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Güngör SA. Synthesis, DNA Binding Properties, Molecular Docking and ADME Studies of Schiff Base Compound Containing Pyridine-Propargyl Group. Chem Biodivers 2023; 20:e202300752. [PMID: 37782576 DOI: 10.1002/cbdv.202300752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023]
Abstract
The structure of the pyridine-based Schiff base compound containing the propargyl group was characterized by NMR spectroscopy. Binding of compound 2 with double-stranded fish sperm DNA (Fsds-DNA) was investigated using viscosity measurement studies and UV/VIS and fluorescence spectral techniques. Binding of compound 2 with Fsds-DNA results in minor hypochromism with no change in absorption maxima and fluorescence quenching with almost no shift in emission maxima, which can be attributed to the groove-binding mode of the interaction. The binding constant was found to be 4.7×104 M-1 . The Fsds-DNA viscosity measurement, KI quenching and NaCl quenching studies and the competitive interaction between compound 2 and ethidium bromide with DNA confirm the proposed binding mode. In addition, interactions between compound 2 and the DNA double helix were analysed by molecular docking study in order to determine the binding mode and binding affinity. As a result of molecular docking, the binding affinity of the 2-DNA complex, which has the most stable conformation -8.10 kcal/mol and it is located in its minor groove. In addition, molecular docking and ADME studies for compound 2 were also performed.
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Affiliation(s)
- Seyit Ali Güngör
- Chemistry Department, Faculty of Science, Kahramanmaras Sütcü Imam University, 46100, Kahramanmaras, Turkey
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2
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Rashid M, Khalid M, Ashraf A, Saleem T, Shafiq I, Shakil MA, Zainab B, El-Kott AF, Yaqub M, Shafiq Z. Multicomponent synthesis of pyrido[2,3- b]pyrazine derivatives: electrochemical DNA sensing, nonlinear optical properties and biological activity. RSC Adv 2023; 13:32160-32174. [PMID: 37920758 PMCID: PMC10619479 DOI: 10.1039/d3ra05365b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023] Open
Abstract
We synthesized novel pyrido[2,3-b]pyrazin based heterocyclic compounds (4-7) and their chemical structures were ascertained by spectral techniques (NMR, FT-IR). Besides experimental investigation, density functional theory (DFT) computations with B3LYP/6-31G(d,p) level of theory were executed to obtain spectroscopic and electronic properties. Nonlinear optical (NLO) properties, frontier molecular orbitals (FMOs), UV-visible, vibrational analysis, natural bond orbitals (NBOs), transition density matrix (TDM) and density of states (DOS) analyses of molecules (4-7) were accomplished at B3LYP/6-31G (d,p) level. Global reactivity parameters (GRPs) were correlated with the band gap (Egap) values; compound 7 with lower Egap (3.444 eV), exhibited smaller value of hardness (1.722 eV) with greater softness value (0.290 eV-1). The dipole moment (μ), average polarizability 〈α〉, first (βtot) and second 〈γ〉 hyper-polarizabilities were calculated for compounds (4-7). Compound 7 showed less Egap, highest absorption wavelength and remarkable NLO response. The highest 〈α〉, βtot and 〈γ〉 values for compound 7 were observed as 3.90 × 10-23, 15.6 × 10-30 and 6.63 × 10-35 esu, respectively. High NLO response revealed that pyrido[2,3-b]pyrazin based heterocyclic compounds had very remarkable contributions towards NLO technological applications. Further compounds (4-7) are utilized for the first time in electrochemical sensing of DNA, in vitro antioxidant and antiurease activity.
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Affiliation(s)
- Muhammad Rashid
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 60800 Pakistan +92-3006559811
| | - Muhammad Khalid
- Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
- Centre for Theoretical and Computational Research, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
| | - Abida Ashraf
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 60800 Pakistan +92-3006559811
- Department of Chemistry, Govt. Graduate College Shah Rukne-Alam Multan Pakistan
| | - Tahira Saleem
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 60800 Pakistan +92-3006559811
| | - Iqra Shafiq
- Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
- Centre for Theoretical and Computational Research, Khwaja Fareed University of Engineering & Information Technology Rahim Yar Khan 64200 Pakistan
| | - Muhammad Azeem Shakil
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 60800 Pakistan +92-3006559811
| | - Briha Zainab
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 60800 Pakistan +92-3006559811
| | - Attalla F El-Kott
- Department of Biology, College of Science, King Khalid University Abha Saudi Arabia
- Department of Zoology, College of Science, Damanhour University Egypt
| | - Muhammad Yaqub
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 60800 Pakistan +92-3006559811
| | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 60800 Pakistan +92-3006559811
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Dorafshan Tabatabai AS, Dehghanian E, Mansouri-Torshizi H. Exploring the Interaction Between the Newly Designed Antitumor Zn(II) Complex and CT-DNA/BSA: Spectroscopic Methods, DFT Computational Analysis, and Docking Simulation. Appl Biochem Biotechnol 2023; 195:6276-6308. [PMID: 36856984 DOI: 10.1007/s12010-023-04394-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2023] [Indexed: 03/02/2023]
Abstract
A new zinc(II) complex formulated as [Zn(pipr-ac)2], where pipr-ac stands for piperidineacetate, was synthesized and structurally identified with the help of experimental and DFT methods. Frontier molecular orbital (FMO) analysis demonstrated that the new complex has higher biological activity compared to the free ligand. Molecular electrostatic potential (MEP) showed the nitrogen atoms and oxygen of carbonyl groups are the active sites of Zn(II) compound. Also, natural bond orbital (NBO) analysis confirmed the charge transfer from the ligating atoms to the metal ion and formation of four coordinated Zn(II) complex. MTT assay illustrated a noticeable cytotoxic activity of the new zinc(II) complex compared to cisplatin on K562 cell line. The CT-DNA and serum albumin (SA) binding of the Zn(II) complex were explored individually. In this regard, UV-Vis spectroscopy and florescence titration revealed the occurrences of fluorescence quenching of CT-DNA/SA by metal compound via static mechanism and creation of hydrogen bonds and van der Waals interactions between them. The binding was further confirmed by viscosity measurement and gel electrophoresis assay for CT-DNA and circular dichroism spectroscopy for SA. Moreover, molecular docking simulation demonstrated that the new compound binds mainly through hydrogen bonds to the groove of DNA and hydrogen bonds and van der Waals interactions to site I of SA.
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Affiliation(s)
| | - Effat Dehghanian
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran.
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Durga Priyadharshini R, Ravi J, Ragunathan P, Vennila KN, Elango KP. Multi-spectroscopic, thermodynamic and molecular simulation studies on binding of pyrroloquinoline quinone with DNA: coexistence of intercalation and groove binding modes. J Biomol Struct Dyn 2023:1-10. [PMID: 37559546 DOI: 10.1080/07391102.2023.2245477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023]
Abstract
The interaction between enzyme-like pyrroloquinoline quinone (PQQ) and calf-thymus DNA (CT-DNA) has been investigated by means of multi-spectroscopic (UV-Vis, fluorescence and circular dichroism), isothermal titration calorimetric (ITC), viscometry and molecular docking and metadynamics simulation techniques. Absorption spectral data suggested the formation of a PQQ/CT-DNA complex, which quenched the fluorescence of PQQ via the dynamic quenching process. The results of CD spectral studies coupled with viscosity measurements, competitive binding assays with Hoechst 33258 and ethidium bromide (EB), KI quenching experiments, gel electrophoresis and DNA melting studies indicated groove binding mode of interaction of PQQ with CT-DNA. ITC experiment revealed that the complex formation is a spontaneous process (ΔGo < 0) with a binding constant of 1.05 × 104 M-1. The observed ΔHo < 0 and ΔSo < 0 pointed out that the complex is stabilized by van der Waals forces along with H-bonding interactions. The outcomes of molecular docking and simulation studies confirmed the binding of PQQ with DNA. The free energy surface (FES) analysis pointed out the existence of an equilibrium between partial intercalation and groove binding modes, which is in good agreement with the competitive binding assays.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- R Durga Priyadharshini
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - Jayashree Ravi
- Centre for Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
| | - Preethi Ragunathan
- Centre for Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
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Ponkarpagam S, Vennila KN, Elango KP. A closer look at the mode of binding of drug pemetrexed with CT-DNA. J Biomol Struct Dyn 2023; 41:3553-3561. [PMID: 35297322 DOI: 10.1080/07391102.2022.2051747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/05/2022] [Indexed: 10/18/2022]
Abstract
The interaction of antifolate drug Pemetrexed (PEM) with CT-DNA has been studied by UV-Vis, fluorescence and circular dichroism spectroscopic techniques. The results of these spectroscopic studies in combination with viscosity measurements, voltammetric and KI quenching studies suggested a less-common mode of binding of PEM with CT-DNA i.e. neither intercalation nor groove binding. Thus, metadynamic (MD) simulation is utilized to decipher the nature of binding of PEM with CT-DNA. Analysis of free energy surfaces obtained in MD simulation, reveals that PEM binds to the 3'- and 5'-ends of the DNA molecule. The thermodynamics of the interaction has been investigated by isothermal titration calorimetric experiment. The analysis shows that PEM binds with CT-DNA strongly with a binding constant of 2.6x109 M-1 and the process is found to be spontaneous (ΔG - 12.84 kcal/mol). Further, positive values of enthalpy (ΔH 6.09 cal/mol) and entropy (ΔS 43.1 cal/mol) changes indicate that the binding is an enthalpically unfavourable and, instead, entropically driven process.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute, (Deemed to be University), Gandhigram, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute, (Deemed to be University), Gandhigram, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute, (Deemed to be University), Gandhigram, India
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Çeşme M, Özaltay A. DNA‐Binding Studies of Ofloxacin Using a Series of Spectroscopic, Electrochemical Techniques and in Silico Approaches. ChemistrySelect 2022. [DOI: 10.1002/slct.202202278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mustafa Çeşme
- Department of Chemistry Faculty of Sciences Kahramanmaras Sütçü İmam University 46040 Kahramanmaras TURKEY
| | - Ayşe Özaltay
- Department of Chemistry Faculty of Sciences Kahramanmaras Sütçü İmam University 46040 Kahramanmaras TURKEY
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Ponkarpagam S, Vennila KN, Elango KP. Intercalation of diafenthiuron insecticide with calf thymus DNA: spectroscopic and molecular dynamics analysis. J Biomol Struct Dyn 2022:1-9. [PMID: 35848349 DOI: 10.1080/07391102.2022.2098824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A series of biophysical experiments like UV-Vis, fluorescence, circular dichroism (CD), competitive displacement assays, voltammetric studies, viscosity measurements and denaturation effect and metadynamics simulation studies were performed to establish the mode of binding of diafenthiuron (DF) insecticide with calf thymus DNA (CT-DNA). Analysis of absorption and fluorescence spectra in Tris-HCl buffer of pH 7.4 indicates the formation of a complex between DF and CT-DNA and the binding constant of which is in the order of 104 M-1. Competitive displacement assay with ethidium bromide (EB) and Hoechst 33258 suggests that the most probable mode of binding of DF with CT-DNA may be via intercalation mode. The results of other experiments such as CD spectral studies, viscosity measurements and the effect of denaturation agent urea support the intercalation of DF with CT-DNA. Thermodynamic parameters (ΔHo, ΔSo and ΔGo) reveal that hydrogen bonds (H-bonds) or van der Waals (vdW) force is the main binding force in the spontaneous interaction between DF and CT-DNA. Molecular dynamics (MD) simulation studies confirmed the intercalation of DF into the base pairs of CT-DNA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
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Erkmen C, Unal DN, Kurbanoglu S, Eren G, Uslu B. Evaluation of the Interaction of Cinacalcet with Calf Thymus dsDNA: Use of Electrochemical, Spectrofluorimetric, and Molecular Docking Methods. Biosensors 2022; 12:bios12050278. [PMID: 35624577 PMCID: PMC9138790 DOI: 10.3390/bios12050278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022]
Abstract
The binding of drugs to DNA plays a critical role in new drug discovery and is important for designing better drugs. In this study, the interaction and binding mode of calf-thymus double-stranded deoxyribonucleic acid (ct-dsDNA) with cinacalcet (CIN) from the calcimimetic drug that mimics the action of calcium on tissues group were investigated. The interaction of CIN with ct-dsDNA was observed by the differential pulse voltammetry (DPV) technique by following the decrease in electrochemical oxidation signals to deoxyguanosine and adenosine. A competitive study was performed on an indicator, methylene blue, to investigate the interaction of the drug with ct-dsDNA by fluorescence spectroscopy. Interaction studies have shown that the binding mode for the interaction of CIN with ct-dsDNA could be groove-binding. According to the results obtained, the binding constant values were found to be 6.30 × 104 M−1 and 3.16 × 105 M−1, respectively, at 25 °C as obtained from the cyclic voltammetry (CV) and spectroscopic techniques. Possible molecular interactions of CIN with dsDNA were explored via molecular docking experiments. The docked structure indicated that CIN could fit well into the minor groove of the DNA through H-bonding and π-π stacking contact with CIN.
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Affiliation(s)
- Cem Erkmen
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey; (C.E.); (D.N.U.); (S.K.)
- The Graduate School of Health Sciences, Ankara University, Ankara 06110, Turkey
| | - Didem Nur Unal
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey; (C.E.); (D.N.U.); (S.K.)
- The Graduate School of Health Sciences, Ankara University, Ankara 06110, Turkey
| | - Sevinc Kurbanoglu
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey; (C.E.); (D.N.U.); (S.K.)
| | - Gokcen Eren
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Etiler, Ankara 06330, Turkey;
| | - Bengi Uslu
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey; (C.E.); (D.N.U.); (S.K.)
- Correspondence:
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Ponkarpagam S, Vennila KN, Elango KP. Investigating binding of insecticide buprofezin to DNA by experimental and metadynamics simulation studies. J Biomol Struct Dyn 2022; 41:3476-3484. [PMID: 35285769 DOI: 10.1080/07391102.2022.2050949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Buprofezin (BUP) is an insecticide which belongs to the thiadiazine structural family and known to damage DNA in mice. Though its toxic effect on human is not known clearly, understanding the mechanism of interaction of BUP with DNA can prove useful when required. Multi-spectroscopic experiments such as UV-Vis, fluorescence, circular dichroism (CD) and 1H NMR coupled with viscosity measurements, urea effect and voltametric studies were performed to ascertain the mode of binding of BUP with calf thymus DNA (CT-DNA). Analysis of UV-Vis and fluorescence spectra indicated the formation of a complex between BUP and CT-DNA. Other experiments such as competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, effect of urea, CD, voltammetric studies and 1H NMR spectral analysis suggested that BUP intercalates into the base pairs of CT-DNA. All these results revealed that the binding mode of BUP with CT-DNA should be intercalation and the binding constant is in the order of 104 M-1. The ΔHo < 0 and ΔSo < 0 suggested that H-bonding or van der Waals force was the main binding force between BUP and CT-DNA. The proposed mode of binding of BUP with CT-DNA has been visualized using in silico molecular docking and metadynamics simulation studies, which showed that the phenyl ring of BUP binds to CT-DNA via π-π stacking interaction in addition to H-bond formation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
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