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Heidari A, Dehghanian E, Razmara Z, Shahraki S, Samareh Delarami H, Heidari Majd M. Effect of Cu(II) compound containing dipicolinic acid on DNA damage: a study of antiproliferative activity and DNA interaction properties by spectroscopic, molecular docking and molecular dynamics approaches. J Biomol Struct Dyn 2024:1-16. [PMID: 38498382 DOI: 10.1080/07391102.2024.2329308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
A polymeric compound formulized as [Cu(µ-dipic)2{Na2(µ-H2O)4]n.2nH2O (I), where dipic is 2,6-pyridine dicarboxylic acid (dipicolinic acid, H2dipic), was synthesized by sonochemical irradiation. The initial in-vitro cytotoxic activity of this complex compared with renowned anticancer drugs like cisplatin, versus HCT116 colon cell lines, shows promising results. This study investigated the interaction mode between compound (I) and calf-thymus DNA utilizing a range of analytical techniques including spectrophotometry, fluorimetry, partition coefficient analysis, viscometry, gel electrophoresis and molecular docking technique. The results obtained from experimental methods reveal complex (I) could bind to CT-DNA via hydrogen bonding and van der Waals forces and the theoretical methods support it. Also, complex (I) indicates nuclease activity in the attendance of H2O2 and can act as an artificial nuclease to cleave DNA with high efficiency.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ameneh Heidari
- Department of Chemistry, Faculty of Science, University of Zabol, Zabol, Iran
| | - Effat Dehghanian
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
| | - Zohreh Razmara
- Department of Chemistry, Faculty of Science, University of Zabol, Zabol, Iran
| | - Somaye Shahraki
- Department of Chemistry, Faculty of Science, University of Zabol, Zabol, Iran
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Luikham S, Bhattacharyya J. On the traditional medicinal plants and plant-derived natural drugs used by indigenous people of Nagaland, India. Nat Prod Res 2024:1-16. [PMID: 38372281 DOI: 10.1080/14786419.2024.2315594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/04/2024] [Indexed: 02/20/2024]
Abstract
An ethnobotanical documentation on the medicinal plants used by local people of Nagaland (North-east India) has been presented here. The study explored 33 plant species (with their local names, indigenous applications, sources/origins, parts of plants used, bioactive compounds present, process of preparing medicines from the plants) belonging to 28 families have been reviewed thoroughly. Some examples are, Catharanthus roseus (Tsuinrinaro, Periwinkle), Acacia pennata (Chakrangaing, Ballikhadira), Adhatoda vasica (Kicharangnaro, Malabar-nut), Ageratum conzyoides (Imchenriza, Billy-goat-weed,/Tropical-white-weed), Alstonia scholaris (Lazarongpang, Blackboard), Rauvolfia serpentina (Per-mozutong, Indian-snakeroot), etc. Plant based drugs are very popular and effective in Nagaland from ancient times but thorough-documentation with scientific-background of effectiveness, active chemical-compounds present, their action-mechanism, etc., are still scanty. Such review can be of useful for pharmacologist, phyto-chemists to a broad group of researchers and may lead to discovery of new sources of novel medicines through traditional therapeutic knowledge.
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Affiliation(s)
- Soching Luikham
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, India
| | - Jhimli Bhattacharyya
- Department of Chemistry, National Institute of Technology Nagaland, Dimapur, India
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Sharma P, Gopi P, Singh S, Rani MSS, Pandya P. Binding studies of sertraline hydrochloride with CT-DNA using experimental and computational techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 300:122910. [PMID: 37257324 DOI: 10.1016/j.saa.2023.122910] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/02/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
Sertraline Hydrochloride (STH) is an antidepressant drug that belongs to the selective serotonin reuptake inhibitor family (SSRIs), which inhibits serotonin uptake in presynaptic nerve fibers. The use of these medications without a legitimate prescription might result in adverse effects, and in rare circumstances, death. The interaction mechanism and binding mode of STH with duplex DNA were extensively investigated using spectroscopic and modeling techniques at different temperatures. The hypochromic shift of the absorption spectra of STH on binding with CT-DNA indicated groove binding. Fluorescence spectroscopic studies showed that CT-DNA quenches the fluorescence intensity of STH through a static quenching mechanism. The thermodynamic parameters indicated that the complex formation was spontaneous, and enthalpy driven. The competitive displacement binding study revealed that STH displaced DAPI from the minor groove of DNA. Molecular docking and molecular dynamics simulations also revealed that the complex was stable over 150 ns and that STH preferred the minor groove of DNA. The binding energy of the stable conformations were evaluated through MM/PBSA methods. A comparison of the bound poses at different timescales showed minor changes in STH structure upon DNA binding. Furthermore, a structural analysis of CT-DNA indicated that STH induced changes in the sugar-phosphate backbone had an impact on the minor groove's width which are in agreement with the CD spectroscopic results. This study provides a better understanding of STH binding with duplex DNA.
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Affiliation(s)
- Palak Sharma
- Amity Institute of Forensic Sciences, Amity University Uttar Pradesh, Noida 201303, India.
| | - Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University Uttar Pradesh, Noida 201303, India.
| | - Shweta Singh
- Amity Institute of Forensic Sciences, Amity University Uttar Pradesh, Noida 201303, India.
| | - Majji Sai Sudha Rani
- Amity Institute of Forensic Sciences, Amity University Uttar Pradesh, Noida 201303, India.
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University Uttar Pradesh, Noida 201303, India.
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Peng S, Chang Y, Zeng X, Lai R, Yang M, Wang D, Zhou X, Shao Y. Selectivity of natural isoquinoline alkaloid assembler in programming poly(dA) into parallel duplex by polyvalent synergy. Anal Chim Acta 2023; 1241:340777. [PMID: 36657870 DOI: 10.1016/j.aca.2022.340777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/04/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
Abstract
Ligand-induced assembly of disordered DNAs attracts much attention due to its potential action in transcription regulation and molecular switches-based sensors. Among natural isoquinoline alkaloids (NIAs), we screened out nitidine (NIT) as polyvalent-binding assembler to program poly(dA) into a parallel duplex assembly at neutral pH. The molecule planarity of NIAs was believed to be a determinant factor in programming the parallel poly(dA) assembly. Poly(dA) with more than six adenines can initiate the synergistic binding of NIT to generate the parallel assembly. It is expected that one A-A pair in duplex can bind one NIT molecule provided that poly(dA) is long enough, suggesting the pivotal role of the polyvalent synergy of NIT in programming the parallel poly(dA) assembly. A gold nanoparticles-based colorimetric method was also developed to screen NIT out of NIAs having the potential to construct the poly(dA) assembly. Our work will inspire more interest in developing polyadenine-based switches and sensors by concentrating NIT within the polyadenine parallel assembly.
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Affiliation(s)
- Shuzhen Peng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yun Chang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xingli Zeng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Rong Lai
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Mujing Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China.
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Fahmy MA, Hassan EE, Farghaly AA, Hassan ZM. Genotoxicity, DNA damage and sperm defects induced by vinblastine. Mol Biol Rep 2023; 50:1059-1068. [PMID: 36394708 PMCID: PMC9889443 DOI: 10.1007/s11033-022-08061-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND The treatment with chemotherapy may develop secondary tumors as a result of chemo genotoxicity. Sperm defects is another complication associated with chemo treatment. In this study the genotoxicity of vinblastine (VB) was estimated in both somatic and germ cells. MATERIALS 85 mice were taken. Four single doses of VB at 3, 4.5, 6 and 10 mg/kg and three successive doses at 3, 4.5 and 6 mg/kg were taken for estimation of chromosomal aberrations (CAs). Four single doses of VB were involved in estimating the DNA fragmentation, and comet assay. For sperm abnormalities mice were injected with three successive doses of VB at 3, 4.5, and 6 mg/kg. RESULTS The results demonstrated a significant frequency of DNA fragmentation in spleen cells and in the percentage of CAs in bone marrow. Numerical and structural aberrations were recorded with a pronounced number of polyploidy metaphases which reached (11.60%) after treatment with 6 mg/kg for three successive days vs zero for control. VB also induced a significant percentage of CAs in spermatocytes in the form of univalent. Sperm defects in the form of coiled tail, absence of acrosome and shapeless head and a significant DNA damage in the testes were recorded. The frequency of sperm abnormalities reached 11.06 ± 0.14 after treatment with highest tested dose (6 mg/kg) vs 3.04 ± 0.19 for control. CONCLUSION VB is genotoxic in somatic and germ cells. Sperm defects induced by VB are of serious concern to future generations and may affect the fertility of cancer survivors.
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Affiliation(s)
- Maha A Fahmy
- Department of Genetics and Cytology, National Research Centre (NRC), Dokki, Giza, Egypt
| | - Entesar E Hassan
- Department of Genetics and Cytology, National Research Centre (NRC), Dokki, Giza, Egypt.
| | - Ayman A Farghaly
- Department of Genetics and Cytology, National Research Centre (NRC), Dokki, Giza, Egypt
| | - Zeinab M Hassan
- Department of Natural Compounds Chemistry Research, National Research Centre (NRC), Dokki, Giza, Egypt
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Gopi P, Singh S, Islam MM, Yadav A, Gupta N, Pandya P. Thermodynamic and structural profiles of multi-target binding of vinblastine in solution. J Mol Recognit 2022; 35:e2989. [PMID: 36054496 DOI: 10.1002/jmr.2989] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 01/05/2023]
Abstract
Structural information about drug-receptor interactions is paramount in drug discovery and subsequent optimization processes. Drugs can bind to multiple potential targets as they contain common chemical entities in their structures. Understanding the details of such interactions offer possibilities for repurposing and developing potent inhibitors of disease pathways. Vinblastine (VLB) is a potent anticancer molecule showing multiple receptor interactions with different affinities and degrees of structural perturbations. We have investigated the multi-target binding profile of VLB with DNA and human serum albumin (HSA) in a dynamic physiological environment using spectroscopic, molecular dynamics simulations, and quantum mechanical calculations to evaluate the structural features, mode, ligand and receptor flexibility, and energetics of complexation. These results confirm that VLB prefers to bind in the major groove of DNA with some inclination toward Thymidine residue and the TR-5 binding site in HSA with its catharanthine half making important contacts with both the receptors. Spectroscopic investigation at multiple temperatures has also proved that VLB binding is entropy driven indicating the major groove and TR-5 binding site of interaction. Finally, the overall binding is facilitated by van der Waals contacts and a few conventional H-bonds. VLB portrays reasonable conformational diversity on binding with multiple receptors.
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Affiliation(s)
- Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University, Uttar Pradesh, Noida, India
| | - Shweta Singh
- Amity Institute of Forensic Sciences, Amity University, Uttar Pradesh, Noida, India
| | | | - Akankasha Yadav
- Department of Chemistry, University of Rajasthan, Jaipur, India
| | - Neelima Gupta
- Department of Chemistry, University of Rajasthan, Jaipur, India
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Uttar Pradesh, Noida, India
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Luikham S, Mavani A, Bhattacharyya J. Deciphering binding affinity, energetics, and base specificity of plant alkaloid Harmane with AT & GC hairpin duplex DNA. LUMINESCENCE 2022; 37:691-701. [DOI: 10.1002/bio.4210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Soching Luikham
- Department of Chemistry National Institute of Technology Nagaland Chumukedima Dimapur Nagaland India
| | - A. Mavani
- Department of Chemistry National Institute of Technology Nagaland Chumukedima Dimapur Nagaland India
| | - Jhimli Bhattacharyya
- Department of Chemistry National Institute of Technology Nagaland Chumukedima Dimapur Nagaland India
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Sohrabi T, Asadzadeh-Lotfabad M, Shafie Z, Amiri Tehranizadeh Z, Saberi MR, Chamani J. Description of the calf thymus DNA-malathion complex behavior by multi-spectroscopic and molecular modeling techniques: EMF at low and high frequency approaches. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:1346-1357. [PMID: 35096292 PMCID: PMC8769509 DOI: 10.22038/ijbms.2021.58083.12907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/07/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Small molecules can bind to DNA via covalent or non-covalent interactions, which results in altering or inhibiting the function of DNA. Thus, understanding the interaction patterns of medicines or other small molecules can be very crucial. In this study, the interaction between malathion and calf thymus DNA (ctDNA), in the absence and presence of electromagnetic field (EMF) at low and high frequencies, was investigated through various spectroscopies and viscosity measurements. MATERIALS AND METHODS The interaction studies were performed by means of absorbance, circular dichroism, fluorescence spectroscopy, viscosity, thermal melting, and molecular modeling techniques. RESULTS The fluorescence intensity of the ctDNA-malathion complex in the presence of EMF, has revealed quenching of fluorescence emission curves. The dynamic interaction and RLS studies have implied the changes in ctDNA-malathion complex throughout the presence of EMF which suggested that hydrophobic forces play the main role in the binding. Studies have revealed that malathion does not have any effect on binding ethidium bromide to ctDNA, which signifies the groove binding. The viscosity of ctDNA increased as the malathion concentration was enlarged. The circular dichroism technique suggested that the ellipticity values of the ctDNA-malathion complex have not increased with enhancing the malathion concentration. Molecular docking and dynamics studies have indicated a potent electrostatic interaction between ctDNA and malathion in the groove binding site. CONCLUSION The results of spectroscopic studies reinforced a potent interaction between malathion and ctDNA in the absence and presence of EMF which can help us for further pharmaceutical drug discoveries.
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Affiliation(s)
- Tahmineh Sohrabi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | | | - Zahra Shafie
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri Tehranizadeh
- Medical Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Saberi
- Medical 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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Alamzeb M, Ali S, Mamoon-Ur-Rashid, Khan B, Ihsanullah, Adnan, Omer M, Ullah A, Ali J, Setzer WN, Salman SM, Khan A, Shah A. Antileishmanial Potential of Berberine Alkaloids From Berberis glaucocarpa Roots: Molecular Docking Suggests Relevant Leishmania Protein Targets. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211031148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Leishmaniases are a spectrum of poverty-linked neglected parasitic diseases that are endemic in 88 countries around the globe and affect millions of people every year. Currently available chemotherapeutic options are inadequate due to side effects, high cost, prolonged treatment, and parasite resistance. Thus, there is an existing need to develop new potent and safer leishmanicidal drugs. Considering the folkloric antiulcer and leishmanicidal use of the genus Berberis and its alkaloids, 5 reported alkaloids, namely berberine (1), palmatine (2), columbamine (3), 8-trichloromethyldihydroberberine (4), and jatrorrhizine (5), were isolated from the roots of Berberis glaucocarpa using classical (column and preparative chromatography) and modern isolation techniques (Sephadex LH-20). Their structures were elucidated and established from 1D and 2D spectroscopic data. The isolated alkaloids displayed excellent antileishmanial potential with IC50 values ranging from 1.50 to 2.56 µM: 1 (1.50 ± 0.53 µM), 2 (2.31 ± 0.37 µM), 3 (2.56 ± 0.48 µM), 4 (1.40 ± 0.90 µM), 5 (2.44 ± 1.34 µM). While the IC50 value for the standard drug (Amphotericin-B) was found to be 1.08 ± 0.95 µM. All of the isolated alkaloids displayed excellent antileishmanial potential as well as minimal cytotoxicity against THP-1 monocytic cells. Molecular docking analysis has revealed Leishmania N-myristoyl transferase, methionyl-tRNA synthetase, pteridine reductase 1, oligopeptidase B, tyrosyl-tRNA synthetase, and/or glycerol-3-phosphate dehydrogenase to be potential protein targets for the alkaloids.
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Affiliation(s)
| | - Saqib Ali
- University of Kotli, Kotli, Pakistan
| | - Mamoon-Ur-Rashid
- Baluchistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Pakistan
| | | | - Ihsanullah
- Institute of Chemical Sciences, University of Swat, Swat, Pakistan
| | - Adnan
- Institute of Chemical Sciences, University of Swat, Swat, Pakistan
| | - Muhammad Omer
- Institute of Chemical Sciences, University of Swat, Swat, Pakistan
| | - Asad Ullah
- Islamia College University, Peshawar, Pakistan
| | - Javed Ali
- Kohat University of Science and Technology (KUST), Kohat, Pakistan
| | | | | | - Ajmal Khan
- Leishmania Diagnostic & Drug Delivery Research Laboratory, University of Peshawar, Peshawar, Pakistan
| | - Akram Shah
- Leishmania Diagnostic & Drug Delivery Research Laboratory, University of Peshawar, Peshawar, Pakistan
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de Araújo RSA, da Silva-Junior EF, de Aquino TM, Scotti MT, Ishiki HM, Scotti L, Mendonça-Junior FJB. Computer-Aided Drug Design Applied to Secondary Metabolites as Anticancer Agents. Curr Top Med Chem 2021; 20:1677-1703. [PMID: 32515312 DOI: 10.2174/1568026620666200607191838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/06/2019] [Accepted: 01/05/2020] [Indexed: 12/11/2022]
Abstract
Computer-Aided Drug Design (CADD) techniques have garnered a great deal of attention in academia and industry because of their great versatility, low costs, possibilities of cost reduction in in vitro screening and in the development of synthetic steps; these techniques are compared with highthroughput screening, in particular for candidate drugs. The secondary metabolism of plants and other organisms provide substantial amounts of new chemical structures, many of which have numerous biological and pharmacological properties for virtually every existing disease, including cancer. In oncology, compounds such as vimblastine, vincristine, taxol, podophyllotoxin, captothecin and cytarabine are examples of how important natural products enhance the cancer-fighting therapeutic arsenal. In this context, this review presents an update of Ligand-Based Drug Design and Structure-Based Drug Design techniques applied to flavonoids, alkaloids and coumarins in the search of new compounds or fragments that can be used in oncology. A systematical search using various databases was performed. The search was limited to articles published in the last 10 years. The great diversity of chemical structures (coumarin, flavonoids and alkaloids) with cancer properties, associated with infinite synthetic possibilities for obtaining analogous compounds, creates a huge chemical environment with potential to be explored, and creates a major difficulty, for screening studies to select compounds with more promising activity for a selected target. CADD techniques appear to be the least expensive and most efficient alternatives to perform virtual screening studies, aiming to selected compounds with better activity profiles and better "drugability".
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Affiliation(s)
| | | | - Thiago Mendonça de Aquino
- Laboratory of Medicinal Chemistry, Nursing and Pharmacy School, Federal University of Alagoas, Maceio-AL, Brazil
| | - Marcus Tullius Scotti
- Laboratory of Medicinal Chemistry, Nursing and Pharmacy School, Federal University of Alagoas, Maceio-AL, Brazil
| | - Hamilton M Ishiki
- University of Western Sao Paulo (Unoeste), Presidente Prudente- SP, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, Joao Pessoa-PB, Brazil
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Morawska K, Ciesielski W, Smarzewska S. First electroanalytical studies of methoxyfenozide and its interactions with dsDNA. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Singh I, Luxami V, Paul K. Synthesis of naphthalimide-phenanthro[9,10-d]imidazole derivatives: In vitro evaluation, binding interaction with DNA and topoisomerase inhibition. Bioorg Chem 2020; 96:103631. [PMID: 32036164 DOI: 10.1016/j.bioorg.2020.103631] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 01/26/2020] [Accepted: 01/28/2020] [Indexed: 12/11/2022]
Abstract
The synthesis and characterization of a series of naphthalimide and phenanthro[9,10-d]imidazole conjugate is described. These compounds are evaluated in vitro for their cytotoxicity towards 60 human cancer cell lines. Derivative 16 shows excellent cytotoxic activity against these cancer cell lines with the range of growth inhibition from -55.78 to 94.53. The most potent derivative (ethylpiperazine, 16) is further studied to evaluate the interaction with ct-DNA using absorption and emission spectroscopy as well as DNA viscosity measurement. The DNA binding studies indicate that compound 16 is significantly interacted with DNA through groove binding having binding constant value of 7.81 × 104 M-1 alongwith partial intercalation between the base pairs of DNA strands. Further, topoisomerase inhibition study suggests that compound 16 is induced apoptosis and inhibits human topoisomerase (Topo-IIα) as a possible intracellular target. Molecular docking study of compound 16 with ct-DNA shows good docking score.
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Affiliation(s)
- Iqubal Singh
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147001, India
| | - Vijay Luxami
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147001, India
| | - Kamaldeep Paul
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala 147001, India.
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13
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Zhang G, Zhou Z, Xu J, Liao Y, Hu X. Groove binding between ferulic acid and calf thymus DNA: spectroscopic methodology combined with chemometrics and molecular docking studies. J Biomol Struct Dyn 2019; 38:2029-2037. [PMID: 31157597 DOI: 10.1080/07391102.2019.1624194] [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] [Indexed: 12/16/2022]
Abstract
Ferulic acid (FA), a dietary phenolic acid compound, is proved to possess numerous biological activities. Hence, this study was devoted to explore the interaction between FA and calf thymus DNA (ctDNA) by UV - vis absorption, fluorescence, circular dichroism (CD) spectroscopy combined with multivariate curve resolution-alternating least-squares (MCR - ALS) and molecular docking studies. The concentration curves and the pure spectra of compositions (FA, ctDNA and FA - ctDNA complex) were obtained by MCR - ALS approach to verify and monitor the interaction of FA with ctDNA. The groove binding mode between FA and ctDNA was confirmed by the results of melting analysis, viscosity measurements, single-stranded DNA experiments, and competitive studies. The binding constant of FA - ctDNA complex was 4.87 × 104 L mol-1 at 298 K. The values of enthalpy (ΔH°) and entropy (ΔS°) changes in the interaction were -16.24 kJ mol-1 and 35.02 J mol-1 K-1, respectively, indicating that the main binding forces were hydrogen bonds and hydrophobic interactions. The result of CD spectra suggested that a decrease in right-handed helicity of ctDNA was induced by FA and the DNA conformational transition from the B-form to the A-form. The results of docking indicated that FA binding with ctDNA in the minor groove. These findings may be conducive to understand the interaction mechanism of FA with ctDNA and the pharmacological effects of FA. Communicated by Ramaswamy H. Sarma[Formula: see text].
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Affiliation(s)
- Guowen Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Zhisheng Zhou
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Jianjian Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Yijing Liao
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Xing Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
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14
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Charak S, Shandilya M, Mehrotra R. RNA targeting by an anthracycline drug: spectroscopic and in silico evaluation of epirubicin interaction with tRNA. J Biomol Struct Dyn 2019; 38:1761-1771. [PMID: 31084352 DOI: 10.1080/07391102.2019.1617786] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Anthracyclines are putative anticancer agents used to treat a wide range of cancers. Among these anthracyclines, epirubicin is derived from the doxorubicin by the subtle difference in the orientation of C4-hydroxyl group at sugar molecule. Epirubicin has great significance as it has propitious anticancer potential with lesser cardiotoxicity and faster elimination from the body. The present study is done to understand the molecular aspect of epirubicin binding to tRNA. We have used various spectroscopic techniques like Fourier transform infrared spectroscopy (FTIR), absorption spectroscopy and circular dichroism to illustrate the binding sites, the extent of binding and conformational changes associated with tRNA after interacting with epirubicin. From infrared studies, we infer that epirubicin interacts with guanine and uracil bases of tRNA. Results obtained from infrared and CD studies suggest that epirubicin complexation with tRNA does not result in any conformational change in tRNA structure. Binding constant (2.1 × 103 M-1) calculated from the absorbance data illustrates that epirubicin has a weak interaction with tRNA molecule. These spectroscopic results like the binding site of epirubicin and binding energy of epirubicin-tRNA complex were also verified by the molecular docking. Results of the present study provide information that aids in the development of efficient RNA targeted drugs from the existing drugs by certain chemical modification in their structure resulting in lesser side effects and better efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sonika Charak
- Physico Mechanical Metrology Division, CSIR-National Physical Laboratory, New Delhi, India
| | - Manish Shandilya
- Amity School of Applied Sciences, Amity University Haryana, Gurgaon, India
| | - Ranjana Mehrotra
- Physico Mechanical Metrology Division, CSIR-National Physical Laboratory, New Delhi, India
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15
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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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16
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Probing the binding of lomefloxacin to a calf thymus DNA-histone H1 complex by multi-spectroscopic and molecular modeling techniques. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.02.031] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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17
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Aneja B, Arif R, Perwez A, Napoleon JV, Hasan P, Rizvi MMA, Azam A, Rahisuddin, Abid M. N-Substituted 1,2,3-Triazolyl-Appended Indole-Chalcone Hybrids as Potential DNA Intercalators Endowed with Antioxidant and Anticancer Properties. ChemistrySelect 2018. [DOI: 10.1002/slct.201702913] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Babita Aneja
- Department of Biosciences; Jamia Millia Islamia; Medicinal Chemistry Laboratory, Jamia Nagar; New Delhi 110025 India
- Department of Chemistry; Jamia Millia Islamia, Jamia Nagar; New Delhi 110025 India
| | - Rizwan Arif
- Department of Chemistry; Jamia Millia Islamia, Jamia Nagar; New Delhi 110025 India
| | - Ahmad Perwez
- Department of Biosciences; Jamia Millia Islamia; Genome Biology Laboratory, Jamia Nagar; New Delhi 110025 India
| | - John V. Napoleon
- Eppley Institute for Research in Cancer and Allied Diseases; University of Nebraska Medical Center; Omaha, NE 68198-6805 USA
| | - Phool Hasan
- Department of Biosciences; Jamia Millia Islamia; Medicinal Chemistry Laboratory, Jamia Nagar; New Delhi 110025 India
| | - M. Moshahid A. Rizvi
- Department of Biosciences; Jamia Millia Islamia; Genome Biology Laboratory, Jamia Nagar; New Delhi 110025 India
| | - Amir Azam
- Department of Chemistry; Jamia Millia Islamia, Jamia Nagar; New Delhi 110025 India
| | - Rahisuddin
- Department of Chemistry; Jamia Millia Islamia, Jamia Nagar; New Delhi 110025 India
| | - Mohammad Abid
- Department of Biosciences; Jamia Millia Islamia; Medicinal Chemistry Laboratory, Jamia Nagar; New Delhi 110025 India
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18
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Haque L, Bhuiya S, Das S. Self-structure assembly in single stranded polyriboadenylic acid by benzophenanthridine alkaloid: Spectroscopic and calorimetric exploration. Int J Biol Macromol 2018; 106:1130-1138. [DOI: 10.1016/j.ijbiomac.2017.08.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023]
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19
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Temerk Y, Ibrahim M, Ibrahim H, Schuhmann W. Comparative studies on the interaction of anticancer drug irinotecan with dsDNA and ssDNA. RSC Adv 2018; 8:25387-25395. [PMID: 35539780 PMCID: PMC9082630 DOI: 10.1039/c8ra03231a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 07/10/2018] [Indexed: 11/21/2022] Open
Abstract
The binding mode and thermodynamic characteristics of the anticancer drug irinotecan (Irino) with dsDNA were investigated. The interaction of Irino with dsDNA indicated its intercalation into the base stacking domain of dsDNA double helix.
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Affiliation(s)
- Yassien Temerk
- Chemistry Department
- Faculty of Science
- Assiut University
- Assiut
- Egypt
| | - Mohamed Ibrahim
- Department of Clinical Pharmacy Research
- Institute for Research and Medical Consultation
- Imam Abdulrahman Bin Faisal University
- Dammam 31441
- Saudi Arabia
| | - Hossieny Ibrahim
- Chemistry Department
- Faculty of Science
- Assiut University
- Assiut
- Egypt
| | - Wolfgang Schuhmann
- Anal. Chem. – Elektroanalytik & Sensorik
- Ruhr-Universitat Bochum
- D-44780 Bochum
- Germany
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20
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Liu F, Tan X, Han X, Li X, Li N, Kang W. Cytotoxicity of Aconitum alkaloid and its interaction with calf thymus DNA by multi-spectroscopic techniques. Sci Rep 2017; 7:14509. [PMID: 29109516 PMCID: PMC5674014 DOI: 10.1038/s41598-017-15240-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 10/23/2017] [Indexed: 12/12/2022] Open
Abstract
The cytotoxicities of three aconitum alkaloids- aconitine, hypaconitine and mesaconitine, and their abilities to bind DNA have been explored. Rat myocardial cells H9c2 were treated with aconitum alkaloids and assessed the cytotoxicities by using MTT assay and flow cytometry. Apoptosis was evidenced by the results of the annexin V/propidium iodide (PI) assay. Aconitine was found to be the most toxic in rat myocardial cells H9c2 in three aconitum alkaloids. At the same time, DNA adducts were isolated and then analyzed by UV-Vis spectroscopy after exposure to alkaloids, which indicated that three alkaloids could bind to DNA in rat myocardial cells H9c2. Furthermore, their binding modes were investigated by UV-Visible, fluorescence, DNA melting studies and ionic strength effect. Results indicated that the interaction between three alkaloids and DNA were intercalation coupled with electrostatic effect. The estimated binding constants were between 4.83 × 105 M-1 to 9.85 × 105 M-1 for three alkaloids at 298 K.
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Affiliation(s)
- Fei Liu
- School of Basic Medical, Hebei University of Chinese Medicine, Shijiazhuang, Hebei Province, China
| | - Xiaoxin Tan
- School of Public Health, Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Xu Han
- Institute of Viral Disease, Hebei Center for Disease Control and Prevention, Shijiazhuang, Hebei Province, China
| | - Xiang Li
- School of Public Health, Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Nan Li
- School of Public Health, Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Weijun Kang
- School of Public Health, Hebei Medical University, Shijiazhuang, Hebei Province, China.
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21
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Das S, da Silva CJ, Silva MDM, Dantas MDDA, de Fátima Â, Góis Ruiz ALT, da Silva CM, de Carvalho JE, Santos JCC, Figueiredo IM, da Silva-Júnior EF, de Aquino TM, de Araújo-Júnior JX, Brahmachari G, Modolo LV. Highly functionalized piperidines: Free radical scavenging, anticancer activity, DNA interaction and correlation with biological activity. J Adv Res 2017; 9:51-61. [PMID: 30046486 PMCID: PMC6057241 DOI: 10.1016/j.jare.2017.10.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 11/23/2022] Open
Abstract
Twenty-five piperidines were studied as potential radical scavengers and antitumor agents. Quantitative interaction of compounds with ctDNA using spectroscopic techniques was also evaluated. Our results demonstrate that the evaluated piperidines possesses different abilities to scavenge the radical 2,2-diphenyl-1-picrylhydrazyl (DPPH) and the anion radical superoxide (•O2−). The piperidine 19 was the most potent radical DPPH scavenger, while the most effective to •O2− scavenger was piperidine 10. In general, U251, MCF7, NCI/ADR-RES, NCI-H460 and HT29 cells were least sensitive to the tested compounds and all compounds were considerably more toxic to the studied cancer cell lines than to the normal cell line HaCaT. The binding mode of the compounds and ctDNA was preferably via intercalation. In addition, these results were confirmed based on theoretical studies. Finally, a linear and exponential correlation between interaction constant (Kb) and GI50 for several human cancer cell was observed.
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Affiliation(s)
- Suvankar Das
- Department of Chemistry, Visva-Bharati (a Central University), Santiniketan 731 235, West Bengal, India
| | - Cristiane J da Silva
- Department of Botany, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marina de M Silva
- Institute of Chemistry and Biotechnology, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | | | - Ângelo de Fátima
- Department of Chemistry, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ana Lúcia T Góis Ruiz
- Chemical, Biological and Agricultural Pluridisciplinary Research Center, Universidade Estadual de Campinas, Paulínia, SP, Brazil
| | - Cleiton M da Silva
- Department of Chemistry, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - João Ernesto de Carvalho
- Chemical, Biological and Agricultural Pluridisciplinary Research Center, Universidade Estadual de Campinas, Paulínia, SP, Brazil
| | - Josué C C Santos
- Institute of Chemistry and Biotechnology, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - Isis M Figueiredo
- Institute of Chemistry and Biotechnology, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - Edeildo F da Silva-Júnior
- Institute of Chemistry and Biotechnology, Universidade Federal de Alagoas, Maceió, AL, Brazil.,Laboratory of Medicinal Chemistry, Nursing and Pharmacy School, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - Thiago M de Aquino
- Institute of Chemistry and Biotechnology, Universidade Federal de Alagoas, Maceió, AL, Brazil.,Laboratory of Medicinal Chemistry, Nursing and Pharmacy School, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - João X de Araújo-Júnior
- Institute of Chemistry and Biotechnology, Universidade Federal de Alagoas, Maceió, AL, Brazil.,Laboratory of Medicinal Chemistry, Nursing and Pharmacy School, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - Goutam Brahmachari
- Department of Chemistry, Visva-Bharati (a Central University), Santiniketan 731 235, West Bengal, India
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22
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Ma L, Wang J, Zhang Y. Probing the Characterization of the Interaction of Aflatoxins B1 and G1 with Calf Thymus DNA In Vitro. Toxins (Basel) 2017; 9:E209. [PMID: 28671585 PMCID: PMC5535156 DOI: 10.3390/toxins9070209] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/20/2017] [Accepted: 06/28/2017] [Indexed: 11/16/2022] Open
Abstract
The binding characterization of aflatoxins with calf thymus DNA (ctDNA) under physiological conditions was investigated. Multispectroscopic techniques, ctDNA melting, viscosity measurements, and molecular docking techniques were employed to elucidate the binding mechanism of the aflatoxins with DNA. The fluorescence results indicated that both aflatoxin B1 (AFB1) and aflatoxin G1 (AFG1) bound to the ctDNA, forming complexes through hydrogen bonding. The binding constants of AFB1 and AFG1 with ctDNA reached up to 10³ L·mol-1 and 10⁴ L·mol-1, respectively, and AFG1 exhibited a higher binding propensity than that of AFB1. Furthermore, both AFB1 and AFG1 bound to the ctDNA through groove binding, as evidenced by the results of the spectroscopic, iodide quenching effect, viscosity, and ctDNA melting measurements. Changes in the circular dichroism signal manifested that both AFB1 and AFG1 induced an increase in the right-handed helicity, but only minimally influenced the base stacking of the DNA. A molecular docking study of the aflatoxin's binding with the DNA revealed a groove binding mode, which was driven mainly by hydrogen bonding. This study of aflatoxin-ctDNA interaction may provide novel insights into the toxicological effect of the mycotoxins.
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Affiliation(s)
- Liang Ma
- College of Food Science, Southwest University, Beibei District, Chongqing 400715, China.
| | - Jiaman Wang
- College of Food Science, Southwest University, Beibei District, Chongqing 400715, China.
| | - Yuhao Zhang
- College of Food Science, Southwest University, Beibei District, Chongqing 400715, China.
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23
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Groove Binding of Vanillin and Ethyl Vanillin to Calf Thymus DNA. J Fluoresc 2017; 27:1815-1828. [DOI: 10.1007/s10895-017-2119-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/14/2017] [Indexed: 10/19/2022]
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24
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Xia K, Zhang G, Gong D. Deciphering the intercalative binding modes of benzoyl peroxide with calf thymus DNA. LUMINESCENCE 2017; 32:988-998. [PMID: 28116811 DOI: 10.1002/bio.3281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 12/13/2016] [Accepted: 12/19/2016] [Indexed: 12/23/2022]
Abstract
The binding of benzoyl peroxide (BPO), a flour brightener, with calf thymus DNA (ctDNA) was predicted by molecular simulation, and this were confirmed using multi-spectroscopic techniques and a chemometrics algorithm. The molecular docking result showed that BPO could insert into the base pairs of ctDNA, and the adenine bases were the preferential binding sites which were validated by the analysis of Fourier transform infrared spectra. The mode of binding of BPO with ctDNA was an intercalation as supported by the results from ctDNA melting and viscosity measurements, iodide quenching effects and competitive binding investigations. The circular dichroism and DNA cleavage assays indicated that BPO induced a conformational change from B-like DNA structure towards to A-like form, but did not lead to significant damage in the DNA. The complexation was driven mainly by hydrogen bonds and hydrophobic interactions. Moreover, the ultraviolet-visible (UV-vis) spectroscopic data matrix was resolved by a multivariate curve resolution-alternating least-squares algorithm. The equilibrium concentration profiles for the components (BPO, ctDNA and BPO-ctDNA complex) were extracted from the highly overlapping composite response to quantitatively monitor the BPO-ctDNA interaction. This study has provided insights into the mechanism of the interaction of BPO with ctDNA and potential hazards of the food additive.
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Affiliation(s)
- Kaixin Xia
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Deming Gong
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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25
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Shahbazy M, Pakravan P, Kompany-Zareh M. Multivariate spectrochemical analysis of interactions of three common Isatin derivatives to calf thymus DNA in vitro. J Biomol Struct Dyn 2016; 35:2539-2556. [DOI: 10.1080/07391102.2016.1225604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Mohammad Shahbazy
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Parvaneh Pakravan
- Department of Chemistry, Zanjan Branch, Islamic Azad University, Zanjan, Iran
| | - Mohsen Kompany-Zareh
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
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26
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Ray B, Agarwal S, Lohani N, Rajeswari MR, Mehrotra R. Structural, conformational and thermodynamic aspects of groove-directed-intercalation of flavopiridol into DNA. J Biomol Struct Dyn 2016; 34:2518-35. [DOI: 10.1080/07391102.2015.1118708] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Bhumika Ray
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Shweta Agarwal
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
| | - Neelam Lohani
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Moganty R. Rajeswari
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Ranjana Mehrotra
- Academy of Scientific & Innovative Research (AcSIR), CSIR-National Physical Laboratory Campus, New Delhi 110012, India
- Quantum Phenomena and Applications, CSIR-National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi 110012, India
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27
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Huang YM, Zheng SJ, Yan J, Yang HQ, Wu D, Wang Q, Li H. Investigation on the interaction of letrozole with herring sperm DNA through spectroscopic and modeling methods. LUMINESCENCE 2015; 31:1077-84. [DOI: 10.1002/bio.3074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/11/2015] [Accepted: 11/12/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Yan-Mei Huang
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Shou-Jun Zheng
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Jin Yan
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Hong-Qin Yang
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Di Wu
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Qing Wang
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Hui Li
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
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28
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Cytotoxicity and DNA interaction of brucine and strychnine—Two alkaloids of semen strychni. Int J Biol Macromol 2015; 77:92-8. [DOI: 10.1016/j.ijbiomac.2015.03.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 03/05/2015] [Accepted: 03/07/2015] [Indexed: 11/21/2022]
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29
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Tao M, Zhang G, Xiong C, Pan J. Characterization of the interaction between resmethrin and calf thymus DNA in vitro. NEW J CHEM 2015. [DOI: 10.1039/c4nj02321h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Resmethrin preferentially binds to the G–C rich region of the ctDNA groove, and the UV-vis spectral matrix is decomposed by MCR-ALS.
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Affiliation(s)
- 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
| | - Chunhong Xiong
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Junhui Pan
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
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30
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Electrochemical studies and spectroscopic investigations on the interaction of an anticancer drug flutamide with DNA and its analytical applications. J Electroanal Chem (Lausanne) 2015. [DOI: 10.1016/j.jelechem.2014.10.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Zhou X, Zhang G, Pan J. Groove binding interaction between daphnetin and calf thymus DNA. Int J Biol Macromol 2014; 74:185-94. [PMID: 25541356 DOI: 10.1016/j.ijbiomac.2014.12.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 12/25/2022]
Abstract
The binding characteristics of daphnetin with calf thymus DNA (ctDNA) were investigated by multispectroscopic and chemometric approaches coupled with DNA viscosity measurements, melting studies and molecular docking technique. The expanded UV-vis spectral data matrix was processed by multivariate curve resolution-alternating least-squares method to obtain the concentration profiles of the components (daphnetin, ctDNA and daphnetin-ctDNA complex) to quantitatively monitor the daphnetin-ctDNA interaction. The groove mode of daphnetin binding to ctDNA was concluded by little change in melting temperature, viscosity of ctDNA and iodide quenching effect as well as increase in single-stranded DNA quenching effect. Moreover, the quantitative data for the competitive binding between daphnetin and Hoechst 33258 for ctDNA obtained by resolving the three-way synchronous fluorescence spectra data using parallel factor analysis modeling further supported the groove binding. The molecular docking visualized the results of the Fourier transform infrared analysis that the adenine and thymine bases in the minor groove of ctDNA were the main binding sites for daphnetin, and the circular dichroism spectra showed that the groove binding of daphnetin to ctDNA led to the conformational change in ctDNA from B-form to A-form. This study revealed the interaction mechanism of daphnetin with ctDNA.
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Affiliation(s)
- Xiaoyue Zhou
- 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.
| | - Junhui Pan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
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32
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Molecular recognition pattern of cytotoxic alkaloid vinblastine with multiple targets. J Mol Graph Model 2014; 54:1-9. [DOI: 10.1016/j.jmgm.2014.09.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/30/2014] [Accepted: 09/02/2014] [Indexed: 11/19/2022]
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Agarwal S, Chadha D, Mehrotra R. Molecular modeling and spectroscopic studies of semustine binding with DNA and its comparison with lomustine–DNA adduct formation. J Biomol Struct Dyn 2014; 33:1653-68. [DOI: 10.1080/07391102.2014.968874] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Lohani N, Narayan Singh H, Agarwal S, Mehrotra R, Rajeswari MR. Interaction of adriamycin with a regulatory element ofhmgb1: spectroscopic and calorimetric approach. J Biomol Struct Dyn 2014; 33:1612-23. [DOI: 10.1080/07391102.2014.967301] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Li Y, Zhang G, Tao M. Binding properties of herbicide chlorpropham to DNA: Spectroscopic, chemometrics and modeling investigations. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 138:109-17. [DOI: 10.1016/j.jphotobiol.2014.05.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/13/2014] [Accepted: 05/15/2014] [Indexed: 01/06/2023]
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Sarioglu OF, Tekiner-Gursacli R, Ozdemir A, Tekinay T. Comparison of Au(III) and Ga(III) ions' binding to calf thymus DNA: spectroscopic characterization and thermal analysis. Biol Trace Elem Res 2014; 160:445-52. [PMID: 25008991 DOI: 10.1007/s12011-014-0059-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/23/2014] [Indexed: 11/30/2022]
Abstract
Metals have been studied as potential chemotherapeutic agents for cancer therapies due to their high reactivity toward a wide variety of substances. The characterization of metal ion-binding capacities is essential to understand the possible effects of metals on target biomolecules. In the present study, biochemical effects of Au(III) and Ga(III) ions on calf thymus DNA (ctDNA) were studied comparatively via bioanalytical, spectroscopic, and thermal methods. Briefly, UV-Vis absorbance spectroscopy, fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and Fourier transform infrared (FT-IR) spectroscopy were utilized for spectroscopic characterization, and isothermal titration calorimetry (ITC) measurements were performed for thermal analysis. Our results reveal that both Au(III) and Ga(III) ions are capable of interacting with ctDNA, and Au(III) ions display a more favorable interaction and a higher binding affinity. ITC analyses indicate that the Au(III)-DNA interaction displays a binding affinity (Ka) around 1.43 × 10(6) M(-1), while a Ka around 1.17 × 10(5) M(-1) was observed for the Ga(III)-DNA binding. It was suggested that both metal ions are unlikely to change the structural B-conformation while interacting with ctDNA.
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Affiliation(s)
- Omer Faruk Sarioglu
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800, Ankara, Turkey
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Agarwal S, Jangir DK, Singh P, Mehrotra R. Spectroscopic analysis of the interaction of lomustine with calf thymus DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 130:281-6. [DOI: 10.1016/j.jphotobiol.2013.11.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 11/09/2013] [Accepted: 11/16/2013] [Indexed: 11/30/2022]
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Šimánek V, Zatloukalová M, Vacek J. Electrochemical Behaviour of Alkaloids: Detection and Interaction with DNA and Proteins. HETEROCYCLES 2014. [DOI: 10.3987/rev-13-sr(s)6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Determination of acetamiprid partial-intercalative binding to DNA by use of spectroscopic, chemometrics, and molecular docking techniques. Anal Bioanal Chem 2013; 405:8871-83. [DOI: 10.1007/s00216-013-7294-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/05/2013] [Accepted: 08/06/2013] [Indexed: 01/07/2023]
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Lin J, Liu Y, Liu L, Song L. Studies on the toxic interaction mechanism between 2-naphthylamine and herring sperm DNA. J Biochem Mol Toxicol 2013; 27:279-85. [PMID: 23625636 DOI: 10.1002/jbt.21488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 03/11/2013] [Accepted: 03/25/2013] [Indexed: 12/30/2022]
Abstract
The toxic interaction between 2-naphthylamine (2-NA) and herring sperm deoxyribonucleic acid (hs-DNA) has been thoroughly investigated by UV absorption, fluorescence, and circular dichroism (CD) spectroscopic methods. UV absorption result indicates that 2-NA may intercalate into the stack base pairs of DNA during the toxic interaction of 2-NA with DNA. A fluorescence quenching study shows that DNA quenches the intrinsic fluorescence of 2-NA via a static pathway. The studies on effects of ionic strength and anionic quenching rule out electrostatic and groove bindings as the dominant binding modes. Further studies on denatured DNA fluorescence quenching and thermal melting studies confirm that the dominant binding mode of 2-NA-DNA is intercalative binding. A CD spectral study shows that the binding interaction of 2-NA with DNA leads to the disorganization of the neat double-helical structure of hs-DNA.
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Affiliation(s)
- Jingjing Lin
- The State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, People's Republic of China
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Zhang Y, Zhang G, Li Y, Hu Y. Probing the binding of insecticide permethrin to calf thymus DNA by spectroscopic techniques merging with chemometrics method. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:2638-2647. [PMID: 23448177 DOI: 10.1021/jf400017f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The binding of permethrin (PE) with calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) was investigated by ultraviolet-visible (UV-vis) absorption, fluorescence, circular dichroism (CD), and Fourier transform infrared (FT-IR) spectroscopy merging with multivariate curve resolution-alternating least-squares (MCR-ALS) chemometrics approach. The MCR-ALS was applied to resolve the combined spectroscopic data matrix, which was obtained by UV-vis and fluorescence methods. The concentration profiles of PE, ctDNA, and PE-ctDNA complex and their pure spectra were then successfully obtained. The PE molecular was found to be able to intercalate into the base pairs of ctDNA as evidenced by decreases in resonance light-scattering signal and iodide-quenching effect and increase in ctDNA viscosity. The results of FT-IR spectra indicated that PE was prone to bind to G-C base pairs of ctDNA, and the molecular docking studies were used to validate and clarify the specific binding. The observed changes in CD signals revealed that the DNA turned into a more highly wound form of B-conformation. The calculated thermodynamic parameters, enthalpy change (ΔH°) and entropy change (ΔS°), suggested that hydrogen bonds and van der Waals forces played a predominant role in the binding of PE to ctDNA.
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Affiliation(s)
- Yue Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University , No. 235, Nanjing East Road, Nanchang 330047, Jiangxi, China
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