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Schlosser J, Ihmels H. Photocontrolled Binding of Styrylnaphthyridine Ligands to Abasic Site-Containing DNA by Reversible [2+2] Cycloaddition and Cycloreversion. Chemistry 2024; 30:e202400423. [PMID: 38545937 DOI: 10.1002/chem.202400423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Indexed: 04/25/2024]
Abstract
Five novel styrylnaphthyridine derivatives were synthesized and shown to operate as photoswitchable, selective ligands for abasic site-containing DNA (AP-DNA), which is an important therapeutic and diagnostic target. These compounds associate with AP-DNA with binding constants of 0.5-8.4×104 M-1 as shown by photometric and fluorimetric titrations. Specifically, these ligands bind preferentially to AP-DNA relative to regularly paired duplex DNA. As a special feature, the association of these ligands with DNA can be controlled by means of a reversible [2+2] photocycloaddition. Upon irradiation at 420 nm the photodimer is formed, which does not bind to AP-DNA. In turn, the naphthyridine is regained with excitation at 315 nm. Most notably, this photoinduced deactivation and release of the DNA ligand can be performed in situ in the presence of AP-DNA, thus providing a tool for on-demand delivery of a DNA binder. Overall, these results provide a promising starting point for the development of functional AP-DNA ligands whose bioactivity can be modulated by light with local and temporal control.
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Affiliation(s)
- Julika Schlosser
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), University of Siegen, Adolf-Reichwein Str. 2, 57068, Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), University of Siegen, Adolf-Reichwein Str. 2, 57068, Siegen, Germany
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2
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Amir M, Aamir Qureshi M, Khan A, Nayeem SM, Ayoub Malik W, Javed S. Exploring the interaction of tepotinib with calf thymus DNA using molecular dynamics simulation and multispectroscopic techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123678. [PMID: 38039637 DOI: 10.1016/j.saa.2023.123678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/05/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
In recent times, there has been a surge in the discovery of drugs that directly interact with DNA, influencing gene expression. As a result, understanding how biomolecules interact with DNA has become a major area of research. One such drug is Tepotinib (TPT), an FDA-approved anti-cancer medication known as a MET tyrosine kinase inhibitor, used in chemotherapy for metastatic non-small cell lung cancer (NSCLC) with MET exon 14 skipping alterations. In our study, we adopted both biophysical and in-silico methods to investigate the binding relationship of TPT and ctDNA. The absorption spectra of ctDNA exhibited a hypochromic effect when titrated with TPT and the binding constant of TPT-ctDNA complex was calculated, Ka = 9.91 × 104 M-1. By computing bimolecular enhancement constant (KB) and thermodynamic enhancement constant (KD) in fluorometric investigations, it was found that the fluorescence enhancement is a result of a static process involving the ctDNA-TPT complex formation in the ground state, as opposed to a dynamic process. The displacement assay results further supported this finding, showing that TPT exhibits a binding preference for minor groove of ct-DNA and was also demonstrated by KI quenching and CD spectroscopy. The molecular docking and molecular dynamic simulations validated TPT's groove binding nature and binding pattern with ctDNA, respectively. Thus, the results of our present investigation offer valuable insights into the interaction between TPT and ctDNA. It is evident that TPT, as an anti-cancer medication, binds to the minor groove of ctDNA.
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Affiliation(s)
- Mohd Amir
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
| | - Mohd Aamir Qureshi
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
| | - Ashma Khan
- Department of Chemistry, Faculty of Sciences, Aligarh Muslim University, Aligarh 202002, India.
| | - Shahid M Nayeem
- Department of Chemistry, Faculty of Sciences, Aligarh Muslim University, Aligarh 202002, India.
| | - Waseem Ayoub Malik
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
| | - Saleem Javed
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
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3
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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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4
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Li SR, Zeng CM, Peng XM, Chen JP, Li S, Zhou CH. Benzopyrone-mediated quinolones as potential multitargeting antibacterial agents. Eur J Med Chem 2023; 262:115878. [PMID: 37866337 DOI: 10.1016/j.ejmech.2023.115878] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023]
Abstract
A new type of benzopyrone-mediated quinolones (BMQs) was rationally designed and efficiently synthesized as novel potential antibacterial molecules to overcome the global increasingly serious drug resistance. Some synthesized BMQs effectively suppressed the growth of the tested strains, outperforming clinical drugs. Notably, ethylidene-derived BMQ 17a exhibited superior antibacterial potential with low MICs of 0.5-2 μg/mL to clinical drugs norfloxacin, it not only displayed rapid bactericidal performance and inhibited bacterial biofilm formation, but also showed low toxicity toward human red blood cells and normal MDA-kb2 cells. Mechanistic investigation demonstrated that BMQ 17a could effectually induce bacterial metabolic disorders and promote the enhancement of reactive oxygen species to disrupt the bacterial antioxidant defense system. It was found that the active molecule BMQ 17a could not only form supramolecular complex with lactate dehydrogenase, which disturbed the biological functions, but also effectively embed into calf thymus DNA, thus affecting the normal function of DNA and achieving cell death. This work would provide an insight into developing new molecules to reduce drug resistance and expand antibacterial spectrum.
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Affiliation(s)
- Shu-Rui Li
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Chun-Mei Zeng
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Xin-Mei Peng
- School of Chemistry and Chemical Engineering, Qiannan Normal University for Nationalities, Duyun, 558000, China.
| | - Jin-Ping Chen
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China
| | - Shuo Li
- School of Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, China.
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, China.
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5
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Das H, Paul L, Chowdhury S, Goswami R, Das S. New insights into self-structure induction in poly (rA) by Quinacrine through non-classical intercalation: Spectroscopic and theoretical perspectives. Int J Biol Macromol 2023; 251:126189. [PMID: 37586624 DOI: 10.1016/j.ijbiomac.2023.126189] [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: 05/17/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023]
Abstract
Self-structure induction in a single stranded polyriboadenylic acid [poly (rA)] is an auspicious physiological phenomenon which switches off protein production in tumor cells. In the present study, the self-structure induction process in poly (rA) moiety was thoroughly investigated using various steady state and time resolved techniques. Optical melting pattern directly evidenced the formation of self-structured assembly in single stranded poly (rA) upon complexation with quinacrine. Further, UV-absorption spectroscopic studies revealed that quinacrine binds to poly (rA) in co-operative fashion and the indication of intercalative mode of binding first came out with the involvement of around two base pairs of poly (rA) in the complexation. Experimental observations established the unconventional or non-classical intercalation of quinacrine molecule inside self-structured duplex poly (rA) moiety. This complexation was accompanied with negative enthalpy change and positive entropy change; suggesting strong van der Waals and the H-bonding interactions as the major governing forces in the complexation. Moreover, ionic strength dependent binding study established that the non-polyelectrolytic forces were the dominating forces. Further, the photo physical behavior of QN was authenticated using time dependent density functional theory (TDDFT) where both the ground and excited states were exploited.
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Affiliation(s)
- Himal Das
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Lopa Paul
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Susmita Chowdhury
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Rapti Goswami
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India
| | - Suman Das
- Biophysical Chemistry Laboratory, Physical Chemistry Section, Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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6
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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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7
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Mati SS, Chowdhury S, Sarkar S, Bera N, Sarkar N. Targeting genomic DNAs and oligonucleotide on base specificity: A comparative spectroscopic, computational and in vitro study. Int J Biol Macromol 2023:124933. [PMID: 37230444 DOI: 10.1016/j.ijbiomac.2023.124933] [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: 02/28/2023] [Revised: 05/10/2023] [Accepted: 05/13/2023] [Indexed: 05/27/2023]
Abstract
Drug discovery in targeted nucleic acid therapeutics encompass several stages and rigorous challenges owing to less specificity of the DNA binders and high failure rate in different stages of clinical trials. In this perspective, we report newly synthesized ethyl 4-(pyrrolo[1,2-a]quinolin-4-yl)benzoate (PQN) with minor groove A-T base pair binding selectivity and encouraging in cell results. This pyrrolo quinolin derivative has shown excellent groove binding ability with three of our inspected genomic DNAs (cpDNA 73 % AT, ctDNA58% AT and mlDNA 28 % AT) with varying A-T and G-C content. Notably in spite of similar binding patterns PQN have strong binding preference with A-T rich groove of genomic cpDNA over the ctDNA and mlDNA. Spectroscopic experiments like steady state absorption and emission results have established the relative binding strengths (Kabs = 6.3 × 105 M-1, 5.6 × 104 M-1, 4.3 × 104 M-1 and Kemiss = 6.1 × 105 M-1, 5.7 × 104 M-1 and 3.5 × 104 M-1 for PQN-cpDNA, PQN-ctDNA and PQN-mlDNA respectively) whereas circular dichroism and thermal melting studies have unveiled the groove binding mechanism. Specific A-T base pair attachment with van der Waals interaction and quantitative hydrogen bonding assessment were characterized by computational modeling. In addition to genomic DNAs, preferential A-T base pair binding in minor groove was also observed with our designed and synthesized deca-nucleotide (primer sequences 5/-GCGAATTCGC-3/ and 3/-CGCTTAAGCG-5/). Cell viability assays (86.13 % in 6.58 μM and 84.01 % in 9.88 μM concentrations) and confocal microscopy revealed low cytotoxicity (IC50 25.86 μM) and efficient perinuclear localization of PQN. We propose PQN with excellent DNA-minor groove binding capacity and intracellular permeation properties, as a lead for further studies encompassing nucleic acid therapeutics.
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Affiliation(s)
- Soumya Sundar Mati
- Department of Chemistry, Government General Degree College, Keshiary, Paschim Medinipur,WB 721135, India.
| | - Sourav Chowdhury
- Structural Biology and Bio-informatics division, CSIR Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Soumen Sarkar
- Department of Chemistry, Balurghat College, Dakshin Dinajpur, WB 733101, India
| | - Nanigopal Bera
- Department of Chemistry, Indian Institute of Technology, Kharagpur, Paschim Medinipur, WB 721302, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology, Kharagpur, Paschim Medinipur, WB 721302, India.
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8
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Gupta S, Aggarwal S, Munde M. New Insights into the Role of Ligand-Binding Modes in GC-DNA Condensation through Thermodynamic and Spectroscopic Studies. ACS OMEGA 2023; 8:4554-4565. [PMID: 36777612 PMCID: PMC9909821 DOI: 10.1021/acsomega.2c01557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 09/20/2022] [Indexed: 06/18/2023]
Abstract
In biological systems, the unprompted assembly of DNA molecules by cationic ligands into condensed structures is ubiquitous. The ability of ligands to provoke DNA packaging is crucial to the molecular organization and functional control of DNA, yet their underlined physical roles have remained elusive. Here, we have examined the DNA condensation mechanism of four cationic ligands, including their primary DNA-binding modes through extensive biophysical studies. We observed contrasting changes for these ligands binding to poly[dGdC]:poly[dGdC] (GC-DNA) and poly[dAdT]:poly[dAdT] (AT-DNA). Based on a CD spectroscopic study, it was confirmed that only GC-DNA undergoes B- to Ψ-type DNA transformation in the presence of ligands. In the fluorescence displacement assay (FDA), the ability of ligands to displace GC-DNA-bound EtBr follows the order: protamine21+ > cohex3+ > Ni2+ > spermine4+, which indicates that there is no direct correlation between the ligand charge and its ability to displace the drug from the DNA, indicating that GC-DNA condensation is not just influenced by electrostatic interaction but ligand-specific interactions may also have played a crucial role. Furthermore, the detailed ITC-binding studies suggested that DNA-ligand interactions are generally driven by unfavorable enthalpy and favorable entropy. The correlations from various studies insinuate that cationic ligands show major groove binding as one of the preferred binding modes during GC-DNA condensation.
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Affiliation(s)
- Sakshi Gupta
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Department
of Applied Science, The NorthCap University, Sector 23-A, Gurgaon, Haryana 122017, India
| | - Soumya Aggarwal
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manoj Munde
- School
of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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9
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Ustimova MA, Fedorov YV, Chmelyuk NS, Abakumov MA, Fedorova OA. Fluorescence turn-on probes for intracellular DNA/RNA distribution based on asymmetric bis(styryl) dyes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 279:121446. [PMID: 35667137 DOI: 10.1016/j.saa.2022.121446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Two bis(styryl) dyes, varying in type of spacer between two mono(styryl) units, were tested for interactions with ct-DNA or cl-RNA. Both compounds showed strong affinity toward ds-DNA/ss-RNA, the binding mode of the interaction is shifting between DNA groove binding to RNA intercalation. Consequently, interaction with DNA shows a stronger flare-up of fluorescence (151 times for dye 1 and 118 times for dye 2) than when binding with RNA (23 times and 36 times correspondingly). The presence of energy transfer in the bis(styryl) system increases the Stokes shift of the dye, so when irradiating the system in the region of 370-380 nm, fluorescence is detected at 610-620 nm. The biological experiments showed that the efficient intracellular fluorescence quench was observed in the DNase digest test suggested that dyes can be applied by recognition of DNA in the presence of RNA molecules.
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Affiliation(s)
- Maria A Ustimova
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, 119991 Moscow, Russia.
| | - Yuri V Fedorov
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, 119991 Moscow, Russia
| | - Nelly S Chmelyuk
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, 117997 Moscow, Russia
| | - Maxim A Abakumov
- Department of Medical Nanobiotechnoilogy, Pirogov Russian National Research Medical University, Ostrovityanova str. 1, 117997 Moscow, Russia
| | - Olga A Fedorova
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, 119991 Moscow, Russia.
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10
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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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11
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Supabowornsathit K, Faikhruea K, Ditmangklo B, Jaroenchuensiri T, Wongsuwan S, Junpra-Ob S, Choopara I, Palaga T, Aonbangkhen C, Somboonna N, Taechalertpaisarn J, Vilaivan T. Dicationic styryl dyes for colorimetric and fluorescent detection of nucleic acids. Sci Rep 2022; 12:14250. [PMID: 35995925 PMCID: PMC9395382 DOI: 10.1038/s41598-022-18460-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/12/2022] [Indexed: 11/26/2022] Open
Abstract
Nucleic acid staining dyes are important tools for the analysis and visualizing of DNA/RNA in vitro and in the cells. Nevertheless, the range of commercially accessible dyes is still rather limited, and they are often very costly. As a result, finding nontoxic, easily accessible dyes, with desirable optical characteristics remains important. Styryl dyes have recently gained popularity as potential biological staining agents with many appealing properties, including a straightforward synthesis procedure, excellent photostability, tunable fluorescence, and high fluorescence quantum yield in the presence of nucleic acid targets with low background fluorescence signals. In addition to fluorescence, styryl dyes are strongly colored and exhibit solvatochromic properties which make them useful as colorimetric stains for low-cost and rapid testing of nucleic acids. In this work, novel dicationic styryl dyes bearing quaternary ammonium groups are designed to improve binding strength and optical response with target nucleic acids which contain a negatively charged phosphate backbone. Optical properties of the newly synthesized styryl dyes have been studied in the presence and absence of nucleic acid targets with the aim to find new dyes that can sensitively and specifically change fluorescence and/or color in the presence of nucleic acid targets. The binding interaction and optical response of the dicationic styryl dyes with nucleic acid were superior to the corresponding monocationic styryl dyes. Applications of the developed dyes for colorimetric detection of DNA in vitro and imaging of cellular nucleic acids are also demonstrated.
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Affiliation(s)
- Kotchakorn Supabowornsathit
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Kriangsak Faikhruea
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Boonsong Ditmangklo
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Theeranuch Jaroenchuensiri
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry (CENP), Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Sutthida Wongsuwan
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry (CENP), Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Sirikarn Junpra-Ob
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Ilada Choopara
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Tanapat Palaga
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Chanat Aonbangkhen
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry (CENP), Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand.,Microbiome Research Unit for Probiotics in Food and Cosmetics, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jaru Taechalertpaisarn
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand.
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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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13
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Delineating molecular interactions within surface active ionic liquids + tartrazine dye solutions: A comparative study with conventional surfactant-DTAC. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Udayan S, Kuriakose AC, Mary P, Sherin DR, Manojkumar TK, Nampoori V, Thomas S. Experimental and theoretical investigation on the nonlinear optical properties of LDS 821 dye in different solvents and DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 272:121011. [PMID: 35158136 DOI: 10.1016/j.saa.2022.121011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Linear and nonlinear optical properties of near-infrared laser grade dye LDS 821 in different solvents and Salmon Deoxyribonucleic acid (DNA) were studied using spectroscopic and Z-scan techniques. UV-Vis absorption spectrum of the dye shows a bathochromic shift with a decrease in the solvent polarity parameter, and in DNA, the dye exhibits a hypochromic shift. The fluorescence spectrum of the dye does not show any notable correlation with the solvent polarity parameter, but in DNA, the fluorescence intensity of the dye decreases with the incremental addition of DNA. Molecular docking studies reveal that the dye intercalates on the major grooves of DNA. Nonlinear optical properties of the dye in different solvents and phosphate buffer solution with varying DNA concentrations were studied using the Z-scan technique using a Q-switched Nd: YAG laser operating at fundamental and second harmonics. A closed and open aperture Z-scan of dye in different solvents was carried out to estimate the nonlinear refractive index, excited-state absorption cross-section, and two-photon absorption coefficient (TPA). The variation in nonlinear optical properties of the dye in different solvents was due to solvent-induced structural modifications. Theoretical investigation on nonlinear optical properties of the dye in different solvents was carried out using density function theory. The theoretical first and second-order hyperpolarizability was calculated using B3LYP functional. The predicated nonlinear optical parameters of the dye in different solvents does not show any direct correlation with solvent polarity. Nonlinear absorption of the dye in phosphate buffer solution (PBS) and DNA were estimated. The nonlinear absorption of the dye in PBS decreases with the addition of DNA. Molecular docking studies were carried out to determine the structural changes induced in dye due to the intercalation with DNA.
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Affiliation(s)
- Sony Udayan
- International School of Photonics, Cochin University of Science and Technology, Cochin, Kerala, India.
| | - Alina C Kuriakose
- International School of Photonics, Cochin University of Science and Technology, Cochin, Kerala, India
| | - Priya Mary
- International School of Photonics, Cochin University of Science and Technology, Cochin, Kerala, India
| | - D R Sherin
- Centre for Computational Modeling and Data Engineering, Indian Institute of Information Technology and Management- Thiruvananthapuram, Kerala, India
| | - T K Manojkumar
- Centre for Computational Modeling and Data Engineering, Indian Institute of Information Technology and Management- Thiruvananthapuram, Kerala, India
| | - Vpn Nampoori
- International School of Photonics, Cochin University of Science and Technology, Cochin, Kerala, India
| | - Sheenu Thomas
- International School of Photonics, Cochin University of Science and Technology, Cochin, Kerala, India
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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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Photophysical Study of Styryl Derivatives with Macrocyclic Host and the Effect of Addition of Cholesterol and Neurotransmitter. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.113842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Quest for the quenching and binding mode of functionalized ZnO QDs with calf thymus DNA: Biophysical and in silico molecular modelling approach. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2021.113562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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18
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Carrascosa E, Bull JN, Martínez-Núñez E, Scholz MS, Buntine JT, Bieske EJ. Photoisomerization of Linear and Stacked Isomers of a Charged Styryl Dye: A Tandem Ion Mobility Study. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2842-2851. [PMID: 34787413 PMCID: PMC8640989 DOI: 10.1021/jasms.1c00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/21/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
The photoisomerization behavior of styryl 9M, a common dye used in material sciences, is investigated using tandem ion mobility spectrometry (IMS) coupled with laser spectroscopy. Styryl 9M has two alkene linkages, potentially allowing for four geometric isomers. IMS measurements demonstrate that at least three geometric isomers are generated using electrospray ionization with the most abundant forms assigned to a combination of EE (major) and ZE (minor) geometric isomers, which are difficult to distinguish using IMS as they have similar collision cross sections. Two additional but minor isomers are generated by collisional excitation of the electrosprayed styryl 9M ions and are assigned to the EZ and ZZ geometric isomers, with the latter predicted to have a π-stacked configuration. The isomer assignments are supported through calculations of equilibrium structures, collision cross sections, and statistical isomerization rates. Photoexcitation of selected isomers using an IMS-photo-IMS strategy shows that each geometric isomer photoisomerizes following absorption of near-infrared and visible light, with the EE isomer possessing a S1 ← S0 electronic transition with a band maximum near 680 nm and shorter wavelength S2 ← S0 electronic transition with a band maximum near 430 nm. The study demonstrates the utility of the IMS-photo-IMS strategy for providing fundamental gas-phase photochemical information on molecular systems with multiple isomerizable bonds.
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Affiliation(s)
- Eduardo Carrascosa
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - James N. Bull
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
- School
of Chemistry, Norwich Research Park, University
of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Emilio Martínez-Núñez
- Departamento
de Química Física, Universidade
de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Michael S. Scholz
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jack T. Buntine
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Evan J. Bieske
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
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19
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Summers PA, Thomas AP, Kench T, Vannier JB, Kuimova MK, Vilar R. Cationic helicenes as selective G4 DNA binders and optical probes for cellular imaging. Chem Sci 2021; 12:14624-14634. [PMID: 34881015 PMCID: PMC8580066 DOI: 10.1039/d1sc04567a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/12/2021] [Indexed: 01/17/2023] Open
Abstract
The important role that G-quadruplex DNA (G4 DNA) structures play in regulating biological processes is becoming widely recognised. These structures have also been proposed to be attractive drug targets. Therefore, there has been significant interest in developing small molecules that can selectively bind to G4 DNA over other topologies. In this paper we investigate the interaction between DNA and helical compounds (helicenes) based on a central carbocation trisubstituted with aromatic rings. We show that the non-planar structure of these helicenes results in a significantly reduced affinity for dsDNA when compared to their planar analogues, whilst maintaining a high affinity for G4 DNA. Additionally, the right- and left-handed enantiomers of one of these helicenes recognise the chiral DNA environments of G4 and dsDNA differently. We show that upon DNA binding the helicenes display a fluorescence switch-on effect, which we have successfully used for cellular imaging in live and fixed U2OS cells, staining mitochondria and the nucleus, respectively.
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Affiliation(s)
- Peter A Summers
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane, White City Campus W12 0BZ UK +44 (0)20 7594 1967 +44 (0)20 7594 8558
| | - Ajesh P Thomas
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane, White City Campus W12 0BZ UK +44 (0)20 7594 1967 +44 (0)20 7594 8558
| | - Timothy Kench
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane, White City Campus W12 0BZ UK +44 (0)20 7594 1967 +44 (0)20 7594 8558
| | - Jean-Baptiste Vannier
- Telomere Replication and Stability Group, Medical Research Council - London Institute of Medical Sciences London W12 0NN UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London London W12 0NN UK
| | - Marina K Kuimova
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane, White City Campus W12 0BZ UK +44 (0)20 7594 1967 +44 (0)20 7594 8558
| | - Ramon Vilar
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London 82 Wood Lane, White City Campus W12 0BZ UK +44 (0)20 7594 1967 +44 (0)20 7594 8558
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20
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Liu H, Lin M, Cui Y, Gan W, Sun J, Li B, Zhao Y. Single-crystal structures of cucurbituril-based supramolecular host-guest complexes for bioimaging. Chem Commun (Camb) 2021; 57:10190-10193. [PMID: 34519729 DOI: 10.1039/d1cc04823f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Two single-crystal structures of cucurbit[n]uril mediated supramolecular complexes were obtained in which [1+3] and [2+3] self-assembly modes are adopted due to the different sizes of cucurbit[7]uril and cucurbit[8]uril. An obvious red-shift in absorption and emission was observed compared to the guest molecule itself which makes them good biolabels.
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Affiliation(s)
- Hui Liu
- College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China.
| | - Min Lin
- College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China.
| | - Yu Cui
- College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China.
| | - Weijin Gan
- College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China.
| | - Jing Sun
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, P. R. China.
| | - Bo Li
- Department of Cardiology, Zibo Central Hospital, Shandong University, Zibo 255000, P. R. China.
| | - Yingjie Zhao
- College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China.
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21
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Alamri MA, Al‐Jahdali M, Al‐Radadi NS, Hussien MA. Characterization, theoretical investigation, and biological applications of Mn(II), Co(II), Ni(II), Cu(II), and Zn(II) complexes of a triazene ligand containing a benzothiazole ring. Appl Organomet Chem 2021. [DOI: 10.1002/aoc.6466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Mona A. Alamri
- Department of Chemistry, Faculty of Science King Abdulaziz University Jeddah Saudi Arabia
- Department of Physics, College of Science and Arts in Dariyah Qassim University Dariyah Saudi Arabia
| | - Mutlaq. Al‐Jahdali
- Department of Chemistry, Faculty of Science King Abdulaziz University Jeddah Saudi Arabia
| | - Najlaa S. Al‐Radadi
- Chemistry Department, College of Science Taibah University Al‐Madinah Al‐Munawarah Saudi Arabia
| | - Mostafa A. Hussien
- Department of Chemistry, Faculty of Science King Abdulaziz University Jeddah Saudi Arabia
- Department of Chemistry, Faculty of Science Port Said University Port Said Egypt
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22
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Ustimova MA, Fedorov YV, Tsvetkov VB, Tokarev SD, Shepel NA, Fedorova OA. Helical aggregates of bis(styryl) dyes formed by DNA templating. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2021.113378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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23
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Kumar S, Nair MS. Deciphering the interaction of flavones with calf thymus DNA and octamer DNA sequence (CCAATTGG) 2. RSC Adv 2021; 11:29354-29371. [PMID: 35479565 PMCID: PMC9040621 DOI: 10.1039/d1ra04101k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/22/2021] [Indexed: 01/18/2023] Open
Abstract
We investigated the interaction of three flavone compounds, baicalein, chrysin and flavone with calf thymus DNA and octamer DNA sequence (CCAATTGG)2. The binding mechanisms of the flavone compounds with both DNA were unveiled using biophysical, thermodynamic and molecular modelling techniques. Absorption and fluorescence titrations confirm the formation of the DNA complexes along with the extent of interaction. Absorption data proposed an intercalation mode of binding. Fluorescence displacement assays using ethidium bromide and Hoechst 33258 data supports a partial intercalation. Potassium iodide quenching substantiated this finding. Circular dichroism data revealed major structural changes on binding with flavones which can arise from intercalation partially or in a tilted arrangement. Analysis of the effect of ionic strength on complex formation eliminated the role of electrostatic interaction in the binding. Differential scanning calorimetric data showed substantial changes in the melting temperatures of complexes and predicted the DNA–baicalein complex as the most stable one. Molecular modelling showcased that the complexes are located near the AT rich region. Docking analysis with different sequences showed that the flavone compounds intercalated with base pairs only with d(CGATCG)2. Binding of flavones induce conformational changes in double stranded DNA.![]()
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Affiliation(s)
- Shailendra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee Uttarakhand-247667 India +91-1332-273560 +91-1332-285790
| | - Maya S Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee Uttarakhand-247667 India +91-1332-273560 +91-1332-285790
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24
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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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25
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Butnarasu C, Barbero N, Viscardi G, Visentin S. Unveiling the interaction between PDT active squaraines with ctDNA: A spectroscopic study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 250:119224. [PMID: 33257241 DOI: 10.1016/j.saa.2020.119224] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 06/12/2023]
Abstract
Squaraine dyes are potential photosensitizers in photodynamic therapy (PDT) due to their ability to release reactive oxygen species (ROS) and cause DNA damage. For this reason, the evaluation and determination of the type of interaction between squaraines and DNA is of the utmost importance. In this study different spectroscopic techniques such as UV-Vis and fluorescence spectroscopies were used to investigate the type of interaction that occurs between two photosensitizers (halogenated squaraines, i.e. Br-C4 and I-C4) and calf thymus DNA (ctDNA). Squaraines were found to bind ctDNA externally following a minor groove binding as they were able to replace Hoechst (a classic groove binder) from the groove of DNA. This binding mode was further supported by iodide quenching studies, ionic strength assay and Florescence Resonance Energy Transfer. Moreover, association (KA) and dissociation (KD) constants were obtained and compared with constants of well-known groove binders.
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Affiliation(s)
- Cosmin Butnarasu
- University of Torino, Department of Molecular Biotechnology and Health Science, Via Quarello15, 10135 Torino, Italy
| | - Nadia Barbero
- University of Torino, Department of Chemistry and NIS Interdepartmental Centre, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Guido Viscardi
- University of Torino, Department of Chemistry and NIS Interdepartmental Centre, Via Pietro Giuria 7, 10125 Torino, Italy
| | - Sonja Visentin
- University of Torino, Department of Molecular Biotechnology and Health Science, Via Quarello15, 10135 Torino, Italy.
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26
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Maurya N, Patel R. Comparative binding analysis of noscapine and piperine with tRNA: A structural perturbation and energetic study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 247:119089. [PMID: 33126137 DOI: 10.1016/j.saa.2020.119089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/05/2020] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
In this study, we have exploring the binding mechanisms of the two anticancer alkaloid noscapine (NOS) and piperine (PIP) with tRNA using different spectroscopy and computational method. Absorbance and emission spectra revealed that both the drugs show strong binding with tRNA, where NOS intercalate between the base pairs of tRNA and PIP binds in the groove of tRNA. Competitive binding study and steady state anisotropy further confirms the intercalative mode of binding between NOS and tRNA and groove binding in PIP-tRNA complex. The observed thermodynamic parameters suggested that NOS-tRNA complex formation is endothermic and entropy driven, however it was exothermic, and enthalpy driven in case of PIP-tRNA complex. CD and time resolved fluorescence studies show the structural perturbations and conformational change in tRNA structure with NOS as well as PIP. Molecular docking studies are comparable with experimental results and further confirmed that the hydrophobic interactions involved in the NOS-tRNA binding, whereas hydrogen binding and van der Waals interactions play important role in the PIP-tRNA complex formation. This study can be useful to understand the potential binding and resultant tRNA damage by alkaloids and deigned new target specific anticancer drug.
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Affiliation(s)
- Neha Maurya
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Rajan Patel
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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27
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Sukanya P, Reddy CVR. Structural investigation, DNA interactions and in vitro anticancer studies of transition metal complexes of 3-(2-(2, 4-dihydroxy benzylidene) hydrazinyl) quinoxalin-2(1H) -one. J Biomol Struct Dyn 2021; 40:6151-6162. [PMID: 33512301 DOI: 10.1080/07391102.2021.1877819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The Schiff base ligand, 3-(2-(2, 4-dihydroxybenzylidene) hydrazinyl) quinoxalin-2(1H)-one (RHQO) has been synthesized and characterized by spectral and single crystal X-ray analysis. The Mn(II), Ni(II) and Cu(II) complexes of RHQO have been synthesized and characterized by FT-IR, UV-VIS, mass, EPR spectra, CHN, thermo gravimetric analysis, magnetic susceptibility and conductivity measurements. The morphology of the ligand and complexes is studied by Scanning Electron Microscopy. The metal complexes formed were found to be polymeric in nature. The abilities of the ligand and its metal complexes to interact and bind with calf thymus DNA (CT-DNA) has been studied by electronic absorption spectroscopy and their quantitative binding strength was evaluated in terms of their intrinsic binding constant (Kb). The cleavage interaction of the ligand and its metal complexes with super coiled pBR 322 DNA has been investigated by agarose gel electrophoresis. Cytotoxicity of the Cu(II) and Ni(II) complexes was evaluated using various cancer cell lines, Human cervical cancer cell line (Hela), B16 melanoma F10(B16-F10), Human ovarian cancer cell (SKOV3) and Breast cancer cell line (MCF7) by MTT assay. The results indicated that the ligand and its metal complexes bind with CT-DNA by groove binding mode and cleaved the supercoiled pBR 322 DNA in to nicked form. The Ni(II) and Cu(II) complexes exhibited anticancer activity without affecting the normal CHO-K1 cell lines. Communicated by Vsevolod Makeev.
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Affiliation(s)
- Panaganti Sukanya
- Department of Chemistry, Vasavi College of Engineering, Hyderabad, India.,Department of Chemistry, Jawaharlal Nehru Technological University Hyderabad, Hyderabad, India
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Kumar CBP, Raghu MS, Prasad KNN, Chandrasekhar S, Jayanna BK, Alharthi FA, Prashanth MK, Kumar KY. Investigation of biological activity of 2,3-disubstituted quinazolin-4(1H)-ones against Mycobacterium tuberculosis and DNA via docking, spectroscopy and DFT studies. NEW J CHEM 2021. [DOI: 10.1039/d0nj03800h] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Docking studies, structural data of DNA binding and molecular dynamics simulations of substituted quinazolin-4(1H)-ones.
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Affiliation(s)
| | - M. S. Raghu
- Department of Chemistry
- New Horizon College of Engineering
- Bengaluru 560 103
- India
| | - K. N. N. Prasad
- Department of Physics
- B N M Institute of Technology
- Bengaluru-560 070
- India
| | - S. Chandrasekhar
- Department of Physics
- B N M Institute of Technology
- Bengaluru-560 070
- India
| | - B. K. Jayanna
- Department of Chemistry
- B N M Institute of Technology
- Bengaluru-560 070
- India
| | - Fahad A. Alharthi
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh
- Saudi Arabia
| | - M. K. Prashanth
- Department of Chemistry
- B N M Institute of Technology
- Bengaluru-560 070
- India
| | - K. Yogesh Kumar
- Department of Chemistry
- School of Engineering and Technology
- Jain University
- Ramanagara
- India
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29
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Ataci N, Kazancioglu EO, Kalındemirtas FD, Kuruca SE, Arsu N. The interaction of light-activatable 2-thioxanthone thioacetic acid with ct-DNA and its cytotoxic activity: Novel theranostic agent. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 239:118491. [PMID: 32485605 DOI: 10.1016/j.saa.2020.118491] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/08/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
In this study, a thioxanthone derivative, 2-Thioxanthone Thioacetic Acid (TXSCH2COOH) was used to analyze the type of binding to calf thymus DNA in a physiological buffer (Tris-HCl buffer solution, pH:7.0). Several spectroscopic techniques were employed including UV-Vis absorption and fluorescence emission spectroscopy and viscosity measurements were also used to clarify the binding mode of TXSCH2COOH to ct-DNA. The intrinsic binding constant Kb of TXSCH2COOH-ct-DNA was found as 2.5 × 103 M-1 from the absorption studies. Increasing of fluorescence emission intensity was found approximately 74.4% by adding ct-DNA to the TXSCH2COOH solution. Fluorescence microscopy was employed to display imaging of the TXSCH2COOH-ct-DNA solution. Increasing of the iodide quenching effect was observed when TXSCH2COOH was added to the double stranded DNA and the calculated quenching constants of TXSCH2COOH and TXSCH2COOH-ct-DNA were found to be 1.89 × 103 M-1 and 1.19 × 104 M-1, respectively. Additionally, the iodide quenching experiment was conducted with single stranded DNA which led to a high Ksv value. All the experimental results including the viscosity values of ct-DNA with TXSCH2COOH demonstrated that the binding of TXSCH2COOH to ct-DNA was most likely groove binding. Furthermore, TXSCH2COOH was found to be an A-T rich minor groove binder. This was confirmed by the displacement assays with Hoechst 33258 compared to Ethidium Bromide. The in vitro cytotoxic activity measurements were performed by MTT assay on HT29 cell line for 72 h. TXSCH2COOH exhibited notable cytotoxic activities compared to the standard chemotherapy drugs, fluorouracil (5-FU), cisplatin in tumorigenic HT29 cell line. The 50% growth-inhibitory concentration (IC50) for TXSCH2COOH was 19,8 μg/mL while 5-FU and cisplatin were 28.9 μg/mL, 20 μg/mL, respectively. The increase in cytotoxic effect when TXSCH2COOH is activated by light indicates the potential of being theranostic cancer drug candidate.
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Affiliation(s)
- Nese Ataci
- Yildiz Technical University, Davutpasa Campus, Department of Chemistry, 34220 Istanbul, Turkey
| | | | | | - Serap Erdem Kuruca
- Istanbul University, Faculty of Medicine, Department of Physiology, 34093 Istanbul, Turkey
| | - Nergis Arsu
- Yildiz Technical University, Davutpasa Campus, Department of Chemistry, 34220 Istanbul, Turkey.
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30
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Maurya N, Imtiyaz K, Alam Rizvi MM, Khedher KM, Singh P, Patel R. Comparative in vitro cytotoxicity and binding investigation of artemisinin and its biogenetic precursors with ctDNA. RSC Adv 2020; 10:24203-24214. [PMID: 35516214 PMCID: PMC9055135 DOI: 10.1039/d0ra02042g] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/22/2020] [Indexed: 12/16/2022] Open
Abstract
Artemisinin (ART) and its biogenetic precursors artemisinic acid (AA) and dihydroartemisinic acid (DHAA) are important traditional medicinal herb compounds with tumor growth inhibition properties. Herein, we have studied the cytotoxicity of ART, AA, and DHAA on different cancer cell lines (H1299, A431, and HCT 116) and investigated in detail their binding mechanisms with ctDNA by using spectroscopy, cyclic voltammetry, and computational methods. The UV absorbance, cyclic voltammetry, DNA helix melting, competition binding, and circular dichroism studies suggested that the complex formation of ART-ctDNA and AA-ctDNA occurs through groove binding. However, in the case of DHAA-ctDNA interaction, electrostatic interaction plays a major role. The thermodynamic parameters, viz., ΔG 0, ΔH 0, and ΔS 0 were calculated, which showed the involvement of hydrogen bonds and van der Waals interactions for drug-ctDNA interaction. FTIR and molecular docking results suggested that ART, AA, and DHAA were bound to the A-T rich region in the minor groove of ctDNA.
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Affiliation(s)
- Neha Maurya
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia New Delhi-110025 India +91 11 26983409 +91 8860634100
| | - Khalid Imtiyaz
- Department of Biosciences, Jamia Millia Islamia New Delhi-110025 India
| | | | - Khaled Mohamed Khedher
- Department of Civil Engineering, College of Engineering, King Khalid University Abha 6421 Saudi Arabia
- Department of Civil Engineering, ISET, DGET Nabeul Tunisia
| | - Prashant Singh
- Department of Chemistry, ARSD College, University of Delhi New Delhi-110021 India
| | - Rajan Patel
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia New Delhi-110025 India +91 11 26983409 +91 8860634100
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31
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Kıpçak F, Tok TT, Duyar H, Seferoğlu Z, Gökoğlu E. Synthesis of new morpholine containing 3-amido-9-ethylcarbazole derivative and studies on its biophysical interactions with calf thymus DNA/HSA. J Biomol Struct Dyn 2020; 39:1561-1571. [PMID: 32093548 DOI: 10.1080/07391102.2020.1734093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this work, we presented the synthesis and investigation of binding properties of the new morpholine containing 3-amido-9-ethylcarbazole derivative (CMR) to calf thymus DNA (ctDNA) and human serum albumin (HSA) by fluorescence spectroscopy, UV absorption spectroscopy and molecular docking method. A decrease in Stern-Volmer constants was obtained with increase in temperature; it shows that static quenching mechanism leads to formation of new CMR-DNA/HSA complexes, which have hydrophobic interaction as the predominant role in the binding modes. Also, binding properties of DNA were investigated with competition assays on two probes (EB and H33258) by absorption, ionic strength and iodide ion quenching methods. The results suggested that CMR entered into the minor groove binding on the A-T region of DNA. The spectral data further confirmed by molecular docking which elicited that CMR complexes have similar interaction and conformation trends to each target, DNA and HSA. The experimental and computational results show that CMR has been classified as a promising molecule in drug designing of other carbazole derivatives.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fulya Kıpçak
- Department of Chemistry, Hacettepe University, Ankara, Turkey
| | - Tugba Taskın Tok
- Department of Chemistry, Gaziantep University, Gaziantep, Turkey.,Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
| | - Halil Duyar
- Department of Chemistry, Gebze Technical University, Kocaeli, Turkey.,Department of Chemistry, Gazi University, Ankara, Turkey
| | | | - Elmas Gökoğlu
- Department of Chemistry, Hacettepe University, Ankara, Turkey
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32
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Das TK, Karmakar S, Maiti S, Kundu S, Saha A. Room temperature synthesis of NIR emitting Ag 2S nanoparticles through aqueous route and its influence on structural modulation of DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117536. [PMID: 31703989 DOI: 10.1016/j.saa.2019.117536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/23/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
Near infra-red (NIR) light emitting nanomaterials had shown great promise in clinical imaging in view of negligible absorption by skin or tissue of mammalian. Thus, it demands for synthesizing stable NIR emitting nanomaterials in water environment. The present work presents synthesis of biologically acceptable luminescent near-IR emitting silver sulfide nanoparticles through an aqueous route using 2-mercaptoethanol. The prepared as-synthesized Ag2S nanoparticles exhibited bright photoluminescence with quantum yield of ca. 4%. X-ray diffraction (XRD) analysis indicated that the products were monoclinic α-Ag2S. Fourier transform infrared spectral analysis revealed that the stretching vibration at 2560 cm-1 responsible for S-H bond of thiol group disappeared suggesting the conjugation of 2-mercaptoethanol with Ag2S nanoparticles. In view of investigating any possible effect on genetic materials, interactions of the synthesized particles with calf thymus DNA was investigated employing Ethidium bromide (EB) as structural probe. To understand the binding mechanism, the UV-vis absorption, fluorescence and circular dichroism (CD) spectroscopic, as well as DNA melting studies measurements were carried out. The observed results confirm that nanoparticles interact with DNA through groove binding.
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Affiliation(s)
- Tushar Kanti Das
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, III/LB-8 Bidhannagar, Kolkata, 700106, India
| | - Sudip Karmakar
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, III/LB-8 Bidhannagar, Kolkata, 700106, India
| | - Susmita Maiti
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, III/LB-8 Bidhannagar, Kolkata, 700106, India
| | - Somashree Kundu
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, III/LB-8 Bidhannagar, Kolkata, 700106, India
| | - Abhijit Saha
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, III/LB-8 Bidhannagar, Kolkata, 700106, India.
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Label-free sensing of abasic DNA using pyrenylamido triazolyl aromatic amino acid scaffold as AIE probe. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2019.112186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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34
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A facile & convenient route for the stereoselective synthesis of Z- isoxazol-5(4H)-ones derivatives catalysed by sodium acetate: Synthesis, multispectroscopic properties, crystal structure with DFT calculations, DNA-binding studies and molecular docking studies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127067] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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35
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Maurya N, Parray ZA, Maurya JK, Islam A, Patel R. Ionic Liquid Green Assembly-Mediated Migration of Piperine from Calf-Thymus DNA: A New Possibility of the Tunable Drug Delivery System. ACS OMEGA 2019; 4:21005-21017. [PMID: 31867492 PMCID: PMC6921251 DOI: 10.1021/acsomega.9b02246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/18/2019] [Indexed: 06/07/2023]
Abstract
Biocompatible surface-active ionic liquid (SAIL) was used first to study the deintercalation process of a well-known natural compound piperine (PIP) as an anticancer drug, obtained from PIP-calf thymus DNA (ctDNA) complex under controlled experimental conditions. In this study, we have been exploring the interaction of PIP in SAIL (1-butyl-3-methylimidazolium octyl sulfate ionic liquid ([C4mim][C8OSO3])), ctDNA, and deintercalation of PIP from the PIP-ctDNA complex through SAIL micelle using various spectroscopic techniques. Absorption, emission, and lifetime decay measurements provide strong evidence of the relocation of PIP molecules from ctDNA to SAIL micelle. Fluorescence quenching and steady-state fluorescence anisotropy were employed to examine the exact location of PIP in different media. Moreover, the surface tension technique was also employed to confirm the release of PIP molecules from the PIP-ctDNA complex in the presence of SAIL. Circular dichroism analysis suggested that SAIL micelle does not perturb the ctDNA structure, which supported the fact that SAIL micelle can be used as a safe vehicle for PIP. Overall, the study highlighted a novel strategy for deintercalation of drug using SAIL because the release of the drug can be controlled over a period by varying the concentration and composition of the SAIL.
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Affiliation(s)
- Neha Maurya
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research
in Basic Sciences and Protein Research Laboratory, Centre for Interdisciplinary
Research in Basic Sciences, Jamia Millia
Islamia, New Delhi 110025, India
| | - Zahoor Ahmad Parray
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research
in Basic Sciences and Protein Research Laboratory, Centre for Interdisciplinary
Research in Basic Sciences, Jamia Millia
Islamia, New Delhi 110025, India
| | - Jitendra Kumar Maurya
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research
in Basic Sciences and Protein Research Laboratory, Centre for Interdisciplinary
Research in Basic Sciences, Jamia Millia
Islamia, New Delhi 110025, India
| | - Asimul Islam
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research
in Basic Sciences and Protein Research Laboratory, Centre for Interdisciplinary
Research in Basic Sciences, Jamia Millia
Islamia, New Delhi 110025, India
| | - Rajan Patel
- Biophysical Chemistry Laboratory, Centre for Interdisciplinary Research
in Basic Sciences and Protein Research Laboratory, Centre for Interdisciplinary
Research in Basic Sciences, Jamia Millia
Islamia, New Delhi 110025, India
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36
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New thiazoldinone substituted 2,6-diarypiperidin-4-one: Synthesis, crystal structure, spectral characterization, binding mode with calf thymus DNA. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.126899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Kumari R, Banerjee S, Roy P, Nath M. Organotin(IV) complexes of NSAID, ibuprofen, X‐ray structure of Ph
3
Sn(IBF), binding and cleavage interaction with DNA and
in vitro
cytotoxic studies of several organotin complexes of drugs. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.5283] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ranjana Kumari
- Department of ChemistryIndian Institute of Technology Roorkee Roorkee 247667 India
| | - Somesh Banerjee
- Department of BiotechnologyIndian Institute of Technology Roorkee Roorkee 247667 India
| | - Partha Roy
- Department of BiotechnologyIndian Institute of Technology Roorkee Roorkee 247667 India
| | - Mala Nath
- Department of ChemistryIndian Institute of Technology Roorkee Roorkee 247667 India
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Kumari S, Halder S, Aggrawal R, Sundar G, Saha SK. Effect of gemini surfactants on binding interactions of Coumarin 485 with calf thymus deoxyribonucleic acid in presence of nanotubes of β-cyclodextrin. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ditmangklo B, Taechalertpaisarn J, Siriwong K, Vilaivan T. Clickable styryl dyes for fluorescence labeling of pyrrolidinyl PNA probes for the detection of base mutations in DNA. Org Biomol Chem 2019; 17:9712-9725. [PMID: 31531484 DOI: 10.1039/c9ob01492f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fluorescent hybridization probes are important tools for rapid, specific and sensitive analysis of genetic mutations. In this work, we synthesized novel alkyne-modified styryl dyes for conjugation with pyrrolidinyl peptide nucleic acid (acpcPNA) by click chemistry for the development of hybridization responsive fluorescent PNA probes. The free styryl dyes generally exhibited weak fluorescence in aqueous media, and the fluorescence was significantly enhanced (up to 125-fold) upon binding with DNA duplexes. Selected styryl dyes that showed good responses with DNA were conjugated with PNA via sequential reductive alkylation-click chemistry. Although these probes showed little fluorescence change when hybridized to complementary DNA, significant fluorescence enhancements were observed in the presence of structural defects including mismatched, abasic and base-inserted DNA targets. The largest increase in fluorescence quantum yield (up to 14.5-fold) was achieved with DNA carrying base insertion. Although a number of probes were designed to give fluorescence response to complementary DNA targets, probes that are responsive to mutations such as single nucleotide polymorphism (SNP), base insertion/deletion and abasic site are less common. Therefore, styryl-dye-labeled acpcPNA is a unique probe that is responsive to structural defects in the duplexes that may be further applied for diagnostic purposes.
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Affiliation(s)
- Boonsong Ditmangklo
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
| | - Jaru Taechalertpaisarn
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand. and National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Khatcharin Siriwong
- Materials Chemistry Research Center, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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Xie X, Zuffo M, Teulade-Fichou MP, Granzhan A. Identification of optimal fluorescent probes for G-quadruplex nucleic acids through systematic exploration of mono- and distyryl dye libraries. Beilstein J Org Chem 2019; 15:1872-1889. [PMID: 31467609 PMCID: PMC6693400 DOI: 10.3762/bjoc.15.183] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/23/2019] [Indexed: 12/20/2022] Open
Abstract
A library of 52 distyryl and 9 mono-styryl cationic dyes was synthesized and investigated with respect to their optical properties, propensity to aggregation in aqueous medium, and capacity to serve as fluorescence “light-up” probes for G-quadruplex (G4) DNA and RNA structures. Among the 61 compounds, 57 dyes showed preferential enhancement of fluorescence intensity in the presence of one or another G4-DNA or RNA structure, while no dye displayed preferential response to double-stranded DNA or single-stranded RNA analytes employed at equivalent nucleotide concentration. Thus, preferential fluorimetric response towards G4 structures appears to be a common feature of mono- and distyryl dyes, including long-known mono-styryl dyes used as mitochondrial probes or protein stains. However, the magnitude of the G4-induced “light-up” effect varies drastically, as a function of both the molecular structure of the dyes and the nature or topology of G4 analytes. Although our results do not allow to formulate comprehensive structure–properties relationships, we identified several structural motifs, such as indole- or pyrrole-substituted distyryl dyes, as well as simple mono-stryryl dyes such as DASPMI [2-(4-(dimethylamino)styryl)-1-methylpyridinium iodide] or its 4-isomer, as optimal fluorescent light-up probes characterized by high fluorimetric response (I/I0 of up to 550-fold), excellent selectivity with respect to double-stranded DNA or single-stranded RNA controls, high quantum yield in the presence of G4 analytes (up to 0.32), large Stokes shift (up to 150 nm) and, in certain cases, structural selectivity with respect to one or another G4 folding topology. These dyes can be considered as promising G4-responsive sensors for in vitro or imaging applications. As a possible application, we implemented a simple two-dye fluorimetric assay allowing rapid topological classification of G4-DNA structures.
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Affiliation(s)
- Xiao Xie
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Sud, Université Paris Saclay, Bât. 110, Centre universitaire Paris Sud, F-91405 Orsay, France
| | - Michela Zuffo
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Sud, Université Paris Saclay, Bât. 110, Centre universitaire Paris Sud, F-91405 Orsay, France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Sud, Université Paris Saclay, Bât. 110, Centre universitaire Paris Sud, F-91405 Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Sud, Université Paris Saclay, Bât. 110, Centre universitaire Paris Sud, F-91405 Orsay, France
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Farooqi SI, Arshad N, Perveen F, Channar PA, Saeed A, Javed A. Aroylthiourea derivatives of ciprofloxacin drug as DNA binder: Theoretical, spectroscopic and electrochemical studies along with cytotoxicity assessment. Arch Biochem Biophys 2019; 666:83-98. [DOI: 10.1016/j.abb.2019.03.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/18/2019] [Accepted: 03/31/2019] [Indexed: 11/26/2022]
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42
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Shahabadi N, Momeni BZ, Zendehcheshm S. Studies on the Interaction of [SnMe 2Cl 2(bu 2bpy)] Complex with ct-DNA Using Multispectroscopic, Atomic Force Microscopy (AFM) and Molecular Docking. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:157-182. [PMID: 31044667 DOI: 10.1080/15257770.2018.1506885] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The interaction of SnMe2Cl2(bu2bpy)complex with calf thymus DNA (ct-DNA) has been explored following, using spectroscopic methods, viscosity measurements, Atomic force microscopy, Thermal denaturation and Molecular docking. It was found that Sn(IV) complex could bind with DNA via intercalation mode as evidenced by hyperchromism and bathochromic in UV-Vis spectrum; these spectral characteristics suggest that the Sn(IV) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. In addition, the fluorescence emission spectra of intercalated methylene blue (MB) with increasing concentrations of SnMe2Cl2(bu2bpy) represented a significant increase of MB intensity as to release MB from MB-DNA system. Positive values of ΔH and ΔS imply that the complex is bound to ct-DNA mainly via the hydrophobic attraction. Large complexes contain the DNA chains with an average size of 859 nm were observed by using AFM for Sn(IV) Complex-DNA. The Fourier transform infrared study showed a major interaction of Sn(IV) complex with G-C and A-T base pairs and a minor perturbation of the backbone PO2 group. Addition of the Sn(IV)complex results in a noticeable rise in the Tm of DNA. In addition, the results of viscosity measurements suggest that SnMe2Cl2(bu2bpy) complex may bind with the classical intercalative mode. From spectroscopic and hydrodynamic studies, it has been found that Sn(IV)complex interacts with DNA by intercalation mode. Optimized docked model of DNA-complex mixture confirmed the experimental results.
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Affiliation(s)
- Nahid Shahabadi
- a Department of Inorganic Chemistry, Faculty of Chemistry , Razi University , Kermanshah , Iran.,b Medical Biology Research Center (MBRC) , Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Badri Z Momeni
- c Department of Chemistry , K. N. Toosi University of Technology , Tehran , Iran
| | - Saba Zendehcheshm
- a Department of Inorganic Chemistry, Faculty of Chemistry , Razi University , Kermanshah , Iran
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Liu H, Zhang Z, Zhao Y, Zhou Y, Xue B, Han Y, Wang Y, Mu X, Zang S, Zhou X, Li Z. A water-soluble two-dimensional supramolecular organic framework with aggregation-induced emission for DNA affinity and live-cell imaging. J Mater Chem B 2019; 7:1435-1441. [PMID: 32255014 DOI: 10.1039/c8tb03206h] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A water-soluble two-dimensional supramolecular organic framework (2D SOF) was prepared via self-assembly of cucurbit[8]uril (CB[8]) and a three-arm flat linker molecule, which contains a benzene ring as the core and three Brooker's merocyanine (BM) analogs as arms. The strong host-guest interactions between BM and CB[8] and the directional head-to-tail stacking modes between the BM arms synergistically led to the formation of a 2D SOF. The structure of the 2D SOF was verified by 1H NMR, 2D 1H NMR NOESY, and DLS characterizations, while the monolayer structure was characterized by Cryo-TEM and AFM measurements. The 2D SOF exhibited an obvious AIE enhancement effect in H2O. In addition, DNA induced photoluminescence enhancement was observed for the monomer. As a result, this AIEgen-based 2D SOF could feature not only as a cell visualizer but also as a tracker for the nucleus in biological imaging due to the dynamic assembly process.
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Affiliation(s)
- Hui Liu
- Key Laboratory of Biobased Polymer Materials, Shandong Provincial Education Department, College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China.
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Dávila–Rodríguez M, Barolli JP, de Oliveira KM, Colina–Vegas L, da Silva Miranda F, Castellano EE, Von Poelhsitz G, Batista AA. Carbonyl–heterobimetallic Ru(II)/Fe(II)–complexes containing polypyridyl ligands: Synthesis, characterization, cellular viability assays and interactions with biomolecules. Arch Biochem Biophys 2018; 660:156-167. [DOI: 10.1016/j.abb.2018.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 12/18/2022]
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Ataci N, Ozcelik E, Arsu N. Spectrophotometric study on binding of 2-thioxanthone acetic acid with ct-DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 204:281-286. [PMID: 29945110 DOI: 10.1016/j.saa.2018.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 05/14/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
Thioxanthone and its derivatives are the most remarkable molecules due to their vast variety of application such as radiation curing that is, until using them as a therapeutic drug. Therefore, in this study it was intended to use 2-Thioxanthone acetic acid with and without NaCl in Tris HCl buffer solution (pH:7.0) to represent the interaction with ct-DNA. The UV-vis absorption spectra of TXCH2COOH in the presence of ct-DNA showed hypochromism and the intrinstic binding constant (Kb) was determined as 6 × 103 L mol-1. The fluoresence intensity of TXCH2COOH with ct-DNA clearly increased up to 101% which indicated that the fluorescence intensity was very sensitive to ct-DNA concentration. The binding constant (K) and the values of number of binding sites (n) and were calculated as 1.8 × 103 L mol-1 and 0.69, respectively. When the quenching constants (Ksv) of free TXCH2COOH and TXCH2COOH, which were bonded with ct-DNA were compared, slightly changed values of Ksv were seen. Moreover, displacement assay with Hoechst 33,258 and viscosity measurements in the presence and absence of NaCl salt also confirmed the binding mode which noted the electrostatic interaction following groove binding between TXCH2COOH and ct-DNA. Last but not least, the salt effect was examined on ct-DNA binding with TXCH2COOH. The results of the experiments indicated that the groove binding was strengthened by NaCl whereas in the high NaCl concentration, the binding ability of TXCH2COOH to ct-DNA was inversely affected.
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Affiliation(s)
- Nese Ataci
- Yildiz Technical University, Chemistry Department, Davutpasa Campus, 34220 Esenler, Istanbul, Turkey
| | - Elif Ozcelik
- Yildiz Technical University, Chemistry Department, Davutpasa Campus, 34220 Esenler, Istanbul, Turkey
| | - Nergis Arsu
- Yildiz Technical University, Chemistry Department, Davutpasa Campus, 34220 Esenler, Istanbul, Turkey.
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Moradi Z, Khorasani-Motlagh M, Rezvani AR, Noroozifar M. Electronic and fluorescent studies on the interaction of DNA and BSA with a new ternary praseodymium complex containing 2,9-dimethyl 1,10-phenanthroline and antibacterial activities testing. J Biomol Struct Dyn 2018; 37:2283-2295. [DOI: 10.1080/07391102.2018.1479657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Zohreh Moradi
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
| | | | - Ali Reza Rezvani
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
| | - Meissam Noroozifar
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
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Mandal P, Sahoo D, Saha S, Chowdhury J. Sensing of Different Human Telomeric G-Quadruplex DNA Topologies by Natural Alkaloid Allocryptopine Using Spectroscopic Techniques. J Phys Chem B 2018; 122:10279-10290. [PMID: 30346761 DOI: 10.1021/acs.jpcb.8b07856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Paulami Mandal
- Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, West Bengal 700032, India
| | - Dibakar Sahoo
- School of Physics, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
| | - Saumen Saha
- Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, West Bengal 700032, India
| | - Joydeep Chowdhury
- Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata, West Bengal 700032, India
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Hu X, Yang D, Yao T, Gao R, Wumaier M, Shi S. Regulation of multi-factors (tail/loop/link/ions) for G-quadruplex enantioselectivity of Δ- and Λ- [Ru(bpy) 2(dppz-idzo)] 2. Dalton Trans 2018; 47:5422-5430. [PMID: 29594288 DOI: 10.1039/c8dt00501j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chiral recognition of DNA molecules is important because much evidence has indicated that transformations of chirality and diverse conformations of DNA are involved in a series of key biological events. Among these, enrichment of G-quadruplexes (GQs) in the genome, and the exploration of their multiple structures, has aroused great interest. Herein, we compared nearly 100 different sequences with 3'-tail sequences of variable length or different linkers or diverse loops and mutative ionic concentrations. All sequences were capable of forming stable GQs, with fluorescence signal enhancement upon binding with Δ- and Λ- [Ru(bpy)2(dppz-idzo)]2+ (Δ/Λ-1). Our results show that multiple factors, including the 3'-tail length, linkers, loop length and ionic concentration, regulate the enantioselectivity of GQs. Furthermore, molecular docking simulations revealed that chiral recognition of GQs depends on the binding site. To the best of our knowledge, this is the first systematic study regarding the regulation of multi-factors for GQ selectivity of chiral Ru-complexes. These results will serve as a useful reference for enantioselective recognition of genomic GQs and may facilitate the development of chiral anticancer agents for targeting GQs.
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Affiliation(s)
- Xiaochun Hu
- Shanghai Key Lab of Chemical Assessment and Sustainability, Department of Chemistry, Tongji University, 1239 Siping Road, 200092 Shanghai, PR China.
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Halder D, Purkayastha P. A flavonol that acts as a potential DNA minor groove binder as also an efficient G-quadruplex loop binder. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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50
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Zhang F, Li G, Lv FL, Jiang GB, Wang HX, Wang MQ, Li S. A far-red fluorescent probe for selective G-quadruplex DNA targeting. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.07.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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