of fluorescent natural product probes that target proteins independently of biochemical function. The resulting probes also suggest targetable pockets for lead discovery. Using human survivin as a model, we demonstrate this method with the discovery of members of the prodiginine family as fluorescent probes to the cancer target survivin.
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Affiliation(s)
- Andrew J Ambrose
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
| | - Nhan T Pham
- School of Biological Sciences and Edinburgh Medical School, Biomedical Sciences, University of Edinburgh The King's Buildings CH Waddington Building 3.07 Max Born Crescent Edinburgh EH9 3BF UK
| | - Jared Sivinski
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
| | - Larissa Guimarães
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
- Departamento de Farmacologia, Universidade de São Paulo São Paulo SP 05508-900 Brazil
| | - Niloufar Mollasalehi
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
| | - Paula Jimenez
- Instituto do Mar, Universidade Federal de São Paulo Santos SP 11.070-100 Brazil
| | - Maria A Abad
- Wellcome Centre for Cell Biology, University of Edinburgh Edinburgh EH9 3BF UK
| | | | - Steven Shave
- School of Biological Sciences and Edinburgh Medical School, Biomedical Sciences, University of Edinburgh The King's Buildings CH Waddington Building 3.07 Max Born Crescent Edinburgh EH9 3BF UK
| | | | - James J La Clair
- Xenobe Research Institute P. O. Box 3052 San Diego CA 92163-1052 USA
| | - Manfred Auer
- School of Biological Sciences and Edinburgh Medical School, Biomedical Sciences, University of Edinburgh The King's Buildings CH Waddington Building 3.07 Max Born Crescent Edinburgh EH9 3BF UK
| | - Eli Chapman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
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Arif A, Ahmad A, Ahmad M. Toxicity assessment of carmine and its interaction with calf thymus DNA. J Biomol Struct Dyn 2020; 39:5861-5871. [DOI: 10.1080/07391102.2020.1794962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Amin Arif
- Department of Biochemistry, Faculty of life sciences, Aligarh Muslim University, Aligarh, India
| | - Ajaz Ahmad
- Department of Biochemistry, Faculty of life sciences, Aligarh Muslim University, Aligarh, India
| | - Masood Ahmad
- Department of Biochemistry, Faculty of life sciences, Aligarh Muslim University, Aligarh, India
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Lin SR, Chen YH, Tseng FJ, Weng CF. The production and bioactivity of prodigiosin: quo vadis? Drug Discov Today 2020; 25:828-836. [PMID: 32251776 DOI: 10.1016/j.drudis.2020.03.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/11/2020] [Accepted: 03/26/2020] [Indexed: 12/13/2022]
Abstract
Prodigiosin (PG), a red tripyrrole pigment, belongs to a member of the prodiginine family and is normally secreted by various sources including Serratia marcescens and other Gram-negative bacteria. The studies of PG have received innovative devotion as a result of reported antimicrobial, larvicidal and anti-nematoid immunomodulation and antitumor properties, owing to its antibiotic and cytotoxic activities. This review provides a comprehensive summary of research undertaken toward the isolation and structural elucidation of the prodiginine family of natural products. Additionally, the current evidence-based understanding of the biological activities and medicinal potential of PG is employed to determine the efficacy, with some reports of information related to pharmacokinetics, pharmacodynamics and toxicology.
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Affiliation(s)
- Shian-Ren Lin
- Graduated Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11041, Taiwan
| | - Yu-Hsin Chen
- National Museum of Marine Biology and Aquarium, Pingtung 94450, Taiwan
| | - Feng-Jen Tseng
- Department of Orthopedics, Hualien Armed Force General Hospital, Hualien 97144, Taiwan
| | - Ching-Feng Weng
- The Center of Translational Medicine, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China; Institute of Respiratory Disease, Department of Basic Medical Science, Xiamen Medical College, Xiamen 361023, Fujian, China.
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9
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Dareini M, Amiri Tehranizadeh Z, Marjani N, Taheri R, Aslani-Firoozabadi S, Talebi A, NayebZadeh Eidgahi N, Saberi MR, Chamani J. A novel view of the separate and simultaneous binding effects of docetaxel and anastrozole with calf thymus DNA: Experimental and in silico approaches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117528. [PMID: 31718965 DOI: 10.1016/j.saa.2019.117528] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
DNA stands as the primary purpose of many anticancer drugs and according to the performed research on this field, some certain changes contain crucial functionalities in the regulated transcription of DNA. Therefore, the interaction between anticancer drugs and DNA play an important role in understanding their function and also provide a better groundwork for producing more efficient and newer drugs. Here, the interaction between Docetaxel (DO) and calf thymus DNA (ct DNA), in the presence and absence of Anastrozole (AN), has been examined through the usage of different methods that include isothermal titration calorimetry, multi-spectroscopic, viscometry, and molecular docking techniques. Interaction studies have been performed by preparing different molar ratios of DO with the constant ct DNA and AN concentration at pH = 6.8. The binding constants have been calculated to be 7.93 × 104 M-1 and 6.27 × 104 M-1, which indicate the strong binding of DO with ct DNA double helix in the absence and presence of AN, respectively. Thermodynamic parameters, which were obtained from fluorescence spectroscopy and isothermal titration calorimetry, have suggested that the binding of DO and AN to ct DNA as binary and ternary systems have been mainly driven by the electrostatic interactions. The relative viscosity of ct DNA has increased upon the addition of DO and AN, which confirms the interaction mode. A competitive binding study has reported that the enhanced emission intensity of ethidium bromide (EB) and acridine orange (AO), in the presence of ct DNA, have been quenched through the addition of DO and Anastrozole as binary and ternary systems. As it is indicated by these findings, DO is capable of displacing EB and AO from their binding site in ct DNA; hence, it can be concluded that DO and AN are able to intercalate into the base pairs of ct DNA in binary and ternary systems. Molecular docking studies have corroborated the mentioned experimental results.
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Affiliation(s)
- Maryam Dareini
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri Tehranizadeh
- Medicinal Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Narges Marjani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Reza Taheri
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | | | - Atiye Talebi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Negar NayebZadeh Eidgahi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Mohammad Reza Saberi
- Medicinal Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran.
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Kheirdoosh F, Pazhavand M, Sariaslani M, Moghadam NH, Salehzadeh S. Multi-spectroscopic and molecular docking studies on the interaction of neotame with calf thymus DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:699-714. [PMID: 32126880 DOI: 10.1080/15257770.2019.1680999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In this paper, we have studied the in vitro binding of neotame (NTM), an artificial sweetener, with native calf thymus DNA using different methods including spectrophotometric, spectrofluorometric, competition experiment, circular dichroism (CD), and viscosimetric techniques. From the spectrophotometric studies, the binding constant (Kb) of NTM-DNA was calculated to be 2 × 103 M-1. The quenching of the intrinsic fluorescence of NTM in the presence of DNA at different temperatures was also used to calculate binding constants (Kb) as well as corresponding number of binding sites (n). Moreover, the obtained results indicated that the quenching mechanism involves static quenching. By comparing the competitive fluorimetric studies with Hoechst 33258, as a known groove probe, and methylene blue, as a known intercalation probe, and iodide quenching experiments it was revealed that NTM strongly binds in the grooves of the DNA helix, which was further confirmed by CD and viscosimetric studies. In addition, a molecular docking method was employed to further investigate the binding interactions between NTM and DNA, and confirm the obtained results.
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Affiliation(s)
- Fahimeh Kheirdoosh
- Department of Applied Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Islamic Republic of Iran
| | - Mahsa Pazhavand
- Department of Applied Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Islamic Republic of Iran
| | - Mahya Sariaslani
- School of paramedical, Kermanshah University of Medical Science, Kermanshah, Iran
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Gan C, Huang X, Zhan J, Liu X, Huang Y, Cui J. Study on the interactions between B-norcholesteryl benzimidazole compounds with ct-DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117525. [PMID: 31703992 DOI: 10.1016/j.saa.2019.117525] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/30/2019] [Accepted: 09/09/2019] [Indexed: 06/10/2023]
Abstract
The study of molecule-DNA interaction is very important for designing an improved therapeutic agent. In previous studies, we synthesized some B-norcholesteryl benzimidazole compounds, and the tests on cancer cells showed that these compounds had good in vitro anti-cancer activities. In order to further investigate mechanism of their actions, three different B-norcholesteryl benzimidazole compounds were selected and interaction of these compounds with the calf thymus DNA (ct-DNA) was monitored by using various methods including UV-Vis and fluorescence spectroscopic techniques, viscosity measurement, and circular dichroism (CD). The results proved a hypochromic effect accompanied with a slight red-shift due to the interaction of the molecules with ct-DNA. According to the UV-Vis and fluorescence spectra, the mentioned compounds were bound to DNA, preferentially through partial intercalation into the DNA helix. Moreover, the ethidium bromide (EB) and Hoechst 33258 competitive binding experiments were also used to confirm the interaction mode of the compounds with ct-DNA. In the Hoechst 33258 displacement experiment, no significant change in the fluorescence intensity was observed. Additional assays such as iodide quenching, viscosity, and CD spectroscopy further confirmed that intercalation should be the major binding mode of the selected compounds with DNA. The cytotoxicity of these three compounds was also evaluated by MTT method, and the results confirmed that binding ability of these compounds to DNA was consistent with their cytotoxicity behavior. The experimental results indicated a higher binding affinity for compound 3 compared to the other compounds. This research provided a better understanding on the molecular mechanism of the interaction between B-norcholesteryl benzimidazole compounds and tumor cells, and offered a beneficial perspective to the designation of novel B-norsteroidal anticancer compounds.
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Affiliation(s)
- Chunfang Gan
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Key Laboratory of Beibu Gulf Environment Change and Resources Utilization, School of Chemistry and Material, Nanning Normal University, Nanning, 530001, PR China.
| | - Xiaotong Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Key Laboratory of Beibu Gulf Environment Change and Resources Utilization, School of Chemistry and Material, Nanning Normal University, Nanning, 530001, PR China
| | - Junyan Zhan
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Key Laboratory of Beibu Gulf Environment Change and Resources Utilization, School of Chemistry and Material, Nanning Normal University, Nanning, 530001, PR China
| | - Xiaolan Liu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Key Laboratory of Beibu Gulf Environment Change and Resources Utilization, School of Chemistry and Material, Nanning Normal University, Nanning, 530001, PR China
| | - Yanmin Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Key Laboratory of Beibu Gulf Environment Change and Resources Utilization, School of Chemistry and Material, Nanning Normal University, Nanning, 530001, PR China
| | - Jianguo Cui
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Key Laboratory of Beibu Gulf Environment Change and Resources Utilization, School of Chemistry and Material, Nanning Normal University, Nanning, 530001, PR China; Guangxi Colleges and University Key Laboratory of Beibu Gulf Oil and Natural Gas Resource Effective Utilization, Beibuwan University, Qinzhou, 535099, PR China.
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12
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Zhang Q, Peng Q, Shu X, Mo D, Jiang D. Spectroscopic analysis of tylosin adsorption on extracellular DNA reveals its interaction mechanism. Colloids Surf B Biointerfaces 2019; 183:110431. [PMID: 31421405 DOI: 10.1016/j.colsurfb.2019.110431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 10/26/2022]
Abstract
Extracellular DNA (eDNA), which is commonly detected in aquatic and terrestrial environments, may be involved in gene transfer, increases in genetic diversity, and evolution. However, it has been reported that some small organic molecules or heavy metal ions can influence the transformation of DNA and even destroy its structure. We previously found that tylosin (TYL, a kind of antibiotic) is adsorbed onto salmon sperm DNA in a mixed solution. However, it is not clear whether this antibiotic affects the structure of DNA, and the mechanism of their interaction needs to be clarified. Therefore, we investigated the adsorption of TYL on different concentrations of salmon sperm DNA using agarose gel electrophoresis, ultraviolet-visible (UV-vis) spectroscopy, fluorescence spectroscopy, and surface enhanced Raman spectroscopy (SERS) to elucidate the interaction mechanism between TYL and DNA. The results showed that the adsorption of TYL decreased with increased concentrations of DNA. The electrophoresis band of pristine DNA was at 5000 bps. The brightness of the DNA band decreased with the TYL concentration and their incubation time. As the concentration of TYL increased, the fluorescence absorption intensity of DNA decreased significantly. Redshift and hyperchromicity were observed in the UV-vis adsorption spectrum with the presence of TYL in DNA solution, and they weakened as the DNA concentration increased. The Raman spectrum intensities of characteristic peaks in the mixed solution were weaker than that of pure TYL solution, and the peak intensity increased with increasing DNA concentration. Even a part of TYL characteristic peaks disappeared in the mixed solution. These results indicated that the pyran and macrolide of TYL might intercalate into the base pair plane of DNA. In addition, electrostatic attraction between TYL and DNA and interactions among TYL molecules may also play a role in the interaction mechanism. However, the double helix structure of DNA was not subject to the interaction of TYL.
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Affiliation(s)
- Qian Zhang
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, 541000, China
| | - Qiuyan Peng
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, 541000, China; College of Environmental Science and Engineering, Guilin University of Technology, Guilin, Guangxi, 541000, China
| | - Xiaohua Shu
- College of Environmental Science and Engineering, Guilin University of Technology, Guilin, Guangxi, 541000, China.
| | - Deqing Mo
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, 541000, China
| | - Dongyun Jiang
- School of Life and Environmental Science, Guilin University of Electronic Technology, Guilin, Guangxi, 541000, China
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Matarlo JS, Krumpe LRH, Heinz WF, Oh D, Shenoy SR, Thomas CL, Goncharova EI, Lockett SJ, O'Keefe BR. The Natural Product Butylcycloheptyl Prodiginine Binds Pre-miR-21, Inhibits Dicer-Mediated Processing of Pre-miR-21, and Blocks Cellular Proliferation. Cell Chem Biol 2019; 26:1133-1142.e4. [PMID: 31155509 DOI: 10.1016/j.chembiol.2019.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 03/15/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022]
Abstract
Identification of RNA-interacting pharmacophores could provide chemical probes and, potentially, small molecules for RNA-based therapeutics. Using a high-throughput differential scanning fluorimetry assay, we identified small-molecule natural products with the capacity to bind the discrete stem-looped structure of pre-miR-21. The most potent compound identified was a prodiginine-type compound, butylcycloheptyl prodiginine (bPGN), with the ability to inhibit Dicer-mediated processing of pre-miR-21 in vitro and in cells. Time-dependent RT-qPCR, western blot, and transcriptomic analyses showed modulation of miR-21 expression and its target genes such as PDCD4 and PTEN upon treatment with bPGN, supporting on-target inhibition. Consequently, inhibition of cellular proliferation in HCT-116 colorectal cancer cells was also observed when treated with bPGN. The discovery that bPGN can bind and modulate the expression of regulatory RNAs such as miR-21 helps set the stage for further development of this class of natural product as a molecular probe or therapeutic agent against miRNA-dependent diseases.
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Affiliation(s)
- Joe S Matarlo
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Lauren R H Krumpe
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Daniel Oh
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Shilpa R Shenoy
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Cheryl L Thomas
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ekaterina I Goncharova
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Biomedical Informatics and Data Science Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Stephen J Lockett
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Barry R O'Keefe
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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14
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Aydoğdu Tığ G, Koyuncu Zeybek D, Zeybek B, Pekyardımcı Ş. Interaction of prednisone with dsDNA at silver nanoparticles/poly(glyoxal-bis(2-hydroxyanil))/dsDNA modified electrode and its analytical application. Bioelectrochemistry 2019; 126:56-63. [DOI: 10.1016/j.bioelechem.2018.11.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 11/06/2018] [Accepted: 11/06/2018] [Indexed: 12/22/2022]
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15
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Tripathi AK. Binding interaction of N-acetylated acridine conjugate with ct-DNA and β-cyclodextrin: Synthesis and photophysical studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 205:497-502. [PMID: 30059876 DOI: 10.1016/j.saa.2018.07.069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/03/2018] [Accepted: 07/23/2018] [Indexed: 05/17/2023]
Abstract
In the present work we are reporting the synthesis and binding interaction of a saturated fatty acid containing 9-aminoacridine derivative (AC-PA) with ct-DNA and β-cyclodextrin (β-CD). From Steady-state fluorescence experiments this newly synthesized 9-aminoacridine derivative, AC-PA, shows more efficient binding interaction with ct-DNA as compared to the 9-aminoacridine (AC). The extent of interaction of AC-PA and AC with ct-DNA was found out by calculating the fluorescence quenching by using Stern-Volmer quenching equation. The calculated quenching constants of AC-PA and AC are (4.5 ± 0.5) × 103M-1 (3.7 ± 0.5) × 103M-1 respectively. The mechanism of fluorescence quenching of AC-PA and AC, were understand by using Stern-Volmer plots as well as time-resolved fluorescence experiments. The fluorescence quenching of AC-PA and AC by ct-DNA are static in nature and take place by formation of ground state complexes. The binding mode between AC-PA and AC were understood by DNA melting analysis experiment. The DNA melting analysis experiments were reveals that the binding interactions between fluorophores (AC-PA and AC) with ct-DNA are intercalative in nature. The melting temperature and mode of binding intercalative mode of binding between AC-PA and AC were further confirmed by DSC and CD experiments. The steady-state and time-resolved fluorescence parameters of AC-PA are quite sensitive towards the formation of inclusion complexes between AC-PA and β-CD. Long hydrophobic tail containing acridine conjugate (AC-PA) shows more efficient binding interactions with the β-CD and the calculated binding constants value of AC-PA is 0.51 × 102M-1. Whereas, the parent molecule, AC not showing any binding interactions with β-CD.
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Affiliation(s)
- Alok Kumar Tripathi
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, India.
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16
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Sun Q, Suo Z, Pu H, Tang P, Gan N, Gan R, Zhai Y, Ding X, Li H. Studies of the binding properties of the food preservative thiabendazole to DNA by computer simulations and NMR relaxation. RSC Adv 2018; 8:20295-20303. [PMID: 35541658 PMCID: PMC9080843 DOI: 10.1039/c8ra03702g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 05/24/2018] [Indexed: 11/22/2022] Open
Abstract
Thiabendazole (TBZ) is a commonly used food preservative and has a wide range of anthelmintic properties. In this study, computer simulations and experiments were conducted to investigate the interaction mechanism of TBZ and herring sperm DNA (hsDNA) at the molecular level. Molecular docking showed that TBZ interacted with DNA in groove mode and bound in A-T and C-G base pair regions. Molecular dynamics (MD) was used to evaluate the stability of the TBZ–DNA complex and found that the three phases in MD and the hydrogen bonds helped maintain the combination. NMR relaxation indicated that TBZ had a certain affinity to hsDNA with a binding constant of 462.43 L mol−1, and the thiazole ring was the main group bound with DNA. Results obtained from fluorescence experiments showed that the binding of TBZ and hsDNA was predominantly driven by enthalpy through a static quenching mechanism. Circular dichroism and viscosity measurements proved the groove binding mode. The FTIR results clarified the conformational changes of DNA, that the DNA helix became shorter and compact, and the DNA structure transformed from B-form to A-form. The groove binding of thiabendazole and hsDNA was studied by computer simulation and experimental methods.![]()
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Affiliation(s)
- Qiaomei Sun
- School of Chemical Engineering, Sichuan University Chengdu 610065 China +86 028 85401207 +86 028 85405220
| | - Zili Suo
- School of Chemical Engineering, Sichuan University Chengdu 610065 China +86 028 85401207 +86 028 85405220
| | - Hongyu Pu
- School of Chemical Engineering, Sichuan University Chengdu 610065 China +86 028 85401207 +86 028 85405220
| | - Peixiao Tang
- School of Chemical Engineering, Sichuan University Chengdu 610065 China +86 028 85401207 +86 028 85405220
| | - Na Gan
- School of Chemical Engineering, Sichuan University Chengdu 610065 China +86 028 85401207 +86 028 85405220
| | - Ruixue Gan
- School of Chemical Engineering, Sichuan University Chengdu 610065 China +86 028 85401207 +86 028 85405220
| | - Yuanming Zhai
- Analytical & Testing Center, Sichuan University Chengdu 610065 China
| | - Xiaohui Ding
- School of Chemical Engineering, Sichuan University Chengdu 610065 China +86 028 85401207 +86 028 85405220
| | - Hui Li
- School of Chemical Engineering, Sichuan University Chengdu 610065 China +86 028 85401207 +86 028 85405220
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17
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Zhang S, Yang H, Zhao L, Gan R, Tang P, Sun Q, Xiong X, Li H. Capecitabine as a minor groove binder of DNA: molecular docking, molecular dynamics, and multi-spectroscopic studies. J Biomol Struct Dyn 2018; 37:1451-1463. [PMID: 29620482 DOI: 10.1080/07391102.2018.1461137] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The interaction mechanism and binding mode of capecitabine with ctDNA was extensively investigated using docking and molecular dynamics simulations, fluorescence and circular dichroism (CD) spectroscopy, DNA thermal denaturation studies, and viscosity measurements. The possible binding mode and acting forces on the combination between capecitabine and DNA had been predicted through molecular simulation. Results indicated that capecitabine could relatively locate stably in the G-C base-pairs-rich DNA minor groove by hydrogen bond and several weaker nonbonding forces. Fluorescence spectroscopy and fluorescence lifetime measurements confirmed that the quenching was static caused by ground state complex formation. This phenomenon indicated the formation of a complex between capecitabine and ctDNA. Fluorescence data showed that the binding constants of the complex were approximately 2 × 104 M-1. Calculated thermodynamic parameters suggested that hydrogen bond was the main force during binding, which were consistent with theoretical results. Moreover, CD spectroscopy, DNA melting studies, and viscosity measurements corroborated a groove binding mode of capecitabine with ctDNA. This binding had no effect on B-DNA conformation.
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Affiliation(s)
- Shuangshuang Zhang
- a College of Chemical Engineering , Sichuan University , Chengdu 610065 , Sichuan , China
| | - Hongqin Yang
- a College of Chemical Engineering , Sichuan University , Chengdu 610065 , Sichuan , China
| | - Ludan Zhao
- a College of Chemical Engineering , Sichuan University , Chengdu 610065 , Sichuan , China
| | - Ruixue Gan
- a College of Chemical Engineering , Sichuan University , Chengdu 610065 , Sichuan , China
| | - Peixiao Tang
- a College of Chemical Engineering , Sichuan University , Chengdu 610065 , Sichuan , China
| | - Qiaomei Sun
- a College of Chemical Engineering , Sichuan University , Chengdu 610065 , Sichuan , China
| | - Xinnuo Xiong
- a College of Chemical Engineering , Sichuan University , Chengdu 610065 , Sichuan , China
| | - Hui Li
- a College of Chemical Engineering , Sichuan University , Chengdu 610065 , Sichuan , China
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18
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Ikhlas S, Ahmad M. Binding studies of guggulsterone-E to calf thymus DNA by multi-spectroscopic, calorimetric and molecular docking studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 190:402-408. [PMID: 28954252 DOI: 10.1016/j.saa.2017.09.065] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/14/2017] [Accepted: 09/20/2017] [Indexed: 06/07/2023]
Abstract
Guggulsterone, a sterol found in plants is used as an ayurvedic medicine for many diseases such as obesity, internal tumors, ulcers etc. E and Z are two isoforms of guggulsterone, wherein guggulsterone-E (GUGE) has also been shown to have anticancer potential. Most of the anticancer drugs target nucleic acids. Therefore, we studied the mode of interaction between ctDNA and GUGE using UV-Vis, fluorescence and CD spectroscopy, isothermal calorimetry along with molecular docking studies. Hoechst 3325, ethidium bromide and rhodamine-B displacement experiments confirms that GUGE binds in the minor groove of DNA. ITC results further suggest these interactions to be feasible and spontaneous with hydrogen bond formation and van der waals interactions. Lastly, molecular docking also suggests GUGE to be a minor groove binder interacting through a single hydrogen bond formation between OH group of GUGE and nitrogen (N3) of adenosine (A6).
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Affiliation(s)
- Shoeb Ikhlas
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Masood Ahmad
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
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19
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Ahmad A, Ahmad M. Deciphering the mechanism of interaction of edifenphos with calf thymus DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 188:244-251. [PMID: 28732283 DOI: 10.1016/j.saa.2017.07.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/10/2017] [Accepted: 07/12/2017] [Indexed: 06/07/2023]
Abstract
Edifenphos is an important organophosphate pesticide with many antifungal and anti-insecticidal properties but it may cause potential hazards to human health. In this work, we have tried to explore the binding mode of action and mechanism of edifenphos to calf thymus DNA (CT-DNA). Several experiments such as ultraviolet-visible absorption spectra and emission spectroscopy showed complex formation between edifenphos and CT-DNA and low binding constant values supporting groove binding mode. These results were further confirmed by circular dichroism (CD), CT-DNA melting studies, viscosity measurements, density functional theory and molecular docking. CD study suggests that edifenphos does not alter native structure of CT-DNA. Isothermal calorimetry reveals that binding of edifenphos with CT-DNA is enthalpy driven process. Competitive binding assay and effect of ionic strength showed that edifenphos binds to CT-DNA via groove binding manner. Hence, edifenphos is a minor groove binder preferably interacting with A-T regions with docking score -6.84kJ/mol.
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Affiliation(s)
- Ajaz Ahmad
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Masood Ahmad
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
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20
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Zulkarnain, Miyan L, Ahmad A, Fazle Alam M, Younus H. Synthesis, single-crystal, DNA interaction, spectrophotometric and spectroscopic characterization of the hydrogen-bonded charge transfer complex of 2-aminopyrimidine with π-acceptor chloranilic acid at different temperature in acetonitrile. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 174:195-208. [DOI: 10.1016/j.jphotobiol.2017.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/23/2017] [Accepted: 07/03/2017] [Indexed: 01/01/2023]
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21
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Li S, Pan J, Zhang G, Xu J, Gong D. Characterization of the groove binding between di-(2-ethylhexyl) phthalate and calf thymus DNA. Int J Biol Macromol 2017; 101:736-746. [DOI: 10.1016/j.ijbiomac.2017.03.136] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 01/03/2023]
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22
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da Silva CM, Silva MM, Reis FS, Ruiz ALTG, de Carvalho JE, Santos JCC, Figueiredo IM, Alves RB, Modolo LV, de Fátima Â. Studies on free radical scavenging, cancer cell antiproliferation, and calf thymus DNA interaction of Schiff bases. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 172:129-138. [PMID: 28549321 DOI: 10.1016/j.jphotobiol.2017.05.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/21/2017] [Accepted: 05/16/2017] [Indexed: 10/19/2022]
Abstract
Thirty-nine Schiff bases were synthesized by performing microwave-assisted condensation of the corresponding aldehydes and aromatic amines. Their reactive nitrogen species (RNS) scavenging activity and inhibitory effects against cancer cell growth were then subsequently investigated. Additionally, the interaction between the calf thymus DNA (ctDNA) and selected Schiff bases was evaluated using fluorescence spectroscopy, and their binding parameters were determined. The yields of the various compounds ranged from moderate to excellent (43-99%) after only a 2-min reaction. The hydroxylated Schiff bases 2, 8, 15, 16, 18, 20, 29, 32, 34, and 37 were found to be potent scavengers of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals with half-maximal scavenging concentration (SC50) values lower than that of the positive control, resveratrol. The presence of hydroxyl substituents on the aromatic rings also proved essential to the cytotoxicity of the compounds. The binding constants (Kb) obtained using fluorescence spectroscopy ranged from 0.37 to 3.07×105Lmol-1, and were strongly influenced by the structure and hydroxylation degree. Schiff bases 3 and 8 showed promising cytotoxic activity, with half-maximal growth inhibitory (GI50) values in the same order of magnitude as those exhibited by the reference drug, doxorubicin against various cell lines. Interestingly, these compounds also showed the highest Kb, suggesting that the cytotoxic activity could be related to their interaction with the DNA of the tumor cells. The results of this study highlighted some Schiff bases as potential lead compounds for the design of new free radical scavengers and anticancer agents.
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Affiliation(s)
- Cleiton M da Silva
- Grupo de Estudos em Química Orgânica e Biológica (GEQOB), Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marina M Silva
- Instituto de Química e Biotecnologia, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - Fabiano S Reis
- Grupo de Estudos em Química Orgânica e Biológica (GEQOB), Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Ana Lúcia T G Ruiz
- Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas (CPQBA), Universidade Estadual de Campinas, Paulínia, SP, Brazil
| | - João E de Carvalho
- Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas (CPQBA), Universidade Estadual de Campinas, Paulínia, SP, Brazil; Grupo de Estudos em Bioquímica de Plantas (GEBioPlan), Departamento de Botânica, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Josué C C Santos
- Instituto de Química e Biotecnologia, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - Isis M Figueiredo
- Instituto de Química e Biotecnologia, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - Rosemeire B Alves
- Grupo de Estudos em Química Orgânica e Biológica (GEQOB), Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luzia V Modolo
- Grupo de Estudos em Bioquímica de Plantas (GEBioPlan), Departamento de Botânica, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ângelo de Fátima
- Grupo de Estudos em Química Orgânica e Biológica (GEQOB), Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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23
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Experimental and molecular modeling studies on the DNA-binding of diazacyclam-based acrocyclic copper complex. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 167:7-14. [DOI: 10.1016/j.jphotobiol.2016.12.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 12/19/2016] [Indexed: 01/03/2023]
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24
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Guo Q, Zhang Z, Song Y, Liu S, Gao W, Qiao H, Guo L, Wang J. Investigation on interaction of DNA and several cationic surfactants with different head groups by spectroscopy, gel electrophoresis and viscosity technologies. CHEMOSPHERE 2017; 168:599-605. [PMID: 27838032 DOI: 10.1016/j.chemosphere.2016.11.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 10/01/2016] [Accepted: 11/05/2016] [Indexed: 06/06/2023]
Abstract
In this study, the interaction between DNA and several cationic surfactants with different head groups such as ethyl hexadecyl dimethyl ammonium bromide (EHDAB), hexadecyl dimethyl benzyl ammonium chloride (HDBAC), and cetyl pyridinium bromide (CPB) were investigated by UV-vis absorption, fluorescence and circular dichroism (CD) spectroscopy, gel electrophoresis, and viscosity technologies. The results show that these cationic surfactants can interact with DNA and major binding modes are electrostatic and hydrophobic. Also, CPB and HDBAC molecules interact with DNA by partial intercalation, and CPB has slightly stronger intercalation than HDBAC, while EHDAB interacts with DNA by non-intercalation. The different head groups of the surfactant molecules can influence the interaction strength. CPB has the stronger interaction with DNA than the others. Moreover, surfactant concentration, the ratio of DNA and fluorescence probe, ionic strength can influence the interaction. The surfactants may interact with DNA by the competition reactions with BR for DNA-BR. The increase of ionic strength may favor the surface binding between DNA and surfactants to some extent. This work provides deep mechanistic insight on the toxicity of cationic surfactants with different head groups to DNA molecules.
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Affiliation(s)
- Qing Guo
- School of Environment, Liaoning University, Shenyang 110036, PR China
| | - Zhaohong Zhang
- School of Environment, Liaoning University, Shenyang 110036, PR China.
| | - Youtao Song
- School of Environment, Liaoning University, Shenyang 110036, PR China
| | - Shuo Liu
- Shenyang Red Cross Hospital, Shenyang 110014, PR China
| | - Wei Gao
- School of Environment, Liaoning University, Shenyang 110036, PR China
| | - Heng Qiao
- School of Environment, Liaoning University, Shenyang 110036, PR China; Pony Testing International Group, Qingdao 266100, PR China
| | - Lili Guo
- School of Environment, Liaoning University, Shenyang 110036, PR China
| | - Jun Wang
- School of Chemistry, Liaoning University, Shenyang 110036, PR China.
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25
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Yang H, Tang P, Tang B, Huang Y, Xiong X, Li H. Novel poly(ADP-ribose) polymerase inhibitor veliparib: biophysical studies on its binding to calf thymus DNA. RSC Adv 2017. [DOI: 10.1039/c6ra28213j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Veliparib, an new anticancer drug in the class of poly (ADP-ribose) polymerase inhibitors, intercalates partially and binds to ctDNA and induces moderate conformational perturbation of the DNA.
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Affiliation(s)
- Hongqin Yang
- College of Chemical Engineering
- Sichuan University
- Chengdu
- China
| | - Peixiao Tang
- College of Chemical Engineering
- Sichuan University
- Chengdu
- China
| | - Bin Tang
- College of Chemical Engineering
- Sichuan University
- Chengdu
- China
| | - Yanmei Huang
- College of Chemical Engineering
- Sichuan University
- Chengdu
- China
| | - Xinnuo Xiong
- College of Chemical Engineering
- Sichuan University
- Chengdu
- China
| | - Hui Li
- College of Chemical Engineering
- Sichuan University
- Chengdu
- China
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26
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Drink E, Dugourd P, Dumont E, Aronssohn N, Antoine R, Loison C. Optical properties of prodigiosin and obatoclax: action spectroscopy and theoretical calculations. Phys Chem Chem Phys 2016; 17:25946-55. [PMID: 26120608 DOI: 10.1039/c5cp01498k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Prodiginine molecules (prodigiosin and obatoclax) are well-known pH-chromic dyes with promising anti-tumor properties. They present multiple tautomeric and rotameric forms. The protonation state and the structure of such flexible ligands in interaction with a protein are crucial to understand and to model the protein's biological activities. The determination of the protonation state via UV/vis absorption is possible if the ligand spectra of the neutral and protonated states are sufficiently different, and also if we can eliminate other factors potentially impacting the spectrum. Upon measuring the absorption spectra of the ligand in solution, varying solvents and pH values, we have determined that the optical properties of prodigiosin and obatoclax depend on the protonation state and not on the solvent permittivity constant. In parallel, action spectroscopy (using tunable lasers coupled to ion traps) in the gas phase of protonated and sodiated prodigiosin and obatoclax molecules has been performed to evaluate the sensitivity of the charge and the conformational state to their optical properties free of solvent. The spectra are interpreted using computational simulations of molecular structures and electronic excitations. The excitation energies are only slightly sensitive to various isomerizations, and may be used to distinguish between protonated and deprotonated states, even in the presence of a sodium counter-ion.
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Affiliation(s)
- Evangeline Drink
- Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne cedex, France.
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27
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Ahmad I, Ahmad A, Ahmad M. Binding properties of pendimethalin herbicide to DNA: multispectroscopic and molecular docking approaches. Phys Chem Chem Phys 2016; 18:6476-85. [PMID: 26862600 DOI: 10.1039/c5cp07351k] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pendimethalin (PND) is a systemic herbicide widely used on rice, cotton, peas, wheat, potatoes, fruits, nuts and other residential and non-residential crops; however, it concurrently exerts toxic effects on beneficial organisms like earthworms, aquatic invertebrates and other non-targeted animals including humans. Most likely, the genotoxicity of agrochemicals/drugs is modulated through cellular distribution of bound DNA. Therefore, the in vitro interaction of PND with calf thymus DNA (ctDNA) has been investigated using various sensitive biophysical techniques to ascertain its binding mechanism. UV-visible absorption and fluorescence spectra suggested the formation of a complex between PND and ctDNA. The binding constant of the PND-ctDNA complex was found to be around 10(4) M(-1) using steady state fluorescence titration. The calculated positive values of enthalpy and entropy changes suggested that the binding reaction was predominantly driven by hydrophobic interactions. Competitive displacement studies using acridine orange (AO), ethidium bromide (EB) and Hoechst dye suggested intercalation of PND molecules into the double helix of ctDNA by replacing the bound AO and EB probes. An increase in the viscosity and melting temperature of ctDNA and a decrease in iodine-quenching also support the intercalative binding of PND with ctDNA. Molecular docking analysis further confirmed the specific binding mode of PND between adjacent 'G-C' base pairs of ctDNA.
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Affiliation(s)
- Irshad Ahmad
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, U.P. 202002, India.
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Affiliation(s)
- Soumya Rastogi
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Daoning Zhang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Jeffery T. Davis
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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Guo L, Zhang Z, Qiao H, Liu M, Shen M, Yuan T, Chen J, Dionysiou DD. Spectroscopic study on interaction between three cationic surfactants with different alkyl chain lengths and DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 151:237-246. [PMID: 26142657 DOI: 10.1016/j.saa.2015.06.114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 06/24/2015] [Accepted: 06/25/2015] [Indexed: 06/04/2023]
Abstract
In this study, the interaction between cationic surfactants with different alkyl chain lengths, such as hexyltrimethyl ammonium bromide (HTAB), dodecyltrimethyl ammonium bromide (DTAB) and cetyltrimethyl ammonium bromide (CTAB), and DNA was investigated by UV-vis spectroscopy, fluorescence spectroscopy and viscosity techniques. The results showed that these three cationic surfactants with different hydrocarbon chain lengths could all interact with DNA. Their binding modes were estimated and their interaction strength was compared. In addition, the effects of the surfactant, NaCl and phosphate ion concentrations on the interaction were reviewed. It is wished that this work would provide some valuable references to investigate the influence of cationic surfactants with different alkyl chain lengths on DNA.
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Affiliation(s)
- Lili Guo
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Zhaohong Zhang
- School of Environmental Science, Liaoning University, Shenyang 110036, China.
| | - Heng Qiao
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Miao Liu
- Department of Endocrinology, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Manli Shen
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Tianxin Yuan
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Jing Chen
- School of Environmental Science, Liaoning University, Shenyang 110036, China
| | - Dionysios D Dionysiou
- Environmental Engineering and Science Program, University of Cincinnati, Cincinnati, OH 45221-0012, USA.
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Interactions of Isophorone Derivatives with DNA: Spectroscopic Studies. PLoS One 2015; 10:e0129817. [PMID: 26069963 PMCID: PMC4466397 DOI: 10.1371/journal.pone.0129817] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 05/12/2015] [Indexed: 12/19/2022] Open
Abstract
Interactions of three new isophorone derivatives, Isoa Isob and Isoc with salmon testes DNA have been investigated using UV-Vis, fluorescence and circular dichroism spectroscopic methods. All the studied compounds interact with DNA through intercalative binding mode. The stoichiometry of the isophorone/DNA adducts was found to be 1:1. The fluorescence quenching data revealed a binding interaction with the base pairs of DNA. The CD data indicate that all the investigated isophorones induce DNA modifications.
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Husain MA, Sarwar T, Rehman SU, Ishqi HM, Tabish M. Ibuprofen causes photocleavage through ROS generation and intercalates with DNA: a combined biophysical and molecular docking approach. Phys Chem Chem Phys 2015; 17:13837-50. [DOI: 10.1039/c5cp00272a] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Ibuprofen is an important nonsteroidal anti inflammatory drug which intercalates with DNA and causes phototoxicity through ROS generation.
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Affiliation(s)
| | - Tarique Sarwar
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | - Sayeed Ur Rehman
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | | | - Mohammad Tabish
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
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32
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Wang L, Tao M, Zhang G, Li S, Gong D. Partial intercalative binding of the food colorant erythrosine to herring sperm DNA. RSC Adv 2015. [DOI: 10.1039/c5ra19626d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Erythrosine partially inserts into the G–C rich region of hsDNA and induces moderate conformational perturbation of the DNA.
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Affiliation(s)
- Langhong Wang
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Mo Tao
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Song Li
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Deming Gong
- School of Biological Sciences
- The University of Auckland
- Auckland 1142
- New Zealand
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