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Kuzpınar E, Al Faysal A, Şenel P, Erdoğan T, Gölcü A. Quantification of mirtazapine in tablets via DNA binding mechanism; development of a new HPLC method. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1234:124019. [PMID: 38309044 DOI: 10.1016/j.jchromb.2024.124019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 02/05/2024]
Abstract
Atypical antidepressant mirtazapine (MIR) is mostly prescribed for the management of major depressive disorder. The identification of MIR in pharmaceutical dosage forms was made possible by developing a novel, quick, sensitive high-performance liquid chromatography (HPLC) approach that was verified in accordance with ICH recommendations. In the first part of this study, HPLC investigations were optimized with regard to variables including pH, working column, mobile phase, temperature, and flow rate. The limit of detection (LOD) was 0.013 ppm, the limit of quantification (LOQ) was 0.044 ppm, and the linear range was computed as 0.5-15 ppm (R2 = 0.9998). The recovery investigation assessed the method's accuracy, which was shown to range between 98.82 and 100.97 %. In the second part, by using UV-vis spectroscopy, HPLC, thermal denaturation, and viscosity measurements, the mechanism of binding interaction of MIR with double-stranded fish sperm deoxyribonucleic acid (dsDNA) has been thoroughly studied. The DNA binding constants (Kb) were determined using UV-Vis absorption and HPLC methods. To investigate the interactions of MIR with dsDNA, molecular docking calculations and additionally, molecular dynamics simulations were performed. Results showed that MIR is located in the minor groove of dsDNA, and in addition to hydrogen bonding, electrostatic interaction is also formed between the aromatic ring of MIR and phosphate oxygen of dsDNA. Finally, a binding characterization study using MIR tablets was also conducted in order to assess the interaction mechanism of the DNA with the drug using the validated analytical procedure developed for the MIR molecule.
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Affiliation(s)
- Ecem Kuzpınar
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Maslak, Istanbul, Türkiye
| | - Abdullah Al Faysal
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Maslak, Istanbul, Türkiye
| | - Pelin Şenel
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Maslak, Istanbul, Türkiye
| | - Taner Erdoğan
- Kocaeli University, Kocaeli Vocational School, Department of Chemistry and Chemical Processing Technologies, Kocaeli, 41140, Türkiye
| | - Ayşegül Gölcü
- Istanbul Technical University, Faculty of Sciences and Letters, Department of Chemistry, Maslak, Istanbul, Türkiye.
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2
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Radwan AS, Salim MM, Elkhoudary MM, Hadad GM, Shaldam MA, Belal F, Magdy G. Study of the binding interaction of salmon sperm DNA with nintedanib, a tyrosine kinase inhibitor using multi-spectroscopic, thermodynamic, and in silico approaches. J Biomol Struct Dyn 2024; 42:1170-1180. [PMID: 37079322 DOI: 10.1080/07391102.2023.2202776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/28/2023] [Indexed: 04/21/2023]
Abstract
The study of the intermolecular binding interaction of small molecules with DNA can guide the rational drug design with greater efficacy and improved or more selective activity. In the current study, nintedanib's binding interaction with salmon sperm DNA (ssDNA) was thoroughly investigated using UV-vis spectrophotometry, spectrofluorimetry, ionic strength measurements, viscosity measurements, thermodynamics, molecular docking, and molecular dynamic simulation techniques under physiologically simulated conditions (pH 7.4). The obtained experimental results showed that nintedanib and ssDNA had an apparent binding interaction. Nintedanib's binding constant (Kb) with ssDNA, as determined using the Benesi-Hildebrand plot, was 7.9 × 104 M-1 at 298 K, indicating a moderate binding affinity. The primary binding contact forces were hydrophobic and hydrogen bonding interactions, as verified by the enthalpy and entropy changes (ΔH0 and ΔS0), which were - 16.25 kJ.mol-1 and 39.30 J mol-1 K-1, respectively. According to the results of UV-vis spectrophotometry, viscosity assays, and competitive binding interactions with ethidium bromide or rhodamine B, the binding mode of nintedanib to ssDNA was minor groove. Molecular docking and molecular dynamic simulation studies showed that nintedanib fitted into the B-DNA minor groove's AT-rich region with high stability. This study can contribute to further understanding of nintedanib's molecular mechanisms and pharmacological effects.
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Affiliation(s)
- Aya Saad Radwan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta, Egypt
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Mohamed M Salim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta, Egypt
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Mahmoud M Elkhoudary
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta, Egypt
| | - Ghada M Hadad
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Moataz A Shaldam
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Fathalla Belal
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Galal Magdy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
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3
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Shaldam M, Tawfik H, Elmansi H, Belal F, Yamaguchi K, Sugiura M, Magdy G. Synthesis, crystallographic, DNA binding, and molecular docking/dynamic studies of a privileged chalcone-sulfonamide hybrid scaffold as a promising anticancer agent. J Biomol Struct Dyn 2023; 41:8876-8890. [PMID: 36310097 DOI: 10.1080/07391102.2022.2138551] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/15/2022] [Indexed: 10/31/2022]
Abstract
In the present study, a drug-like molecular hybrid structure between chalcone and sulfonamide moieties was synthesized and characterized. The structural peculiarities of the synthesized hybrid were further verified by means of single crystal X-ray crystallography. Furthermore, its biological activity as an anticancer agent was evaluated. The synthesized model of chalcone-sulfonamide hybrid 3 was found to have potent anticancer properties against the studied cancer cell lines. Hence, the in vitro binding interaction of hybrid 3 with Calf thymus DNA (CT-DNA) was studied at a simulated physiological pH to confirm its anticancer activity for the first time. This was investigated by applying different spectroscopic techniques, ionic strength measurements, viscosity measurements, thermodynamics, molecular dynamic simulation and molecular docking studies. The obtained results showed a clear binding interaction between hybrid 3 and CT-DNA with a moderate affinity via a minor groove binding mechanism. The binding constant (Kb) at 298 K calculated from the Benesi-Hildebrand equation was found to be 3.49 × 104 M-1. The entropy and enthalpy changes (ΔS0 and ΔH0) were 204.65 J mol-1 K-1 and 35.08 KJ mol-1, respectively, indicating that hydrophobic interactions constituted the major binding forces. The results obtained from molecular docking and dynamic simulation studies confirmed the minor groove binding interaction and the stability of the formed complex. This study can contribute to further understanding of the molecular mechanism of hybrid 3 as a potential antitumor agent and can also guide future clinical and pharmacological studies for rational drug design with enhanced or more selective activity and greater efficacy.[Figure: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Moataz Shaldam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Haytham Tawfik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Heba Elmansi
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Fathalla Belal
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Koki Yamaguchi
- Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan
| | - Masaharu Sugiura
- Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, Japan
| | - Galal Magdy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
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4
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Batibay GS, Keser Karaoglan G, Gumrukcu Kose G, Ozcelik Kazancioglu E, Metin E, Danisman Kalindemirtas F, Erdem Kuruca S, Arsu N. DNA groove binder and significant cytotoxic activity on human colon cancer cells: Potential of a dimeric zinc (II) phthalocyanine derivative. Biophys Chem 2023; 295:106974. [PMID: 36827854 DOI: 10.1016/j.bpc.2023.106974] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
The interaction of a multi-component system consisting of benzene-1,4-diyldimethanimine-bridged dimeric zinc-phthalocyanine groups (4OMPCZ) with calf thymus DNA (ct-DNA) was investigated using UV-Vis absorption, fluorescence emission spectroscopy methods, and viscosity measurements. The binding constant, Kb, which is an important parameter to gain information about the binding mode, was found as 9.7 × 107 M-1 from the UV-Vis absorption studies. Another important spectrophotometric tool is competitive displacement assays with Ethidium bromide and Hoechst 33342. Through this experiment, a higher KSV value was obtained with Hoechst for the phthalocyanine derivative, 4OMPCZ, and the ct-DNA complex than with ethidium bromide. Additionally, molecular docking studies were conducted to calculate the theoretical binding constant and visualize the interactions of 4OMPCZ with a model DNA. According to docking results, although the interactions are mainly located in the major groove of the DNA helix, due to the wrapping, these interactions can also be extended to the minor groove of the DNA. Spectrophotometric, molecular docking, and viscosity studies revealed that the interaction of 4OMPCZ with DNA is likely to be via the major and minor grooves. The in vitro cytotoxic activity of 4OMPCZ was evaluated by MTT assay on human colon cancer cells (HT29) after 72 h of treatment. 4OMPCZ indicated significant cytotoxic activity when stimulated with UV light compared to the standard chemotherapy drugs, fluorouracil (5-FU), and cisplatin on HT29 colon cancer cells. The IC50 value of 4OMPCZ displayed considerably lower concentrations compared to the standard drugs, 5-FU, and cisplatin.
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Affiliation(s)
- Gonul S Batibay
- Yildiz Technical University, Department of Chemistry, Davutpasa Campus, 34220 Istanbul, Turkey
| | - Gulnur Keser Karaoglan
- Yildiz Technical University, Department of Chemistry, Davutpasa Campus, 34220 Istanbul, Turkey
| | - Gulsah Gumrukcu Kose
- Yildiz Technical University, Department of Chemistry, Davutpasa Campus, 34220 Istanbul, Turkey
| | | | - Eyup Metin
- Yildiz Technical University, Department of Chemistry, Davutpasa Campus, 34220 Istanbul, Turkey; Turkish-German University, Department of Materials Science and Technology, 34820 Istanbul, Turkey
| | - Ferdane Danisman Kalindemirtas
- Erzincan Binali Yildirim University, Faculty of Medicine, Department of Physiology, Erzincan 24100, Turkey; Istanbul University, Faculty of Medicine, Department of Physiology, 34093 Istanbul, Turkey
| | - Serap Erdem Kuruca
- Atlas University, Faculty of Medicine, Department of Physiology, Istanbul 34403, Turkey; Istanbul University, Faculty of Medicine, Department of Physiology, 34093 Istanbul, Turkey
| | - Nergis Arsu
- Yildiz Technical University, Department of Chemistry, Davutpasa Campus, 34220 Istanbul, Turkey.
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Jeevitha Rani J, Mary Imelda Jayaseeli A, Sankarganesh M, Nandini Asha R. Bovine serum albumin interaction, molecular docking, anticancer and antimicrobial activities of Co(II) Schiff base complex derived from Nophen ligand. J Biomol Struct Dyn 2023; 41:1895-1903. [PMID: 35037822 DOI: 10.1080/07391102.2022.2026249] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this report, synthesis, characterization, biological and molecular modeling studies of Nophen Schiff base [N,N-bis(2-hydroxy-1-naphthaldehyde)-o-phenylenediamine] and Co(II)-Nophen complex have been furnished. BSA binding affinities of the ligand and Co(II)-Nophen complex have been appraised by UV-visible, fluorescence and cyclic voltammetric techniques. Spectroscopic measurements indicate strong binding of the complex with BSA protein through static quenching mechanism with binding constant in the order of 104 M-1. The negative shift of the peak potential in cyclic voltammetry suggested an electrostatic interaction. Molecular docking analysis reveals significant binding affinity (-6.3 kcal/mol) of the complex towards BSA protein. It is amazing that the in vitro cytotoxicity of Co(II)-Nophen complex against A549 cell lines (Human lung carcinoma cells) has remarkable potentials with 29 ± 1.2 µM as IC50 value. Comparing the biological activity towards microorganisms, Co(II)-Nophen complex show substantial response than the Nophen ligand.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- J Jeevitha Rani
- Post Graduate and Research Center of Chemistry, Jayaraj Annapackiam College for Women (Autonomous), Affiliated to Mother Teresa Women's University, Kodaikanal, Periyakulam, Theni, Tamil Nadu, India
| | - A Mary Imelda Jayaseeli
- Post Graduate and Research Center of Chemistry, Jayaraj Annapackiam College for Women (Autonomous), Affiliated to Mother Teresa Women's University, Kodaikanal, Periyakulam, Theni, Tamil Nadu, India
| | - M Sankarganesh
- Department of Chemistry, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| | - R Nandini Asha
- Department of Chemistry, Pope's College (Autonomous), Sawyerpuram, Thoothukudi, Tamil Nadu, India
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6
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Dehkordi MF, Farhadian S, Hashemi-Shahraki F, Rahmani B, Darzi S, Dehghan G. The interaction mechanism of candidone with calf thymus DNA: A multi-spectroscopic and MD simulation study. Int J Biol Macromol 2023; 235:123713. [PMID: 36801300 DOI: 10.1016/j.ijbiomac.2023.123713] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/11/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023]
Abstract
In this investigation, the effects of candidone on the structure and conformation of DNA were evaluated by spectroscopic methods, molecular dynamics simulation, and molecular docking studies. Fluorescence emission peaks, ultraviolet-visible spectra, and molecular docking exhibited the complex formation between candidone and DNA in a groove-binding mode. Fluorescence spectroscopy results also showed a static quenching mechanism of DNA in the presence of candidone. Moreover, thermodynamic parameters demonstrated that candidone spontaneously bound to DNA with a high binding affinity. The hydrophobic interactions were the dominant forces over the binding process. Based on the Fourier transform infrared data candidone tended to attach to the A-T base pairs of the minor grooves of DNA. The thermal denaturation and circular dichroism measurements displayed that candidone caused a slight change in the DNA structure, which was confirmed by the molecular dynamics simulation results. According to the obtained findings from the molecular dynamic simulation, the structural flexibility and dynamics of DNA were altered to a more extended structure.
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Affiliation(s)
- Mahvash Farajzadeh Dehkordi
- Department of Molecular Medicine, Qazvin University of Medical Sciences, Qazvin, Iran; Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Fatemeh Hashemi-Shahraki
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Babak Rahmani
- Department of Molecular Medicine, Qazvin University of Medical Sciences, Qazvin, Iran; Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran.
| | - Sina Darzi
- Health Products Safety Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Gholamreza Dehghan
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
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7
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Shahabadi N, Abdoli Z, Mardani Z, Hadidi S, Shiri F, Soltani L. DNA interaction studies of a cobalt(III) complex containing β-amino alcohol ligand by spectroscopic and molecular docking methods. J Biomol Struct Dyn 2023; 41:12545-12551. [PMID: 36650998 DOI: 10.1080/07391102.2023.2166994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023]
Abstract
In the present research, the feasibility of a Cobalt(III) complex containing β-amino alcohol ligands for affinity with the target calf thymus DNA is demonstrated. In the title complex, [Co(C11H15N2O2)2]Cl, the Co(III) atom is six-coordinated with four N atoms and two O atoms from (2-[(E)-({2-[(2-Hydroxyethyl) amino]ethyl}imino)methyl]phenol) ligand (L). To investigate the molecular interaction between the synthesized complex and DNA, some multi-spectroscopic approaches associated with molecular docking were employed in the physiological buffer (pH 7.4). The results indicated that the Co(III) complex proved to be a minor groove binder with a preference for the A-T region, which was substantiated by displacement studies with Hoechst33258 and Methylene blue (MB) as minor groove binder and intercalator. In addition, the results of the molecular docking study revealed that the Co(III) complex approached the gap between the DNA minor grooves near the spot where the Hoechst was. Furthermore, the results of the cytotoxicity and apoptosis tests for the MCF-7 cell line were also indicative of the positive effects of the complex on controlling the growth and viability of breast cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Zahra Abdoli
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Zahra Mardani
- Department of Inorganic Chemistry, Faculty of Chemistry, Urmia University, Urmia, Iran
| | - Saba Hadidi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Farshad Shiri
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Leila Soltani
- Department of Animal Sciences, College of Agriculture and Natural Resources, Razi University, Kermanshah, Iran
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Madku SR, Sahoo BK, Lavanya K, Reddy RS, Bodapati ATS. DNA binding studies of antifungal drug posaconazole using spectroscopic and molecular docking methods. Int J Biol Macromol 2023; 225:745-756. [PMID: 36414083 DOI: 10.1016/j.ijbiomac.2022.11.137] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/15/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022]
Abstract
The binding studies of DNA with small molecules have been an emerging field of research all the time since DNA as the genetic material is a major biological target for various drugs. Interpretation of small molecule-DNA binding helps in understanding their interactions with designing new drugs of greater medicinal activity. Posaconazole is an antifungal drug in the class of triazoles which are known to possess numerous pharmacological properties. In this work, the nature of the binding of posaconazole with calf-thymus DNA has been studied using spectroscopic techniques and molecular docking studies. A binding constant of the order of 103 M-1 was observed from UV-visible and fluorescence studies for the interaction between posaconazole and calf-thymus DNA. The fluorescence property of posaconazole was found to be quenched by calf-thymus DNA with a quenching constant of the order of 103 M-1. Competitive displacement of ethidium bromide and Hoechst 33258 by posaconazole using fluorescence technique suggested minor groove binding of posaconazole in calf-thymus DNA. Confirmation of the binding mode was further complemented by the viscosity measurement and DNA melting studies followed by KI quenching experiments. The studies on the effect of ionic strength on the binding suggested a possible role of electrostatic force in the interaction. Molecular docking studies reflected a crescent shape of the posaconazole within the minor groove of calf-thymus DNA validating the experimental findings showing the residues involved in the interaction.
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Affiliation(s)
- Shravya Rao Madku
- Department of Chemistry, St. Francis College for Women, Hyderabad 500016, India; Department of Chemistry, GITAM School of Science, GITAM Deemed to be University Hyderabad Campus, 502329, India
| | - Bijaya Ketan Sahoo
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University Hyderabad Campus, 502329, India.
| | - K Lavanya
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University Hyderabad Campus, 502329, India; Department of H&S (Chemistry), Gokaraju Rangaraju Institute of Engineering and Technology, Hyderabad 500090, India
| | - Ragaiahgari Srinivas Reddy
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University Hyderabad Campus, 502329, India; Department of Chemistry, B V Raju Institute of Technology (BVRIT), Narsapur 502313, India
| | - Anna Tanuja Safala Bodapati
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University Hyderabad Campus, 502329, India; Chemistry Division, BS&H Department, BVRIT College of Engineering for Women, Hyderabad 500090, India
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Ahmadi Oskooei F, Mehrzad J, Asoodeh A, Motavalizadehkakhky A. Multi-spectroscopic characteristics of olive oil-based Quercetin nanoemulsion (QuNE) interactions with calf thymus DNA and its anticancer activity. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Bilge S, Dogan-Topal B, Taskin Tok T, Atici EB, Sınağ A, Ozkan SA. Investigation of the interaction between anticancer drug ibrutinib and double-stranded DNA by electrochemical and molecular docking techniques. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Multi-spectroscopic, thermodynamic, and molecular docking/dynamic approaches for characterization of the binding interaction between calf thymus DNA and palbociclib. Sci Rep 2022; 12:14723. [PMID: 36042232 PMCID: PMC9427788 DOI: 10.1038/s41598-022-19015-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Studying the binding interaction between biological macromolecules and small molecules has formed the core of different research aspects. The interaction of palbociclib with calf thymus DNA at simulated physiological conditions (pH 7.4) was studied using different approaches, including spectrophotometry, spectrofluorimetry, FT-IR spectroscopy, viscosity measurements, ionic strength measurements, thermodynamic, molecular dynamic simulation, and docking studies. The obtained findings showed an apparent binding interaction between palbociclib and calf thymus DNA. Groove binding mode was confirmed from the findings of competitive binding studies with ethidium bromide or rhodamine B, UV–Vis spectrophotometry, and viscosity assessment. The binding constant (Kb) at 298 K calculated from the Benesi–Hildebrand equation was found to be 6.42 × 103 M−1. The enthalpy and entropy changes (∆H0 and ∆S0) were − 33.09 kJ mol−1 and 61.78 J mol−1 K−1, respectively, showing that hydrophobic and hydrogen bonds constitute the primary binding forces. As indicated by the molecular docking results, palbociclib fits into the AT-rich region of the B-DNA minor groove with four base pairs long binding site. The dynamic performance and stability of the formed complex were also evaluated using molecular dynamic simulation studies. The in vitro study of the intermolecular binding interaction of palbociclib with calf thymus DNA could guide future clinical and pharmacological studies for the rational drug scheming with enhanced or more selective activity and greater efficacy.
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12
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Intrinsically Fluorescent Anti-Cancer Drugs. BIOLOGY 2022; 11:biology11081135. [PMID: 36009762 PMCID: PMC9405238 DOI: 10.3390/biology11081135] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022]
Abstract
At present, about one-third of the total protein targets in the pharmaceutical research sector are kinase-based. While kinases have been attractive targets to combat many diseases, including cancer, selective kinase inhibition has been challenging, because of the high degree of structural homology in the active site where many kinase inhibitors bind. Despite efficacy as cancer drugs, kinase inhibitors can exhibit limited target specificity and rationalizing their target profiles in the context of precise molecular mechanisms or rearrangements is a major challenge for the field. Spectroscopic approaches such as infrared, Raman, NMR and fluorescence have the potential to provide significant insights into drug-target and drug-non-target interactions because of sensitivity to molecular environment. This review places a spotlight on the significance of fluorescence for extracting information related to structural properties, discovery of hidden conformers in solution and in target-bound state, binding properties (e.g., location of binding sites, hydrogen-bonding, hydrophobicity), kinetics as well as dynamics of kinase inhibitors. It is concluded that the information gleaned from an understanding of the intrinsic fluorescence from these classes of drugs may aid in the development of future drugs with improved side-effects and less disease resistance.
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Ponkarpagam S, Vennila KN, Elango KP. Intercalation of diafenthiuron insecticide with calf thymus DNA: spectroscopic and molecular dynamics analysis. J Biomol Struct Dyn 2022:1-9. [PMID: 35848349 DOI: 10.1080/07391102.2022.2098824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A series of biophysical experiments like UV-Vis, fluorescence, circular dichroism (CD), competitive displacement assays, voltammetric studies, viscosity measurements and denaturation effect and metadynamics simulation studies were performed to establish the mode of binding of diafenthiuron (DF) insecticide with calf thymus DNA (CT-DNA). Analysis of absorption and fluorescence spectra in Tris-HCl buffer of pH 7.4 indicates the formation of a complex between DF and CT-DNA and the binding constant of which is in the order of 104 M-1. Competitive displacement assay with ethidium bromide (EB) and Hoechst 33258 suggests that the most probable mode of binding of DF with CT-DNA may be via intercalation mode. The results of other experiments such as CD spectral studies, viscosity measurements and the effect of denaturation agent urea support the intercalation of DF with CT-DNA. Thermodynamic parameters (ΔHo, ΔSo and ΔGo) reveal that hydrogen bonds (H-bonds) or van der Waals (vdW) force is the main binding force in the spontaneous interaction between DF and CT-DNA. Molecular dynamics (MD) simulation studies confirmed the intercalation of DF into the base pairs of CT-DNA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
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14
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Kou SB, Zhou KL, Lin ZY, Lou YY, Wang BL, Shi JH, Liu YX. Investigation of binding characteristics of ritonavir with calf thymus DNA with the help of spectroscopic techniques and molecular simulation. J Biomol Struct Dyn 2022; 40:2908-2916. [PMID: 33164672 DOI: 10.1080/07391102.2020.1844057] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The binding behavior of ritonavir (RTV), a HIV/AIDS protease inhibitor, with ct-DNA was characterized through multiple testing technologies and theoretical calculation. The findings revealed that the RTV-DNA complex was formed through the noncovalent interaction mainly including conventional hydrogen bonds and carbon hydrogen bonds as well as hydrophobic interactions (pi-alkyl interactions). The stoichiometry and binding constant of the RTV-DNA complex were 1:1 and 1.87 × 103 M-1 at 298 K, respectively, indicating that RTV has moderate affinity with ct-DNA. The findings confirmed that RTV binds to the minor groove of DNA. The outcomes of CD experiments showed that the binding with RTV changed the conformation of DNA slightly. However, the conformation of RTV had obvious changes after binding to DNA, meaning that the flexibility of RTV molecule played an important role in stabilizing the RTV-DNA complex. Meanwhile, the results of DFT calculation revealed that the RTV and DNA interaction caused the changes in the frontier molecular orbitals, dipole moment and atomic charge distribution of RTV, altering the chemical properties of RTV when it bound to DNA. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Song-Bo Kou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Kai-Li Zhou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Zhen-Yi Lin
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Yan-Yue Lou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Bao-Li Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Jie-Hua Shi
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Ying-Xin Liu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
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15
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Goswami S, Ghosh R, Prasanthan P, Kishore N. Mode of interaction of altretamine with calf thymus DNA: biophysical insights. J Biomol Struct Dyn 2022; 41:3728-3740. [PMID: 35343872 DOI: 10.1080/07391102.2022.2054472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Insights into drug-DNA interactions have importance in medicinal chemistry as it has a major role in the evolution of new therapeutic drugs. Therefore, binding studies of small molecules with DNA are of significant interest. Spectroscopy, coupled with measurements of viscosity and molecular docking studies were employed to obtain mechanistic insights into the binding of altretamine with calf thymus DNA (CT-DNA). The UV-visible spectroscopic measurements study confirmed altretamine-CT-DNA complex formation with affinity constant ([15.68 ± 0.04] × 103 M-1), a value associated with groove binding phenomenon. The associated thermodynamic signatures suggest enthalpically driven interactions. The values of standard molar free energy change (ΔGmo) -(23.93 ± 0.23) kJ mol-1, enthalpy change (ΔvHHmo) -(50.84 ± 0.19) kJ mol-1 and entropy change (ΔSmo) -(90.29 ± 0.12) JK-1 mol-1 indicate the binding is thermodynamically favorable and an important role of the hydrogen bonds and Van der Waals interactions in the binding of altretamine with CT-DNA. Circular dichroism spectroscopy indicated insignificant conformational changes in the DNA backbone upon interaction with altretamine suggesting no distortion and/or unstacking of the base pairs in the DNA helix. UV-melting study suggested that the thermal stability of the DNA backbone is not affected by the binding of the drug. Competitive displacement assays with ethidium bromide, Hoechst-33258 and DAPI established the binding of altretamine with CT-DNA in the minor groove. The mode of binding was further confirmed by viscosity and molecular docking studies. Molecular docking further ascertained binding of altretamine in the minor groove of the CT-DNA, preferably with the A-T rich sequences.
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Affiliation(s)
- Sathi Goswami
- Department of Chemistry, Indian Institute of Technology Bombay, Maharashtra, India
| | - Ritutama Ghosh
- Department of Chemistry, Indian Institute of Technology Bombay, Maharashtra, India
| | - Pooja Prasanthan
- Department of Chemistry, Indian Institute of Technology Bombay, Maharashtra, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Maharashtra, India
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16
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Ponkarpagam S, Vennila KN, Elango KP. Investigating binding of insecticide buprofezin to DNA by experimental and metadynamics simulation studies. J Biomol Struct Dyn 2022; 41:3476-3484. [PMID: 35285769 DOI: 10.1080/07391102.2022.2050949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Buprofezin (BUP) is an insecticide which belongs to the thiadiazine structural family and known to damage DNA in mice. Though its toxic effect on human is not known clearly, understanding the mechanism of interaction of BUP with DNA can prove useful when required. Multi-spectroscopic experiments such as UV-Vis, fluorescence, circular dichroism (CD) and 1H NMR coupled with viscosity measurements, urea effect and voltametric studies were performed to ascertain the mode of binding of BUP with calf thymus DNA (CT-DNA). Analysis of UV-Vis and fluorescence spectra indicated the formation of a complex between BUP and CT-DNA. Other experiments such as competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, effect of urea, CD, voltammetric studies and 1H NMR spectral analysis suggested that BUP intercalates into the base pairs of CT-DNA. All these results revealed that the binding mode of BUP with CT-DNA should be intercalation and the binding constant is in the order of 104 M-1. The ΔHo < 0 and ΔSo < 0 suggested that H-bonding or van der Waals force was the main binding force between BUP and CT-DNA. The proposed mode of binding of BUP with CT-DNA has been visualized using in silico molecular docking and metadynamics simulation studies, which showed that the phenyl ring of BUP binds to CT-DNA via π-π stacking interaction in addition to H-bond formation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
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17
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García-Quiroz J, Cárdenas-Ochoa N, García-Becerra R, Morales-Guadarrama G, Méndez-Pérez EA, Santos-Cuevas C, Ramírez-Nava GJ, Segovia-Mendoza M, Prado-García H, Avila E, Larrea F, Díaz L. Antitumoral effects of dovitinib in triple-negative breast cancer are synergized by calcitriol in vivo and in vitro. J Steroid Biochem Mol Biol 2021; 214:105979. [PMID: 34438041 DOI: 10.1016/j.jsbmb.2021.105979] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/25/2021] [Accepted: 08/18/2021] [Indexed: 12/21/2022]
Abstract
Chemotherapy is a standard therapeutic option for triple-negative breast cancer (TNBC); however, its effectiveness is often compromised by drug-related toxicity and resistance development. Herein, we aimed to evaluate whether an improved antineoplastic effect could be achieved in vitro and in vivo in TNBC by combining dovitinib, a multi-kinase inhibitor, with calcitriol, a natural anticancer hormone. In vitro, cell proliferation and cell-cycle distribution were studied by sulforhodamine B-assays and flow cytometry. In vivo, dovitinib/calcitriol effects on tumor growth, angiogenesis, and endothelium activation were evaluated in xenografted mice by caliper measures, Itgb3/VEGFR2-immunohistochemistry and 99mTc-Ethylenediamine-N,N-diacetic acid/hydrazinonicotinamyl-Glu[cyclo(Arg-Gly-Asp-D-Phe-Lys)]2 (99mTc-RGD2)-tumor uptake. The drug combination elicited a synergistically improved antiproliferative effect in TNBC-derived cells, which allowed a 7-fold and a 3.3-fold dovitinib dose-reduction in MBCDF-Tum and HCC-1806 cells, respectively. Mechanistically, the co-treatment induced a cell cycle profile suggestive of cell death and DNA damage (accumulation of cells in SubG1, S, and G2/M phases), increased the number of multinucleated cells and inhibited tumor growth to a greater extent than each compound alone. Tumor uptake of 99mTc-RGD2 was reduced by dovitinib, suggesting angiogenesis inhibition, which was corroborated by decreased endothelial cell growth, tumor-vessel density and VEGFR2 expression. In summary, calcitriol synergized dovitinib anticancer effects in vitro and in vivo, allowing for a significant dose-reduction of dovitinib while maintaining its antiproliferative potency. Our results suggest the beneficial convergence of independent antitumor mechanisms of dovitinib and calcitriol to inhibit TNBC-tumor growth.
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Affiliation(s)
- Janice García-Quiroz
- Departamento de Biología de la Reproducción Dr. Carlos Gual Castro, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga No. 15, Belisario Domínguez Sección XVI, Tlalpan, 14080, Ciudad de México, Mexico.
| | - Nohemí Cárdenas-Ochoa
- Departamento de Biología de la Reproducción Dr. Carlos Gual Castro, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga No. 15, Belisario Domínguez Sección XVI, Tlalpan, 14080, Ciudad de México, Mexico.
| | - Rocío García-Becerra
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, 04510, Ciudad de México, Mexico.
| | - Gabriela Morales-Guadarrama
- Departamento de Biología de la Reproducción Dr. Carlos Gual Castro, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga No. 15, Belisario Domínguez Sección XVI, Tlalpan, 14080, Ciudad de México, Mexico.
| | - Edgar A Méndez-Pérez
- Departamento de Biología de la Reproducción Dr. Carlos Gual Castro, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga No. 15, Belisario Domínguez Sección XVI, Tlalpan, 14080, Ciudad de México, Mexico.
| | - Clara Santos-Cuevas
- Departamento de Materiales Radioactivos, Instituto Nacional de Investigaciones Nucleares, Ocoyoacac, 52750, Estado de México, Mexico.
| | - Gerardo J Ramírez-Nava
- Departamento de Materiales Radioactivos, Instituto Nacional de Investigaciones Nucleares, Ocoyoacac, 52750, Estado de México, Mexico.
| | - Mariana Segovia-Mendoza
- Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán, 04510, Ciudad de México, Mexico.
| | - Heriberto Prado-García
- Departamento de Enfermedades Crónico-Degenerativas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, Belisario Domínguez Sección XVI, C.P. 14080, Tlalpan, Ciudad de México, Mexico.
| | - Euclides Avila
- Departamento de Biología de la Reproducción Dr. Carlos Gual Castro, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga No. 15, Belisario Domínguez Sección XVI, Tlalpan, 14080, Ciudad de México, Mexico.
| | - Fernando Larrea
- Departamento de Biología de la Reproducción Dr. Carlos Gual Castro, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga No. 15, Belisario Domínguez Sección XVI, Tlalpan, 14080, Ciudad de México, Mexico.
| | - Lorenza Díaz
- Departamento de Biología de la Reproducción Dr. Carlos Gual Castro, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga No. 15, Belisario Domínguez Sección XVI, Tlalpan, 14080, Ciudad de México, Mexico.
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18
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Magdy G, Belal F, Abdel Hakiem AF, Abdel-Megied AM. Salmon sperm DNA binding study to cabozantinib, a tyrosine kinase inhibitor: Multi-spectroscopic and molecular docking approaches. Int J Biol Macromol 2021; 182:1852-1862. [PMID: 34062156 DOI: 10.1016/j.ijbiomac.2021.05.164] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022]
Abstract
In the current work, the binding interaction of cabozantinib with salmon sperm DNA (SS-DNA) was studied under simulated physiological conditions (pH 7.4) using fluorescence emission spectroscopy, UV-Vis absorption spectroscopy, viscosity measurement, ionic strength measurement, FT-IR spectroscopy, and molecular modeling methods. The obtained experimental data demonstrated an apparent binding interaction of cabozantinib with SS-DNA. The binding constant (Kb) of cabozantinib with SS-DNA evaluated from the Benesi-Hildebrand plot was equal to 5.79 × 105 at 298 K. The entropy and enthalpy changes (∆S0 and ∆H0) in the binding interaction of SS-DNA with cabozantinib were 44.13 J mol-1 K-1 and -19.72 KJ mol-1, respectively, demonstrating that the basic binding interaction forces are hydrophobic and hydrogen bonding interactions. Results from UV-Vis absorption spectroscopy, competitive binding interaction with rhodamine B or ethidium bromide, and viscosity measurements revealed that cabozantinib binds to SS-DNA via minor groove binding. The molecular docking results revealed that cabozantinib fits into the AT-rich region of the B-DNA minor groove and the binding site of cabozantinib was 4 base pairs long. Moreover, cabozantinib has eight active torsions, implying a high degree of flexibility in its structure, which played a significant role in the formation of a stable cabozantinib-DNA complex.
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Affiliation(s)
- Galal Magdy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, P.O. Box 33511, Egypt.
| | - Fathalla Belal
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura, P.O. Box 35516, Egypt
| | - Ahmed Faried Abdel Hakiem
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, P.O. Box 33511, Egypt
| | - Ahmed M Abdel-Megied
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, P.O. Box 33511, Egypt; Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine Street, Baltimore, MD 21201, USA
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19
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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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20
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Liu JJ, Liu XR, Zhao SS, Yang ZW, Yang Z. Syntheses, crystal structures, thermal stabilities, CT-DNA, and BSA binding characteristics of a new acylhydrazone and its Co(II), Cu(II), and Zn(II) complexes. J COORD CHEM 2020. [DOI: 10.1080/00958972.2020.1758316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Jing-Jing Liu
- Chemistry and Chemical Engineering, Xi'an University of Science and Technology, Xi'an, PR China
| | - Xiang-Rong Liu
- Chemistry and Chemical Engineering, Xi'an University of Science and Technology, Xi'an, PR China
| | - Shun-Sheng Zhao
- Chemistry and Chemical Engineering, Xi'an University of Science and Technology, Xi'an, PR China
| | - Zai-Wen Yang
- Chemistry and Chemical Engineering, Xi'an University of Science and Technology, Xi'an, PR China
| | - Zheng Yang
- Chemistry and Chemical Engineering, Xi'an University of Science and Technology, Xi'an, PR China
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21
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Nasir MH, Jabeen E, Qureshi R, Ansari FL, Shaukat A, Nasir U, Ahmed A. Investigation of redox mechanism and DNA binding of novel 2-(x-nitrophenyl)-5-nitrobenzimidazole (x = 2, 3 and 4). Biophys Chem 2019; 258:106316. [PMID: 31986436 DOI: 10.1016/j.bpc.2019.106316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 02/08/2023]
Abstract
The present study describes the investigation of the binding modes of potential anti-cancerous nitrophenyl derivatives of 2-(x-nitrophenyl)-5-nitrobenzimidazole with calf thymus DNA. The -2-(x-nitrophenyl)-5-nitrobenzimidazoles under investigation differ only in position x of nitro group in nitrophenyl substituent relative to benzimidazole moiety leading to 1-NPNB (x = 2), 2-NPNB (x = 3) and 3-NPNB (x = 4). The DFT calculations predicted that derivatives were electrochemically reducible which was then confirmed by cyclic voltammetry. In cyclic voltammetry, the second reversible peak was dependent on first irreversible reduction. This revealed that electrochemical irreversible process was governed by some other process which was then followed by reversible second electron transfer. Thus, ECE (electron transfer leading to coupled chemical reaction followed by another electron transfer process) mechanism was attributed for electrochemical reduction. Experimental results based on UV-Vis spectroscopy vaguely showed intercalation of 1-NPNB, 2-NPNB and 3-NPNB into DNA which was assisted by cyclic voltammetry. However, thermal melting and florescence spectroscopy unambiguously established intercalation for all three compounds. Molecular docking analysis ascertained in pocket stacking of 5-nitrobenzimidazole moiety in 1-NPNB and 2-NPNB while nitro phenyl substitution in 3-NPNB stacks between DNA base pair during intercalation which was in agreement with DFT computed molecular geometry. Therefore, the relative positions of nitro group and 5-nitrobenzimidazole moieties in 2-(x-nitrophenyl)- 5-nitrobenzimidazole influenced the DNA binding pattern of compounds during intercalation. The cytotoxicity of these compounds was comparable to standard drug doxorubicin against both cancerous (MCF-7) and normal (MCF-10A) breast cells which depicts their anti-cancerous potential.
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Affiliation(s)
- Mehwish H Nasir
- Department of Chemistry, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Erum Jabeen
- Department of Chemistry, Faculty of Sciences, Allama Iqbal Open University, 44000 Islamabad, Pakistan.
| | - Rumana Qureshi
- Department of Chemistry, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Farzana L Ansari
- Department of Chemistry, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Awais Shaukat
- Department of Chemistry, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Usman Nasir
- Department of Electrical Engineering, COMSAT Institute of IT, Islamabad, Pakistan.
| | - Aftab Ahmed
- Department of Science Education, Faculty of Education, Iqbal Open University, Islamabad, Pakistan
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22
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Xu F, Chen J, Wu Q, Gu W, Shen Y, Lu C, Zhang Y, Liu S, Liao H. The antitumor molecular mechanism of Alisma orientalis with c-myc DNA: multi-spectroscopic analysis and molecular simulation. J Biomol Struct Dyn 2019; 38:4189-4209. [DOI: 10.1080/07391102.2019.1688687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Fei Xu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jun Chen
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Qinan Wu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Wei Gu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuqing Shen
- Department of Neurology, Taizhou Second People’s Hospital, Taizhou, China
| | - Cai Lu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yun Zhang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shengjin Liu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Haiying Liao
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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23
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Luo YJ, Wang BL, Kou SB, Lin ZY, Zhou KL, Lou YY, Shi JH. Assessment on the binding characteristics of dasatinib, a tyrosine kinase inhibitor to calf thymus DNA: insights from multi-spectroscopic methodologies and molecular docking as well as DFT calculation. J Biomol Struct Dyn 2019; 38:4210-4220. [PMID: 31581883 DOI: 10.1080/07391102.2019.1676824] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The binding characteristics of calf thymus DNA (ct-DNA) with dasatinib (DSTN), a tyrosine kinase inhibitor was assessed through multi-spectroscopic methodologies and viscosity measurement combined with molecular docking as well as DFT calculation to understand the binding mechanism, affinity of DSTN onto ct-DNA, effect of DSTN on ct-DNA conformation, and among others. The results confirmed DSTN bound onto ct-DNA, leading to forming the DSTN-ct-DNA complex with the binding constant of 4.82 × 103 M-1 at 310 K. DSTN preferentially inserted to the minor groove of ct-DNA with rich A-T region, that was the binding mode of DSTN onto ct-DNA was groove binding. The enthalpic change (ΔH0) and entropic change (ΔS0) during the binding process of DSTN with ct-DNA were 128.9 kJ mol-1 and 489.2 J mol-1 K-1, respectively, confirming clearly that the association of DSTN with ct-DNA was an endothermic process and the dominative driven-force was hydrophobic interaction. Meanwhile, the results also indicated that there was a certain extent of electrostatic force and hydrogen bonding, but they maybe play an auxiliary role. The CD measurement results confirmed the alteration in the helical configuration of ct-DNA but almost no change in the base stacking after binding DSTN. The results revealed that there was the obvious change in the conformation, the dipole moment, and the atomic charge distribution of DSTN in the B-DNA complexes, compared with free DSTN, to satisfy the conformational adaptation. From the obtained fronitier molecular orbitals of DSTN, it can be inferred that the nature of DSTN alters with the change of the environment around DSTN. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yu-Jie Luo
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Bao-Li Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Song-Bo Kou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Zhen-Yi Lin
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Kai-Li Zhou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Yan-Yue Lou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Jie-Hua Shi
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
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24
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Chen X, Wang B, Zhou K, Lou Y, Kou S, Lin Z, Shi J. Characterizing the Binding Interaction between Erlotinib and Calf Thymus DNA In Vitro Using Multi‐Spectroscopic Methodologies and Viscosity Measurement Combined with Molecular Docking and DFT Calculation. ChemistrySelect 2019. [DOI: 10.1002/slct.201900089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xue‐Jun Chen
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
| | - Bao‐Li Wang
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
| | - Kai‐Li Zhou
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
| | - Yan‐Yue Lou
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
| | - Song‐Bo Kou
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
| | - Zhen‐Yi Lin
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
| | - Jie‐Hua Shi
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
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25
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Shi JH, Pan DQ, Zhou KL, Lou YY. Exploring the binding interaction between herring sperm DNA and sunitinib: insights from spectroscopic and molecular docking approaches. J Biomol Struct Dyn 2018; 37:837-845. [DOI: 10.1080/07391102.2018.1445033] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jie-Hua Shi
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Dong-Qi Pan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Kai-Li Zhou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yan-Yue Lou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310032, China
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